Citrus Sinensis ID: 038591

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--
Protein Sequence
KKTAGAVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK
Secondary Structure (PSIPRED)
ccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHcccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHccccccccHHHHHHHHHHHcccEcccccc
Coil and Loop (DISEMBL)
KKTAGAVINmrkldegtepdtprQIQRARlgkkmsqpdlanqinqrpqvvseyengkavpnqTVLAKMEKAIGVKLRVKIRK
Flexible Loop (DISEMBL)
kktagavinmrkldegtepdtprQIQRArlgkkmsqpdlaNQINQRPQVVSEyengkavpnqtvlakmekaigvklrvkirk
Low Complexity Region (SEG)
KKTAGAVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK
Disordered region (IsUnstruct)
**********************************************************************AIGV********
Disordered Region (DISOPRED)
****************TEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV****
Disordered Region (DISEMBL)
KKTAGAVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK
Disordered Region (DISPRO)
***********KLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR*****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
KKTAGAVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK
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	82	2.2.26 [Sep-21-2011]
Q9LV58	148	Multiprotein-bridging fac	yes	no	1.0	0.554	0.644	3e-21
O14467	151	Multiprotein-bridging fac	yes	no	0.817	0.443	0.535	3e-14
Q9LXT3	142	Multiprotein-bridging fac	no	no	0.939	0.542	0.447	5e-14
Q9SJI8	142	Multiprotein-bridging fac	no	no	0.939	0.542	0.435	2e-13
Q6FJN0	151	Multiprotein-bridging fac	yes	no	0.841	0.456	0.506	3e-13
P14327	104	Vegetative-specific prote	yes	no	0.743	0.586	0.573	3e-13
Q752P7	152	Multiprotein-bridging fac	yes	no	0.841	0.453	0.493	3e-13
P69736	148	Endothelial differentiati	yes	no	0.865	0.479	0.468	9e-13
Q9JMG1	148	Endothelial differentiati	yes	no	0.865	0.479	0.468	9e-13
O94700	148	Multiprotein-bridging fac	yes	no	0.646	0.358	0.566	3e-12

>sp|Q9LV58|MBF1C_ARATH Multiprotein-bridging factor 1c OS=Arabidopsis thaliana GN=MBF1C PE=1 SV=1

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 64/90 (71%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K TA  VIN +KL+E TEP        +    IQ+ARL KKMSQ DLA QIN+R QVV E
Sbjct: 59  KSTAVPVINTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQE 118

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 119 YENGKAVPNQAVLAKMEKVLGVKLRGKIGK 148

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators. Involved in the tolerance to heat and osmotic stress by partially activating the ethylene-response signal transduction pathway.
Arabidopsis thaliana (taxid: 3702)

>sp|O14467|MBF1_YEAST Multiprotein-bridging factor 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MBF1 PE=1 SV=2

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 38/71 (53%), Positives = 53/71 (74%), Gaps = 4/71 (5%)

Query: 7   VINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66
           ++  +KLD    P+  R I RAR  KKMSQ DLA +IN++P VV++YE  +A+PNQ VL+
Sbjct: 71  IVKPKKLD----PNVGRAISRARTDKKMSQKDLATKINEKPTVVNDYEAARAIPNQQVLS 126

Query: 67  KMEKAIGVKLR 77
           K+E+A+GVKLR
Sbjct: 127 KLERALGVKLR 137

Transcriptional coactivator that stimulates GCN4-dependent transcriptional activity by bridging the DNA-binding region of GCN4 and TBP (SPT15), thereby recruiting TBP to GCN4-bound promoters.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9LXT3|MBF1B_ARATH Multiprotein-bridging factor 1b OS=Arabidopsis thaliana GN=MBF1B PE=2 SV=1

 Score = 76.3 bits (186), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 38/85 (44%), Positives = 59/85 (69%), Gaps = 8/85 (9%)

Query: 3   TAGAVINMRKLDEGTE--------PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54
           ++G  +N +KLD+ TE         +  + I +AR  KK++Q  LA+ IN++PQV+ EYE
Sbjct: 57  SSGTSLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQVIQEYE 116

Query: 55  NGKAVPNQTVLAKMEKAIGVKLRVK 79
           +GKA+PNQ +L+K+E+A+G KLR K
Sbjct: 117 SGKAIPNQQILSKLERALGAKLRGK 141

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJI8|MBF1A_ARATH Multiprotein-bridging factor 1a OS=Arabidopsis thaliana GN=MBF1A PE=2 SV=1

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 57/85 (67%), Gaps = 8/85 (9%)

Query: 3   TAGAVINMRKLDEGTE--------PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54
           ++G  +N + LD+ TE         +  + I +AR  KK++Q  LA  IN++PQV+ EYE
Sbjct: 57  SSGTSLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYE 116

Query: 55  NGKAVPNQTVLAKMEKAIGVKLRVK 79
           +GKA+PNQ +L+K+E+A+G KLR K
Sbjct: 117 SGKAIPNQQILSKLERALGAKLRGK 141

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6FJN0|MBF1_CANGA Multiprotein-bridging factor 1 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=MBF1 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 52/73 (71%), Gaps = 4/73 (5%)

Query: 7   VINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66
           ++  +KLD     +  + I R R  KKMSQ DLA +IN++P V+++YE G+A+PNQ VL 
Sbjct: 71  IVKPKKLD----ANVGKTIARVRTEKKMSQKDLATKINEKPTVINDYEAGRAIPNQQVLG 126

Query: 67  KMEKAIGVKLRVK 79
           KME+A+GVKLR K
Sbjct: 127 KMERALGVKLRGK 139

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

>sp|P14327|VSH7_DICDI Vegetative-specific protein H7 OS=Dictyostelium discoideum GN=cinD-1 PE=2 SV=2

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/61 (57%), Positives = 48/61 (78%)

Query: 19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78
          P  P+ IQRAR   KM+Q +LA +IN+RP V++EYE+G A+P+Q VL+K+EKA+ VKLR 
Sbjct: 37 PSVPQAIQRARNALKMTQKELAFKINERPGVINEYESGSAIPSQAVLSKLEKALNVKLRG 96

Query: 79 K 79
          K
Sbjct: 97 K 97

Dictyostelium discoideum (taxid: 44689)

>sp|Q752P7|MBF1_ASHGO Multiprotein-bridging factor 1 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=MBF1 PE=3 SV=1

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 52/73 (71%), Gaps = 4/73 (5%)

Query: 7   VINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66
           ++  +KLD    P   R I + R  K M+Q DLA +IN++P V+++YE G+A+PNQ +LA
Sbjct: 72  IVKPKKLD----PSVGRAIAKGRGDKGMTQKDLATRINEKPTVINDYEAGRAIPNQQILA 127

Query: 67  KMEKAIGVKLRVK 79
           KME+A+GVKLR K
Sbjct: 128 KMERALGVKLRGK 140

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

>sp|P69736|EDF1_RAT Endothelial differentiation-related factor 1 OS=Rattus norvegicus GN=Edf1 PE=1 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 53/79 (67%), Gaps = 8/79 (10%)

Query: 9   NMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
           N  KLD  TE         +  + IQR R  K ++Q DLA +IN++PQV+++YE+G+A+P
Sbjct: 57  NTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIP 116

Query: 61  NQTVLAKMEKAIGVKLRVK 79
           N  VL K+E+AIG+KLR K
Sbjct: 117 NNQVLGKIERAIGLKLRGK 135

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. Might function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Rattus norvegicus (taxid: 10116)

>sp|Q9JMG1|EDF1_MOUSE Endothelial differentiation-related factor 1 OS=Mus musculus GN=Edf1 PE=1 SV=1

 Score = 72.0 bits (175), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 53/79 (67%), Gaps = 8/79 (10%)

Query: 9   NMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
           N  KLD  TE         +  + IQR R  K ++Q DLA +IN++PQV+++YE+G+A+P
Sbjct: 57  NTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIP 116

Query: 61  NQTVLAKMEKAIGVKLRVK 79
           N  VL K+E+AIG+KLR K
Sbjct: 117 NNQVLGKIERAIGLKLRGK 135

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. Might function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Mus musculus (taxid: 10090)

>sp|O94700|MBF1_SCHPO Multiprotein-bridging factor 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mbf1 PE=3 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 45/53 (84%)

Query: 25  IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
           IQ+ R  K  +Q DL+ +IN++PQVV++YE+G+A+PNQ VL+KME+A+G+KLR
Sbjct: 82  IQKGRQAKGWAQKDLSQRINEKPQVVNDYESGRAIPNQQVLSKMERALGIKLR 134

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	82
225445278	144	PREDICTED: multiprotein-bridging factor	0.987	0.562	0.651	3e-21
147852829	144	hypothetical protein VITISV_034625 [Viti	0.987	0.562	0.640	4e-21
19225065	145	ethylene-responsive transciptional coact	1.0	0.565	0.622	1e-20
21553721	148	ethylene-responsive transcriptional coac	1.0	0.554	0.644	1e-19
297831282	148	ATMBF1C/MBF1C [Arabidopsis lyrata subsp.	1.0	0.554	0.644	1e-19
15230125	148	multiprotein-bridging factor 1c [Arabido	1.0	0.554	0.644	1e-19
449443143	145	PREDICTED: multiprotein-bridging factor	0.939	0.531	0.635	2e-19
255546543	146	Multiprotein-bridging factor, putative [	1.0	0.561	0.6	2e-19
350535769	146	ethylene-responsive transcriptional coac	1.0	0.561	0.6	3e-19
357500453	146	Ethylene-responsive transciptional coact	1.0	0.561	0.611	4e-18

>gi|225445278|ref|XP_002284605.1| PREDICTED: multiprotein-bridging factor 1c [Vitis vinifera]

 Score =  105 bits (262), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 58/89 (65%), Positives = 65/89 (73%), Gaps = 8/89 (8%)

Query: 2   KTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEY 53
           K A  ++N RKLDEGTEP        D  + IQ+ARL KKMSQ +LA  IN+RPQVV EY
Sbjct: 56  KKAAPIMNTRKLDEGTEPAALDRVSVDVRQLIQKARLEKKMSQAELAKLINERPQVVQEY 115

Query: 54  ENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           ENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 116 ENGKAVPNQAVLAKMEKVLGVKLRGKISK 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147852829|emb|CAN79519.1| hypothetical protein VITISV_034625 [Vitis vinifera]

 Score =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 57/89 (64%), Positives = 65/89 (73%), Gaps = 8/89 (8%)

Query: 2   KTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEY 53
           K A  ++N RKLDEGTEP        D  + IQ+ARL KKMSQ +LA  IN+RPQVV EY
Sbjct: 56  KKAAPIMNTRKLDEGTEPAALDRVSVDVRQLIQKARLEKKMSQAELAKLINERPQVVQEY 115

Query: 54  ENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           EBGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 116 EBGKAVPNQAVLAKMEKVLGVKLRGKISK 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|19225065|gb|AAL32037.2|AF439278_1 ethylene-responsive transciptional coactivator-like protein [Retama raetam]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/90 (62%), Positives = 65/90 (72%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           +KTAG V+  RKLDE  EP        +    IQ+ARL KKMSQ ++A QIN+RPQVV E
Sbjct: 56  EKTAGPVVYARKLDEAAEPAALERVAGEVRHAIQKARLEKKMSQAEVAKQINERPQVVQE 115

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VLAKME+ +GVKLR KI K
Sbjct: 116 YENGKAVPNQAVLAKMERVLGVKLRGKIGK 145

Source: Retama raetam

Species: Retama raetam

Genus: Retama

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21553721|gb|AAM62814.1| ethylene-responsive transcriptional coactivator, putative [Arabidopsis thaliana]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 64/90 (71%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K TA  VIN +KL+E TEP        +    IQ+ARL KKMSQ DLA QIN+R QVV E
Sbjct: 59  KSTAVPVINTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQE 118

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 119 YENGKAVPNQAVLAKMEKVLGVKLRGKIGK 148

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831282|ref|XP_002883523.1| ATMBF1C/MBF1C [Arabidopsis lyrata subsp. lyrata] gi|297329363|gb|EFH59782.1| ATMBF1C/MBF1C [Arabidopsis lyrata subsp. lyrata]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 64/90 (71%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K TA  VIN +KL+E TEP        +    IQ+ARL KKMSQ DLA QIN+R QVV E
Sbjct: 59  KSTAVPVINTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQE 118

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 119 YENGKAVPNQAVLAKMEKVLGVKLRGKIGK 148

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15230125|ref|NP_189093.1| multiprotein-bridging factor 1c [Arabidopsis thaliana] gi|75274343|sp|Q9LV58.1|MBF1C_ARATH RecName: Full=Multiprotein-bridging factor 1c gi|9294040|dbj|BAB01997.1| ethylene-responsive transcriptional coactivator-like protein [Arabidopsis thaliana] gi|28466837|gb|AAO44027.1| At3g24500 [Arabidopsis thaliana] gi|110735899|dbj|BAE99925.1| putative ethylene-responsive transcriptional coactivator [Arabidopsis thaliana] gi|332643384|gb|AEE76905.1| multiprotein-bridging factor 1c [Arabidopsis thaliana]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 58/90 (64%), Positives = 64/90 (71%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K TA  VIN +KL+E TEP        +    IQ+ARL KKMSQ DLA QIN+R QVV E
Sbjct: 59  KSTAVPVINTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQE 118

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct: 119 YENGKAVPNQAVLAKMEKVLGVKLRGKIGK 148

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443143|ref|XP_004139340.1| PREDICTED: multiprotein-bridging factor 1c-like [Cucumis sativus] gi|449521076|ref|XP_004167557.1| PREDICTED: multiprotein-bridging factor 1c-like [Cucumis sativus]

 Score = 99.8 bits (247), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 54/85 (63%), Positives = 62/85 (72%), Gaps = 8/85 (9%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           KK   A +N RKL+EGTEP        +  + IQ+ARL KKMSQ +LA QIN+R QVV E
Sbjct: 56  KKVTAAPVNARKLEEGTEPAALDRVAVEVRQAIQKARLEKKMSQAELAKQINERTQVVQE 115

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLR 77
           YENGKAVPNQ VLAKMEK +GVKLR
Sbjct: 116 YENGKAVPNQAVLAKMEKVLGVKLR 140

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255546543|ref|XP_002514331.1| Multiprotein-bridging factor, putative [Ricinus communis] gi|223546787|gb|EEF48285.1| Multiprotein-bridging factor, putative [Ricinus communis]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 54/90 (60%), Positives = 66/90 (73%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K  AG V+N +KLDEGTEP        +  + IQ+ARL KKMSQ +LA  IN++P+VV E
Sbjct: 57  KAAAGPVVNAKKLDEGTEPAALDRVAPEVRQAIQKARLEKKMSQAELAKLINEQPKVVQE 116

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPN+ +LAKMEK +GVKLR KI K
Sbjct: 117 YENGKAVPNKAILAKMEKVLGVKLRGKIGK 146

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350535769|ref|NP_001234468.1| ethylene-responsive transcriptional coactivator [Solanum lycopersicum] gi|5669634|gb|AAD46402.1|AF096246_1 ethylene-responsive transcriptional coactivator [Solanum lycopersicum] gi|161898092|gb|ABX80140.1| multiprotein bridging factor ER24 [Solanum lycopersicum]

 Score = 99.0 bits (245), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 54/90 (60%), Positives = 63/90 (70%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           KK A   +N+RKLDE  EP        D  + IQ+AR+ KKMSQ DLA +IN+R QVV+E
Sbjct: 56  KKAATLAVNVRKLDEAAEPAALEKLPVDVRQAIQKARIEKKMSQADLAKKINERTQVVAE 115

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAVPNQ VL KME  +GVKLR KI K
Sbjct: 116 YENGKAVPNQLVLGKMENVLGVKLRGKIHK 145

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500453|ref|XP_003620515.1| Ethylene-responsive transciptional coactivator-like protein [Medicago truncatula] gi|355495530|gb|AES76733.1| Ethylene-responsive transciptional coactivator-like protein [Medicago truncatula]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 55/90 (61%), Positives = 61/90 (67%), Gaps = 8/90 (8%)

Query: 1   KKTAGAVINMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSE 52
           K TAG V+N RKLDE  EP        +    IQ+ARL KKMSQ DLA  IN+R QVV E
Sbjct: 57  KATAGPVLNARKLDEAAEPAALERVGGEVRHAIQKARLDKKMSQGDLAKLINERVQVVQE 116

Query: 53  YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           YENGKAV NQ VL KME+ +GVKLR KI K
Sbjct: 117 YENGKAVINQGVLGKMERVLGVKLRGKIGK 146

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	82
TAIR|locus:2091747	148	MBF1C "multiprotein bridging f	1.0	0.554	0.655	1.9e-21
SGD|S000007253	151	MBF1 "Transcriptional coactiva	0.817	0.443	0.535	5.4e-15
TAIR|locus:2098994	142	MBF1B "multiprotein bridging f	0.939	0.542	0.458	1.1e-14
TAIR|locus:2041509	142	MBF1A "multiprotein bridging f	0.939	0.542	0.447	3e-14
WB|WBGene00003148	156	mbf-1 [Caenorhabditis elegans	0.865	0.455	0.518	3e-14
DICTYBASE|DDB_G0273775	104	cinD-2 "putative helix-turn-he	0.743	0.586	0.573	4.9e-14
DICTYBASE|DDB_G0273061	104	cinD-1 "putative helix-turn-he	0.743	0.586	0.573	4.9e-14
MGI|MGI:1891227	148	Edf1 "endothelial differentiat	0.865	0.479	0.468	3.4e-13
RGD|1308073	148	Edf1 "endothelial differentiat	0.865	0.479	0.468	3.4e-13
CGD|CAL0003442	151	MBF1 [Candida albicans (taxid:	0.841	0.456	0.452	4.4e-13

TAIR|locus:2091747 MBF1C "multiprotein bridging factor 1C" [Arabidopsis thaliana (taxid:3702)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 59/90 (65%), Positives = 65/90 (72%)

Query:     1 KKTAGAVINMRKLDEGTEP---DTPR-----QIQRARLGKKMSQPDLANQINQRPQVVSE 52
             K TA  VIN +KL+E TEP   D  +      IQ+ARL KKMSQ DLA QIN+R QVV E
Sbjct:    59 KSTAVPVINTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQE 118

Query:    53 YENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
             YENGKAVPNQ VLAKMEK +GVKLR KI K
Sbjct:   119 YENGKAVPNQAVLAKMEKVLGVKLRGKIGK 148

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003713 "transcription coactivator activity" evidence=IGI;ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

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

GO:0009408 "response to heat" evidence=IEP;RCA

GO:0009414 "response to water deprivation" evidence=IEP

GO:0005730 "nucleolus" evidence=IDA

GO:0006457 "protein folding" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

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

GO:0009873 "ethylene mediated signaling pathway" evidence=TAS

SGD|S000007253 MBF1 "Transcriptional coactivator" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 38/71 (53%), Positives = 53/71 (74%)

Query:     7 VINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66
             ++  +KLD    P+  R I RAR  KKMSQ DLA +IN++P VV++YE  +A+PNQ VL+
Sbjct:    71 IVKPKKLD----PNVGRAISRARTDKKMSQKDLATKINEKPTVVNDYEAARAIPNQQVLS 126

Query:    67 KMEKAIGVKLR 77
             K+E+A+GVKLR
Sbjct:   127 KLERALGVKLR 137

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

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

GO:0005634 "nucleus" evidence=IEA;IC

GO:0003713 "transcription coactivator activity" evidence=IDA

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

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

GO:0005737 "cytoplasm" evidence=IEA

TAIR|locus:2098994 MBF1B "multiprotein bridging factor 1B" [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 39/85 (45%), Positives = 60/85 (70%)

Query:     3 TAGAVINMRKLDEGTE-------P-DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54
             ++G  +N +KLD+ TE       P +  + I +AR  KK++Q  LA+ IN++PQV+ EYE
Sbjct:    57 SSGTSLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQVIQEYE 116

Query:    55 NGKAVPNQTVLAKMEKAIGVKLRVK 79
             +GKA+PNQ +L+K+E+A+G KLR K
Sbjct:   117 SGKAIPNQQILSKLERALGAKLRGK 141

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003713 "transcription coactivator activity" evidence=IGI;ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

TAIR|locus:2041509 MBF1A "multiprotein bridging factor 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 38/85 (44%), Positives = 58/85 (68%)

Query:     3 TAGAVINMRKLDEGTE-------P-DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54
             ++G  +N + LD+ TE       P +  + I +AR  KK++Q  LA  IN++PQV+ EYE
Sbjct:    57 SSGTSLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYE 116

Query:    55 NGKAVPNQTVLAKMEKAIGVKLRVK 79
             +GKA+PNQ +L+K+E+A+G KLR K
Sbjct:   117 SGKAIPNQQILSKLERALGAKLRGK 141

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003713 "transcription coactivator activity" evidence=IGI;ISS

GO:0005634 "nucleus" evidence=ISM

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

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

GO:0005730 "nucleolus" evidence=IDA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

WB|WBGene00003148 mbf-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 183 (69.5 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 41/79 (51%), Positives = 54/79 (68%)

Query:     9 NMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
             N  +LDE TE            + +Q+AR  K  +Q DL+ QIN++PQVV EYE+GKAVP
Sbjct:    64 NTLRLDEETEELHHQKVALSLGKVMQQARATKGWTQKDLSTQINEKPQVVGEYESGKAVP 123

Query:    61 NQTVLAKMEKAIGVKLRVK 79
             NQ ++AKME+A+GVKLR K
Sbjct:   124 NQQIMAKMERALGVKLRGK 142

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

DICTYBASE|DDB_G0273775 cinD-2 "putative helix-turn-helix transcription factor" [Dictyostelium discoideum (taxid:44689)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 35/61 (57%), Positives = 48/61 (78%)

Query:    19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78
             P  P+ IQRAR   KM+Q +LA +IN+RP V++EYE+G A+P+Q VL+K+EKA+ VKLR 
Sbjct:    37 PSVPQAIQRARNALKMTQKELAFKINERPGVINEYESGSAIPSQAVLSKLEKALNVKLRG 96

Query:    79 K 79
             K
Sbjct:    97 K 97

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISS

GO:0003713 "transcription coactivator activity" evidence=ISS

DICTYBASE|DDB_G0273061 cinD-1 "putative helix-turn-helix transcription factor" [Dictyostelium discoideum (taxid:44689)]

 Score = 181 (68.8 bits), Expect = 4.9e-14, P = 4.9e-14
 Identities = 35/61 (57%), Positives = 48/61 (78%)

Query:    19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78
             P  P+ IQRAR   KM+Q +LA +IN+RP V++EYE+G A+P+Q VL+K+EKA+ VKLR 
Sbjct:    37 PSVPQAIQRARNALKMTQKELAFKINERPGVINEYESGSAIPSQAVLSKLEKALNVKLRG 96

Query:    79 K 79
             K
Sbjct:    97 K 97

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISS

GO:0003713 "transcription coactivator activity" evidence=ISS

MGI|MGI:1891227 Edf1 "endothelial differentiation-related factor 1" [Mus musculus (taxid:10090)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 37/79 (46%), Positives = 53/79 (67%)

Query:     9 NMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
             N  KLD  TE         +  + IQR R  K ++Q DLA +IN++PQV+++YE+G+A+P
Sbjct:    57 NTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIP 116

Query:    61 NQTVLAKMEKAIGVKLRVK 79
             N  VL K+E+AIG+KLR K
Sbjct:   117 NNQVLGKIERAIGLKLRGK 135

GO:0003677 "DNA binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005516 "calmodulin binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=ISO

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

RGD|1308073 Edf1 "endothelial differentiation-related factor 1" [Rattus norvegicus (taxid:10116)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 37/79 (46%), Positives = 53/79 (67%)

Query:     9 NMRKLDEGTEP--------DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
             N  KLD  TE         +  + IQR R  K ++Q DLA +IN++PQV+++YE+G+A+P
Sbjct:    57 NTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIP 116

Query:    61 NQTVLAKMEKAIGVKLRVK 79
             N  VL K+E+AIG+KLR K
Sbjct:   117 NNQVLGKIERAIGLKLRGK 135

GO:0003713 "transcription coactivator activity" evidence=IEA;ISO

GO:0005516 "calmodulin binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA;ISO

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

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

GO:0004402 "histone acetyltransferase activity" evidence=ISO

GO:0008168 "methyltransferase activity" evidence=ISO

CGD|CAL0003442 MBF1 [Candida albicans (taxid:5476)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 33/73 (45%), Positives = 55/73 (75%)

Query:     7 VINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66
             V+ ++K+D        + IQ+AR  KK++Q +LA ++N++P V+++YE G+A+PNQ +LA
Sbjct:    72 VVAVKKVDVSVG----KAIQQARQEKKLTQKELATKVNEKPNVINDYEAGRAIPNQQLLA 127

Query:    67 KMEKAIGVKLRVK 79
             K+E+A+GVKLR K
Sbjct:   128 KLERALGVKLRGK 140

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.7.1.22	LOW CONFIDENCE prediction!
4th Layer	2.7.7.1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	82
COG1813	165	COG1813, COG1813, Predicted transcription factor,	5e-10
smart00530	56	smart00530, HTH_XRE, Helix-turn-helix XRE-family l	2e-09
cd00093	58	cd00093, HTH_XRE, Helix-turn-helix XRE-family like	4e-09
pfam01381	55	pfam01381, HTH_3, Helix-turn-helix	8e-09
PHA01976	67	PHA01976, PHA01976, helix-turn-helix protein	2e-05
PRK06424	144	PRK06424, PRK06424, transcription factor; Provisio	1e-04
pfam12844	64	pfam12844, HTH_19, Helix-turn-helix domain	2e-04
TIGR00270	154	TIGR00270, TIGR00270, TIGR00270 family protein	0.001
COG1396	120	COG1396, HipB, Predicted transcriptional regulator	0.004

>gnl|CDD|224726 COG1813, COG1813, Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

 Score = 52.1 bits (125), Expect = 5e-10
 Identities = 23/63 (36%), Positives = 37/63 (58%)

Query: 19  PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78
            D   +I+ AR  + +SQ DLA ++ ++  V+   E G+A PN  V  K+EK +G+KL  
Sbjct: 78  EDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVE 137

Query: 79  KIR 81
           K+ 
Sbjct: 138 KVD 140

Length = 165

>gnl|CDD|197775 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 48.3 bits (116), Expect = 2e-09
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          ++  R  K ++Q +LA ++      +S  ENGK  P+   L K+ KA+GV L 
Sbjct: 2  LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54

Length = 56

>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 47.2 bits (113), Expect = 4e-09
 Identities = 18/54 (33%), Positives = 30/54 (55%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +++  R  K ++Q +LA ++      +S  ENGK  P+   L K+ KA+GV L
Sbjct: 2  ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Length = 58

>gnl|CDD|201759 pfam01381, HTH_3, Helix-turn-helix

 Score = 46.4 bits (111), Expect = 8e-09
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          ++  R    +SQ +LA ++      +S+ ENGK  P+   L K+ +A+GV L 
Sbjct: 1  LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53

This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the Neisseria gonorrhoeae phage associated protein NGO0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family. Length = 55

>gnl|CDD|177330 PHA01976, PHA01976, helix-turn-helix protein

 Score = 38.0 bits (88), Expect = 2e-05
 Identities = 16/55 (29%), Positives = 30/55 (54%)

Query: 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            Q+ +AR  +  S P+L+ +   R  ++ ++E  K +PN   L ++  A+GV L
Sbjct: 4  AIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58

Length = 67

>gnl|CDD|102369 PRK06424, PRK06424, transcription factor; Provisional

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 20  DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           D    ++ AR    MSQ DLA +I +R  V++  E G  +P+     K+EK +G+ L
Sbjct: 84  DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL 140

Length = 144

>gnl|CDD|205103 pfam12844, HTH_19, Helix-turn-helix domain

 Score = 35.6 bits (83), Expect = 2e-04
 Identities = 18/54 (33%), Positives = 32/54 (59%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +++  R  K +SQ DLA ++      +S+ ENGK+ P+   L K+ +A+GV +
Sbjct: 2  ERLKELREAKGLSQEDLAEKLGISKSYLSKIENGKSDPSADKLKKIAEALGVDV 55

Members of this family contains a DNA-binding helix-turn-helix domain. Length = 64

>gnl|CDD|129371 TIGR00270, TIGR00270, TIGR00270 family protein

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 20  DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79
           D    I+R R  +  SQ  LA +I ++  ++ + EN +  P   V+ K+EK + +KLR +
Sbjct: 69  DYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQ 128

Query: 80  I 80
           +
Sbjct: 129 V 129

[Hypothetical proteins, Conserved]. Length = 154

>gnl|CDD|224314 COG1396, HipB, Predicted transcriptional regulators [Transcription]

 Score = 33.5 bits (75), Expect = 0.004
 Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAV-PNQTVLAKMEKAIGVKL 76
           +++  R  K +SQ +LA ++      +S  E G++  P+  +LA++  A+GV L
Sbjct: 4  ERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSL 58

Length = 120

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	82
PHA01976	67	helix-turn-helix protein	99.76
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	99.75
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	99.73
COG1476	68	Predicted transcriptional regulators [Transcriptio	99.72
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	99.71
PRK06424	144	transcription factor; Provisional	99.68
PRK08359	176	transcription factor; Validated	99.67
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	99.65
PRK09726	88	antitoxin HipB; Provisional	99.65
TIGR00270	154	conserved hypothetical protein TIGR00270.	99.64
PRK09706	135	transcriptional repressor DicA; Reviewed	99.64
TIGR02607	78	antidote_HigA addiction module antidote protein, H	99.59
PRK13890	120	conjugal transfer protein TrbA; Provisional	99.57
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	99.57
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	99.56
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	99.56
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	99.55
PRK10072	96	putative transcriptional regulator; Provisional	99.54
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	99.49
PRK04140	317	hypothetical protein; Provisional	99.48
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.43
KOG3398	135	consensus Transcription factor MBF1 [Transcription	99.41
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.4
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	99.38
COG1813	165	Predicted transcription factor, homolog of eukaryo	99.38
PHA00542	82	putative Cro-like protein	99.28
COG2944	104	Predicted transcriptional regulator [Transcription	99.26
PRK10856	331	cytoskeletal protein RodZ; Provisional	99.25
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	99.21
COG3620	187	Predicted transcriptional regulator with C-termina	99.2
COG3093	104	VapI Plasmid maintenance system antidote protein [	99.11
PRK13355	517	bifunctional HTH-domain containing protein/aminotr	99.08
PRK02866	147	cyanate hydratase; Validated	99.02
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	98.98
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	98.93
TIGR00673	150	cynS cyanate hydratase. Alternate names include cy	98.92
COG3655	73	Predicted transcriptional regulator [Transcription	98.91
COG1709	241	Predicted transcriptional regulator [Transcription	98.89
PF13413	62	HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_	98.86
COG1395	313	Predicted transcriptional regulator [Transcription	98.83
COG1396	120	HipB Predicted transcriptional regulators [Transcr	98.76
PF08667	147	BetR: BetR domain; InterPro: IPR013975 CheY-like p	98.65
PHA01083	149	hypothetical protein	98.58
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	98.54
COG5499	120	Predicted transcription regulator containing HTH d	98.49
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	98.47
COG1426	284	Predicted transcriptional regulator contains Xre-l	98.45
PF08965	118	DUF1870: Domain of unknown function (DUF1870); Int	98.29
COG3636	100	Predicted transcriptional regulator [Transcription	98.28
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	98.24
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	98.19
COG4800	170	Predicted transcriptional regulator with an HTH do	98.18
COG2522	119	Predicted transcriptional regulator [General funct	98.08
PF13693	78	HTH_35: Winged helix-turn-helix DNA-binding; PDB:	98.0
COG3423	82	Nlp Predicted transcriptional regulator [Transcrip	97.98
PRK08099	399	bifunctional DNA-binding transcriptional repressor	97.97
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	97.87
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	97.74
PRK10344	92	DNA-binding transcriptional regulator Nlp; Provisi	97.7
PRK09526	342	lacI lac repressor; Reviewed	97.66
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	97.65
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	97.65
PRK09492	315	treR trehalose repressor; Provisional	97.62
PHA00675	78	hypothetical protein	97.62
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	97.62
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	97.62
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	97.62
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	97.61
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	97.61
TIGR02844	80	spore_III_D sporulation transcriptional regulator	97.61
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	97.57
PRK14987	331	gluconate operon transcriptional regulator; Provis	97.57
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.56
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	97.56
PF04814	180	HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N te	97.53
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	97.51
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	97.5
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	97.42
PHA02591	83	hypothetical protein; Provisional	97.39
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.39
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.38
COG1609	333	PurR Transcriptional regulators [Transcription]	97.36
PRK03975	141	tfx putative transcriptional regulator; Provisiona	97.36
COG5606	91	Uncharacterized conserved small protein [Function	97.31
COG4197	96	Uncharacterized protein conserved in bacteria, pro	97.27
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	97.23
PRK10423	327	transcriptional repressor RbsR; Provisional	97.2
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	97.15
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	97.11
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	97.07
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	97.04
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	97.01
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	97.0
PF12728	51	HTH_17: Helix-turn-helix domain	96.99
TIGR01764	49	excise DNA binding domain, excisionase family. An	96.87
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	96.85
PF13518	52	HTH_28: Helix-turn-helix domain	96.82
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.79
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	96.77
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.76
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	96.75
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	96.75
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	96.73
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	96.71
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	96.7
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.63
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.57
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	96.52
PRK08558	238	adenine phosphoribosyltransferase; Provisional	96.5
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	96.49
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	96.4
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	96.37
PRK01381	99	Trp operon repressor; Provisional	96.37
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	96.36
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	96.31
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	96.31
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	96.2
PRK15418	318	transcriptional regulator LsrR; Provisional	96.2
PRK13698	323	plasmid-partitioning protein; Provisional	96.18
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	96.17
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	96.16
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	96.16
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	96.15
COG1342	99	Predicted DNA-binding proteins [General function p	96.13
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	96.09
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	96.08
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	96.07
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	96.01
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	96.0
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	95.98
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.95
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.9
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.9
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	95.89
TIGR00180	187	parB_part ParB-like partition proteins. This model	95.88
COG1513	151	CynS Cyanate lyase [Inorganic ion transport and me	95.88
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	95.84
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	95.84
COG1318	182	Predicted transcriptional regulators [Transcriptio	95.82
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	95.81
TIGR02054	120	MerD mercuric resistence transcriptional repressor	95.8
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	95.79
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	95.77
PRK04217	110	hypothetical protein; Provisional	95.71
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	95.69
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	95.69
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	95.68
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.67
PF13551	112	HTH_29: Winged helix-turn helix	95.66
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	95.65
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	95.64
KOG3802	398	consensus Transcription factor OCT-1, contains POU	95.63
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.62
TIGR03764	258	ICE_PFGI_1_parB integrating conjugative element, P	95.62
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.61
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	95.6
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	95.6
PRK13749	121	transcriptional regulator MerD; Provisional	95.55
PRK09413	121	IS2 repressor TnpA; Reviewed	95.54
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	95.51
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	95.51
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.51
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.48
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	95.47
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	95.47
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	95.47
PRK00118	104	putative DNA-binding protein; Validated	95.45
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	95.43
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.43
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	95.43
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	95.41
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	95.41
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	95.39
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	95.38
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	95.37
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	95.36
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	95.34
PRK15043	243	transcriptional regulator MirA; Provisional	95.33
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	95.33
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	95.3
smart00351	125	PAX Paired Box domain.	95.29
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.26
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	95.26
PRK04132	846	replication factor C small subunit; Provisional	95.22
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	95.21
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	95.17
PF14590	166	DUF4447: Domain of unknown function (DUF4447); PDB	95.14
PRK10840	216	transcriptional regulator RcsB; Provisional	95.13
PRK11891	429	aspartate carbamoyltransferase; Provisional	95.12
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	95.11
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	95.09
COG3415	138	Transposase and inactivated derivatives [DNA repli	95.08
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	95.07
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	95.03
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	94.99
COG1522	154	Lrp Transcriptional regulators [Transcription]	94.98
PF07638	185	Sigma70_ECF: ECF sigma factor	94.97
cd00131	128	PAX Paired Box domain	94.94
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	94.92
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	94.88
PRK10458	467	DNA cytosine methylase; Provisional	94.84
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.83
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	94.8
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	94.78
PF13309	64	HTH_22: HTH domain	94.74
PRK13752	144	putative transcriptional regulator MerR; Provision	94.71
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	94.64
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	94.63
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	94.62
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	94.62
PF13730	55	HTH_36: Helix-turn-helix domain	94.54
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	94.53
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	94.52
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	94.52
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	94.51
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	94.46
PRK13182	175	racA polar chromosome segregation protein; Reviewe	94.46
PRK11169	164	leucine-responsive transcriptional regulator; Prov	94.44
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	94.43
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	94.37
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	94.37
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	94.32
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	94.28
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	94.26
PRK00430	95	fis global DNA-binding transcriptional dual regula	94.23
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	94.22
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	94.22
PF13556	59	HTH_30: PucR C-terminal helix-turn-helix domain; P	94.2
PRK01905	77	DNA-binding protein Fis; Provisional	94.12
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	94.07
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	94.02
PRK12469	481	RNA polymerase factor sigma-54; Provisional	94.01
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	94.01
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	93.98
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	93.91
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.91
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	93.89
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	93.88
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.86
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	93.83
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	93.83
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	93.79
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	93.75
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	93.73
PF10078	89	DUF2316: Uncharacterized protein conserved in bact	93.66
PRK13413	200	mpi multiple promoter invertase; Provisional	93.61
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	93.58
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	93.54
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	93.52
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	93.49
PRK09954	362	putative kinase; Provisional	93.48
PF06322	64	Phage_NinH: Phage NinH protein; InterPro: IPR01045	93.47
COG2512	258	Predicted membrane-associated trancriptional regul	93.45
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	93.4
COG3413	215	Predicted DNA binding protein [General function pr	93.29
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	93.29
PRK05572	252	sporulation sigma factor SigF; Validated	93.27
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	93.22
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	93.19
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	93.17
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	93.14
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	93.06
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	93.06
COG1974	201	LexA SOS-response transcriptional repressors (RecA	93.06
PRK11608	326	pspF phage shock protein operon transcriptional ac	93.05
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	93.05
PRK09480	194	slmA division inhibitor protein; Provisional	93.02
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	93.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	92.97
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	92.97
PRK13509	251	transcriptional repressor UlaR; Provisional	92.92
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	92.81
PRK06759	154	RNA polymerase factor sigma-70; Validated	92.8
PRK08215	258	sporulation sigma factor SigG; Reviewed	92.79
PF07471	164	Phage_Nu1: Phage DNA packaging protein Nu1; InterP	92.74
PRK09391	230	fixK transcriptional regulator FixK; Provisional	92.71
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	92.68
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	92.68
PRK11924	179	RNA polymerase sigma factor; Provisional	92.68
PRK00215	205	LexA repressor; Validated	92.65
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	92.64
PRK15320	251	transcriptional activator SprB; Provisional	92.6
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	92.47
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	92.46
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	92.44
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	92.36
PRK12519	194	RNA polymerase sigma factor; Provisional	92.34
COG2973	103	TrpR Trp operon repressor [Transcription]	92.33
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	92.31
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	92.3
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	92.27
PHA01082	133	putative transcription regulator	92.24
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	92.17
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	92.16
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	92.15
PF06892	162	Phage_CP76: Phage regulatory protein CII (CP76); I	92.07
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	91.97
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	91.97
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	91.96
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	91.94
PRK13869	405	plasmid-partitioning protein RepA; Provisional	91.9
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	91.87
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	91.8
TIGR03453	387	partition_RepA plasmid partitioning protein RepA.	91.76
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	91.73
PRK09047	161	RNA polymerase factor sigma-70; Validated	91.72
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	91.71
COG1309	201	AcrR Transcriptional regulator [Transcription]	91.7
PRK15115	444	response regulator GlrR; Provisional	91.69
PRK14165	217	winged helix-turn-helix domain-containing protein/	91.69
COG5484	279	Uncharacterized conserved protein [Function unknow	91.62
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	91.59
PRK08583	257	RNA polymerase sigma factor SigB; Validated	91.54
PRK10365	441	transcriptional regulatory protein ZraR; Provision	91.54
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	91.53
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	91.53
PRK08301	234	sporulation sigma factor SigE; Reviewed	91.44
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	91.4
PRK15201	198	fimbriae regulatory protein FimW; Provisional	91.36
PRK10046	225	dpiA two-component response regulator DpiA; Provis	91.33
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	91.33
PRK13919	186	putative RNA polymerase sigma E protein; Provision	91.33
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	91.32
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	91.25
TIGR03613	202	RutR pyrimidine utilization regulatory protein R.	91.22
PRK12529	178	RNA polymerase sigma factor; Provisional	91.22
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	91.21
PRK12537	182	RNA polymerase sigma factor; Provisional	91.17
COG1508	444	RpoN DNA-directed RNA polymerase specialized sigma	91.16
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	91.12
PF11268	170	DUF3071: Protein of unknown function (DUF3071); In	91.1
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	91.05
COG2197	211	CitB Response regulator containing a CheY-like rec	91.05
PRK12423	202	LexA repressor; Provisional	90.96
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	90.96
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	90.95
PRK13832	520	plasmid partitioning protein; Provisional	90.94
PRK12534	187	RNA polymerase sigma factor; Provisional	90.93
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	90.92
TIGR02366	176	DHAK_reg probable dihydroxyacetone kinase regulato	90.92
cd08316	97	Death_FAS_TNFRSF6 Death domain of FAS or TNF recep	90.88
PRK12547	164	RNA polymerase sigma factor; Provisional	90.85
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	90.83
COG4565	224	CitB Response regulator of citrate/malate metaboli	90.83
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	90.82
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	90.81
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	90.8
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	90.76
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	90.74
COG3355	126	Predicted transcriptional regulator [Transcription	90.71
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	90.7
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	90.67
PRK12523	172	RNA polymerase sigma factor; Reviewed	90.67
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	90.65
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	90.64
PRK15008	212	HTH-type transcriptional regulator RutR; Provision	90.61
PRK09975	213	DNA-binding transcriptional regulator EnvR; Provis	90.61
COG1654	79	BirA Biotin operon repressor [Transcription]	90.59
PRK03573	144	transcriptional regulator SlyA; Provisional	90.53
PRK12511	182	RNA polymerase sigma factor; Provisional	90.52
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	90.5
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	90.47
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	90.43
PRK12530	189	RNA polymerase sigma factor; Provisional	90.4
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	90.4
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	90.39
PRK12532	195	RNA polymerase sigma factor; Provisional	90.36
PRK05803	233	sporulation sigma factor SigK; Reviewed	90.36
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	90.31
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	90.29
PRK13777	185	transcriptional regulator Hpr; Provisional	90.28
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	90.28
PRK12513	194	RNA polymerase sigma factor; Provisional	90.27
PRK10668	215	DNA-binding transcriptional repressor AcrR; Provis	90.27
PRK11050	152	manganese transport regulator MntR; Provisional	90.27
PRK12524	196	RNA polymerase sigma factor; Provisional	90.24
PRK15424	538	propionate catabolism operon regulatory protein Pr	90.23
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	90.2
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	90.18
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	90.08
PRK12516	187	RNA polymerase sigma factor; Provisional	90.08
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	90.08
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	90.07
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	89.96
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	89.95
TIGR03384	189	betaine_BetI transcriptional repressor BetI. BetI	89.93
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	89.92
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	89.91
PF04760	54	IF2_N: Translation initiation factor IF-2, N-termi	89.86
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	89.85
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	89.85
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	89.85
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	89.82
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	89.82
PRK09508	314	leuO leucine transcriptional activator; Reviewed	89.8
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	89.72
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	89.7
PRK05602	186	RNA polymerase sigma factor; Reviewed	89.69
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	89.67
PRK12514	179	RNA polymerase sigma factor; Provisional	89.66
PF05043	87	Mga: Mga helix-turn-helix domain; InterPro: IPR007	89.64
PRK06930	170	positive control sigma-like factor; Validated	89.61
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	89.5
PRK12528	161	RNA polymerase sigma factor; Provisional	89.49
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	89.46
PRK12536	181	RNA polymerase sigma factor; Provisional	89.42
PRK12682	309	transcriptional regulator CysB-like protein; Revie	89.4
PRK12525	168	RNA polymerase sigma factor; Provisional	89.4
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	89.38
PRK05022	509	anaerobic nitric oxide reductase transcription reg	89.37
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	89.34
PRK09483	217	response regulator; Provisional	89.3
PRK12542	185	RNA polymerase sigma factor; Provisional	89.3
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	89.27
PRK11202	203	DNA-binding transcriptional repressor FabR; Provis	89.26
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	89.18
PRK12527	159	RNA polymerase sigma factor; Reviewed	89.12
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	89.11
COG2963	116	Transposase and inactivated derivatives [DNA repli	89.07
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	89.05
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	88.99
PRK12526	206	RNA polymerase sigma factor; Provisional	88.97
PRK12545	201	RNA polymerase sigma factor; Provisional	88.96
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	88.93
PRK14996	192	TetR family transcriptional regulator; Provisional	88.91
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	88.9
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	88.89
PRK12518	175	RNA polymerase sigma factor; Provisional	88.88
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	88.86
PHA02535	581	P terminase ATPase subunit; Provisional	88.81
PRK00767	197	transcriptional regulator BetI; Validated	88.79
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	88.78
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	88.75
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	88.74
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	88.71
PHA00738	108	putative HTH transcription regulator	88.71
PRK12533	216	RNA polymerase sigma factor; Provisional	88.7
TIGR03826	137	YvyF flagellar operon protein TIGR03826. This gene	88.63
PRK11557	278	putative DNA-binding transcriptional regulator; Pr	88.58
PRK14845	1049	translation initiation factor IF-2; Provisional	88.52
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	88.48
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	88.43
PRK12515	189	RNA polymerase sigma factor; Provisional	88.4
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	88.39
cd08804	84	Death_ank2 Death domain of Ankyrin-2. Death Domain	88.35
PRK12517	188	RNA polymerase sigma factor; Provisional	88.34
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	88.33
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	88.32
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	88.3
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	88.3
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	88.29
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	88.29
PRK12546	188	RNA polymerase sigma factor; Provisional	88.24
PRK12522	173	RNA polymerase sigma factor; Provisional	88.2
PRK12520	191	RNA polymerase sigma factor; Provisional	88.16
PRK15482	285	transcriptional regulator MurR; Provisional	88.11
PRK06811	189	RNA polymerase factor sigma-70; Validated	88.07
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	87.94
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	87.93
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	87.93
PRK12540	182	RNA polymerase sigma factor; Provisional	87.91
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	87.82
PRK12541	161	RNA polymerase sigma factor; Provisional	87.81
PRK11337	292	DNA-binding transcriptional repressor RpiR; Provis	87.75
TIGR03454	325	partition_RepB plasmid partitioning protein RepB.	87.75
PRK11569	274	transcriptional repressor IclR; Provisional	87.74
PRK08295	208	RNA polymerase factor sigma-70; Validated	87.7
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	87.67
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	87.66
COG1737	281	RpiR Transcriptional regulators [Transcription]	87.6
PRK10086	311	DNA-binding transcriptional regulator DsdC; Provis	87.59
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	87.57
PRK03601	275	transcriptional regulator HdfR; Provisional	87.47
PRK12543	179	RNA polymerase sigma factor; Provisional	87.42
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	87.41
PRK09415	179	RNA polymerase factor sigma C; Reviewed	87.41
PRK10870	176	transcriptional repressor MprA; Provisional	87.41
PRK07405	317	RNA polymerase sigma factor SigD; Validated	87.37
PRK07670	251	RNA polymerase sigma factor SigD; Validated	87.37
PF14174	53	YycC: YycC-like protein	87.35
COG2207	127	AraC AraC-type DNA-binding domain-containing prote	87.33
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	87.26
PRK12531	194	RNA polymerase sigma factor; Provisional	87.21
PRK06704	228	RNA polymerase factor sigma-70; Validated	87.2
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	87.09
PF10743	87	Phage_Cox: Regulatory phage protein cox; InterPro:	87.03
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	87.02
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	87.01
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	87.0
PRK12539	184	RNA polymerase sigma factor; Provisional	86.82
PRK12512	184	RNA polymerase sigma factor; Provisional	86.79
PRK05901	509	RNA polymerase sigma factor; Provisional	86.74
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	86.68
PRK13756	205	tetracycline repressor protein TetR; Provisional	86.57
PRK11922	231	RNA polymerase sigma factor; Provisional	86.5
PRK12538	233	RNA polymerase sigma factor; Provisional	86.45
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	86.43
PRK10216	319	DNA-binding transcriptional regulator YidZ; Provis	86.42
PRK12535	196	RNA polymerase sigma factor; Provisional	86.41
PRK15369	211	two component system sensor kinase SsrB; Provision	86.4

>PHA01976 helix-turn-helix protein

Probab=99.76  E-value=4.7e-18  Score=90.89  Aligned_cols=58  Identities=28%  Similarity=0.476  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|+..|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||++++
T Consensus         3 ~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~   60 (67)
T PHA01976          3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDW   60 (67)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4789999999999999999999999999999999999999999999999999999875

>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=99.75  E-value=5.4e-18  Score=89.94  Aligned_cols=57  Identities=32%  Similarity=0.493  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|+..|+||.+||+.+|+++++|++||+|...|+...+.+||++|||++++
T Consensus         1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~   57 (64)
T PF12844_consen    1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDE   57 (64)
T ss_dssp             HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHH
Confidence            689999999999999999999999999999999999999999999999999999875

>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=99.73  E-value=9.7e-18  Score=86.49  Aligned_cols=54  Identities=35%  Similarity=0.487  Sum_probs=49.9

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus         1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~   54 (55)
T PF01381_consen    1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEY   54 (55)
T ss_dssp             HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHH
T ss_pred             CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            688999999999999999999999999999999999999999999999999864

; 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 ....

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=99.72  E-value=2.4e-17  Score=88.31  Aligned_cols=57  Identities=19%  Similarity=0.309  Sum_probs=54.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+++.+|...|+||.+||+.+|||++||..||+|+..|++....+||+.|++++++.
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedI   60 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDI   60 (68)
T ss_pred             hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHHH
Confidence            489999999999999999999999999999999999999999999999999998763

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=99.71  E-value=1.2e-16  Score=82.60  Aligned_cols=56  Identities=21%  Similarity=0.310  Sum_probs=53.6

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      .+.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+|+++||+++
T Consensus         3 ~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lgv~l   58 (58)
T TIGR03070         3 IGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALGLEL   58 (58)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence            37899999999999999999999999999999999999999999999999999985

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.

>PRK06424 transcription factor; Provisional

Probab=99.68  E-value=2.7e-16  Score=95.54  Aligned_cols=59  Identities=34%  Similarity=0.487  Sum_probs=57.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      +.+|+.+|+.+||||.+||+.+|+++++|++||+|...|+.+.+.+|+++||+++.|++
T Consensus        86 g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~  144 (144)
T PRK06424         86 AELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA  144 (144)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence            89999999999999999999999999999999999999999999999999999999864

>PRK08359 transcription factor; Validated

Probab=99.67  E-value=3.6e-16  Score=97.50  Aligned_cols=59  Identities=15%  Similarity=0.241  Sum_probs=57.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      +.+|+.+|+.+||||.+||..+|++.++|++||+|...|+.+.+.+||++|||++.+..
T Consensus        87 ~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~  145 (176)
T PRK08359         87 AERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERV  145 (176)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccccc
Confidence            99999999999999999999999999999999999999999999999999999997753

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

Probab=99.65  E-value=2.5e-16  Score=83.70  Aligned_cols=59  Identities=27%  Similarity=0.456  Sum_probs=51.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |..|+.+|+..|+||.++|+.+|+|+++|++||+|.. .|+.+.+.+||.+||+++++.+
T Consensus         3 g~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~~~~   62 (64)
T PF13560_consen    3 GRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPDERA   62 (64)
T ss_dssp             HHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHHHHc
Confidence            6889999999999999999999999999999999999 5999999999999999988754

>PRK09726 antitoxin HipB; Provisional

Probab=99.65  E-value=1.2e-15  Score=85.79  Aligned_cols=57  Identities=18%  Similarity=0.323  Sum_probs=55.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|...|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++-
T Consensus        14 ~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~   70 (88)
T PRK09726         14 ANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL   70 (88)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcch
Confidence            889999999999999999999999999999999999999999999999999999764

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=99.64  E-value=8.1e-16  Score=94.41  Aligned_cols=58  Identities=31%  Similarity=0.472  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +.+|+.+|+.+||||.+||+.+|+++++|++||+|...|+.+.+.+|+++||+++++.
T Consensus        71 g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~el  128 (154)
T TIGR00270        71 GIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQ  128 (154)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHH
Confidence            8999999999999999999999999999999999999999999999999999999773

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=99.64  E-value=1e-15  Score=91.88  Aligned_cols=58  Identities=22%  Similarity=0.262  Sum_probs=55.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|...|+||.+||+.+|||+++|++||+|...|+.+.+.+||++|||+++.
T Consensus         6 ~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~   63 (135)
T PRK09706          6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTW   63 (135)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4899999999999999999999999999999999999999999999999999999763

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=99.59  E-value=1.1e-14  Score=79.70  Aligned_cols=57  Identities=16%  Similarity=0.154  Sum_probs=54.5

Q ss_pred             CHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           21 TPRQIQ-RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        21 ~~~~lk-~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .|++|+ .+|+..|+|+.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
T Consensus         5 ~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~   62 (78)
T TIGR02607         5 PGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPE   62 (78)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHH
Confidence            478999 899999999999999999999999999999999999999999999999975

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.

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=99.57  E-value=1.2e-14  Score=86.10  Aligned_cols=58  Identities=19%  Similarity=0.283  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.++..+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++
T Consensus         6 ~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~~   63 (120)
T PRK13890          6 FFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPL   63 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            4788999999999999999999999999999999999999999999999999997654

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=99.57  E-value=9.4e-15  Score=91.59  Aligned_cols=58  Identities=22%  Similarity=0.283  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+...+.+||++||+++++
T Consensus         8 ~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~   65 (185)
T PRK09943          8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSE   65 (185)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            4899999999999999999999999999999999999999999999999999999865

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=99.56  E-value=8.1e-15  Score=98.20  Aligned_cols=70  Identities=19%  Similarity=0.250  Sum_probs=60.9

Q ss_pred             hhhccCCCCCCC---HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           10 MRKLDEGTEPDT---PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        10 ~~~~~~~~~~~~---~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      |+.+..+...|.   |.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        15 ~~~~~~~~~~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l   87 (309)
T PRK08154         15 MTGAAAEEAPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL   87 (309)
T ss_pred             CCCCccchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHH
Confidence            333444444443   9999999999999999999999999999999999999999999999999999998753

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=99.56  E-value=8.5e-15  Score=82.65  Aligned_cols=60  Identities=23%  Similarity=0.320  Sum_probs=54.6

Q ss_pred             CCCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           16 GTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        16 ~~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ....+.+..|+.+|+..|+||  ||+++||++++|++||+|...|+.+.+.+||++||+++.
T Consensus        28 ~~~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~   87 (89)
T TIGR02684        28 GDPAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT   87 (89)
T ss_pred             CCHHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence            344455889999999999995  999999999999999999999999999999999999875

gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.

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

Probab=99.55  E-value=1.8e-14  Score=76.02  Aligned_cols=56  Identities=23%  Similarity=0.310  Sum_probs=43.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +|+.++..+|+|+.+||+.+|++++++++|.+|. ..|+.+.+.+||.+|||+++|.
T Consensus         1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el   57 (63)
T PF13443_consen    1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEEL   57 (63)
T ss_dssp             HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHHC
T ss_pred             CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHHH
Confidence            5889999999999999999999999999999998 7999999999999999999874

>PRK10072 putative transcriptional regulator; Provisional

Probab=99.54  E-value=5.9e-14  Score=80.18  Aligned_cols=56  Identities=18%  Similarity=0.298  Sum_probs=52.3

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .+..|+.+|...|+||.+||+.+|+|.+||++||+|.+.|+...+. +++++|++|.
T Consensus        34 ~~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P~   89 (96)
T PRK10072         34 SFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANPA   89 (96)
T ss_pred             ChHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCHH
Confidence            5778999999999999999999999999999999999999999954 9999999983

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=99.49  E-value=1.3e-13  Score=84.36  Aligned_cols=56  Identities=20%  Similarity=0.229  Sum_probs=52.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA--VPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~--~p~~~~~~~la~~lgv~~~   77 (82)
                      ..+|+.+|...||||.+||+.+|||+++|++||+|..  .|+.+.+.+||++|||++.
T Consensus        27 ~~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~   84 (150)
T TIGR02612        27 EGWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFV   84 (150)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHH
Confidence            5789999999999999999999999999999999975  4899999999999999964

Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).

>PRK04140 hypothetical protein; Provisional

Probab=99.48  E-value=1.4e-13  Score=92.58  Aligned_cols=57  Identities=26%  Similarity=0.352  Sum_probs=55.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|+..||||.+||+.+|+|+++|++||+|...|+.+.+.+|+++||+++.+
T Consensus       128 GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~~  184 (317)
T PRK04140        128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTK  184 (317)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChHH
Confidence            999999999999999999999999999999999999999999999999999998644

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=99.43  E-value=1.2e-12  Score=65.33  Aligned_cols=54  Identities=33%  Similarity=0.500  Sum_probs=51.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |+.+|...++|+.+||+.+|+++.+|++|++|...|+.+.+..++++||++++.
T Consensus         2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~   55 (56)
T smart00530        2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE   55 (56)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChhh
Confidence            677899999999999999999999999999999999999999999999999864

>KOG3398 consensus Transcription factor MBF1 [Transcription]

Probab=99.41  E-value=1.4e-12  Score=76.83  Aligned_cols=78  Identities=50%  Similarity=0.709  Sum_probs=70.8

Q ss_pred             ccchhhhhhhccCCCCCCC--------HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591            3 TAGAVINMRKLDEGTEPDT--------PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~--------~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      .-+.+++.+++|++.+...        |..|...|..+||||++||.+++=.++.|..||+|+..|+...+.++.++|||
T Consensus        48 q~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgv  127 (135)
T KOG3398|consen   48 QHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGV  127 (135)
T ss_pred             cCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhce
Confidence            3456788899988777664        89999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 038591           75 KLRVKI   80 (82)
Q Consensus        75 ~~~e~~   80 (82)
                      .++.++
T Consensus       128 Klrgk~  133 (135)
T KOG3398|consen  128 KLRGKN  133 (135)
T ss_pred             eccccc
Confidence            988765

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=99.40  E-value=3e-12  Score=64.31  Aligned_cols=56  Identities=32%  Similarity=0.504  Sum_probs=52.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..|+.++...|+|+.++|..+|+++.+|++|++|...|+...+..|++.||++++.
T Consensus         2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~~   57 (58)
T cd00093           2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE   57 (58)
T ss_pred             hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChhh
Confidence            56888899999999999999999999999999999999999999999999998764

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

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

Probab=99.38  E-value=2.9e-12  Score=75.72  Aligned_cols=62  Identities=24%  Similarity=0.327  Sum_probs=55.0

Q ss_pred             CCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           17 TEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        17 ~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ...+.+..|+.+|...|+||.+||+.+|+++++|++||+|...|+.. +..+++.|+++++..
T Consensus        62 ~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~~l  123 (127)
T TIGR03830        62 DGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPELL  123 (127)
T ss_pred             cCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChHHH
Confidence            34556899999999999999999999999999999999999888865 688889999998653

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.

>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

Probab=99.38  E-value=2.4e-12  Score=79.32  Aligned_cols=58  Identities=38%  Similarity=0.570  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +++|+.+|+.+||||++||.+++++.+.|.+||+|...|+...+.+|.++||+.+.++
T Consensus        81 ~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~  138 (165)
T COG1813          81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK  138 (165)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence            8999999999999999999999999999999999999999999999999999998765

>PHA00542 putative Cro-like protein

Probab=99.28  E-value=5.2e-11  Score=66.23  Aligned_cols=54  Identities=17%  Similarity=0.278  Sum_probs=48.7

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG   73 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg   73 (82)
                      +....+..++...|+|+.+||+.+|||+++|++||+|. ..|+.+.+.+||+++-
T Consensus        18 ~~~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~   72 (82)
T PHA00542         18 QRPDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVL   72 (82)
T ss_pred             cCHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            34667888899999999999999999999999999998 5899999999999863

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=99.26  E-value=3.2e-11  Score=69.46  Aligned_cols=49  Identities=24%  Similarity=0.390  Sum_probs=43.8

Q ss_pred             CCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591           17 TEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL   65 (82)
Q Consensus        17 ~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~   65 (82)
                      ...+.+..|+.+|+..|+||.+||..+|+|.+||++||+|...|+-..+
T Consensus        41 ~~~ls~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Al   89 (104)
T COG2944          41 VKTLSPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAAL   89 (104)
T ss_pred             CCCCCHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHH
Confidence            3446699999999999999999999999999999999999999886553

>PRK10856 cytoskeletal protein RodZ; Provisional

Probab=99.25  E-value=2.5e-11  Score=82.34  Aligned_cols=58  Identities=16%  Similarity=0.221  Sum_probs=53.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ------TVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~------~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+||||.+||+++++++++|++||+|...+..      ..+..+|++||++.++
T Consensus        15 ~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~   78 (331)
T PRK10856         15 TGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEE   78 (331)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHH
Confidence            489999999999999999999999999999999999887776      4589999999999875

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

Probab=99.21  E-value=5.1e-11  Score=65.90  Aligned_cols=56  Identities=23%  Similarity=0.293  Sum_probs=46.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ...|..+++..||||.++|+.+|++++.|+++++| ...++.+.+..++..+|..++
T Consensus        20 ~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~   76 (80)
T PF13744_consen   20 MAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE   76 (80)
T ss_dssp             HHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence            56688999999999999999999999999999998 468999999999999998764

>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]

Probab=99.20  E-value=8.8e-11  Score=72.42  Aligned_cols=52  Identities=21%  Similarity=0.395  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      .+-|+..|+..|+||++||+..|+|+++|.++|.|+..|.+.++.+|.++|-
T Consensus         7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~   58 (187)
T COG3620           7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALE   58 (187)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence            6789999999999999999999999999999999999999999999998874

>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]

Probab=99.11  E-value=4.2e-10  Score=64.74  Aligned_cols=57  Identities=16%  Similarity=0.225  Sum_probs=52.3

Q ss_pred             CHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           21 TPRQIQR-ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        21 ~~~~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .|+.|++ +.+..|+|+.+||+.+||++.+|+.+.+|++.++.+++.+|+++||.+++
T Consensus        10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe   67 (104)
T COG3093          10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE   67 (104)
T ss_pred             chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence            4888855 66778999999999999999999999999999999999999999999875

>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional

Probab=99.08  E-value=5.3e-10  Score=79.14  Aligned_cols=57  Identities=23%  Similarity=0.364  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQI-----NQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~-----gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|+..|+||.+||+.+     +|++++|++||+|+..|+.+.+..||++|||+++.
T Consensus         5 ~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~   66 (517)
T PRK13355          5 AERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDW   66 (517)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            6899999999999999999996     69999999999999999999999999999999864

>PRK02866 cyanate hydratase; Validated

Probab=99.02  E-value=2e-09  Score=65.50  Aligned_cols=57  Identities=18%  Similarity=0.176  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.|..+|.++|+|++++|+.+|+|+.++..++.|+..++.+.+.+||++||++.+.
T Consensus         7 ~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~~   63 (147)
T PRK02866          7 TEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDA   63 (147)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHHH
Confidence            567899999999999999999999999999999999999999999999999988654

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=98.98  E-value=4.6e-09  Score=57.26  Aligned_cols=46  Identities=11%  Similarity=0.242  Sum_probs=39.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      +.+++..|...|+||.+||+.+|      +|+++|++||+|.  .+..++.+|-
T Consensus        13 ~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~--ls~~n~~kl~   64 (75)
T smart00352       13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLK   64 (75)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcC--ccHHHHHHHH
Confidence            89999999999999999999999      5999999999974  4566655553

>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=98.93  E-value=6.5e-10  Score=59.41  Aligned_cols=53  Identities=21%  Similarity=0.355  Sum_probs=39.5

Q ss_pred             HHHHHHHhCCCCH-HHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           24 QIQRARLGKKMSQ-PDLANQINQRPQVVS-EYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        24 ~lk~~r~~~g~s~-~elA~~~gis~~~i~-~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .|+.+++..|++. .+||+.+|||+++|+ .|......| .+.+.+||..+||+++
T Consensus         2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~~gvsl~   56 (66)
T PF07022_consen    2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALETGVSLD   56 (66)
T ss_dssp             HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHHH---HH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHHHCcCHH
Confidence            5777888888765 699999999999999 899877676 9999999999999986

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.

>TIGR00673 cynS cyanate hydratase

Probab=98.92  E-value=1e-08  Score=62.58  Aligned_cols=56  Identities=11%  Similarity=0.124  Sum_probs=53.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .+.|..++.++|+|.+++|+.+|+|+..+..++.|+..++.+.+.+||++||++-+
T Consensus        10 t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~e   65 (150)
T TIGR00673        10 ADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDED   65 (150)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCHH
Confidence            57788999999999999999999999999999999999999999999999998754

Alternate names include cyanate lyase, cyanase and cyanate hydrolase.

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=98.91  E-value=6e-09  Score=56.55  Aligned_cols=58  Identities=21%  Similarity=0.212  Sum_probs=52.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .-++..++..++++..+||+.+|||.++++.+.+|+ ..+.++++.+||++|.|.|.|.
T Consensus         4 ~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDi   62 (73)
T COG3655           4 AVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDI   62 (73)
T ss_pred             hHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhhe
Confidence            456788899999999999999999999999999886 4689999999999999999764

>COG1709 Predicted transcriptional regulator [Transcription]

Probab=98.89  E-value=3.1e-09  Score=68.21  Aligned_cols=52  Identities=27%  Similarity=0.465  Sum_probs=48.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAV-PNQTVLAKMEKAI   72 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~-p~~~~~~~la~~l   72 (82)
                      .|+.|+.+|+..++||.|||+.+|+|++.|+.||.|++. |....+.++-.+|
T Consensus        28 pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          28 PGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             hhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence            499999999999999999999999999999999999877 9999988887766

>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A

Probab=98.86  E-value=9.6e-09  Score=54.36  Aligned_cols=55  Identities=24%  Similarity=0.375  Sum_probs=41.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC--CCCCCH----HHHHHHHHHhCCCCcc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG--KAVPNQ----TVLAKMEKAIGVKLRV   78 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g--~~~p~~----~~~~~la~~lgv~~~e   78 (82)
                      +|+.+|+.+|+|..++|..++|+.++|..+|+|  ...|+.    ..+..+|++||++.++
T Consensus         1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~   61 (62)
T PF13413_consen    1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDE   61 (62)
T ss_dssp             -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHH
T ss_pred             ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCccc
Confidence            488999999999999999999999999999999  445654    3488999999998764

>COG1395 Predicted transcriptional regulator [Transcription]

Probab=98.83  E-value=1.4e-08  Score=68.22  Aligned_cols=56  Identities=23%  Similarity=0.316  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      |+.|++.|++.|+|.-+||..+|+|+.+|++||+|...|+.+.+.+|-..||.++-
T Consensus       127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv  182 (313)
T COG1395         127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIV  182 (313)
T ss_pred             hHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchhh
Confidence            99999999999999999999999999999999999999999999999999998764

>COG1396 HipB Predicted transcriptional regulators [Transcription]

Probab=98.76  E-value=8.2e-08  Score=52.01  Aligned_cols=56  Identities=29%  Similarity=0.503  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~   77 (82)
                      +.+++.+|...|+|+.++|..+|++..+++.||+|.. .|+...+..++..|+++..
T Consensus         3 ~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~   59 (120)
T COG1396           3 GERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLD   59 (120)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCHH
Confidence            6789999999999999999999999999999999988 9999999999999888654

>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems

Probab=98.65  E-value=1.1e-07  Score=58.01  Aligned_cols=59  Identities=17%  Similarity=0.161  Sum_probs=54.2

Q ss_pred             CCHHHHHHHHHhCCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQRARLGKKMSQ----PDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~----~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ...++|+.+...+|+.+    .+||+.||+|.+++++-.+|+...+...+.+|++.||+++++
T Consensus         5 ~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d~   67 (147)
T PF08667_consen    5 AIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPDE   67 (147)
T ss_pred             HHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHHH
Confidence            34789999999999876    679999999999999999999999999999999999999875

BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].

>PHA01083 hypothetical protein

Probab=98.58  E-value=2.3e-07  Score=56.41  Aligned_cols=56  Identities=13%  Similarity=0.280  Sum_probs=48.1

Q ss_pred             HHHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCcc
Q 038591           23 RQIQRARLGKKM-SQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        23 ~~lk~~r~~~g~-s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.|....+..++ +-++||..+||+++.|++|.+| ++.++.+.+..||+.+|+++.+
T Consensus         5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~e   62 (149)
T PHA01083          5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEI   62 (149)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            445666666654 5589999999999999999999 9999999999999999999853

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

Probab=98.54  E-value=3.6e-07  Score=46.05  Aligned_cols=41  Identities=20%  Similarity=0.249  Sum_probs=34.0

Q ss_pred             HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           38 DLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        38 elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      +||+.+|+|++||++|++|...++...   +..++..||+.++.
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~~   45 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNA   45 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence            799999999999999999986666444   56688899987753

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

>COG5499 Predicted transcription regulator containing HTH domain [Transcription]

Probab=98.49  E-value=4.3e-07  Score=52.72  Aligned_cols=55  Identities=20%  Similarity=0.233  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      -+.|+.+++..|+|+.+||..+| |.+.+|++.+|++..+.+.+.+|.+-||++.+
T Consensus        62 ve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~  116 (120)
T COG5499          62 VEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPAD  116 (120)
T ss_pred             HHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHH
Confidence            57889999999999999999998 67999999999999999999999999999875

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

Probab=98.47  E-value=1.1e-06  Score=43.82  Aligned_cols=42  Identities=17%  Similarity=0.250  Sum_probs=33.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKL   76 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~   76 (82)
                      |.+|+|+.+|+|.+|||++.+|...++.++   +..+++.+|..+
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~p   45 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYRP   45 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence            578999999999999999999988887776   455566666554

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 ....

>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]

Probab=98.45  E-value=8.3e-07  Score=59.34  Aligned_cols=59  Identities=20%  Similarity=0.290  Sum_probs=50.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCH----HHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA--VPNQ----TVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~--~p~~----~~~~~la~~lgv~~~e~   79 (82)
                      .|++|++.|+++|||+.|+|.+++|.+.++..+|+|..  .|..    ..+..+|+++|++.++.
T Consensus         4 ~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l   68 (284)
T COG1426           4 LGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDEL   68 (284)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHHH
Confidence            48999999999999999999999999999999999943  3432    35789999999998753

>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins

Probab=98.29  E-value=5.6e-06  Score=48.79  Aligned_cols=51  Identities=14%  Similarity=0.140  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN--QRPQVVSEYENGKAVPNQTVLAKMEKAI   72 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~g~~~p~~~~~~~la~~l   72 (82)
                      +..|+.+|...++|+.|.|..++  ++..+..+||+|...++.+.+..+....
T Consensus         3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~   55 (118)
T PF08965_consen    3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMK   55 (118)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            56789999999999999999999  9999999999999999998887776543

; PDB: 1S4K_A.

>COG3636 Predicted transcriptional regulator [Transcription]

Probab=98.28  E-value=1.9e-06  Score=49.05  Aligned_cols=54  Identities=17%  Similarity=0.190  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ...+-..-...||||  +|++.|+|+..+++-.+...+|+++++.+++++||+.+.
T Consensus        40 ~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~   93 (100)
T COG3636          40 AAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLS   93 (100)
T ss_pred             HHHHHHHHHhcCHHH--HHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCceee
Confidence            444444556678877  999999999999999999999999999999999998653

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=98.24  E-value=6e-06  Score=44.36  Aligned_cols=44  Identities=16%  Similarity=0.142  Sum_probs=36.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      +|+.|+|+.+|+|.+||+++.+|...++.+.   +..+++.+|..++
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~   47 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPN   47 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence            4789999999999999999999987766544   6667888887665

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=98.19  E-value=8.9e-06  Score=46.27  Aligned_cols=47  Identities=13%  Similarity=0.130  Sum_probs=34.7

Q ss_pred             HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591           22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      ..|+.-+..  ..++||+|+|..+|||.+||++++++-...+++.-..|
T Consensus        42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l   90 (94)
T TIGR01321        42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFL   90 (94)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHH
Confidence            344444432  47899999999999999999999999775554444443

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.

>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]

Probab=98.18  E-value=1.1e-05  Score=49.01  Aligned_cols=54  Identities=17%  Similarity=0.180  Sum_probs=48.3

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI   72 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l   72 (82)
                      .+-++..|+.+..+.|+|..|||++.|+.++|++++.+| +.|..+++.+|-+.+
T Consensus        14 ~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti   67 (170)
T COG4800          14 GEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI   67 (170)
T ss_pred             hhHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhC-CCccHHHHHHHHHHH
Confidence            344588899999999999999999999999999999999 789999998887765

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=98.08  E-value=1.5e-05  Score=47.11  Aligned_cols=34  Identities=24%  Similarity=0.226  Sum_probs=30.0

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           26 QRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      +.++++ |+||.++|+.+|+|+++||+|.+|++.+
T Consensus        16 ~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522          16 KELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence            455565 9999999999999999999999998774

>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A

Probab=98.00  E-value=2e-05  Score=43.42  Aligned_cols=55  Identities=15%  Similarity=0.068  Sum_probs=41.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ...|+.....+|+|..+||+..|++++|+++...   .|....-..||+++|+++.+.
T Consensus         4 ~adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal~---r~~pk~E~~IA~aLgv~P~eI   58 (78)
T PF13693_consen    4 RADIKAALRKRGTSLAALSREAGLSSSTLRNALR---RPWPKGERIIADALGVPPEEI   58 (78)
T ss_dssp             HHHHHHHHCTTS--HHHHHHHHSS-HHHHHHTTT---SS-HHHHHHHHHHTTS-HHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHHHh
Confidence            4567777778999999999999999999999874   556667788999999998763

>COG3423 Nlp Predicted transcriptional regulator [Transcription]

Probab=97.98  E-value=7.2e-05  Score=40.89  Aligned_cols=59  Identities=17%  Similarity=0.135  Sum_probs=47.3

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ......-|....+.+|+|...|+.+.|+|++|+.+.... ..|..+  ..||.++||++.|.
T Consensus         6 ~dWh~adI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r-p~pkgE--riIA~algv~P~eI   64 (82)
T COG3423           6 QDWHPADIIAALKKKGTSLAALSREAGLSSSTLANALDR-PWPKGE--RIIADALGVPPEEI   64 (82)
T ss_pred             ccCCHHHHHHHHHHccccHHHHHHHcCCCHHHHHHHHcC-CCchHH--HHHHHHhCCCHHHh
Confidence            445566677778889999999999999999999999863 344444  56899999999874

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=97.97  E-value=2.2e-05  Score=54.69  Aligned_cols=47  Identities=15%  Similarity=0.252  Sum_probs=43.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCcc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|+|..+||+.+|+|.++++++|||+ ..|+.+.+.+|+++|||+...
T Consensus         2 ~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~~   49 (399)
T PRK08099          2 QGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR   49 (399)
T ss_pred             CCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChhh
Confidence            68999999999999999999999995 579999999999999998643

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=97.87  E-value=4.3e-05  Score=50.90  Aligned_cols=48  Identities=15%  Similarity=0.207  Sum_probs=44.8

Q ss_pred             CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           33 KMSQPDLANQINQRP-QVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        33 g~s~~elA~~~gis~-~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      .+|-.+||+.+|++. ++++.+++|+++++...+.+++.+||.+..|.+
T Consensus        27 ~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~~   75 (271)
T TIGR02147        27 AFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEALGLDEKEAA   75 (271)
T ss_pred             CcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            699999999999876 999999999999999999999999999988754

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

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

Probab=97.74  E-value=8.6e-05  Score=37.00  Aligned_cols=31  Identities=16%  Similarity=0.147  Sum_probs=22.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .|..+.+  |+|..++|+.+|+|++||++|.+-
T Consensus        10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred             HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3444444  999999999999999999999864

>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional

Probab=97.70  E-value=0.0005  Score=38.75  Aligned_cols=58  Identities=16%  Similarity=0.034  Sum_probs=46.0

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .....-|......+|+|...|+...|++.+|+.+...   .|-+.-=..||++||+.+.+.
T Consensus         7 DWH~adI~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~---rp~PKgEriIA~aLGv~P~eI   64 (92)
T PRK10344          7 DWHPADIIAGLRKKGTSMAAESRRNGLSSSTLANALS---RPWPKGEMIIAKALGTDPWVI   64 (92)
T ss_pred             CCCHHHHHHHHHHcCCcHHHHHHHcCCChHHHHHHHc---CCCchHHHHHHHHHCcCHHHh
Confidence            4455667777777999999999999999999999876   333344467999999998764

>PRK09526 lacI lac repressor; Reviewed

Probab=97.66  E-value=0.00015  Score=48.40  Aligned_cols=47  Identities=15%  Similarity=0.026  Sum_probs=38.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      +..|.+|+|+.+|||.+|||++.||...++.++   +..+++.||..++.
T Consensus         4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~   53 (342)
T PRK09526          4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNR   53 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            357999999999999999999999987676655   66677778876653

>TIGR01481 ccpA catabolite control protein A

Probab=97.65  E-value=0.0002  Score=47.54  Aligned_cols=45  Identities=16%  Similarity=0.164  Sum_probs=37.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .|.+|+|+.+|||.+|||++.||...++.++   +.+.++.||..++.
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~   49 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNA   49 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence            4789999999999999999999987777666   56678888887653

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.

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=97.65  E-value=0.00022  Score=47.50  Aligned_cols=47  Identities=19%  Similarity=0.135  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCCcc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM---EKAIGVKLRV   78 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l---a~~lgv~~~e   78 (82)
                      ...|.+|+|+.+|||.+|||+..||...++.++-.++   ++.||..++.
T Consensus         5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~~   54 (342)
T PRK10014          5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNR   54 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCH
Confidence            3589999999999999999999999888887775544   8888887653

>PRK09492 treR trehalose repressor; Provisional

Probab=97.62  E-value=0.00023  Score=46.97  Aligned_cols=46  Identities=15%  Similarity=0.122  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .+|.+|+|+.+|||.+|||++.||...++.++   +.+.++.+|..++.
T Consensus         4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~   52 (315)
T PRK09492          4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPSK   52 (315)
T ss_pred             CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            47999999999999999999999987777666   44567788876653

>PHA00675 hypothetical protein

Probab=97.62  E-value=0.00019  Score=39.29  Aligned_cols=37  Identities=16%  Similarity=0.109  Sum_probs=31.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      -+.|+.+++..|.|..+||..+|+|+++|++|.+|+.
T Consensus        28 V~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~   64 (78)
T PHA00675         28 VERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER   64 (78)
T ss_pred             HHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence            4556666667899999999999999999999999864

>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=97.62  E-value=0.00019  Score=35.38  Aligned_cols=34  Identities=24%  Similarity=0.259  Sum_probs=24.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+.+..++. .|+|..++|+.+|||++||++|.+.
T Consensus        11 ~~~i~~l~~-~G~si~~IA~~~gvsr~TvyR~l~~   44 (45)
T PF02796_consen   11 IEEIKELYA-EGMSIAEIAKQFGVSRSTVYRYLNK   44 (45)
T ss_dssp             HHHHHHHHH-TT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred             HHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            455666554 5699999999999999999999763

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 ....

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=97.62  E-value=0.00023  Score=47.47  Aligned_cols=44  Identities=14%  Similarity=0.055  Sum_probs=36.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      +|.+|+|+.+|+|.+|||++.||...++.++   +.++++.+|..++
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn   48 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS   48 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            4899999999999999999999977676555   6677778887664

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=97.62  E-value=0.00024  Score=47.10  Aligned_cols=44  Identities=16%  Similarity=0.111  Sum_probs=36.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA---VPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~---~p~~~~---~~~la~~lgv~~~   77 (82)
                      +|.+|+|+.+|||.+|||++.||..   .++.++   +.+.++.||..++
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~elgY~pn   50 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN   50 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHhCCCCC
Confidence            5889999999999999999999975   466655   5566778887665

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=97.61  E-value=0.00026  Score=46.83  Aligned_cols=45  Identities=13%  Similarity=0.097  Sum_probs=36.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .|.+|+|+.+|+|++|||++.||...++.++   +...++.+|..++.
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~   49 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSK   49 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            5899999999999999999999977666655   55567778877653

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

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=97.61  E-value=0.00024  Score=47.56  Aligned_cols=45  Identities=11%  Similarity=0.083  Sum_probs=37.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .|.+|+|+.+|||.+|||++.||...++.++   +.+.++.||..++-
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~   49 (343)
T PRK10727          2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNA   49 (343)
T ss_pred             CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence            4889999999999999999999987777665   66667788877653

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=97.61  E-value=0.00075  Score=37.35  Aligned_cols=50  Identities=8%  Similarity=0.019  Sum_probs=40.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG   73 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg   73 (82)
                      ..+..++. ..+|..++|+.+|+|..||++..++. ..++.++-.++-.+..
T Consensus        10 ~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844        10 EIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD   60 (80)
T ss_pred             HHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence            34455667 88999999999999999999999985 6788888777766554

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.

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

Probab=97.57  E-value=0.00021  Score=37.54  Aligned_cols=42  Identities=29%  Similarity=0.276  Sum_probs=30.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      ..| ++..||+.+|||+++|++|  + ..++......|..+-+-.+
T Consensus         8 ~~G-~~~~lAkalGVs~~aVs~W--~-~~IP~~ra~~Ie~~T~G~l   49 (60)
T PF14549_consen    8 YFG-GQSKLAKALGVSPQAVSQW--G-ERIPAERAYQIEKLTNGKL   49 (60)
T ss_dssp             HHS-SHHHHHHHHTS-HHHHHHH--H-TS--HHHHHHHHHHTTTSS
T ss_pred             HHC-CHHHHHHHHCCCHHHHHHh--c-CccCHHHHHHHHHHhCCce
Confidence            345 7899999999999999999  3 4566777788877665433

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=97.57  E-value=0.00019  Score=47.72  Aligned_cols=46  Identities=13%  Similarity=0.156  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      ..|.+|+|+.+|||.+|||++.||...++.++   +.++++.||..++.
T Consensus         5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~   53 (331)
T PRK14987          5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNR   53 (331)
T ss_pred             CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCccH
Confidence            47999999999999999999999987776665   56677888877653

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.56  E-value=0.00047  Score=37.53  Aligned_cols=40  Identities=20%  Similarity=0.256  Sum_probs=32.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      .|...|+|+.|+|+.+|+|+++|..+.++  .+....+.+++
T Consensus        27 ~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~~   66 (73)
T TIGR03879        27 AREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKLA   66 (73)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHHH
Confidence            36679999999999999999999999985  34444555554

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.

>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family

Probab=97.56  E-value=0.00054  Score=41.11  Aligned_cols=54  Identities=2%  Similarity=-0.029  Sum_probs=44.1

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKA   71 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~   71 (82)
                      .-+....+..+....|++++++|..+|+|++|++++-++...++.+.-.++..+
T Consensus        21 ~Glp~~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l   74 (133)
T TIGR02293        21 RGLPIGALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV   74 (133)
T ss_pred             cCCCHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence            345578888899999999999999999999999999987667776665555443

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.

>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1

Probab=97.53  E-value=0.00039  Score=43.75  Aligned_cols=51  Identities=10%  Similarity=0.012  Sum_probs=35.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI   72 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l   72 (82)
                      .+.||.++..++|+|.++++.+|||.++||+|.+-....+...=..|-..|
T Consensus       120 keeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~Wy  170 (180)
T PF04814_consen  120 KEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRWY  170 (180)
T ss_dssp             HHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHHH
Confidence            889999999999999999999999999999999755555555544444443

This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=97.51  E-value=0.00042  Score=46.42  Aligned_cols=44  Identities=20%  Similarity=0.224  Sum_probs=36.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      .|.+|+|+.+|||.+|||++.||...++.++   +.+.++.+|..++
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn   48 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPN   48 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            5889999999999999999999977666555   6666777887665

>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain

Probab=97.50  E-value=0.00086  Score=36.66  Aligned_cols=47  Identities=11%  Similarity=0.253  Sum_probs=36.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      +..++..|...|+||.+++..+|      .|+++|+++|+  -..+...+.+|-=
T Consensus        13 a~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~--L~LS~kn~~klkP   65 (75)
T PF00157_consen   13 AKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEA--LQLSFKNMCKLKP   65 (75)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHT--TTSCHHHHHHHHH
T ss_pred             HHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHh--cccCHHHHHHHHH
Confidence            57788999999999999999886      58999999998  4567777666543

The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=97.42  E-value=0.00058  Score=45.33  Aligned_cols=44  Identities=20%  Similarity=0.204  Sum_probs=35.8

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC---CCCHHH---HHHHHHHhCCCCcc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKA---VPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~---~p~~~~---~~~la~~lgv~~~e   78 (82)
                      |.+|+|+.+|||.+|||++.||..   .++.++   +.++++.+|..++.
T Consensus         1 ti~dIA~~aGVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~   50 (327)
T TIGR02417         1 TLSDIAKLAGVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQPNI   50 (327)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCCCH
Confidence            578999999999999999999975   466665   55678888887753

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.

>PHA02591 hypothetical protein; Provisional

Probab=97.39  E-value=0.00053  Score=37.68  Aligned_cols=31  Identities=13%  Similarity=0.179  Sum_probs=26.4

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.....+.|+||.++|+.+|++..+|++|..
T Consensus        51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4444556899999999999999999999975

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

Probab=97.39  E-value=0.00028  Score=34.62  Aligned_cols=31  Identities=23%  Similarity=0.249  Sum_probs=20.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..++ ..|+|+.++|+.+|++++||+++..
T Consensus        12 ~I~~l~-~~G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen   12 QIEALL-EQGMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             HHHHHH-CS---HHHHHHHTT--HHHHHHHHH
T ss_pred             HHHHHH-HcCCCHHHHHHHHCcCcHHHHHHHh
Confidence            355554 5899999999999999999999763

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

Probab=97.38  E-value=0.00056  Score=33.79  Aligned_cols=33  Identities=18%  Similarity=0.347  Sum_probs=26.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+.+.-++|+.++|+.+|+|.++++++.+
T Consensus         7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~   39 (48)
T PF13412_consen    7 KILNYLRENPRITQKELAEKLGISRSTVNRYLK   39 (48)
T ss_dssp             HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            456778888889999999999999999998764

...

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=97.36  E-value=0.00079  Score=45.70  Aligned_cols=44  Identities=18%  Similarity=0.191  Sum_probs=36.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      .|.+|+|+.+|||.+|||++.||...++.++   +.+.++.+|.-++
T Consensus         1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~kV~~a~~elgY~pN   47 (333)
T COG1609           1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPN   47 (333)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            3789999999999999999999988777665   6666777777654

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=97.36  E-value=0.00034  Score=42.55  Aligned_cols=46  Identities=13%  Similarity=0.226  Sum_probs=34.0

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCC---CCHHHHHHHHHHhCCCC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENGKAV---PNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~---p~~~~~~~la~~lgv~~   76 (82)
                      ...|+||+|+|+.+|+|+++|+.||++-..   -...++ ++++.++.++
T Consensus        18 r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~   66 (141)
T PRK03975         18 RERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPV   66 (141)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCe
Confidence            369999999999999999999999986211   112233 6777777654

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=97.31  E-value=0.00062  Score=38.15  Aligned_cols=57  Identities=21%  Similarity=0.171  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      +..|..+.+..+++|+++|+.+||+++.+|.+.+|+. ..+.+.+.......|..++-
T Consensus        30 ~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~~   87 (91)
T COG5606          30 MMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEIDV   87 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCcccc
Confidence            6677888899999999999999999999999999964 56788888888888877653

>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]

Probab=97.27  E-value=0.00021  Score=40.39  Aligned_cols=44  Identities=20%  Similarity=0.261  Sum_probs=38.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCcc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG--VKLRV   78 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg--v~~~e   78 (82)
                      .|+.+|..+|+|+++|++|-+|.+.........|.++.+  |+..|
T Consensus        14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~e   59 (96)
T COG4197          14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREE   59 (96)
T ss_pred             cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhcCCccHHH
Confidence            488899999999999999999999999899999999888  65544

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=97.23  E-value=0.00049  Score=45.79  Aligned_cols=44  Identities=14%  Similarity=0.145  Sum_probs=35.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAV--PNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~--p~~~~---~~~la~~lgv~~~   77 (82)
                      .|.+|+|+.+|||.+|||++.||...  ++.++   +.++++.||..++
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn   50 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTS   50 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCc
Confidence            48899999999999999999998742  55444   6677888887665

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=97.20  E-value=0.0012  Score=43.70  Aligned_cols=41  Identities=15%  Similarity=0.124  Sum_probs=33.9

Q ss_pred             HHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           37 PDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      +|+|+.+|||.+|||++.||...++.++   +.+.++.+|..++
T Consensus         2 ~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn   45 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS   45 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcc
Confidence            6899999999999999999987777666   5556777887665

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

Probab=97.15  E-value=0.001  Score=32.23  Aligned_cols=23  Identities=9%  Similarity=0.297  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+||+++||.+|++.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~   23 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            57899999999999999999854

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.

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

Probab=97.11  E-value=0.00067  Score=38.19  Aligned_cols=25  Identities=16%  Similarity=0.137  Sum_probs=19.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.||||.|+|+++|.|+++|+++..
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~   25 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLA   25 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHG
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4799999999999999999999875

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

>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=97.07  E-value=0.00089  Score=34.86  Aligned_cols=26  Identities=12%  Similarity=0.175  Sum_probs=23.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      -.|+++.++|+.+|++.+||+.|..-
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r   36 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKDR   36 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHHh
Confidence            36999999999999999999999864

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

>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=97.04  E-value=0.00011  Score=41.52  Aligned_cols=46  Identities=13%  Similarity=0.143  Sum_probs=35.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .-..++|..+|+.+|++.++||+|-++    -...+..++.+|+..+.+.
T Consensus        20 rlA~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v~~~   65 (91)
T PF05269_consen   20 RLASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGVEDS   65 (91)
T ss_dssp             HHHHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTHHHH
T ss_pred             HHHHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhccccc
Confidence            345678999999999999999999764    3456677777777766543

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.

>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=97.01  E-value=0.0027  Score=30.74  Aligned_cols=33  Identities=9%  Similarity=-0.072  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|....+..+.++.+.|+.+|||++|+++-.
T Consensus         7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~kl   39 (42)
T PF02954_consen    7 KQLIRQALERCGGNVSKAARLLGISRRTLYRKL   39 (42)
T ss_dssp             HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence            456888889999999999999999999998753

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 ....

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=97.00  E-value=0.0019  Score=39.14  Aligned_cols=26  Identities=27%  Similarity=0.350  Sum_probs=24.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..|+||+|+|+.+|+|+++|+.+++.
T Consensus        19 ~~GlTq~EIAe~LgiS~stV~~~e~r   44 (137)
T TIGR00721        19 EKGLSQKEIAKELKTTRANVSAIEKR   44 (137)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            59999999999999999999999975

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

>PF12728 HTH_17: Helix-turn-helix domain

Probab=96.99  E-value=0.0016  Score=32.51  Aligned_cols=28  Identities=11%  Similarity=0.201  Sum_probs=23.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      +|..|+|+.+|||++||.+|.+....|.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~   29 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPP   29 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCe
Confidence            6889999999999999999987554444

>TIGR01764 excise DNA binding domain, excisionase family

Probab=96.87  E-value=0.0023  Score=31.04  Aligned_cols=27  Identities=11%  Similarity=0.188  Sum_probs=23.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      +|..|+|+.+|+|+++|.+|.+....|
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~   28 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELP   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence            688999999999999999999654444

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).

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

Probab=96.85  E-value=0.0013  Score=38.93  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ||.+|||+.+|+|++||++|-.
T Consensus         1 MT~eELA~~tG~srQTINrWvR   22 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVR   22 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHH
Confidence            6899999999999999999975

The function of this family is unknown.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=96.82  E-value=0.0042  Score=30.74  Aligned_cols=24  Identities=13%  Similarity=0.148  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|.|..++|..+|||+++|.+|.+
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~   34 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIK   34 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHH
Confidence            477999999999999999999975

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

Probab=96.79  E-value=0.0021  Score=29.61  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=17.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|..|+|+.+|+++.||++...
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~   24 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILK   24 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHH
Confidence            47899999999999999999764

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=96.77  E-value=0.0034  Score=30.70  Aligned_cols=23  Identities=22%  Similarity=0.264  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+|++++||..|++-
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~   23 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERI   23 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999864

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.

>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=96.76  E-value=0.0021  Score=33.68  Aligned_cols=24  Identities=13%  Similarity=0.368  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +++..++|+.+|||.+||+.|-+-
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHhhh
Confidence            589999999999999999999764

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 [].

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

Probab=96.75  E-value=0.006  Score=32.02  Aligned_cols=22  Identities=18%  Similarity=0.439  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|||++||..|+.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4788999999999999999985

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.

>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=96.75  E-value=0.0017  Score=30.96  Aligned_cols=23  Identities=17%  Similarity=0.341  Sum_probs=19.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCC
Q 038591           35 SQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      |..|+|+.+|||+.||..||.-.
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~G   23 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYEREG   23 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCC
Confidence            45789999999999999999753

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 ....

>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=96.73  E-value=0.0063  Score=30.19  Aligned_cols=29  Identities=14%  Similarity=0.196  Sum_probs=24.4

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++-..++|..|+|+.+|+|.++|+++..
T Consensus        14 ~~~y~~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen   14 RLRYFEGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             HHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence            34557899999999999999999999875

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 ....

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=96.71  E-value=0.0037  Score=35.18  Aligned_cols=27  Identities=11%  Similarity=0.180  Sum_probs=24.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ...|+|..++|+.+|+|++||++|.+|
T Consensus        47 l~~G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        47 LKQGKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            457999999999999999999999885

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.

>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=96.70  E-value=0.0037  Score=31.53  Aligned_cols=32  Identities=9%  Similarity=0.152  Sum_probs=24.6

Q ss_pred             HHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKK-MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+....+ +|..+||+.+|||..||.+..+
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~   37 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIK   37 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            3555655554 9999999999999999998754

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 ....

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

Probab=96.63  E-value=0.0039  Score=36.23  Aligned_cols=35  Identities=11%  Similarity=0.113  Sum_probs=29.2

Q ss_pred             HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+.+..+|  .-.|+||.+.|..+|||++|+.++.+.
T Consensus        44 ~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~   80 (106)
T PF02001_consen   44 VDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILES   80 (106)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence            56666655  468999999999999999999999863

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.57  E-value=0.0025  Score=38.19  Aligned_cols=28  Identities=21%  Similarity=0.228  Sum_probs=25.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..++|+||+++|+.+|.++..||.+|..
T Consensus        19 lRekG~tQ~eIA~~L~TTraNvSaIEkr   46 (143)
T COG1356          19 LREKGLTQSEIARILKTTRANVSAIEKR   46 (143)
T ss_pred             hhhccccHHHHHHHHccchhhHHHHHHH
Confidence            3568999999999999999999999974

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

Probab=96.52  E-value=0.0048  Score=32.29  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+||+++|+..|++
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~   22 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4788999999999999999996

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

>PRK08558 adenine phosphoribosyltransferase; Provisional

Probab=96.50  E-value=0.015  Score=38.15  Aligned_cols=41  Identities=17%  Similarity=0.354  Sum_probs=35.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      -+|-+||++.+|++.+.+++|-+|...|+.+....+.+.+.
T Consensus        23 ~~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~   63 (238)
T PRK08558         23 TYTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLG   63 (238)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHH
Confidence            37999999999999999999999999999887666665444

>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=96.49  E-value=0.0024  Score=32.50  Aligned_cols=34  Identities=21%  Similarity=0.258  Sum_probs=24.4

Q ss_pred             HHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           23 RQIQRA-RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        23 ~~lk~~-r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +.+.-+ +-+.|.++.++|...||+.+||+.|...
T Consensus        11 eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen   11 EKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             HHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            344443 2468889999999999999999999875

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.

>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins

Probab=96.40  E-value=0.036  Score=31.07  Aligned_cols=58  Identities=16%  Similarity=0.143  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQI-NQRPQVVSEYENGKAVPNQ------TVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e~g~~~p~~------~~~~~la~~lgv~~~e~   79 (82)
                      ...|+..+...+++|+.||+.+ |.|+.+++.+.+.-..-+.      +...++-..|..+-+++
T Consensus        15 ~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~L~~~gre~y~RM~nWL~~~e~~r   79 (87)
T PF02376_consen   15 ARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPKPWNKLKPKGREPYIRMYNWLSLPEEER   79 (87)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHCSTHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCCCHHHcCccccHHHHHHHHHhcCCHHHH
Confidence            6788999999999999999976 9999999999985332222      22566777776665443

The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.

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

Probab=96.37  E-value=0.0066  Score=31.05  Aligned_cols=24  Identities=21%  Similarity=0.337  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.|..|||+.+|||++|++....
T Consensus        22 R~~tl~elA~~lgis~st~~~~LR   45 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLR   45 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHH
Confidence            478999999999999999998764

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

>PRK01381 Trp operon repressor; Provisional

Probab=96.37  E-value=0.0094  Score=34.24  Aligned_cols=53  Identities=8%  Similarity=0.077  Sum_probs=38.4

Q ss_pred             HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591           22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      +.|++-++.  .-++||.|+|..+|||..||++--+.-...+...-..|...++-
T Consensus        42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~   96 (99)
T PRK01381         42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK   96 (99)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence            555555543  34599999999999999999998776444456666666666553

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

Probab=96.36  E-value=0.0052  Score=32.39  Aligned_cols=22  Identities=18%  Similarity=0.342  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+||+++||..||.
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~   22 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999985

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

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

Probab=96.31  E-value=0.0051  Score=32.30  Aligned_cols=23  Identities=17%  Similarity=0.349  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+|||+++|..|++-
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~   23 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYERE   23 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHT
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHh
Confidence            46789999999999999999863

>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=96.31  E-value=0.01  Score=29.22  Aligned_cols=35  Identities=23%  Similarity=0.281  Sum_probs=24.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..|..++... +|+.+.|+..||+++||++..+|..
T Consensus         7 ~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~   41 (45)
T PF05225_consen    7 KAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP   41 (45)
T ss_dssp             HHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred             HHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3455555333 9999999999999999999998854

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.

>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=96.20  E-value=0.01  Score=26.24  Aligned_cols=24  Identities=13%  Similarity=0.194  Sum_probs=21.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+++..++|+.+|++.++|++|.
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHhC
Confidence            468899999999999999999873

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

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=96.20  E-value=0.01  Score=40.39  Aligned_cols=52  Identities=10%  Similarity=0.110  Sum_probs=37.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN-----GK--------AVPNQTVLAKMEKAIGVK   75 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~-----g~--------~~p~~~~~~~la~~lgv~   75 (82)
                      ++-++-=..|+||.|+|+++|+|+.+|+++.+     |-        .....+.-..|.+.||+.
T Consensus        20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk   84 (318)
T PRK15418         20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQ   84 (318)
T ss_pred             HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCC
Confidence            34444456799999999999999999999964     31        112344556777777754

>PRK13698 plasmid-partitioning protein; Provisional

Probab=96.18  E-value=0.013  Score=40.13  Aligned_cols=35  Identities=14%  Similarity=0.059  Sum_probs=30.0

Q ss_pred             HHHH-HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQI-QRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~l-k~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |... +.+....|+||++||+.+|+|+++|++..+-
T Consensus       164 A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl  199 (323)
T PRK13698        164 GLRYASRLQNEFAGNISALADAENISRKIITRCINT  199 (323)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            5555 5577789999999999999999999999764

>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=96.17  E-value=0.02  Score=27.75  Aligned_cols=31  Identities=13%  Similarity=0.182  Sum_probs=24.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSE   52 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~   52 (82)
                      ...|..+......|..++|+.+|+|++++.+
T Consensus         6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~   36 (42)
T PF13404_consen    6 RKILRLLQEDGRRSYAELAEELGLSESTVRR   36 (42)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHCcCHHHHHH
Confidence            4567888888999999999999999999875

...

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=96.16  E-value=0.012  Score=30.83  Aligned_cols=22  Identities=14%  Similarity=0.185  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||+++|..|+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~   22 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER   22 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999964

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=96.16  E-value=0.0097  Score=35.26  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC-C-----------CHHH-----HHHHHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAV-P-----------NQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~-p-----------~~~~-----~~~la~~lgv~~~e~   79 (82)
                      |+..|+|+.+|||..||.-||.-.-. |           +.+.     +...++.+|++++|.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEEC   63 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            57889999999999999999963222 2           1222     344566777777653

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.

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

Probab=96.15  E-value=0.0096  Score=34.52  Aligned_cols=22  Identities=14%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||+.||..||+
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~   22 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEK   22 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.13  E-value=0.0089  Score=34.10  Aligned_cols=34  Identities=12%  Similarity=0.055  Sum_probs=28.2

Q ss_pred             HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -+.|..+|  .-.|++|.|.|.++|||++|+.+..+
T Consensus        36 ~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~   71 (99)
T COG1342          36 IEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLT   71 (99)
T ss_pred             HHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence            45555554  56899999999999999999999876

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

Probab=96.09  E-value=0.012  Score=40.17  Aligned_cols=54  Identities=13%  Similarity=0.169  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----C--------CCCCCHHHHHHHHHHhCCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN-----G--------KAVPNQTVLAKMEKAIGVK   75 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~-----g--------~~~p~~~~~~~la~~lgv~   75 (82)
                      ..++.++--..|+||.|+|+++|||+.+|+++.+     |        ......+.-..|.+.||++
T Consensus        15 ~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~   81 (321)
T COG2390          15 LARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK   81 (321)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence            4566677778899999999999999999999964     3        1122344557777888876

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

Probab=96.08  E-value=0.0021  Score=34.37  Aligned_cols=32  Identities=13%  Similarity=0.270  Sum_probs=25.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|... ...|.|..++|...||++++|++|..
T Consensus        14 ~~v~~~-~~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen   14 QAVREY-LESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             HHHHHH-HHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHH-HHCCCceEeeecccccccccccHHHH
Confidence            344444 34689999999999999999999975

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.

>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=96.07  E-value=0.012  Score=29.98  Aligned_cols=33  Identities=15%  Similarity=0.192  Sum_probs=27.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+....++++.+||+.+++++++++++.+
T Consensus         7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~   39 (59)
T PF01047_consen    7 RILRILYENGGITQSELAEKLGISRSTVTRIIK   39 (59)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHH
Confidence            456778888999999999999999999998864

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 ....

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

Probab=96.01  E-value=0.012  Score=34.51  Aligned_cols=46  Identities=20%  Similarity=0.273  Sum_probs=32.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC-CC----------CHHH-----HHHHHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA-VP----------NQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~-~p----------~~~~-----~~~la~~lgv~~~e~   79 (82)
                      |+..|+|+.+|||..||.-||+-.- .|          +...     +...++.+|+++++.
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~GLl~p~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI   62 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEI   62 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5789999999999999999996322 22          1122     445666777777653

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

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

Probab=96.00  E-value=0.0015  Score=40.49  Aligned_cols=46  Identities=13%  Similarity=0.174  Sum_probs=2.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      -.-+|++++|+.+|++.+|||+.-+|+..-+..-+.-|..+|...+
T Consensus        47 l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~   92 (160)
T PF04552_consen   47 LKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSV   92 (160)
T ss_dssp             --------------------------------------S-----SS
T ss_pred             CcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccc
Confidence            3468999999999999999999999987766666778888887665

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.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=95.98  E-value=0.033  Score=30.33  Aligned_cols=36  Identities=31%  Similarity=0.483  Sum_probs=26.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      +...+|..+|||+++|++|  |...| ......|..+-+
T Consensus        12 s~~kvA~aLGIs~~AVsQW--Ge~VP-e~rA~~ie~~T~   47 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVP-EGRAMRLQEASG   47 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH--hccCc-HHHHHHHHHHhC
Confidence            6778999999999999999  65444 444455555443

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.95  E-value=0.028  Score=38.11  Aligned_cols=55  Identities=24%  Similarity=0.140  Sum_probs=43.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      -..++++.+-.+++|..+|..+|+++.+++++.+|...-....-.+|+.+++...
T Consensus         8 ~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~~~   62 (297)
T COG2842           8 IKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEKKG   62 (297)
T ss_pred             HHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcCcCchHHHHHHHHHHHHcCCC
Confidence            4678888999999999999999999999999999833333445567777776554

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

Probab=95.90  E-value=0.027  Score=29.93  Aligned_cols=33  Identities=9%  Similarity=0.039  Sum_probs=26.2

Q ss_pred             HHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKK--MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+...-+  ++..+||+.+|++..++++...
T Consensus        10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~   44 (68)
T smart00550       10 KILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY   44 (68)
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            44555565545  9999999999999999998854

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

>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=95.90  E-value=0.032  Score=26.90  Aligned_cols=26  Identities=15%  Similarity=0.262  Sum_probs=23.5

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|+++.++|+.+|++..+|++|.+
T Consensus        23 ~~~~~~~~~ia~~~~~s~~~i~~~~~   48 (55)
T cd06171          23 FGEGLSYEEIAEILGISRSTVRQRLH   48 (55)
T ss_pred             HhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34799999999999999999999875

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

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

Probab=95.89  E-value=0.0089  Score=36.36  Aligned_cols=25  Identities=8%  Similarity=0.295  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..|+.++|+.+||+++|+++|-+..
T Consensus        34 r~T~~eiAee~Gis~~tLYrWr~~~   58 (142)
T PF13022_consen   34 RRTQAEIAEEVGISRSTLYRWRQQN   58 (142)
T ss_dssp             -S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred             cchHHHHHHHhCCCHHHHHHHHhcC
Confidence            4789999999999999999998754

>TIGR00180 parB_part ParB-like partition proteins

Probab=95.88  E-value=0.042  Score=34.51  Aligned_cols=48  Identities=15%  Similarity=0.134  Sum_probs=36.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      +..++.+....|+|+.++|+.+|+|+++|+++..=-. .+.+.+..+..
T Consensus       109 a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~  156 (187)
T TIGR00180       109 AQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE  156 (187)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence            5566666666899999999999999999999987433 44455555544

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]

Probab=95.88  E-value=0.079  Score=31.99  Aligned_cols=56  Identities=18%  Similarity=0.149  Sum_probs=49.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ...|-...+.+|+|-.++++.+|.+...+....-|+...+.+.+.+++..||.+-+
T Consensus        10 ~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~~   65 (151)
T COG1513          10 ADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDED   65 (151)
T ss_pred             HHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCHH
Confidence            34555667789999999999999999999999999999999999999999998644

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=95.84  E-value=0.016  Score=28.63  Aligned_cols=25  Identities=8%  Similarity=0.224  Sum_probs=23.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|++..++|+.+|+|+++|..+..
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5799999999999999999999875

lux regulon (activates the bioluminescence operon

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=95.84  E-value=0.034  Score=30.14  Aligned_cols=40  Identities=13%  Similarity=0.129  Sum_probs=27.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      +.....-..+|..+||+.+|+|+++|.++-+.-..-+...
T Consensus        26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e   65 (77)
T PF01418_consen   26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE   65 (77)
T ss_dssp             HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred             HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence            3445566789999999999999999999987555545444

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.

>COG1318 Predicted transcriptional regulators [Transcription]

Probab=95.82  E-value=0.017  Score=36.34  Aligned_cols=32  Identities=22%  Similarity=0.312  Sum_probs=29.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      +|...|+|.+++|+.+|.+++||.++..|...
T Consensus        56 arekag~Ti~EIAeelG~TeqTir~hlkgetk   87 (182)
T COG1318          56 AREKAGMTISEIAEELGRTEQTVRNHLKGETK   87 (182)
T ss_pred             HHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence            56899999999999999999999999998654

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

Probab=95.81  E-value=0.021  Score=31.82  Aligned_cols=23  Identities=9%  Similarity=0.229  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|..|+|+.+|||++||..||.
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~   23 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEE   23 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHH
Confidence            46889999999999999999985

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.

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=95.80  E-value=0.023  Score=33.66  Aligned_cols=47  Identities=17%  Similarity=0.173  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC-CCCC-----------HHH-----HHHHHHHhCCCCccc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK-AVPN-----------QTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~-~~p~-----------~~~-----~~~la~~lgv~~~e~   79 (82)
                      .+|..|||+.+|+|..||..||.-. -.|.           ...     +...++.+|+++++.
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI   66 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGEL   66 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5899999999999999999998632 2222           222     445556777777653

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.

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

Probab=95.79  E-value=0.019  Score=33.16  Aligned_cols=23  Identities=22%  Similarity=0.426  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..++|+.+|||+.||..||.-
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~   23 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKE   23 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999863

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.

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

Probab=95.77  E-value=0.018  Score=34.03  Aligned_cols=46  Identities=13%  Similarity=0.194  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC-C-----------CCCHHH-----HHHHHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGK-A-----------VPNQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~-~-----------~p~~~~-----~~~la~~lgv~~~e~   79 (82)
                      |+..|||+.+|||+.||.-||+-. -           ..+.+.     +....+.+|++++|.
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEI   63 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578899999999999999998632 1           222222     345556778877653

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.

>PRK04217 hypothetical protein; Provisional

Probab=95.71  E-value=0.032  Score=32.64  Aligned_cols=30  Identities=10%  Similarity=-0.018  Sum_probs=26.1

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           26 QRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.++...|+|++++|+.+|+|.+||+++..
T Consensus        51 i~l~~~eGlS~~EIAk~LGIS~sTV~r~L~   80 (110)
T PRK04217         51 LRLVDYEGLTQEEAGKRMGVSRGTVWRALT   80 (110)
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345566899999999999999999999876

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=95.69  E-value=0.022  Score=34.30  Aligned_cols=23  Identities=22%  Similarity=0.316  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |+..|||+.+|+|..||.-||+-
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~~   23 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEK   23 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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

Probab=95.69  E-value=0.021  Score=33.84  Aligned_cols=23  Identities=17%  Similarity=0.208  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |+..|+|+.+|||+.||..||+-
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~   23 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEI   23 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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

>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=95.68  E-value=0.017  Score=30.72  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.++++..+
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~   50 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILK   50 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHH
Confidence            468999999999999999998764

...

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.67  E-value=0.047  Score=26.58  Aligned_cols=31  Identities=16%  Similarity=0.128  Sum_probs=25.2

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..+....+++..++|+.+++++++++++..
T Consensus         6 l~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~   36 (53)
T smart00420        6 LELLAQQGKVSVEELAELLGVSEMTIRRDLN   36 (53)
T ss_pred             HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            4445555679999999999999999988764

>PF13551 HTH_29: Winged helix-turn helix

Probab=95.66  E-value=0.024  Score=32.06  Aligned_cols=26  Identities=12%  Similarity=0.277  Sum_probs=22.6

Q ss_pred             HhCCC-CHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKM-SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~-s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|+ |..++|+.+|+|++||++|.+
T Consensus         8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~   34 (112)
T PF13551_consen    8 LAEGVSTIAEIARRLGISRRTVYRWLK   34 (112)
T ss_pred             HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            45688 599999999999999999954

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

Probab=95.65  E-value=0.0043  Score=31.18  Aligned_cols=28  Identities=7%  Similarity=0.167  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      ++.+|+++.+|+|.+|+.++.+....|.
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~   31 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKDGKFPK   31 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHHHH---
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhcccCCC
Confidence            5678999999999999999987544543

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.

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

Probab=95.64  E-value=0.025  Score=32.46  Aligned_cols=22  Identities=23%  Similarity=0.247  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..+||+.+|+|..||.-||.
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~   22 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYID   22 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=95.63  E-value=0.018  Score=40.25  Aligned_cols=48  Identities=10%  Similarity=0.221  Sum_probs=39.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEKA   71 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~~   71 (82)
                      +..+|..|...|+||.|+...+|      .|.+||.++|.  -..++.++-+|-=.
T Consensus       212 AK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEA--LqLSFKNMCKLKPL  265 (398)
T KOG3802|consen  212 AKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEA--LQLSFKNMCKLKPL  265 (398)
T ss_pred             HHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHh--hccCHHHHhhhHHH
Confidence            78888889999999999999998      69999999997  45666666555433

>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=95.62  E-value=0.035  Score=27.71  Aligned_cols=31  Identities=19%  Similarity=0.113  Sum_probs=21.9

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +=.++-..|+|..|+|+.+|+|+++|..+..
T Consensus        18 i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~   48 (54)
T PF08281_consen   18 IFLLRYFQGMSYAEIAEILGISESTVKRRLR   48 (54)
T ss_dssp             HHHHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3345567899999999999999999998753

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.

>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein

Probab=95.62  E-value=0.029  Score=37.31  Aligned_cols=42  Identities=14%  Similarity=0.228  Sum_probs=30.8

Q ss_pred             CCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           32 KKMSQPDLANQINQ-----RPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        32 ~g~s~~elA~~~gi-----s~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      .++||.+||+.+|-     |+++|++++.--..+.......|+.-+|
T Consensus       135 ~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~~glG  181 (258)
T TIGR03764       135 ESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLYSGLG  181 (258)
T ss_pred             CCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHHccCC
Confidence            68999999999976     9999999987544444455455544443

Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.

>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=95.61  E-value=0.027  Score=28.88  Aligned_cols=32  Identities=16%  Similarity=0.140  Sum_probs=26.8

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+..+.+...+|..++|+.+|+|..||.+-.+
T Consensus         5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~   36 (57)
T PF08220_consen    5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDLN   36 (57)
T ss_pred             HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence            45666777889999999999999999988644

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

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=95.60  E-value=0.023  Score=27.09  Aligned_cols=31  Identities=19%  Similarity=0.195  Sum_probs=21.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      ..+++..++|..+|+|++++++...-....+
T Consensus         6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t   36 (42)
T PF00165_consen    6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT   36 (42)
T ss_dssp             -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence            3579999999999999999999876443333

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

Probab=95.60  E-value=0.022  Score=33.79  Aligned_cols=22  Identities=23%  Similarity=0.326  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|+|+.+|||..||..||+
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~   22 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK   22 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>PRK13749 transcriptional regulator MerD; Provisional

Probab=95.55  E-value=0.026  Score=33.50  Aligned_cols=47  Identities=13%  Similarity=0.162  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC------------CCCCHHH-----HHHHHHHhCCCCccc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK------------AVPNQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~------------~~p~~~~-----~~~la~~lgv~~~e~   79 (82)
                      .+|..|||+.+|+|..||.-||.-.            +..+...     +...++.+|++++|.
T Consensus         3 ~~tIgelA~~~gvS~~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI   66 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL   66 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            4789999999999999999998532            1222222     344456788887664

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=95.54  E-value=0.04  Score=32.39  Aligned_cols=26  Identities=12%  Similarity=0.054  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|.|..++|..+|||+++|++|-+
T Consensus        26 ~~~g~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413         26 FEPGMTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45699999999999999999999965

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=95.51  E-value=0.027  Score=34.67  Aligned_cols=51  Identities=18%  Similarity=0.322  Sum_probs=35.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC-----------CHHH-----HHHHHHHhCCCCccc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVP-----------NQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p-----------~~~~-----~~~la~~lgv~~~e~   79 (82)
                      +...=++..|+|+.+|||..||..||.-.-.+           +.+.     +.+.++.+|++++|.
T Consensus         7 ~~~~~~~IgevAk~~gvs~~TlRyYE~~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eI   73 (154)
T PRK15002          7 RIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATI   73 (154)
T ss_pred             hhcccccHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence            34456899999999999999999999632111           2222     445566777777653

>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=95.51  E-value=0.059  Score=30.25  Aligned_cols=34  Identities=15%  Similarity=0.197  Sum_probs=27.0

Q ss_pred             HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.|++-++  -..|.||.++|+.+|+|..||++.-+
T Consensus        36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr   71 (87)
T PF01371_consen   36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR   71 (87)
T ss_dssp             HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            45555544  35799999999999999999998754

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 ....

>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=95.51  E-value=0.029  Score=28.59  Aligned_cols=33  Identities=18%  Similarity=0.215  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKK--MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+...-+  +|+.+||+.++++++++++..+
T Consensus         9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~   43 (62)
T PF12802_consen    9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVK   43 (62)
T ss_dssp             HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34555666666  8999999999999999998754

...

>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=95.48  E-value=0.064  Score=27.58  Aligned_cols=24  Identities=13%  Similarity=0.219  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|+.+|+++++++++.+
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~   47 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLK   47 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            458999999999999999998765

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

Probab=95.47  E-value=0.03  Score=31.99  Aligned_cols=23  Identities=17%  Similarity=0.189  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|+|+.+|||+.||..||+-
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~   24 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKL   24 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999863

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.

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

Probab=95.47  E-value=0.04  Score=27.83  Aligned_cols=29  Identities=14%  Similarity=0.217  Sum_probs=22.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++.+.|++..++|+.+|-|+..|.+|.++
T Consensus        15 ~m~qlG~s~~~isr~i~RSr~~Ir~yl~d   43 (50)
T PF11427_consen   15 VMHQLGMSLREISRRIGRSRTCIRRYLKD   43 (50)
T ss_dssp             HHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred             HHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence            56789999999999999999999999875

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

Probab=95.47  E-value=0.029  Score=32.33  Aligned_cols=23  Identities=13%  Similarity=0.159  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..++|+.+|||++||..||.-
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~   23 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI   23 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            47889999999999999999863

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=95.45  E-value=0.051  Score=31.48  Aligned_cols=30  Identities=17%  Similarity=0.093  Sum_probs=26.1

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           26 QRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.++-..|+|..++|+.+|+|++||+++..
T Consensus        26 l~L~y~eg~S~~EIAe~lGIS~~TV~r~L~   55 (104)
T PRK00118         26 MELYYLDDYSLGEIAEEFNVSRQAVYDNIK   55 (104)
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345667899999999999999999999865

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=95.43  E-value=0.058  Score=30.18  Aligned_cols=26  Identities=4%  Similarity=0.045  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -+.|++..++|...|||..|.++|..
T Consensus        22 v~~g~~~a~aA~~~gVS~~Ta~kW~~   47 (85)
T PF13011_consen   22 VEQGWPVAHAAAEFGVSRRTAYKWLA   47 (85)
T ss_pred             HHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence            35899999999999999999999964

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

Probab=95.43  E-value=0.022  Score=28.76  Aligned_cols=28  Identities=21%  Similarity=0.166  Sum_probs=24.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+-..|.+..++|...|||++|+++|-+
T Consensus        14 ~~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen   14 MYLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             HHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            3456799999999999999999999875

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

Probab=95.43  E-value=0.032  Score=31.80  Aligned_cols=22  Identities=9%  Similarity=0.190  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||++||..||.
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~   22 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE   22 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4788999999999999999975

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

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=95.41  E-value=0.027  Score=27.09  Aligned_cols=24  Identities=13%  Similarity=0.202  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+++.++|+.+|+|++++++..+
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~   30 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLK   30 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHH
Confidence            468999999999999999998764

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=95.41  E-value=0.057  Score=27.49  Aligned_cols=30  Identities=3%  Similarity=-0.011  Sum_probs=25.6

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +..++.-..+++.+.|+.+||+.+++.+.-
T Consensus         7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~C   36 (52)
T PF02042_consen    7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRC   36 (52)
T ss_pred             HHHHHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence            567788899999999999999988877664

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=95.39  E-value=0.034  Score=33.61  Aligned_cols=23  Identities=22%  Similarity=0.294  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|+|+.+|||+.||..||.-
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~   24 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQ   24 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999863

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=95.38  E-value=0.032  Score=33.30  Aligned_cols=23  Identities=17%  Similarity=0.231  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|+|+.+|||+.||..||.-
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~   24 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKN   24 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999863

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.

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

Probab=95.37  E-value=0.022  Score=32.47  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=20.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||++|+..||.
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~   22 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWET   22 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999975

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.

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

Probab=95.36  E-value=0.034  Score=31.38  Aligned_cols=23  Identities=9%  Similarity=0.206  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+|||+.||..||+-
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~   23 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI   23 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            47889999999999999999963

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.

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

Probab=95.34  E-value=0.036  Score=31.55  Aligned_cols=23  Identities=39%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|+|+.+|||..||..||.-
T Consensus         1 y~i~e~A~~~gvs~~tlR~Ye~~   23 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYESL   23 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            46789999999999999999863

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.

>PRK15043 transcriptional regulator MirA; Provisional

Probab=95.33  E-value=0.039  Score=36.44  Aligned_cols=46  Identities=13%  Similarity=0.238  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc--C----------CCCCCHHHHHHHH-----HHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN--G----------KAVPNQTVLAKME-----KAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~--g----------~~~p~~~~~~~la-----~~lgv~~~e   78 (82)
                      -++..++|+.+|||+.|+..||.  |          .+..+.+.+..|.     ...|+++.+
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~e   65 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSK   65 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHH
Confidence            47899999999999999999983  4          2334455555554     556666654

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

Probab=95.33  E-value=0.025  Score=31.98  Aligned_cols=26  Identities=12%  Similarity=0.054  Sum_probs=22.7

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ....+|+.|||+.+|++++++++..+
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~   69 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIK   69 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHH
Confidence            46689999999999999999999643

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

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

Probab=95.30  E-value=0.038  Score=31.32  Aligned_cols=22  Identities=14%  Similarity=0.315  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|+|++||..||+
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~   22 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEE   22 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999986

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.

>smart00351 PAX Paired Box domain

Probab=95.29  E-value=0.055  Score=32.03  Aligned_cols=25  Identities=16%  Similarity=0.126  Sum_probs=22.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|.|+.++|+.+|||++||++|.+
T Consensus        31 ~~G~s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       31 QNGVRPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3799999999999999999999954

>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=95.26  E-value=0.018  Score=28.80  Aligned_cols=31  Identities=10%  Similarity=0.186  Sum_probs=23.3

Q ss_pred             HHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+.. ..++|..|+|+.+|+++++++++.+
T Consensus         9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen    9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            333433 3458999999999999999999865

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.

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

Probab=95.26  E-value=0.04  Score=31.10  Aligned_cols=22  Identities=14%  Similarity=0.273  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|+|+.+|+|+.||..||.
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~   22 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH   22 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PRK04132 replication factor C small subunit; Provisional

Probab=95.22  E-value=0.041  Score=42.04  Aligned_cols=43  Identities=28%  Similarity=0.484  Sum_probs=40.4

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           36 QPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+++|++.||....+-.|..|++.|++..-.+||++||+++++
T Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  462 (846)
T PRK04132        420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK  462 (846)
T ss_pred             HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence            4789999999999999999999999999999999999999865

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

Probab=95.21  E-value=0.041  Score=31.40  Aligned_cols=22  Identities=9%  Similarity=0.194  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|||++||..||+
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~   23 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES   23 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6789999999999999999986

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

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

Probab=95.17  E-value=0.036  Score=33.15  Aligned_cols=22  Identities=23%  Similarity=0.273  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|||+.+|||..||.-||+
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE~   22 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEA   22 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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

>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B

Probab=95.14  E-value=0.23  Score=30.03  Aligned_cols=44  Identities=16%  Similarity=0.160  Sum_probs=32.6

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ   62 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~   62 (82)
                      .+++-.++.+|...|+|..++|+..+.|..-|-.||.|....+.
T Consensus         6 glnaie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~   49 (166)
T PF14590_consen    6 GLNAIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG   49 (166)
T ss_dssp             ---HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred             cchHHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence            34577889999999999999999999999999999999766543

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=95.13  E-value=0.098  Score=32.84  Aligned_cols=61  Identities=15%  Similarity=0.218  Sum_probs=38.6

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCCcccc
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      +......-++ -..|+|.+|+|+.+++|..||..+.+.    -...+...+..++.-.-.++.++|
T Consensus       151 Lt~rE~evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~~~  216 (216)
T PRK10840        151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD  216 (216)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCcccCC
Confidence            4444443333 357999999999999999999988754    122344444455544455555543

>PRK11891 aspartate carbamoyltransferase; Provisional

Probab=95.12  E-value=0.039  Score=39.20  Aligned_cols=35  Identities=14%  Similarity=0.148  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+.|+.++...|||..+||+++|++..++.+|.--
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p   39 (429)
T PRK11891          5 QAFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP   39 (429)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence            35689999999999999999999999999999843

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

Probab=95.11  E-value=0.046  Score=30.92  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc-CCC-----------CCCHHH-----HHHHHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN-GKA-----------VPNQTV-----LAKMEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~-g~~-----------~p~~~~-----~~~la~~lgv~~~e~   79 (82)
                      +|..|+|+.+|||+.||..||+ |--           ..+...     +....+.+|+++.+.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI   63 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEI   63 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            4788999999999999999985 321           222222     344566777777653

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.

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

Probab=95.09  E-value=0.047  Score=30.72  Aligned_cols=22  Identities=14%  Similarity=0.249  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|+++++|..|++
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~   22 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE   22 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999975

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.

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

Probab=95.08  E-value=0.029  Score=34.08  Aligned_cols=26  Identities=15%  Similarity=0.234  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|+|.+++|.++|+|.+|+.+|.+
T Consensus        18 ~~~G~S~re~Ak~~gvs~sTvy~wv~   43 (138)
T COG3415          18 VGEGLSCREAAKRFGVSISTVYRWVR   43 (138)
T ss_pred             HHcCccHHHHHHHhCccHHHHHHHHH
Confidence            45799999999999999999999964

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=95.07  E-value=0.047  Score=29.47  Aligned_cols=31  Identities=10%  Similarity=0.193  Sum_probs=25.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      +...|++..+|+|++||+++.+....|....
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk   44 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK   44 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccCCCCCCee
Confidence            4567899999999999999999877776543

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=95.03  E-value=0.052  Score=35.91  Aligned_cols=33  Identities=15%  Similarity=0.255  Sum_probs=27.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|-.+|-..++|++|+|+.+|||.++||+++.
T Consensus       202 k~Vl~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         202 KLVLVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             HHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence            344456667799999999999999999999986

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

Probab=94.99  E-value=0.049  Score=30.38  Aligned_cols=22  Identities=23%  Similarity=0.212  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..++|+.+|||+.||..||.
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~   23 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER   23 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999995

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.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=94.98  E-value=0.065  Score=32.12  Aligned_cols=32  Identities=19%  Similarity=0.319  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      -..|+.+......++.++|+.+|+|++++.+-
T Consensus        11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R   42 (154)
T COG1522          11 RRILRLLQEDARISNAELAERVGLSPSTVLRR   42 (154)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence            56788889999999999999999999998765

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=94.97  E-value=0.073  Score=33.25  Aligned_cols=33  Identities=15%  Similarity=0.237  Sum_probs=26.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++=.++.-.|+|..|+|..+|+|+.||.+...
T Consensus       141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~  173 (185)
T PF07638_consen  141 RRVVELRFFEGLSVEEIAERLGISERTVRRRLR  173 (185)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334445667899999999999999999988654

>cd00131 PAX Paired Box domain

Probab=94.94  E-value=0.041  Score=32.79  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|+.++|..+|||++||++|.+
T Consensus        31 ~~G~s~~~iA~~~~Vs~~tV~r~i~   55 (128)
T cd00131          31 QSGIRPCDISRQLRVSHGCVSKILN   55 (128)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4799999999999999999999954

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

Probab=94.92  E-value=0.056  Score=31.24  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|+|+.+|||..||..||+-
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~   23 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLR   23 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            47789999999999999999863

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,

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

Probab=94.88  E-value=0.057  Score=30.63  Aligned_cols=22  Identities=18%  Similarity=0.289  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|||++||..|++
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~   23 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR   23 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999975

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.

>PRK10458 DNA cytosine methylase; Provisional

Probab=94.84  E-value=0.15  Score=36.62  Aligned_cols=48  Identities=17%  Similarity=0.243  Sum_probs=36.2

Q ss_pred             HHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCC---CCHHHHHHHHHHhCCC
Q 038591           28 ARLGKKMSQPDLANQIN------QRPQVVSEYENGKAV---PNQTVLAKMEKAIGVK   75 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~---p~~~~~~~la~~lgv~   75 (82)
                      .+...+++|+++|..++      .+..++.+|++|...   ++...+..|-..+.-.
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (467)
T PRK10458         24 EKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLPKP   80 (467)
T ss_pred             HHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcccC
Confidence            34557899999999997      789999999999763   3446566666665433

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

Probab=94.83  E-value=0.061  Score=27.69  Aligned_cols=32  Identities=19%  Similarity=0.159  Sum_probs=25.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|+.+....++|..++|+.+|+++++++.-.
T Consensus        14 ~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL   45 (61)
T PF12840_consen   14 RILRLLASNGPMTVSELAEELGISQSTVSYHL   45 (61)
T ss_dssp             HHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34555667789999999999999999998753

...

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=94.80  E-value=0.04  Score=31.98  Aligned_cols=22  Identities=14%  Similarity=0.170  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|||..||.-||.
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~   22 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYER   22 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHH
Confidence            5788999999999999999986

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

Probab=94.78  E-value=0.065  Score=30.31  Aligned_cols=23  Identities=13%  Similarity=0.198  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |+..|||+.+|+|.+||..||+-
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~~   23 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLRE   23 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57789999999999999999963

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.

>PF13309 HTH_22: HTH domain

Probab=94.74  E-value=0.031  Score=29.44  Aligned_cols=21  Identities=14%  Similarity=0.162  Sum_probs=18.8

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 038591           35 SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~   55 (82)
                      +...+|+.+|||+.||++|.+
T Consensus        44 av~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   44 AVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHcC
Confidence            668999999999999999863

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=94.71  E-value=0.06  Score=32.73  Aligned_cols=23  Identities=9%  Similarity=0.159  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++..+||+.+|||..||.-||+
T Consensus         7 ~~~IgevAk~~Gvs~~TLRyYE~   29 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQR   29 (144)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            48999999999999999999986

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

Probab=94.64  E-value=0.072  Score=30.88  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|||+.||..||+
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~   22 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE   22 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Confidence            5788999999999999999986

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.

>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=94.63  E-value=0.065  Score=28.11  Aligned_cols=33  Identities=6%  Similarity=0.005  Sum_probs=27.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+..+....++|..++|+.+|+++++++++.+
T Consensus        12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~   44 (68)
T PF01978_consen   12 KVYLALLKNGPATAEEIAEELGISRSTVYRALK   44 (68)
T ss_dssp             HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344556677889999999999999999998764

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.

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

Probab=94.62  E-value=0.14  Score=25.25  Aligned_cols=22  Identities=18%  Similarity=0.095  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|.+++|+.+|+|..||.++.+
T Consensus        28 ~s~~~vA~~~~vs~~TV~ri~~   49 (52)
T PF13542_consen   28 RSFKDVARELGVSWSTVRRIFD   49 (52)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Confidence            6999999999999999999865

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

Probab=94.62  E-value=0.063  Score=26.44  Aligned_cols=25  Identities=8%  Similarity=0.133  Sum_probs=22.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|..++|+.+|+|+.+|..+..
T Consensus        13 ~~~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4799999999999999999999865

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

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.54  E-value=0.058  Score=27.02  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=19.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 038591           35 SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~   55 (82)
                      |++.+|+.+|+|+.||.++.+
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~   47 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIK   47 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            899999999999999999865

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

Probab=94.53  E-value=0.052  Score=31.64  Aligned_cols=22  Identities=27%  Similarity=0.318  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||+.||..||.
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~   22 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEE   22 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

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

Probab=94.52  E-value=0.05  Score=32.13  Aligned_cols=22  Identities=14%  Similarity=0.286  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|+|+.+|||+.||..||.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~   22 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQR   22 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=94.52  E-value=0.077  Score=26.25  Aligned_cols=24  Identities=21%  Similarity=0.201  Sum_probs=21.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           35 SQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      |+.+.|+.+|++.++|+++.+|..
T Consensus        19 S~~eAa~~lg~~~~~I~~~~~~~~   42 (53)
T smart00497       19 SIREAAKYLGISHSSISKYLNTGK   42 (53)
T ss_pred             CHHHHHHHhCCCHHHHHHHHhCCC
Confidence            788999999999999999999854

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

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

Probab=94.51  E-value=0.052  Score=31.78  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||+.||.-||+
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~   22 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYER   22 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

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

Probab=94.46  E-value=0.08  Score=31.41  Aligned_cols=23  Identities=17%  Similarity=0.254  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..++|+.+|||++||..||+-
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~   24 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH   24 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999863

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

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=94.46  E-value=0.065  Score=33.73  Aligned_cols=22  Identities=23%  Similarity=0.480  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|||+.||.+|+.
T Consensus         1 mti~evA~~lGVS~~TLRrw~k   22 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVK   22 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999973

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=94.44  E-value=0.071  Score=32.82  Aligned_cols=32  Identities=13%  Similarity=0.233  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      -..|..+.+...+|..++|+.+|+|++++.+-
T Consensus        17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~R   48 (164)
T PRK11169         17 RNILNELQKDGRISNVELSKRVGLSPTPCLER   48 (164)
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHH
Confidence            56778888999999999999999999997653

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=94.43  E-value=0.05  Score=33.49  Aligned_cols=24  Identities=13%  Similarity=0.235  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+++.||++..+
T Consensus       142 ~~~t~~~iA~~lG~tretvsR~l~  165 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTITRLLG  165 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHHH
Confidence            358999999999999999999754

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.

>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=94.37  E-value=0.063  Score=26.29  Aligned_cols=30  Identities=13%  Similarity=0.161  Sum_probs=23.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+.. ..++..|+|+.+|+++++|++..+
T Consensus         8 l~~L~~-~~~~~~el~~~l~~s~~~vs~hL~   37 (47)
T PF01022_consen    8 LKLLSE-GPLTVSELAEELGLSQSTVSHHLK   37 (47)
T ss_dssp             HHHHTT-SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHh-CCCchhhHHHhccccchHHHHHHH
Confidence            344444 778999999999999999998753

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 ....

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=94.37  E-value=0.055  Score=32.82  Aligned_cols=22  Identities=18%  Similarity=0.268  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|+|+.+|||+.||.-||.
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~   23 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYES   23 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=94.32  E-value=0.14  Score=27.91  Aligned_cols=30  Identities=7%  Similarity=0.103  Sum_probs=23.9

Q ss_pred             HHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           25 IQRARLG-KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        25 lk~~r~~-~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      |..+-.. .++|..++|+.+|+++++++++.
T Consensus        11 l~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l   41 (91)
T smart00346       11 LRALAEEPGGLTLAELAERLGLSKSTAHRLL   41 (91)
T ss_pred             HHHHHhCCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            3444343 47999999999999999999884

>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth

Probab=94.28  E-value=0.049  Score=28.39  Aligned_cols=33  Identities=9%  Similarity=0.005  Sum_probs=24.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      |.++-...|  |.+.|+.+||+++.|++..+-.++
T Consensus         6 L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR~   38 (59)
T PF09048_consen    6 LAEYVKEHG--QAKAARALGVTQSAISKALRAGRN   38 (59)
T ss_dssp             HHHHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-E
T ss_pred             HHHHHHHhC--hHHHHHHcCCcHHHHHHHHHcCCc
Confidence            445555566  999999999999999999876554

Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....

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

Probab=94.26  E-value=0.063  Score=32.03  Aligned_cols=22  Identities=32%  Similarity=0.436  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|||+.+|||+.||.-||+
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~   22 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTR   22 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=94.23  E-value=0.17  Score=28.69  Aligned_cols=34  Identities=6%  Similarity=-0.086  Sum_probs=29.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+..+.+.|+.+||+++|+.+...
T Consensus        57 r~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLk   90 (95)
T PRK00430         57 APLLDMVMQYTRGNQTRAALMLGINRGTLRKKLK   90 (95)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3457777888899999999999999999988765

>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=94.22  E-value=0.058  Score=27.46  Aligned_cols=26  Identities=19%  Similarity=0.339  Sum_probs=22.1

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|.+..++|+.+|+|+.||..+.+
T Consensus        15 l~~G~~~~eIA~~l~is~~tV~~~~~   40 (58)
T PF00196_consen   15 LAQGMSNKEIAEELGISEKTVKSHRR   40 (58)
T ss_dssp             HHTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred             HHhcCCcchhHHhcCcchhhHHHHHH
Confidence            45799999999999999999998754

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 ....

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

Probab=94.22  E-value=0.092  Score=31.67  Aligned_cols=22  Identities=18%  Similarity=0.243  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|||+.||..||.
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~   23 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQ   23 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999985

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.

>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B

Probab=94.20  E-value=0.22  Score=25.56  Aligned_cols=39  Identities=15%  Similarity=0.172  Sum_probs=29.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      ..+.+..+.|+.++|.++|+..           .+.+|.+.+|+++++-+
T Consensus        10 ~~~~n~~~tA~~L~iHrNTl~y-----------Rl~ki~~l~g~dl~~~~   48 (59)
T PF13556_consen   10 ENNGNISKTARALHIHRNTLRY-----------RLKKIEELLGLDLDDPE   48 (59)
T ss_dssp             HTTT-HHHHHHHHTS-HHHHHH-----------HHHHHHHHHS--TTSHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHH-----------HHHHHHHHHCcCCCCHH
Confidence            4678999999999999999976           56788888888887643

>PRK01905 DNA-binding protein Fis; Provisional

Probab=94.12  E-value=0.2  Score=27.19  Aligned_cols=34  Identities=6%  Similarity=-0.101  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+..+....+.++.+.|+.+||+++++++...
T Consensus        39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklk   72 (77)
T PRK01905         39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQ   72 (77)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4567778888899999999999999999988765

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

Probab=94.07  E-value=0.11  Score=30.48  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|||..||.-||+
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~   22 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYED   22 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999986

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.

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=94.02  E-value=0.12  Score=25.23  Aligned_cols=25  Identities=16%  Similarity=0.088  Sum_probs=22.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.++|..++|+++|+++++++++-.
T Consensus        14 ~~~~s~~~Ia~~~gvs~~~~y~~f~   38 (47)
T PF00440_consen   14 YEAVSIRDIARRAGVSKGSFYRYFP   38 (47)
T ss_dssp             TTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHhCCHHHHHHHHccchhhHHHHcC
Confidence            4678999999999999999998754

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=94.01  E-value=0.025  Score=40.64  Aligned_cols=45  Identities=16%  Similarity=0.169  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      +-|+.+++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|...+
T Consensus       368 kPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v  412 (481)
T PRK12469        368 KPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKL  412 (481)
T ss_pred             cCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhcccc
Confidence            358999999999999999999999987777777777777887554

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=94.01  E-value=0.15  Score=32.72  Aligned_cols=28  Identities=29%  Similarity=0.275  Sum_probs=24.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +-..|+|+.++|+.+|+|+.+|+++++.
T Consensus       195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~  222 (231)
T TIGR02885       195 RYFKDKTQTEVANMLGISQVQVSRLEKK  222 (231)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3346999999999999999999999864

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.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=93.98  E-value=0.19  Score=30.07  Aligned_cols=35  Identities=14%  Similarity=0.280  Sum_probs=30.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      .+|..++|..+|+|.++++++.+       ..+.+||..||.
T Consensus       100 ~~t~~~Ia~~l~iS~~t~~r~r~-------~~l~kla~~lG~  134 (134)
T TIGR01636       100 PLTLVGLAQQLFISKSTAYRLRN-------HIIEAVAEELGM  134 (134)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHHHhCc
Confidence            46999999999999999999976       477888888873

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.

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

Probab=93.91  E-value=0.078  Score=31.94  Aligned_cols=22  Identities=18%  Similarity=0.217  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..++|+.+|||+.||..||.
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye~   22 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYTN   22 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999985

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.91  E-value=0.18  Score=30.14  Aligned_cols=34  Identities=6%  Similarity=0.066  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.++++++++++..+
T Consensus        43 ~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~   76 (144)
T PRK11512         43 FKVLCSIRCAACITPVELKKVLSVDLGALTRMLD   76 (144)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445666666789999999999999999998743

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

Probab=93.89  E-value=0.12  Score=30.50  Aligned_cols=22  Identities=23%  Similarity=0.356  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|||+.||..||.
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~   22 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYES   22 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>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=93.88  E-value=0.25  Score=25.31  Aligned_cols=35  Identities=23%  Similarity=0.320  Sum_probs=28.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++|++           .+..|.+.||+++-+++
T Consensus        15 s~~~AA~~l~is~~~vs~-----------~i~~LE~~lg~~Lf~r~   49 (60)
T PF00126_consen   15 SISAAAEELGISQSAVSR-----------QIKQLEEELGVPLFERS   49 (60)
T ss_dssp             SHHHHHHHCTSSHHHHHH-----------HHHHHHHHHTS-SEEEC
T ss_pred             CHHHHHHHhhccchHHHH-----------HHHHHHHHhCCeEEEEC
Confidence            677799999999999998           45778888888887664

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 ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.86  E-value=0.16  Score=30.88  Aligned_cols=34  Identities=12%  Similarity=0.096  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      +....|..+......|..++|+.+|+|++++.+-
T Consensus        10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~R   43 (153)
T PRK11179         10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVR   43 (153)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            3466778888889999999999999999997654

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=93.83  E-value=0.21  Score=26.17  Aligned_cols=27  Identities=11%  Similarity=0.094  Sum_probs=22.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ......+..+||+.+|+|.++|++...
T Consensus         9 L~~~~~~~~eLa~~l~vS~~tv~~~l~   35 (69)
T TIGR00122         9 LADNPFSGEKLGEALGMSRTAVNKHIQ   35 (69)
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            445568899999999999999988754

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.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=93.83  E-value=0.074  Score=33.04  Aligned_cols=24  Identities=13%  Similarity=0.153  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+++.+|++..+
T Consensus       148 ~~~t~~~iA~~lG~tretvsR~l~  171 (202)
T PRK13918        148 IYATHDELAAAVGSVRETVTKVIG  171 (202)
T ss_pred             ecCCHHHHHHHhCccHHHHHHHHH
Confidence            357999999999999999999754

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=93.79  E-value=0.023  Score=40.22  Aligned_cols=45  Identities=11%  Similarity=0.155  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      +-||.+++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|.-.+
T Consensus       317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~  361 (429)
T TIGR02395       317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGV  361 (429)
T ss_pred             cCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCcc
Confidence            358999999999999999999999987666666666777776433

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

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=93.75  E-value=0.22  Score=28.15  Aligned_cols=34  Identities=15%  Similarity=0.304  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|..+.....+|..++|+.+|+|++++++..+
T Consensus         6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~   39 (108)
T smart00344        6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVK   39 (108)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3456667777789999999999999999987643

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

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=93.73  E-value=0.084  Score=31.15  Aligned_cols=21  Identities=19%  Similarity=0.286  Sum_probs=19.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 038591           35 SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..|||+.+|||+.||..||.
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye~   21 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYER   21 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            467999999999999999986

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.

>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function

Probab=93.66  E-value=0.32  Score=27.43  Aligned_cols=36  Identities=17%  Similarity=0.167  Sum_probs=31.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ...|++-.+..|+|..++|..+|+|...|.++.+=+
T Consensus        12 ~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~   47 (89)
T PF10078_consen   12 RQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK   47 (89)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence            456777778899999999999999999999998743

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=93.61  E-value=0.11  Score=32.80  Aligned_cols=32  Identities=16%  Similarity=0.353  Sum_probs=26.2

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+..+ ...|+|..++|+.+|||++|+++|.+.
T Consensus       164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            44444 356999999999999999999999863

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=93.58  E-value=0.091  Score=32.82  Aligned_cols=23  Identities=9%  Similarity=0.253  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+++||..+|+++.+++++.+
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~  190 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLK  190 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            58999999999999999999864

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=93.54  E-value=0.12  Score=23.98  Aligned_cols=19  Identities=21%  Similarity=0.289  Sum_probs=17.5

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q 038591           35 SQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~   53 (82)
                      |..+.|+.+|++.++|+++
T Consensus        18 Si~eAa~~l~i~~~~I~~~   36 (37)
T PF07453_consen   18 SIREAARYLGISHSTISKY   36 (37)
T ss_pred             CHHHHHHHhCCCHHHHHHh
Confidence            7889999999999999876

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=93.52  E-value=0.03  Score=39.95  Aligned_cols=45  Identities=11%  Similarity=0.182  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      +-||++++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|...+
T Consensus       342 kPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~  386 (455)
T PRK05932        342 KPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAV  386 (455)
T ss_pred             cCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhccccc
Confidence            358999999999999999999999987656556666666776544

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=93.49  E-value=0.12  Score=25.68  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             C-CHHHHHHHhCCCHHHHHHHHc
Q 038591           34 M-SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~-s~~elA~~~gis~~~i~~~e~   55 (82)
                      + |+.+||+.+|+|++++.+..+
T Consensus        20 l~s~~~la~~~~vs~~tv~~~l~   42 (60)
T smart00345       20 LPSERELAAQLGVSRTTVREALS   42 (60)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            5 899999999999999988653

>PRK09954 putative kinase; Provisional

Probab=93.48  E-value=0.18  Score=34.43  Aligned_cols=34  Identities=12%  Similarity=0.060  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|+.+++...+|+.++|+.+|+|+++|.+..+
T Consensus         6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~   39 (362)
T PRK09954          6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIM   39 (362)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3467888888899999999999999999998865

>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH

Probab=93.47  E-value=0.2  Score=26.30  Aligned_cols=30  Identities=13%  Similarity=0.210  Sum_probs=24.0

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..+.--+|.|+|+.+++++.||.+|-..
T Consensus        10 elLi~~~GnqtEvaR~l~c~R~TVrKY~~D   39 (64)
T PF06322_consen   10 ELLIETYGNQTEVARRLGCNRATVRKYSRD   39 (64)
T ss_pred             HHHHHHhCcHHHHHHHhcccHHHHHHHhcc
Confidence            333444458999999999999999999765

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

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=93.45  E-value=0.14  Score=34.03  Aligned_cols=34  Identities=15%  Similarity=0.140  Sum_probs=30.6

Q ss_pred             HHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKK-MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+.|+.++..-| ++|.||.+.+|.|++|++++.+
T Consensus       198 ~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~  232 (258)
T COG2512         198 KEILDLIRERGGRITQAELRRALGLSKTTVSRILR  232 (258)
T ss_pred             HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHH
Confidence            677888888888 9999999999999999999864

>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=93.40  E-value=0.09  Score=30.32  Aligned_cols=27  Identities=15%  Similarity=0.219  Sum_probs=19.7

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      -.-++|..|+|+.+|||+++|+.+.+-
T Consensus        30 y~eDlSlsEIAe~~~iSRqaV~d~ikr   56 (101)
T PF04297_consen   30 YEEDLSLSEIAEELGISRQAVYDSIKR   56 (101)
T ss_dssp             CTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            346899999999999999999998753

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.

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=93.29  E-value=0.12  Score=33.14  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+.++||+.+|||++|++...+
T Consensus       178 ~~~l~dLA~~lGISkst~~ehLR  200 (215)
T COG3413         178 RVSLKDLAKELGISKSTLSEHLR  200 (215)
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            56999999999999999998875

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=93.29  E-value=0.11  Score=34.42  Aligned_cols=23  Identities=17%  Similarity=0.328  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|++++|+.+|||+.+|++++.
T Consensus       236 ~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       236 KLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            79999999999999999999986

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=93.27  E-value=0.23  Score=32.41  Aligned_cols=28  Identities=25%  Similarity=0.273  Sum_probs=24.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +-..|+|+.++|+.+|+|+++|+++++.
T Consensus       214 ~~~~~~s~~eIA~~lgis~~~V~~~~~r  241 (252)
T PRK05572        214 RYFKDKTQSEVAKRLGISQVQVSRLEKK  241 (252)
T ss_pred             HHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4446999999999999999999999864

>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=93.22  E-value=0.12  Score=26.85  Aligned_cols=26  Identities=23%  Similarity=0.391  Sum_probs=21.2

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ....++..++|+.+|+|+++++...+
T Consensus        19 ~~~~v~~~~iA~~L~vs~~tvt~ml~   44 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGVSPPTVTEMLK   44 (60)
T ss_dssp             CTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCccHHHHHHHHCCChHHHHHHHH
Confidence            44678999999999999999998753

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 ....

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=93.19  E-value=0.28  Score=25.20  Aligned_cols=32  Identities=16%  Similarity=0.173  Sum_probs=25.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+-....++..++|..+|+|..+|.++.+
T Consensus        10 Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~   41 (59)
T PF08280_consen   10 LLELLLKNKWITLKELAKKLNISERTIKNDIN   41 (59)
T ss_dssp             HHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            34555567789999999999999999998764

; PDB: 2WTE_A 3SQN_A.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=93.17  E-value=0.29  Score=25.58  Aligned_cols=24  Identities=17%  Similarity=0.289  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+|..++|+.+|+|..++.++...
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~   24 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKK   24 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            368889999999999998888753

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=93.14  E-value=0.15  Score=30.14  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=20.8

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVS   51 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~   51 (82)
                      ++--.|+|.+|+|+.+|+|.+||.
T Consensus       118 l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209       118 MKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHhhc
Confidence            445679999999999999999985

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.

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

Probab=93.06  E-value=0.19  Score=31.37  Aligned_cols=22  Identities=23%  Similarity=0.315  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|||+.+|||+.||..||.
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~   23 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER   23 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999986

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

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

Probab=93.06  E-value=0.2  Score=26.38  Aligned_cols=30  Identities=7%  Similarity=0.094  Sum_probs=22.6

Q ss_pred             HHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           26 QRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        26 k~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+.. ...++-.|+|+.+|+|..++..|.+
T Consensus         7 ~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~   37 (62)
T PF04703_consen    7 EYIKEQNGPLKTREIADALGLSIYQARYYLE   37 (62)
T ss_dssp             HHHHHHTS-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            33444 5789999999999999999998864

>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]

Probab=93.06  E-value=0.18  Score=32.44  Aligned_cols=49  Identities=14%  Similarity=0.089  Sum_probs=43.4

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      ..+++.+.++.++++..|+++ ++..|.++-..++...+....+.|+..-
T Consensus         6 rrq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g   54 (201)
T COG1974           6 RRQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKG   54 (201)
T ss_pred             HHHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcCC
Confidence            356778899999999999999 9999999999999999999999887653

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=93.05  E-value=0.23  Score=33.76  Aligned_cols=34  Identities=15%  Similarity=0.099  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++..+
T Consensus       288 r~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk  321 (326)
T PRK11608        288 KELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK  321 (326)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4457777788899999999999999999998875

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

Probab=93.05  E-value=0.31  Score=28.80  Aligned_cols=28  Identities=11%  Similarity=-0.021  Sum_probs=24.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|..|+|..+|+|+++|.....
T Consensus       124 l~~~~~~~~~eIA~~lgis~~tv~~~~~  151 (161)
T TIGR02985       124 LSRFEGKSYKEIAEELGISVKTVEYHIS  151 (161)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445799999999999999999998764

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.

>PRK09480 slmA division inhibitor protein; Provisional

Probab=93.02  E-value=0.1  Score=32.05  Aligned_cols=28  Identities=14%  Similarity=0.178  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .+.|..++|+.+|||+++++.+-.++..
T Consensus        29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~~   56 (194)
T PRK09480         29 ERITTAKLAARVGVSEAALYRHFPSKAR   56 (194)
T ss_pred             CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence            5899999999999999999999887654

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=93.00  E-value=0.12  Score=32.98  Aligned_cols=23  Identities=17%  Similarity=0.299  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|++++|..+|+++.++++..+
T Consensus       184 ~lt~~~iA~~lG~sr~tvsR~l~  206 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLLG  206 (235)
T ss_pred             cccHHHHHHHhCCcHHHHHHHHH
Confidence            48999999999999999999753

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=92.97  E-value=0.18  Score=33.60  Aligned_cols=44  Identities=11%  Similarity=0.115  Sum_probs=33.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..|+|++|+|+.+|+|.++|..+...    ....+.......+++++.
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~r----AlkkLr~~l~~~~~~~~~  283 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVE----ALKKLRRILERDGVDREA  283 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHhhhhhhc
Confidence            56899999999999999999999864    344555555566666553

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).

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

Probab=92.97  E-value=0.15  Score=29.52  Aligned_cols=25  Identities=12%  Similarity=0.052  Sum_probs=22.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|+|..++|+.+|+|+++|+++.+
T Consensus       124 ~~g~s~~eIA~~l~~s~~~v~~~~~  148 (158)
T TIGR02937       124 LEGLSYKEIAEILGISVGTVKRRLK  148 (158)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4699999999999999999999875

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.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=92.92  E-value=0.26  Score=32.42  Aligned_cols=32  Identities=6%  Similarity=0.009  Sum_probs=26.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++.+.+...++..|||+.+|+|..|+.+..+
T Consensus        10 Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~   41 (251)
T PRK13509         10 LLELLAQLGFVTVEKVIERLGISPATARRDIN   41 (251)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            45556666779999999999999999988754

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=92.81  E-value=0.29  Score=31.02  Aligned_cols=33  Identities=15%  Similarity=0.111  Sum_probs=27.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+...-++|+.+||+.+|+++++|++..+
T Consensus         5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~   37 (203)
T TIGR02702         5 DILSYLLKQGQATAAALAEALAISPQAVRRHLK   37 (203)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345666667789999999999999999988743

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=92.80  E-value=0.35  Score=28.70  Aligned_cols=28  Identities=11%  Similarity=-0.100  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|..|+|+.+|+|.++|..+..
T Consensus       117 l~~~~~~s~~EIA~~l~is~~tV~~~~~  144 (154)
T PRK06759        117 ERFFVGKTMGEIALETEMTYYQVRWIYR  144 (154)
T ss_pred             HHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445799999999999999999998864

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=92.79  E-value=0.3  Score=31.97  Aligned_cols=28  Identities=25%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +-..|+|+.++|+.+|+|+.+|++++..
T Consensus       221 ~~~~~~t~~eIA~~lgis~~~V~~~~~~  248 (258)
T PRK08215        221 RFFQGKTQMEVAEEIGISQAQVSRLEKA  248 (258)
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3346999999999999999999999863

>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit

Probab=92.74  E-value=0.081  Score=32.98  Aligned_cols=23  Identities=13%  Similarity=0.382  Sum_probs=18.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++.++||+.+|||.+||.+|..
T Consensus         2 ~vnk~~lA~i~gvS~~ti~~W~~   24 (164)
T PF07471_consen    2 KVNKKELAEIFGVSERTIDKWQR   24 (164)
T ss_dssp             EEEHHHHHHHTT--HHHHHHHTT
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            35789999999999999999974

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=92.71  E-value=0.14  Score=32.80  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .+|+.++|..+|+++.++++..
T Consensus       179 ~lt~~~IA~~lGisretlsR~L  200 (230)
T PRK09391        179 PMSRRDIADYLGLTIETVSRAL  200 (230)
T ss_pred             cCCHHHHHHHHCCCHHHHHHHH
Confidence            4799999999999999999965

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=92.68  E-value=0.15  Score=34.10  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++|+.++|+.+|||+.+|++++.
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~  270 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEK  270 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            379999999999999999999986

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

Probab=92.68  E-value=0.34  Score=28.33  Aligned_cols=35  Identities=9%  Similarity=0.132  Sum_probs=28.8

Q ss_pred             CHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           21 TPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        21 ~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+.|+.+- ...++|+.|+|..+|||.++|+.+..
T Consensus        58 d~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lk   93 (119)
T PF01710_consen   58 DRDELKALVEENPDATLRELAERLGVSPSTIWRALK   93 (119)
T ss_pred             cHHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHH
Confidence            355676664 45789999999999999999999885

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 [].

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=92.68  E-value=0.23  Score=29.99  Aligned_cols=26  Identities=12%  Similarity=0.047  Sum_probs=23.4

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|++..++|+.+|+|+.+|.++..
T Consensus       138 ~~~~~~~~eIA~~lgis~~tv~~~~~  163 (179)
T PRK11924        138 YVEGLSYREIAEILGVPVGTVKSRLR  163 (179)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34699999999999999999999875

>PRK00215 LexA repressor; Validated

Probab=92.65  E-value=0.32  Score=30.76  Aligned_cols=25  Identities=24%  Similarity=0.349  Sum_probs=21.3

Q ss_pred             hCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQ-RPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gi-s~~~i~~~e~   55 (82)
                      ...+|+.|||+.+|+ +++|++++.+
T Consensus        21 ~~~~s~~ela~~~~~~~~~tv~~~l~   46 (205)
T PRK00215         21 GYPPSRREIADALGLRSPSAVHEHLK   46 (205)
T ss_pred             CCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            345699999999999 9999999943

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=92.64  E-value=0.3  Score=31.94  Aligned_cols=32  Identities=16%  Similarity=0.141  Sum_probs=26.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+..+.+...+++.|||+.+|+|..||++..+
T Consensus         9 Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~   40 (240)
T PRK10411          9 IVDLLLNHTSLTTEALAEQLNVSKETIRRDLN   40 (240)
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            45566677889999999999999999988754

>PRK15320 transcriptional activator SprB; Provisional

Probab=92.60  E-value=0.15  Score=33.13  Aligned_cols=26  Identities=23%  Similarity=0.302  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|+|++|+|+.+++|.+||+.+.+
T Consensus       176 LAkG~SNKEIAekL~LS~KTVSTYKn  201 (251)
T PRK15320        176 LSSGHPAIELAKKFGLGTKTVSIYRK  201 (251)
T ss_pred             HHcCCCHHHHHHHhccchhhHHHHHH
Confidence            46799999999999999999999865

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=92.47  E-value=0.33  Score=33.16  Aligned_cols=34  Identities=12%  Similarity=0.043  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++..+
T Consensus       294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk  327 (329)
T TIGR02974       294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR  327 (329)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4567777888899999999999999999998764

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

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=92.46  E-value=0.3  Score=28.15  Aligned_cols=34  Identities=18%  Similarity=-0.009  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        31 ~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~   64 (118)
T TIGR02337        31 WRILRILAEQGSMEFTQLANQACILRPSLTGILA   64 (118)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHH
Confidence            3456666677889999999999999999988743

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=92.44  E-value=0.37  Score=31.25  Aligned_cols=27  Identities=11%  Similarity=0.172  Sum_probs=24.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|++++|..+|+|..+|++++.
T Consensus       195 ~~~~~~t~~EIA~~lgis~~~V~q~~~  221 (231)
T PRK12427        195 YYQHEMSLKEIALVLDLTEARICQLNK  221 (231)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            445699999999999999999999886

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

Probab=92.36  E-value=0.42  Score=29.24  Aligned_cols=27  Identities=11%  Similarity=0.100  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|.+||.....
T Consensus       146 ~~~~g~s~~EIA~~lgis~~tVk~~l~  172 (183)
T TIGR02999       146 RFFAGLTVEEIAELLGVSVRTVERDWR  172 (183)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            455799999999999999999988754

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.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=92.34  E-value=0.24  Score=30.70  Aligned_cols=27  Identities=15%  Similarity=0.161  Sum_probs=23.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|.++|..+..
T Consensus       153 ~~~~g~s~~EIA~~lgis~~tV~~~l~  179 (194)
T PRK12519        153 AYYEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             hhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            344699999999999999999998875

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=92.33  E-value=0.89  Score=26.13  Aligned_cols=51  Identities=14%  Similarity=0.218  Sum_probs=33.7

Q ss_pred             HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591           22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI   72 (82)
Q Consensus        22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l   72 (82)
                      |.+++-+.  -...+||.|++..+|+|-.+|.+=-|.-...+.+.-.-+.+.+
T Consensus        47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l   99 (103)
T COG2973          47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL   99 (103)
T ss_pred             HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence            55555443  3568999999999999988888744443333444445555544

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

Probab=92.31  E-value=0.39  Score=30.66  Aligned_cols=27  Identities=19%  Similarity=0.225  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|++++|+.+|+|+++|+.+..
T Consensus       190 ~y~~~~s~~eIA~~lgis~~~v~~~~~  216 (227)
T TIGR02980       190 RFFEDKTQSEIAERLGISQMHVSRLLR  216 (227)
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334699999999999999999999875

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.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=92.30  E-value=0.23  Score=31.55  Aligned_cols=37  Identities=14%  Similarity=0.125  Sum_probs=28.9

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +.....+-++ -..|+|.+|+|+++++|+.||..+.+.
T Consensus       138 LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~  175 (207)
T PRK15411        138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGN  175 (207)
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHH
Confidence            5555555543 457999999999999999999998753

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=92.27  E-value=0.45  Score=28.57  Aligned_cols=28  Identities=18%  Similarity=0.152  Sum_probs=23.8

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|..+|.....
T Consensus       120 l~~~~~~s~~EIA~~lgis~~tV~~~l~  147 (163)
T PRK07037        120 MYRLHGETQKDIARELGVSPTLVNFMIR  147 (163)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455799999999999999999998743

>PHA01082 putative transcription regulator

Probab=92.24  E-value=0.11  Score=30.88  Aligned_cols=31  Identities=16%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      +.|+|..|.|+.+--|..+|.+|-.|+..|+
T Consensus        28 eCgLsveeaa~LCfKsVrtVk~WD~G~~IPP   58 (133)
T PHA01082         28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPP   58 (133)
T ss_pred             ccCccHHHHHHHHHHhHHHHhhccCCCcCCh
Confidence            5799999999999999999999999987665

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=92.17  E-value=0.35  Score=33.77  Aligned_cols=34  Identities=9%  Similarity=-0.061  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++..+
T Consensus       419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~  452 (457)
T PRK11361        419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ  452 (457)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4567777888899999999999999999988654

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=92.16  E-value=0.41  Score=23.73  Aligned_cols=25  Identities=16%  Similarity=0.121  Sum_probs=21.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ....+..++++.+|+|++++++..+
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~   32 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLK   32 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHH
Confidence            5678999999999999999988754

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=92.15  E-value=0.44  Score=28.80  Aligned_cols=27  Identities=15%  Similarity=-0.010  Sum_probs=23.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+++|..+|+|..+|..+..
T Consensus       140 ~~~~~~s~~eIA~~lgis~~tV~~~l~  166 (182)
T PRK09652        140 REIEGLSYEEIAEIMGCPIGTVRSRIF  166 (182)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            335699999999999999999998765

>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII

Probab=92.07  E-value=1.1  Score=27.84  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=37.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHhC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK--AVPNQTVLAKMEKAIG   73 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~--~~p~~~~~~~la~~lg   73 (82)
                      -..++.+-...+  ..+||..+|++++++.+-.|..  ..++...+..|+++-|
T Consensus        11 ~~Ac~~fa~~h~--~~~lA~~lGm~~~~LrNKLNP~q~H~Lt~~el~~i~~~Tg   62 (162)
T PF06892_consen   11 DEACRAFAKNHN--MAALAERLGMNPQTLRNKLNPEQPHKLTVDELIAITDATG   62 (162)
T ss_pred             HHHHHHHHHhcC--HHHHHHHhCCCHHHHHHHcCCCCCCCCCHHHHHHHHHHhC
Confidence            345566666665  5789999999999999999874  3567888888777654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=91.97  E-value=0.29  Score=25.82  Aligned_cols=31  Identities=23%  Similarity=0.336  Sum_probs=21.4

Q ss_pred             HHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQR-ARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|+. ++....+|..|||..+++++++|..+.
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL   35 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFGISPEAVEAML   35 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3455 456667899999999999999876653

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=91.97  E-value=0.4  Score=33.62  Aligned_cols=34  Identities=6%  Similarity=-0.007  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++..+
T Consensus       428 ~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~  461 (463)
T TIGR01818       428 RPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK  461 (463)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3457777788899999999999999999988653

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

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

Probab=91.96  E-value=0.13  Score=31.98  Aligned_cols=27  Identities=7%  Similarity=-0.038  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|..|+|+.+|+|..+|.....
T Consensus       143 ~~~~g~s~~EIA~~lgis~~tVk~~l~  169 (193)
T TIGR02947       143 ADVEGFAYKEIAEIMGTPIGTVMSRLH  169 (193)
T ss_pred             hhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344599999999999999999998875

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=91.94  E-value=0.42  Score=31.23  Aligned_cols=25  Identities=24%  Similarity=0.210  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|+|++++|+.+|+|+.+|+++++
T Consensus       220 ~~~~t~~eIA~~lgis~~~V~~~~~  244 (254)
T TIGR02850       220 FEGKTQMEVAEEIGISQAQVSRLEK  244 (254)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4589999999999999999999986

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.

>PRK13869 plasmid-partitioning protein RepA; Provisional

Probab=91.90  E-value=0.42  Score=33.55  Aligned_cols=43  Identities=7%  Similarity=0.156  Sum_probs=34.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHHHHHhCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN------------GKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~------------g~~~p~~~~~~~la~~lgv   74 (82)
                      +.+|..|+|+.+||+.+||..|+.            |.+..+.+.+..+.+.|+-
T Consensus        47 r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~~  101 (405)
T PRK13869         47 RKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLAG  101 (405)
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHHh
Confidence            367999999999999999999953            3445677788888888863

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=91.87  E-value=0.45  Score=28.02  Aligned_cols=30  Identities=3%  Similarity=-0.043  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      ..++..+||+.+|+|+.++.++.......+
T Consensus        24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s   53 (127)
T PRK11511         24 SPLSLEKVSERSGYSKWHLQRMFKKETGHS   53 (127)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            358999999999999999999987543333

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=91.80  E-value=0.42  Score=30.90  Aligned_cols=26  Identities=12%  Similarity=0.303  Sum_probs=23.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..++|++++|+.+|+|+++|++++..
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~~  219 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIESK  219 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHH
Confidence            46799999999999999999999864

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.

>TIGR03453 partition_RepA plasmid partitioning protein RepA

Probab=91.76  E-value=0.39  Score=33.33  Aligned_cols=43  Identities=5%  Similarity=0.151  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHhCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG------------KAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g------------~~~p~~~~~~~la~~lgv   74 (82)
                      .-+|..|+|+.+|++++||..||.-            .+..+.+.+..|...+..
T Consensus        32 ~~~~i~eva~~~gv~~~tlr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~   86 (387)
T TIGR03453        32 RKFTSGEVAKLLGVSDSYLRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQ   86 (387)
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHh
Confidence            3589999999999999999999753            333466777777777654

Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=91.73  E-value=0.52  Score=28.32  Aligned_cols=28  Identities=14%  Similarity=0.145  Sum_probs=24.4

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++- .|++.+++|+.+|+|.++|.....
T Consensus       122 ~l~~-~g~s~~eIA~~lgis~~tV~~~i~  149 (166)
T PRK09639        122 LLRF-SGYSYKEIAEALGIKESSVGTTLA  149 (166)
T ss_pred             HHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455 899999999999999999998864

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=91.72  E-value=0.53  Score=28.08  Aligned_cols=27  Identities=15%  Similarity=0.079  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|.+|+|+.+|+|..+|.....
T Consensus       118 ~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (161)
T PRK09047        118 RYWEDMDVAETAAAMGCSEGSVKTHCS  144 (161)
T ss_pred             HHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence            445699999999999999999998765

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=91.71  E-value=0.36  Score=31.58  Aligned_cols=33  Identities=9%  Similarity=0.158  Sum_probs=26.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+.....+|..|+|+.+|++++|++++.+
T Consensus        18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~   50 (257)
T PRK15090         18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQ   50 (257)
T ss_pred             HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            444555455679999999999999999999854

>COG1309 AcrR Transcriptional regulator [Transcription]

Probab=91.70  E-value=0.14  Score=30.00  Aligned_cols=27  Identities=7%  Similarity=-0.002  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+++++++++..++.
T Consensus        31 ~~~t~~~Ia~~agvs~~~~Y~~f~~K~   57 (201)
T COG1309          31 AATTVDEIAKAAGVSKGTLYRHFPSKE   57 (201)
T ss_pred             CCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence            468899999999999999999987754

>PRK15115 response regulator GlrR; Provisional

Probab=91.69  E-value=0.38  Score=33.56  Aligned_cols=34  Identities=6%  Similarity=-0.094  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus       400 ~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~  433 (444)
T PRK15115        400 LNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS  433 (444)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4567777888899999999999999999988765

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

Probab=91.69  E-value=0.2  Score=32.55  Aligned_cols=25  Identities=16%  Similarity=0.244  Sum_probs=21.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..++|+.+||+.+++|+++++++.+
T Consensus        19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk   43 (217)
T PRK14165         19 TVKISSSEFANHTGTSSKTAARILK   43 (217)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3468999999999999999999854

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=91.62  E-value=0.21  Score=33.40  Aligned_cols=27  Identities=19%  Similarity=0.378  Sum_probs=23.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      -.||...++|+++|||+.||..|-+..
T Consensus        17 l~gmk~~dIAeklGvspntiksWKrr~   43 (279)
T COG5484          17 LKGMKLKDIAEKLGVSPNTIKSWKRRD   43 (279)
T ss_pred             HhhccHHHHHHHhCCChHHHHHHHHhc
Confidence            357999999999999999999998643

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=91.59  E-value=0.54  Score=25.60  Aligned_cols=34  Identities=15%  Similarity=0.142  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++++.++|+.+++++++|++..+
T Consensus        13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~   46 (101)
T smart00347       13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLD   46 (101)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHH
Confidence            3455666666679999999999999999988754

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=91.54  E-value=0.54  Score=30.70  Aligned_cols=27  Identities=15%  Similarity=0.207  Sum_probs=24.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|+.|+|+.+|+|..+|..+..
T Consensus       217 ~~~~g~s~~eIA~~l~is~~tV~~~~~  243 (257)
T PRK08583        217 TFIENLSQKETGERLGISQMHVSRLQR  243 (257)
T ss_pred             HHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345799999999999999999999875

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=91.54  E-value=0.5  Score=32.81  Aligned_cols=34  Identities=12%  Similarity=-0.010  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus       407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~  440 (441)
T PRK10365        407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  440 (441)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence            4467777888899999999999999999987543

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

Probab=91.53  E-value=0.22  Score=29.14  Aligned_cols=24  Identities=17%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|.|..++|...+||.+||.+|..
T Consensus        17 ~g~s~~eaa~~F~VS~~Tv~~W~k   40 (119)
T PF01710_consen   17 KGKSIREAAKRFGVSRNTVYRWLK   40 (119)
T ss_pred             ccchHHHHHHHhCcHHHHHHHHHH
Confidence            488999999999999999999965

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 [].

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

Probab=91.53  E-value=0.61  Score=27.78  Aligned_cols=26  Identities=23%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +.-.|++.+|+|+.+|+|.++|....
T Consensus       123 ~~~~g~~~~eIA~~l~is~~tv~~~l  148 (159)
T TIGR02989       123 RYQRGVSLTALAEQLGRTVNAVYKAL  148 (159)
T ss_pred             HHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence            45579999999999999999998764

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).

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=91.44  E-value=0.27  Score=31.59  Aligned_cols=25  Identities=20%  Similarity=0.393  Sum_probs=22.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|.+|+|+.+|+|..||.+...
T Consensus       196 ~eg~s~~EIA~~lgis~~tVk~~~~  220 (234)
T PRK08301        196 GEEKTQKEVADMLGISQSYISRLEK  220 (234)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3699999999999999999998864

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=91.40  E-value=1.3  Score=24.96  Aligned_cols=26  Identities=4%  Similarity=-0.078  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..++..++|+.+|+|+.++.+..+..
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~f~~~   45 (107)
T PRK10219         20 QPLNIDVVAKKSGYSKWYLQRMFRTV   45 (107)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            35899999999999999999887653

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=91.36  E-value=0.33  Score=31.00  Aligned_cols=37  Identities=3%  Similarity=0.006  Sum_probs=28.1

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +......-++ -..|+|.+|+|+.+++|+.||..+-+.
T Consensus       134 LSpRErEVLrLLAqGkTnKEIAe~L~IS~rTVkth~sr  171 (198)
T PRK15201        134 FSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRS  171 (198)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            4444444443 467999999999999999999987653

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=91.33  E-value=0.26  Score=31.29  Aligned_cols=23  Identities=9%  Similarity=0.179  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+|.+|+|+.+|+|+.||.++..
T Consensus       177 g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        177 QHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             CcCHHHHHHHhCccHHHHHHHHH
Confidence            68999999999999999998864

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=91.33  E-value=0.5  Score=34.44  Aligned_cols=34  Identities=6%  Similarity=-0.110  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|....+..+.++.+.|+.+|||++|+++..+
T Consensus       492 r~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk  525 (526)
T TIGR02329       492 ALAVRAALERFGGDRDAAAKALGISRTTLWRRLK  525 (526)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4567788888999999999999999999998764

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=91.33  E-value=0.61  Score=28.63  Aligned_cols=27  Identities=4%  Similarity=-0.041  Sum_probs=23.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.....
T Consensus       147 ~~~~~~s~~eIA~~lgis~~~V~~~l~  173 (186)
T PRK13919        147 LYYQGYTHREAAQLLGLPLGTLKTRAR  173 (186)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            445699999999999999999998765

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=91.32  E-value=0.63  Score=27.87  Aligned_cols=28  Identities=18%  Similarity=-0.008  Sum_probs=23.6

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.+||.....
T Consensus       117 l~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (160)
T PRK09642        117 AHYLEEKSYQEIALQEKIEVKTVEMKLY  144 (160)
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455699999999999999999977654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=91.25  E-value=0.58  Score=30.71  Aligned_cols=27  Identities=19%  Similarity=0.245  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|++++|..+|+|..+|+++..
T Consensus       215 ~y~~~~s~~eIA~~lgvs~~~V~~~~~  241 (256)
T PRK07408        215 VFLHDLTQKEAAERLGISPVTVSRRVK  241 (256)
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334699999999999999999999976

>TIGR03613 RutR pyrimidine utilization regulatory protein R

Probab=91.22  E-value=0.24  Score=30.71  Aligned_cols=29  Identities=14%  Similarity=0.009  Sum_probs=24.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .+.|..++|+.+|||+.+++.+-.++...
T Consensus        27 ~~~s~~~IA~~agvs~~~lY~hF~sKe~L   55 (202)
T TIGR03613        27 HGTSLEQIAELAGVSKTNLLYYFPSKDAL   55 (202)
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence            46899999999999999999998765443

This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=91.22  E-value=0.71  Score=28.39  Aligned_cols=28  Identities=21%  Similarity=0.243  Sum_probs=24.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|.+||.....
T Consensus       138 L~~~~g~s~~EIA~~lgis~~tVk~~l~  165 (178)
T PRK12529        138 MATLDGMKQKDIAQALDIALPTVKKYIH  165 (178)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456699999999999999999988764

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=91.21  E-value=0.55  Score=30.25  Aligned_cols=27  Identities=7%  Similarity=0.155  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|.+|+|+.+|+|.++|..+..
T Consensus       196 ~~~~g~s~~EIA~~lgis~~tV~~~~~  222 (236)
T PRK06986        196 YYQEELNLKEIGAVLGVSESRVSQIHS  222 (236)
T ss_pred             HhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            445699999999999999999998875

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=91.17  E-value=0.62  Score=28.66  Aligned_cols=28  Identities=11%  Similarity=0.146  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.++|..+..
T Consensus       144 l~~~~~~s~~eIA~~lgis~~tV~~~l~  171 (182)
T PRK12537        144 HAYVDGCSHAEIAQRLGAPLGTVKAWIK  171 (182)
T ss_pred             HHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence            3445799999999999999999998865

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

Probab=91.16  E-value=0.15  Score=36.41  Aligned_cols=43  Identities=16%  Similarity=0.191  Sum_probs=35.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      ++.+++|+.+|++.+|||+.-+++..-+..-+..|-.+|-..+
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i  373 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSL  373 (444)
T ss_pred             ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhc
Confidence            8999999999999999999999987666666666666665544

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

Probab=91.12  E-value=0.36  Score=24.40  Aligned_cols=21  Identities=24%  Similarity=0.278  Sum_probs=18.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 038591           35 SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..++|+.+|+|++++++..+
T Consensus        27 ~~~~la~~~~is~~~v~~~l~   47 (66)
T cd07377          27 SERELAEELGVSRTTVREALR   47 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
Confidence            599999999999999988654

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

>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed

Probab=91.10  E-value=0.38  Score=30.20  Aligned_cols=36  Identities=25%  Similarity=0.361  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+.+..|+ .|...|.|..|+|+..|++...|.+|+.
T Consensus        56 ~L~PReIQ-arIRaGas~eeVA~~~G~~~~rV~rfa~   91 (170)
T PF11268_consen   56 SLRPREIQ-ARIRAGASAEEVAEEAGVPVERVRRFAG   91 (170)
T ss_pred             CCCHHHHH-HHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence            34455554 5777899999999999999999999864

Currently no function is known.

>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=91.05  E-value=0.38  Score=29.89  Aligned_cols=30  Identities=13%  Similarity=0.232  Sum_probs=23.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhC-CCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQIN-QRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~g-is~~~i~~~e   54 (82)
                      .|+++. ..|+|..++|..|| +|+++|-..-
T Consensus        10 ~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~   40 (162)
T PF07750_consen   10 RLRKLW-AEGLSASQIARQLGGVSRNAVIGKA   40 (162)
T ss_pred             HHHHHH-HcCCCHHHHHHHhCCcchhhhhhhh
Confidence            444444 47999999999999 9999876543

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 [].

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=91.05  E-value=0.31  Score=31.17  Aligned_cols=38  Identities=24%  Similarity=0.377  Sum_probs=28.8

Q ss_pred             CCCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           19 PDTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        19 ~~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+....+.-++ -..|+|.+|+|+++++|..||..+-+.
T Consensus       148 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~  186 (211)
T COG2197         148 LLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSN  186 (211)
T ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHH
Confidence            34445554443 468999999999999999999887654

>PRK12423 LexA repressor; Provisional

Probab=90.96  E-value=0.68  Score=29.44  Aligned_cols=32  Identities=13%  Similarity=0.050  Sum_probs=24.7

Q ss_pred             HHHHHHHHHhCCC--CHHHHHHHhC-CCHHHHHHH
Q 038591           22 PRQIQRARLGKKM--SQPDLANQIN-QRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~--s~~elA~~~g-is~~~i~~~   53 (82)
                      -..|.......|+  |..|||+.+| .|+++++..
T Consensus        12 l~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~   46 (202)
T PRK12423         12 LAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKH   46 (202)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHH
Confidence            3456666666777  9999999999 589888754

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=90.96  E-value=0.62  Score=29.53  Aligned_cols=33  Identities=9%  Similarity=0.155  Sum_probs=25.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+....++++.++|+.+|+|++|+++..+
T Consensus       147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~  179 (203)
T TIGR01884       147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR  179 (203)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            444555554678999999999999999988754

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

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

Probab=90.95  E-value=0.8  Score=23.26  Aligned_cols=30  Identities=13%  Similarity=0.137  Sum_probs=23.3

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..+.. .+++..++|+.+|++..+++++.+
T Consensus        13 l~~l~~-~~~~~~ei~~~~~i~~~~i~~~l~   42 (78)
T cd00090          13 LRLLLE-GPLTVSELAERLGLSQSTVSRHLK   42 (78)
T ss_pred             HHHHHH-CCcCHHHHHHHHCcCHhHHHHHHH
Confidence            444444 349999999999999999988764

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.

>PRK13832 plasmid partitioning protein; Provisional

Probab=90.94  E-value=0.91  Score=33.17  Aligned_cols=33  Identities=12%  Similarity=0.082  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...++.+. ..|+|+.++|..+|+|+.+|+++..
T Consensus       108 a~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlll  140 (520)
T PRK13832        108 WRAIERLV-ALGWTEEAIAVALALPVRQIRKLRL  140 (520)
T ss_pred             HHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            45556665 7999999999999999999999654

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=90.93  E-value=0.65  Score=28.57  Aligned_cols=28  Identities=11%  Similarity=0.139  Sum_probs=24.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|..+|.....
T Consensus       148 l~~~~g~s~~eIA~~lgis~~~v~~~l~  175 (187)
T PRK12534        148 TAFFEGITYEELAARTDTPIGTVKSWIR  175 (187)
T ss_pred             HHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence            3445799999999999999999998765

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

Probab=90.92  E-value=0.43  Score=29.42  Aligned_cols=28  Identities=14%  Similarity=0.092  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|.+||.....
T Consensus       138 l~~~~gls~~EIA~~l~i~~~tVks~l~  165 (182)
T COG1595         138 LRYLEGLSYEEIAEILGISVGTVKSRLH  165 (182)
T ss_pred             hHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4555699999999999999999998875

>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator

Probab=90.92  E-value=0.3  Score=29.69  Aligned_cols=35  Identities=17%  Similarity=0.128  Sum_probs=26.6

Q ss_pred             HHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           23 RQIQRARLGK---KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        23 ~~lk~~r~~~---g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..+-++..+.   .+|.+++|+++|||++|++.+-..+
T Consensus        10 ~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK   47 (176)
T TIGR02366        10 KAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK   47 (176)
T ss_pred             HHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence            3444455555   4799999999999999999886653

The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.

>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6

Probab=90.88  E-value=1.6  Score=24.95  Aligned_cols=37  Identities=5%  Similarity=0.032  Sum_probs=30.1

Q ss_pred             HHHHHHHHHhCCCC-HHHHHHHhCCCHHHHHHHHcCCC
Q 038591           22 PRQIQRARLGKKMS-QPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        22 ~~~lk~~r~~~g~s-~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ...|..+.+..++. -++||+.+|+|...|..++....
T Consensus         8 ~~~l~~Ia~~~~~~~wK~faR~lglse~~Id~I~~~~~   45 (97)
T cd08316           8 SKHIPDIADVMTLKDVKKFVRKSGLSEPKIDEIKLDNP   45 (97)
T ss_pred             HHhhHHHHHHcCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence            45677777878875 58999999999999999997643

Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=90.85  E-value=0.76  Score=27.79  Aligned_cols=28  Identities=11%  Similarity=-0.105  Sum_probs=24.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|+.+|.....
T Consensus       123 l~~~~g~s~~eIA~~lgis~~tV~~~l~  150 (164)
T PRK12547        123 LIGASGFSYEDAAAICGCAVGTIKSRVS  150 (164)
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445799999999999999999988765

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=90.83  E-value=0.61  Score=30.84  Aligned_cols=27  Identities=22%  Similarity=0.261  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|+.++|+.+|+|..+|++++.
T Consensus       227 ~y~~~~t~~EIA~~lgis~~~V~~~~~  253 (264)
T PRK07122        227 RFFESMTQTQIAERVGISQMHVSRLLA  253 (264)
T ss_pred             HhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334699999999999999999999875

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=90.83  E-value=0.48  Score=30.95  Aligned_cols=25  Identities=12%  Similarity=0.280  Sum_probs=22.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+|..++|+.+|+|+.|+.+|..
T Consensus       171 ~~~~Taeela~~~giSRvTaRRYLe  195 (224)
T COG4565         171 DQELTAEELAQALGISRVTARRYLE  195 (224)
T ss_pred             CCccCHHHHHHHhCccHHHHHHHHH
Confidence            4679999999999999999999864

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=90.82  E-value=0.66  Score=28.74  Aligned_cols=28  Identities=11%  Similarity=-0.123  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|..+|.....
T Consensus       141 L~~~~g~s~~EIA~~lgis~~tVk~~l~  168 (185)
T PRK09649        141 LTQLLGLSYADAAAVCGCPVGTIRSRVA  168 (185)
T ss_pred             hHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4566799999999999999999988764

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=90.81  E-value=0.76  Score=27.88  Aligned_cols=28  Identities=11%  Similarity=0.052  Sum_probs=23.6

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|..+|.....
T Consensus       129 L~~~~g~s~~EIA~~lgis~~tV~~~l~  156 (173)
T PRK09645        129 RSYYRGWSTAQIAADLGIPEGTVKSRLH  156 (173)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4455699999999999999999977654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=90.80  E-value=0.32  Score=32.58  Aligned_cols=25  Identities=12%  Similarity=0.157  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .|+|.+|+|+.+|+|+.+|++++..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~  268 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEAR  268 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            5899999999999999999999863

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=90.76  E-value=0.81  Score=27.92  Aligned_cols=28  Identities=11%  Similarity=0.035  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|++.+|+|+.+|+|..+|.....
T Consensus       111 l~~~~g~s~~eIA~~lgis~~tV~~~l~  138 (170)
T TIGR02959       111 LTELEGLSQQEIAEKLGLSLSGAKSRVQ  138 (170)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456799999999999999999988764

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).

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=90.74  E-value=0.39  Score=24.68  Aligned_cols=31  Identities=23%  Similarity=0.267  Sum_probs=22.0

Q ss_pred             HHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRAR-LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+. ....+++.+||+.++++++++++..+
T Consensus         9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~   40 (68)
T PF13463_consen    9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIK   40 (68)
T ss_dssp             HHHHT--TS-BEHHHHHHHTT--HHHHHHHHH
T ss_pred             HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44444 56789999999999999999998754

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=90.71  E-value=0.74  Score=27.60  Aligned_cols=34  Identities=12%  Similarity=0.052  Sum_probs=28.3

Q ss_pred             HHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -+.+..+. ....+|..+||+.++.+++|+++..+
T Consensus        30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~   64 (126)
T COG3355          30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQ   64 (126)
T ss_pred             HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHH
Confidence            45566677 57889999999999999999998754

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=90.70  E-value=0.7  Score=26.43  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++++.+||..+++++++|++..+
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~   65 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIK   65 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHH
Confidence            569999999999999999998754

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=90.67  E-value=0.6  Score=32.59  Aligned_cols=34  Identities=6%  Similarity=0.008  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus       407 ~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~  440 (445)
T TIGR02915       407 REAVRKAIARVDGNIARAAELLGITRPTLYDLMK  440 (445)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3456677788899999999999999999988654

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).

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=90.67  E-value=0.82  Score=27.83  Aligned_cols=28  Identities=14%  Similarity=0.179  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|.++|.....
T Consensus       130 L~~~~g~s~~EIA~~lgis~~tV~~~l~  157 (172)
T PRK12523        130 YNRLDGMGHAEIAERLGVSVSRVRQYLA  157 (172)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455799999999999999999998764

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=90.65  E-value=0.56  Score=30.81  Aligned_cols=36  Identities=14%  Similarity=0.051  Sum_probs=27.9

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL   65 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~   65 (82)
                      .-..+|..+||+.+|+|++||.++-+--..-+...+
T Consensus        31 ~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~   66 (284)
T PRK11302         31 TAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDF   66 (284)
T ss_pred             HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHH
Confidence            345789999999999999999999875444444443

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=90.64  E-value=0.62  Score=32.78  Aligned_cols=34  Identities=6%  Similarity=-0.025  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+..+.+.|+.+|||++|+++-.+
T Consensus       431 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~  464 (469)
T PRK10923        431 RTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLK  464 (469)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3457777788899999999999999999988664

>PRK15008 HTH-type transcriptional regulator RutR; Provisional

Probab=90.61  E-value=0.29  Score=30.92  Aligned_cols=36  Identities=14%  Similarity=0.040  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAK   67 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~   67 (82)
                      .+.|..++|+.+|||..+|+.+-.++...-...+..
T Consensus        37 ~~~s~~dIA~~aGvs~gtiY~hF~sKe~L~~a~~~~   72 (212)
T PRK15008         37 HGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQ   72 (212)
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHCCCHHHHHHHHHHH
Confidence            357899999999999999999987765444444333

>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional

Probab=90.61  E-value=0.27  Score=30.77  Aligned_cols=28  Identities=14%  Similarity=0.063  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .++|..++|+.+|||+.|++.+-.++..
T Consensus        30 ~~~ti~~Ia~~agvsk~t~Y~~F~sKe~   57 (213)
T PRK09975         30 SNTTLNDIADAANVTRGAIYWHFENKTQ   57 (213)
T ss_pred             ccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence            3689999999999999999999876543

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=90.59  E-value=0.86  Score=25.09  Aligned_cols=21  Identities=19%  Similarity=0.137  Sum_probs=19.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q 038591           34 MSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+||+.+|+|+.+|.+..
T Consensus        20 ~SGe~La~~LgiSRtaVwK~I   40 (79)
T COG1654          20 VSGEKLAEELGISRTAVWKHI   40 (79)
T ss_pred             ccHHHHHHHHCccHHHHHHHH
Confidence            899999999999999998764

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=90.53  E-value=0.35  Score=28.77  Aligned_cols=32  Identities=16%  Similarity=0.087  Sum_probs=25.0

Q ss_pred             HHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+... -++|+.+||+.+++++++|++..+
T Consensus        36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~   68 (144)
T PRK03573         36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLD   68 (144)
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHH
Confidence            35555443 468999999999999999998753

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=90.52  E-value=0.55  Score=29.16  Aligned_cols=27  Identities=7%  Similarity=-0.109  Sum_probs=23.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|.++|.....
T Consensus       123 ~~~eg~s~~EIA~~lgis~~tV~~~l~  149 (182)
T PRK12511        123 VAIEGLSYQEAAAVLGIPIGTLMSRIG  149 (182)
T ss_pred             HHHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence            445699999999999999999998864

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=90.50  E-value=0.3  Score=31.19  Aligned_cols=23  Identities=4%  Similarity=-0.113  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       169 ~~t~~~lA~~lG~sretvsR~L~  191 (226)
T PRK10402        169 HEKHTQAAEYLGVSYRHLLYVLA  191 (226)
T ss_pred             cchHHHHHHHHCCcHHHHHHHHH
Confidence            36899999999999999999643

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=90.47  E-value=0.99  Score=23.47  Aligned_cols=26  Identities=12%  Similarity=0.073  Sum_probs=21.7

Q ss_pred             HhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQ-RPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gi-s~~~i~~~e~   55 (82)
                      ....++..++|..+|+ +++++++.-.
T Consensus        47 ~~~~~~~~~ia~~~g~~s~~~f~r~Fk   73 (84)
T smart00342       47 RDTDLSVTEIALRVGFSSQSYFSRAFK   73 (84)
T ss_pred             HcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            3346999999999999 9999988764

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=90.43  E-value=0.52  Score=30.62  Aligned_cols=23  Identities=22%  Similarity=0.277  Sum_probs=21.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++..|||+.+|+|.++|..||.-
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~~   24 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDR   24 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999964

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.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=90.40  E-value=0.8  Score=28.45  Aligned_cols=28  Identities=7%  Similarity=0.005  Sum_probs=23.8

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|.+||.....
T Consensus       145 L~~~~g~s~~EIA~~lgis~~tVk~~l~  172 (189)
T PRK12530        145 MREYLELSSEQICQECDISTSNLHVLLY  172 (189)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445699999999999999999988764

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=90.40  E-value=1.1  Score=29.20  Aligned_cols=51  Identities=12%  Similarity=-0.053  Sum_probs=33.9

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHH
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEK   70 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~   70 (82)
                      +......-++ -..|+|.+|+|+.+++|+.||..+...    -...+...+..++.
T Consensus       144 LS~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~eLv~~A~  199 (217)
T PRK13719        144 VTKYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDELLIILH  199 (217)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            4444444443 457999999999999999999888653    22334444444443

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=90.39  E-value=0.93  Score=25.79  Aligned_cols=35  Identities=17%  Similarity=0.144  Sum_probs=26.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      -|....|+.+|+|++++++.           +..|.+.||+++-++
T Consensus        17 gSis~AA~~L~iS~stvs~~-----------I~~LE~~lg~~Lf~R   51 (99)
T TIGR00637        17 GSISQAAKDAGISYKSAWDY-----------IRAMNNLSGEPLVER   51 (99)
T ss_pred             CCHHHHHHHHCCCHHHHHHH-----------HHHHHHHhCCCeEEe
Confidence            36677999999999999874           456666777766554

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.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=90.36  E-value=0.52  Score=29.29  Aligned_cols=27  Identities=4%  Similarity=-0.085  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|..|+|+.+|+|..||.....
T Consensus       148 ~~~~g~s~~EIA~~lgis~~tVk~~l~  174 (195)
T PRK12532        148 KEILGFSSDEIQQMCGISTSNYHTIMH  174 (195)
T ss_pred             HHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            455699999999999999999988764

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=90.36  E-value=0.38  Score=30.97  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+++|+.+|+|.++|.++..
T Consensus       194 e~~S~~EIA~~lgis~~tV~~~~~  217 (233)
T PRK05803        194 KEKTQREIAKALGISRSYVSRIEK  217 (233)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            578999999999999999999864

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=90.31  E-value=0.83  Score=23.02  Aligned_cols=28  Identities=11%  Similarity=0.111  Sum_probs=24.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +-..|.+..++|..+++|+.||......
T Consensus        15 l~~~G~s~~eia~~l~is~~tV~~h~~~   42 (65)
T COG2771          15 LVAQGKSNKEIARILGISEETVKTHLRN   42 (65)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4567899999999999999999887653

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=90.29  E-value=0.89  Score=26.79  Aligned_cols=30  Identities=17%  Similarity=0.162  Sum_probs=23.8

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      |..+...-.++..++|+.+|+++++|++-.
T Consensus        22 L~~L~~~~~~~v~ela~~l~lsqstvS~HL   51 (117)
T PRK10141         22 VLLLRESGELCVCDLCTALDQSQPKISRHL   51 (117)
T ss_pred             HHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            344444456899999999999999999864

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=90.28  E-value=0.64  Score=29.48  Aligned_cols=33  Identities=12%  Similarity=-0.072  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....|+||.+||+.++++++|++++.
T Consensus        48 ~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l   80 (185)
T PRK13777         48 HHILWIAYHLKGASISEIAKFGVMHVSTAFNFS   80 (185)
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHH
Confidence            355666677789999999999999999988753

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

Probab=90.28  E-value=0.84  Score=29.13  Aligned_cols=27  Identities=7%  Similarity=0.132  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|.+|+|+.+|+|..+|..+..
T Consensus       187 ~y~~~~s~~eIA~~lgis~~tV~~~~~  213 (224)
T TIGR02479       187 YYYEELNLKEIGEVLGLTESRVSQIHS  213 (224)
T ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            345699999999999999999998765

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.

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=90.27  E-value=0.42  Score=29.66  Aligned_cols=25  Identities=8%  Similarity=0.057  Sum_probs=22.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|+|..|+|+.+|+|..+|.....
T Consensus       153 ~~g~s~~EIA~~lgis~~tV~~~l~  177 (194)
T PRK12513        153 HGDLELEEIAELTGVPEETVKSRLR  177 (194)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3599999999999999999987754

>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional

Probab=90.27  E-value=0.24  Score=31.07  Aligned_cols=28  Identities=14%  Similarity=-0.026  Sum_probs=23.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      +.|..++|+.+|+|+.+++.+..++...
T Consensus        31 ~~t~~~Ia~~agvs~~tlY~~F~sKe~L   58 (215)
T PRK10668         31 ATSLADIAKAAGVTRGAIYWHFKNKSDL   58 (215)
T ss_pred             cCCHHHHHHHhCCChHHHHHHCCCHHHH
Confidence            5689999999999999999998765443

>PRK11050 manganese transport regulator MntR; Provisional

Probab=90.27  E-value=0.71  Score=28.12  Aligned_cols=25  Identities=16%  Similarity=0.169  Sum_probs=22.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .-++++.++|+.+++++++|+++.+
T Consensus        49 ~~~~t~~eLA~~l~is~stVsr~l~   73 (152)
T PRK11050         49 VGEARQVDIAARLGVSQPTVAKMLK   73 (152)
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3578999999999999999999863

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=90.24  E-value=0.86  Score=28.40  Aligned_cols=28  Identities=18%  Similarity=0.260  Sum_probs=24.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|++.+|+|+.+|+|..||.....
T Consensus       147 L~~~~g~s~~eIA~~lgis~~tV~~~l~  174 (196)
T PRK12524        147 LRHIEGLSNPEIAEVMEIGVEAVESLTA  174 (196)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4455799999999999999999998875

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=90.23  E-value=0.67  Score=33.93  Aligned_cols=34  Identities=12%  Similarity=-0.022  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|.......+.++...|+.+|||++|+++..+
T Consensus       499 r~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk  532 (538)
T PRK15424        499 AATLQQALERFNGDKTAAANYLGISRTTLWRRLK  532 (538)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4567778888899999999999999999999875

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=90.20  E-value=0.41  Score=30.75  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+|+|+.+|+|+++|..+.+
T Consensus       193 e~~S~~EIAe~lgis~~tV~~~~~  216 (227)
T TIGR02846       193 RRKTQREIAKILGISRSYVSRIEK  216 (227)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            689999999999999999988764

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.

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

Probab=90.18  E-value=0.83  Score=27.65  Aligned_cols=28  Identities=18%  Similarity=0.296  Sum_probs=23.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.++|.....
T Consensus       130 l~~~~g~s~~eiA~~lgis~~tv~~~l~  157 (169)
T TIGR02954       130 LRYYHDLTIKEIAEVMNKPEGTVKTYLH  157 (169)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445699999999999999999988764

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.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=90.08  E-value=0.45  Score=30.40  Aligned_cols=37  Identities=16%  Similarity=0.305  Sum_probs=27.3

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +......-++ -..|+|.+++|+.+++|+.||..+-..
T Consensus       135 LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~  172 (207)
T PRK11475        135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFN  172 (207)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4444444332 357999999999999999999887653

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=90.08  E-value=0.91  Score=28.28  Aligned_cols=28  Identities=7%  Similarity=-0.089  Sum_probs=24.1

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|..+|.....
T Consensus       127 L~~~~g~s~~EIA~~Lgis~~tVk~~l~  154 (187)
T PRK12516        127 LVGASGFAYEEAAEICGCAVGTIKSRVN  154 (187)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455799999999999999999988764

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=90.08  E-value=0.91  Score=28.74  Aligned_cols=28  Identities=11%  Similarity=0.000  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|++.+|+|+.+|+|..+|.....
T Consensus       149 L~~~~g~s~~EIA~~Lgis~~tV~~~l~  176 (203)
T PRK09647        149 LCDIEGLSYEEIAATLGVKLGTVRSRIH  176 (203)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456799999999999999999988764

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=90.07  E-value=0.68  Score=27.23  Aligned_cols=30  Identities=7%  Similarity=0.001  Sum_probs=22.7

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      -|+.+....| +.+++++.+|||++||..-.
T Consensus        41 Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rL   70 (113)
T PF09862_consen   41 FIKLFIKNRG-NLKEMEKELGISYPTVRNRL   70 (113)
T ss_pred             HHHHHHHhcC-CHHHHHHHHCCCcHHHHHHH
Confidence            3444445444 89999999999999998743

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=89.96  E-value=0.37  Score=30.79  Aligned_cols=24  Identities=25%  Similarity=0.273  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+++|+.+|+|+.||..+.+
T Consensus       177 ~g~s~~eIA~~l~iS~~Tv~~~~~  200 (239)
T PRK10430        177 YEFSTDELANAVNISRVSCRKYLI  200 (239)
T ss_pred             CCcCHHHHHHHhCchHHHHHHHHH
Confidence            799999999999999999998865

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=89.95  E-value=0.52  Score=31.08  Aligned_cols=30  Identities=13%  Similarity=0.163  Sum_probs=25.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSE   52 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~   52 (82)
                      ..|+.+.+..-++.+|||+.+|||..||.+
T Consensus         9 ~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR   38 (253)
T COG1349           9 KILELLKEKGKVSVEELAELFGVSEMTIRR   38 (253)
T ss_pred             HHHHHHHHcCcEEHHHHHHHhCCCHHHHHH
Confidence            455667777789999999999999999988

>TIGR03384 betaine_BetI transcriptional repressor BetI

Probab=89.93  E-value=0.37  Score=29.36  Aligned_cols=28  Identities=18%  Similarity=0.293  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .+.|..++|+.+|+|..+++.+..++..
T Consensus        27 ~~~s~~~IA~~agvsk~~ly~~F~sK~~   54 (189)
T TIGR03384        27 LDVTIAQIARRAGVSSGIISHYFGGKQG   54 (189)
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence            3678999999999999999998765443

BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.

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

Probab=89.92  E-value=0.84  Score=27.33  Aligned_cols=28  Identities=14%  Similarity=0.149  Sum_probs=24.1

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.++|.....
T Consensus       121 l~~~~g~s~~eIA~~lgis~~tV~~~l~  148 (162)
T TIGR02983       121 LRYYEDLSEAQVAEALGISVGTVKSRLS  148 (162)
T ss_pred             hHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445799999999999999999998765

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.

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=89.91  E-value=0.15  Score=34.72  Aligned_cols=34  Identities=12%  Similarity=0.358  Sum_probs=30.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC---------CCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN---------QRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g---------is~~~i~~~e~   55 (82)
                      +++.++.|...|+||.|++..+-         +|++||-++|+
T Consensus       223 AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFES  265 (385)
T KOG1168|consen  223 AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFES  265 (385)
T ss_pred             HHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeee
Confidence            89999999999999999998772         68999999986

>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2

Probab=89.86  E-value=0.098  Score=26.35  Aligned_cols=42  Identities=14%  Similarity=0.216  Sum_probs=27.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH---cCC------CCCCHHHHHHHHHHhCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYE---NGK------AVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e---~g~------~~p~~~~~~~la~~lgv   74 (82)
                      +++..|||+.+|++...|-...   .|.      ...+.+.+..|+..||+
T Consensus         3 ~i~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~~   53 (54)
T PF04760_consen    3 KIRVSELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFGV   53 (54)
T ss_dssp             EE-TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH--
T ss_pred             ceEHHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhCc
Confidence            4677899999999987776665   352      23456667888888875

It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=89.85  E-value=0.48  Score=28.05  Aligned_cols=24  Identities=21%  Similarity=0.142  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|..++|+.+|+|..+|.....
T Consensus       120 ~g~s~~eIA~~lgis~~tv~~~l~  143 (154)
T TIGR02950       120 KEFSYKEIAELLNLSLAKVKSNLF  143 (154)
T ss_pred             ccCcHHHHHHHHCCCHHHHHHHHH
Confidence            489999999999999999988754

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=89.85  E-value=0.93  Score=29.81  Aligned_cols=27  Identities=7%  Similarity=0.103  Sum_probs=24.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..++|..|+|..+|+|.++|++++.
T Consensus       217 ~y~e~~t~~EIA~~lgis~~~V~~~~~  243 (257)
T PRK05911        217 YYYEELVLKEIGKILGVSESRVSQIHS  243 (257)
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334699999999999999999999976

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=89.85  E-value=0.89  Score=29.63  Aligned_cols=28  Identities=14%  Similarity=0.249  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..|+|+.+|+|.++|..+..
T Consensus       216 l~~~~g~s~~eIA~~lgis~~~V~~~~~  243 (255)
T TIGR02941       216 CTFEENLSQKETGERLGISQMHVSRLQR  243 (255)
T ss_pred             HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445799999999999999999998875

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=89.82  E-value=0.63  Score=28.45  Aligned_cols=26  Identities=8%  Similarity=0.072  Sum_probs=22.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      --.|++.+++|+.+|+|..+|.....
T Consensus       149 ~~~~~s~~eIA~~lgis~~~v~~~l~  174 (187)
T PRK09641        149 YIEDLSLKEISEILDLPVGTVKTRIH  174 (187)
T ss_pred             HhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34699999999999999999988764

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

Probab=89.82  E-value=1.1  Score=28.12  Aligned_cols=46  Identities=9%  Similarity=0.038  Sum_probs=32.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC--CCCCCHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENG--KAVPNQTVLAKM   68 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g--~~~p~~~~~~~l   68 (82)
                      ..++.+----++|....|..+|||..|+.+|-..  ...-.++.+..-
T Consensus         9 ~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDDWDk~RaA   56 (165)
T PF08822_consen    9 DAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGDDWDKARAA   56 (165)
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            3445555557899999999999999999999752  122355554433

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

>PRK09508 leuO leucine transcriptional activator; Reviewed

Probab=89.80  E-value=1.2  Score=29.52  Aligned_cols=37  Identities=16%  Similarity=0.225  Sum_probs=27.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      .-|....|+.+|+|+++||+           .+..|.+.||+++-+|.
T Consensus        36 ~gs~s~AA~~L~isQpavS~-----------~I~~LE~~lg~~LF~R~   72 (314)
T PRK09508         36 EQNITRAAHNLGMSQPAVSN-----------AVARLKVMFNDELFVRY   72 (314)
T ss_pred             cCCHHHHHHHhCCCHHHHHH-----------HHHHHHHhhCCCcEEEc
Confidence            34566799999999999998           45666677777765554

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

Probab=89.72  E-value=1.1  Score=26.94  Aligned_cols=28  Identities=14%  Similarity=0.285  Sum_probs=23.4

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|..|+|+.+|+|.++|.....
T Consensus       133 l~~~~g~s~~eIA~~l~is~~tv~~~l~  160 (170)
T TIGR02952       133 LRFGQNLPIAEVARILGKTEGAVKILQF  160 (170)
T ss_pred             HHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445699999999999999999987653

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.

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=89.70  E-value=0.83  Score=30.65  Aligned_cols=25  Identities=16%  Similarity=0.389  Sum_probs=22.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..++|.+|+|+.+|+|+.+|.+++.
T Consensus       267 ~~~~Tl~EIa~~lgiS~erVrq~~~  291 (298)
T TIGR02997       267 GEPLTLAEIGRRLNLSRERVRQIEA  291 (298)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3589999999999999999999986

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).

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=89.69  E-value=0.92  Score=27.91  Aligned_cols=28  Identities=7%  Similarity=0.036  Sum_probs=24.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|..|+|+.+|+|..+|.....
T Consensus       139 l~~~~g~s~~EIA~~lgis~~tV~~~l~  166 (186)
T PRK05602        139 LQYYQGLSNIEAAAVMDISVDALESLLA  166 (186)
T ss_pred             HHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence            3455799999999999999999999875

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=89.67  E-value=0.59  Score=30.80  Aligned_cols=32  Identities=13%  Similarity=0.076  Sum_probs=25.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+..+.+...++..|||+.+|+|..||.+-.
T Consensus         9 ~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL   40 (256)
T PRK10434          9 AILEYLQKQGKTSVEELAQYFDTTGTTIRKDL   40 (256)
T ss_pred             HHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHH
Confidence            34455566667999999999999999998753

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=89.66  E-value=1  Score=27.49  Aligned_cols=27  Identities=11%  Similarity=0.103  Sum_probs=23.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.....
T Consensus       141 ~~~~g~s~~eIA~~lgis~~tV~~~l~  167 (179)
T PRK12514        141 AYLEGLSYKELAERHDVPLNTMRTWLR  167 (179)
T ss_pred             HHHcCCCHHHHHHHHCCChHHHHHHHH
Confidence            345699999999999999999988764

>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=89.64  E-value=0.45  Score=25.96  Aligned_cols=46  Identities=20%  Similarity=0.166  Sum_probs=32.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      ..+..+-.....|..++|+.+++|.+|+.+..+        .+....+.+|+.+
T Consensus        20 ~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~--------~l~~~l~~~~l~i   65 (87)
T PF05043_consen   20 QLLKLLLNNEYVSIEDLAEELFISRSTIYRDIK--------KLNKYLKKYGLKI   65 (87)
T ss_dssp             HHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHH--------HHHHHHHCCT-EE
T ss_pred             HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHH--------HHHHHHHHcCeEE
Confidence            445666778899999999999999999999754        4555566666655

The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.

>PRK06930 positive control sigma-like factor; Validated

Probab=89.61  E-value=1.1  Score=27.93  Aligned_cols=28  Identities=18%  Similarity=0.264  Sum_probs=24.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..++|+.+|+|.++|..+..
T Consensus       125 L~~~eg~s~~EIA~~lgiS~~tVk~~l~  152 (170)
T PRK06930        125 MHRGYGLSYSEIADYLNIKKSTVQSMIE  152 (170)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3456899999999999999999999875

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=89.50  E-value=0.5  Score=30.49  Aligned_cols=24  Identities=17%  Similarity=0.303  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+|+|+.+|+|..||.....
T Consensus       197 eg~s~~EIA~~Lgis~~tV~~~l~  220 (234)
T TIGR02835       197 TEKTQKEVADMLGISQSYISRLEK  220 (234)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            589999999999999999988764

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.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=89.49  E-value=1.2  Score=26.73  Aligned_cols=28  Identities=14%  Similarity=0.169  Sum_probs=23.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|..|+|+.+|+|.+||.....
T Consensus       124 L~~~~g~s~~EIA~~l~is~~tV~~~l~  151 (161)
T PRK12528        124 LAQVDGLGYGEIATELGISLATVKRYLN  151 (161)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455799999999999999999987653

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=89.46  E-value=0.43  Score=30.43  Aligned_cols=22  Identities=18%  Similarity=0.155  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .+|+.++|..+|+++.+|++..
T Consensus       173 ~~t~~~iA~~lG~tretvsR~l  194 (236)
T PRK09392        173 PYEKRVLASYLGMTPENLSRAF  194 (236)
T ss_pred             eCCHHHHHHHhCCChhHHHHHH
Confidence            4678999999999999999975

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=89.42  E-value=0.81  Score=28.12  Aligned_cols=27  Identities=11%  Similarity=-0.093  Sum_probs=23.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|.+|+|+.+|+|.++|.....
T Consensus       141 ~~~~g~s~~EIA~~l~is~~tV~~~l~  167 (181)
T PRK12536        141 VKLEGLSVAETAQLTGLSESAVKVGIH  167 (181)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            445799999999999999999998764

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=89.40  E-value=0.72  Score=30.52  Aligned_cols=47  Identities=15%  Similarity=0.348  Sum_probs=33.9

Q ss_pred             HHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           23 RQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        23 ~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      ..|+.+..  +.|.|....|+.+|+|+++||+.           +..|.+.||+++-+|.
T Consensus         4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~-----------I~~LE~~lg~~LF~R~   52 (309)
T PRK12682          4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKA-----------IIELEEELGIEIFIRH   52 (309)
T ss_pred             HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHH-----------HHHHHHHhCCeeEEEC
Confidence            34555543  34678999999999999999984           4566677777765553

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=89.40  E-value=0.9  Score=27.59  Aligned_cols=26  Identities=4%  Similarity=0.142  Sum_probs=22.9

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +--.|+|.+|+|+.+|+|..||....
T Consensus       130 ~~~eg~s~~EIA~~l~is~~tV~~~l  155 (168)
T PRK12525        130 SQLEGLTYVEIGERLGVSLSRIHQYM  155 (168)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            44569999999999999999998775

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=89.38  E-value=0.73  Score=30.36  Aligned_cols=29  Identities=17%  Similarity=0.274  Sum_probs=23.9

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      +..+.+...++..|||+.++||..||++.
T Consensus        11 l~~l~~~~~~~~~ela~~l~vS~~TiRRd   39 (252)
T PRK10906         11 IELVKQQGYVSTEELVEHFSVSPQTIRRD   39 (252)
T ss_pred             HHHHHHcCCEeHHHHHHHhCCCHHHHHHH
Confidence            44455555699999999999999999985

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=89.37  E-value=0.91  Score=32.73  Aligned_cols=34  Identities=9%  Similarity=0.036  Sum_probs=29.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.+..+..+...|+.+|||++|+++..+
T Consensus       470 r~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk  503 (509)
T PRK05022        470 RQLIRQALAQHQGNWAAAARALELDRANLHRLAK  503 (509)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4567888888999999999999999999988765

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=89.34  E-value=1.2  Score=27.22  Aligned_cols=27  Identities=19%  Similarity=0.153  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|++.+++|..+|+|.++|.....
T Consensus       152 ~~~~g~s~~eIA~~lgis~~~v~~~l~  178 (189)
T TIGR02984       152 RHLEGLSFAEVAERMDRSEGAVSMLWV  178 (189)
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344699999999999999999988754

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).

>PRK09483 response regulator; Provisional

Probab=89.30  E-value=1.6  Score=26.75  Aligned_cols=45  Identities=18%  Similarity=0.349  Sum_probs=32.2

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv   74 (82)
                      -..|+|.+++|+.+++|..||..+.+.    -...+...+..+|.-.|+
T Consensus       160 ~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l~~~a~~~~~  208 (217)
T PRK09483        160 ITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGL  208 (217)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCC
Confidence            368999999999999999999888753    122345555556555553

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=89.30  E-value=1.1  Score=27.58  Aligned_cols=28  Identities=4%  Similarity=0.024  Sum_probs=23.6

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|.+||.....
T Consensus       133 l~~~~g~s~~EIA~~lgis~~tVk~~l~  160 (185)
T PRK12542        133 YKVFYNLTYQEISSVMGITEANVRKQFE  160 (185)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455799999999999999999988653

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=89.27  E-value=0.88  Score=29.88  Aligned_cols=33  Identities=15%  Similarity=0.145  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+..+.....++..+||+.+|||..||.+-.+
T Consensus        11 ~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~   43 (252)
T PRK10681         11 QLLQALKRSDKLHLKDAAALLGVSEMTIRRDLN   43 (252)
T ss_pred             HHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHH
Confidence            345556667779999999999999999987643

>PRK11202 DNA-binding transcriptional repressor FabR; Provisional

Probab=89.26  E-value=0.29  Score=30.75  Aligned_cols=29  Identities=10%  Similarity=0.029  Sum_probs=24.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .++|..++|+.+|+|+.+++++..++...
T Consensus        31 ~~~si~~IA~~Agvs~~t~Y~hF~sKe~L   59 (203)
T PRK11202         31 SSLSLREVAREAGIAPTSFYRHFRDMDEL   59 (203)
T ss_pred             ccCCHHHHHHHhCCCcchHHHHCCCHHHH
Confidence            35799999999999999999998765443

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=89.18  E-value=0.62  Score=28.82  Aligned_cols=26  Identities=4%  Similarity=0.028  Sum_probs=22.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      --.|+|.+|+|+.+|+|.++|.....
T Consensus       147 ~~~g~s~~EIA~~lgis~~tV~~~l~  172 (188)
T PRK09640        147 FVAELEFQEIADIMHMGLSATKMRYK  172 (188)
T ss_pred             HhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34589999999999999999998865

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=89.12  E-value=1.3  Score=26.49  Aligned_cols=28  Identities=14%  Similarity=0.135  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|.++|.....
T Consensus       116 l~~~~~~s~~eIA~~lgis~~tv~~~l~  143 (159)
T PRK12527        116 LRKLEGLSHQQIAEHLGISRSLVEKHIV  143 (159)
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4455799999999999999999988764

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

Probab=89.11  E-value=0.85  Score=29.64  Aligned_cols=31  Identities=10%  Similarity=0.117  Sum_probs=24.9

Q ss_pred             HHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+-. ..++|..|+|+.+|++++|++++.+
T Consensus        15 L~~l~~~~~~~~l~eia~~lglpksT~~RlL~   46 (248)
T TIGR02431        15 IEAFGAERPRLTLTDVAEATGLTRAAARRFLL   46 (248)
T ss_pred             HHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            444433 4679999999999999999999864

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.

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

Probab=89.07  E-value=1.2  Score=25.53  Aligned_cols=32  Identities=6%  Similarity=0.042  Sum_probs=25.7

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQ-RPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gi-s~~~i~~~e~   55 (82)
                      .+-.+....|.|..++|+..|| +.+++++|-.
T Consensus        15 ~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~   47 (116)
T COG2963          15 EAVALYLRGGDTVSEVAREFGIVSATQLYKWRI   47 (116)
T ss_pred             HHHHHHHhcCccHHHHHHHhCCCChHHHHHHHH
Confidence            4444556678899999999996 9999998854

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=89.05  E-value=1.1  Score=27.70  Aligned_cols=28  Identities=18%  Similarity=0.001  Sum_probs=23.8

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|+.+|.....
T Consensus       149 l~~~~g~s~~eIA~~lgis~~tv~~~l~  176 (193)
T PRK11923        149 LREFDGLSYEDIASVMQCPVGTVRSRIF  176 (193)
T ss_pred             hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3456799999999999999999988764

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=88.99  E-value=0.45  Score=29.62  Aligned_cols=21  Identities=19%  Similarity=0.234  Sum_probs=19.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q 038591           34 MSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e   54 (82)
                      +|++++|+.+|+|.+||++..
T Consensus        76 ~t~~~ia~~l~iS~~Tv~r~i   96 (165)
T PF05732_consen   76 ATQKEIAEKLGISKPTVSRAI   96 (165)
T ss_pred             eeHHHHHHHhCCCHHHHHHHH
Confidence            589999999999999999874

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=88.97  E-value=1.2  Score=28.02  Aligned_cols=27  Identities=26%  Similarity=0.171  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.....
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tV~~~l~  191 (206)
T PRK12526        165 VYFQELSQEQLAQQLNVPLGTVKSRLR  191 (206)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345699999999999999999987753

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=88.96  E-value=1.2  Score=27.97  Aligned_cols=28  Identities=11%  Similarity=0.007  Sum_probs=23.8

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|.+||.....
T Consensus       150 L~~~eg~s~~EIA~~lgis~~tVk~~l~  177 (201)
T PRK12545        150 MREFLDFEIDDICTELTLTANHCSVLLY  177 (201)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455799999999999999999987754

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=88.93  E-value=0.97  Score=29.04  Aligned_cols=26  Identities=12%  Similarity=0.012  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..|+|.+|+|+.+++|..||..+...
T Consensus       168 ~~G~s~~eIA~~L~iS~~TVk~~~~~  193 (216)
T PRK10100        168 RIGASNNEIARSLFISENTVKTHLYN  193 (216)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            45999999999999999999988753

>PRK14996 TetR family transcriptional regulator; Provisional

Probab=88.91  E-value=0.37  Score=29.78  Aligned_cols=28  Identities=11%  Similarity=0.035  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .+.|..++|+.+|+|+.+++.+..++..
T Consensus        27 ~~tSi~~Ia~~aGvsk~~lY~~F~sK~~   54 (192)
T PRK14996         27 AAMTVRRIASEAQVAAGQVHHHFSSAGE   54 (192)
T ss_pred             hhccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence            3578999999999999999999876543

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

Probab=88.90  E-value=0.57  Score=32.08  Aligned_cols=33  Identities=27%  Similarity=0.321  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..++ ..|+|..++|+.||..++||++=..
T Consensus        13 R~~I~~l~-~~~~S~reIA~~LgRh~sTIsRElk   45 (318)
T COG2826          13 RYEIERLL-KAKMSIREIAKQLNRHHSTISRELK   45 (318)
T ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCcchhhHHHh
Confidence            34455555 6799999999999999999998654

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=88.89  E-value=2.7  Score=27.41  Aligned_cols=43  Identities=19%  Similarity=0.223  Sum_probs=30.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|..|+|..+|||..||....+.    -...+...+...|-.+|
T Consensus       192 a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~v~~a~~~g  238 (240)
T PRK10188        192 AEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATG  238 (240)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence            67999999999999999999887654    12334444444444443

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=88.88  E-value=0.61  Score=28.32  Aligned_cols=25  Identities=16%  Similarity=0.089  Sum_probs=22.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|+|..|+|+.+|+|..+|.....
T Consensus       134 ~~g~s~~eIA~~lg~s~~tv~~~l~  158 (175)
T PRK12518        134 LEDLPQKEIAEILNIPVGTVKSRLF  158 (175)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3599999999999999999988764

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=88.86  E-value=1.1  Score=29.53  Aligned_cols=32  Identities=9%  Similarity=-0.086  Sum_probs=24.7

Q ss_pred             HHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+-.. .++|..|+|+.+|++++|++++.+
T Consensus        16 iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~   48 (263)
T PRK09834         16 VLRALNRLDGGATVGLLAELTGLHRTTVRRLLE   48 (263)
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34444443 359999999999999999999853

>PHA02535 P terminase ATPase subunit; Provisional

Probab=88.81  E-value=0.49  Score=34.97  Aligned_cols=24  Identities=4%  Similarity=0.300  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |+|..++|+.+|++++||++|-.-
T Consensus        18 G~sv~eIA~~LGv~~~Tl~~W~kr   41 (581)
T PHA02535         18 GWTVAEIAEELGLKSRTIYSWKER   41 (581)
T ss_pred             CCCHHHHHHHhCCChhHHHHHhcc
Confidence            999999999999999999999764

>PRK00767 transcriptional regulator BetI; Validated

Probab=88.79  E-value=0.53  Score=28.89  Aligned_cols=29  Identities=17%  Similarity=0.226  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .+.|..++|+.+|+|+.+++.+..++...
T Consensus        28 ~~~s~~~Ia~~aGvs~gslY~~F~~Ke~L   56 (197)
T PRK00767         28 LDATIAQIARRAGVSTGIISHYFGGKDGL   56 (197)
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHhCCHHHH
Confidence            35789999999999999999998665443

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=88.78  E-value=0.82  Score=27.94  Aligned_cols=27  Identities=7%  Similarity=0.115  Sum_probs=23.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|+.+|.....
T Consensus       148 ~~~~g~s~~eIA~~lgis~~~v~~~l~  174 (187)
T TIGR02948       148 KYMEDLSLKEISEILDLPVGTVKTRIH  174 (187)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345699999999999999999998764

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

>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins

Probab=88.75  E-value=0.99  Score=22.68  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=16.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSE   52 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~   52 (82)
                      ..+|-.+||+.+|+++.+|.+
T Consensus        27 ~~vSS~~La~~~gi~~~qVRK   47 (50)
T PF06971_consen   27 ERVSSQELAEALGITPAQVRK   47 (50)
T ss_dssp             SEE-HHHHHHHHTS-HHHHHH
T ss_pred             eeECHHHHHHHHCCCHHHhcc
Confidence            457889999999999999875

These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=88.74  E-value=1.4  Score=27.18  Aligned_cols=27  Identities=19%  Similarity=0.266  Sum_probs=23.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|..||.....
T Consensus       151 ~~~~g~s~~EIA~~lgis~~tV~~~l~  177 (189)
T PRK09648        151 RVVVGLSAEETAEAVGSTPGAVRVAQH  177 (189)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            445699999999999999999988764

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=88.71  E-value=0.81  Score=30.41  Aligned_cols=32  Identities=19%  Similarity=0.138  Sum_probs=25.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+..++....++..|||+.+|||..||.+-.
T Consensus        21 ~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL   52 (269)
T PRK09802         21 QIIQRLRQQGSVQVNDLSALYGVSTVTIRNDL   52 (269)
T ss_pred             HHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHH
Confidence            34455666667999999999999999997753

>PHA00738 putative HTH transcription regulator

Probab=88.71  E-value=1.2  Score=26.00  Aligned_cols=32  Identities=6%  Similarity=-0.070  Sum_probs=24.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+...-.++..+|++.+++|+++||+-.
T Consensus        16 ~IL~lL~~~e~~~V~eLae~l~lSQptVS~HL   47 (108)
T PHA00738         16 KILELIAENYILSASLISHTLLLSYTTVLRHL   47 (108)
T ss_pred             HHHHHHHHcCCccHHHHHHhhCCCHHHHHHHH
Confidence            33444554446999999999999999999864

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=88.70  E-value=0.81  Score=29.38  Aligned_cols=27  Identities=19%  Similarity=0.031  Sum_probs=23.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|.++|.....
T Consensus       146 ~y~eg~s~~EIAe~LgiS~~tVk~~L~  172 (216)
T PRK12533        146 RELEDMSYREIAAIADVPVGTVMSRLA  172 (216)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344699999999999999999988764

>TIGR03826 YvyF flagellar operon protein TIGR03826

Probab=88.63  E-value=1.3  Score=26.96  Aligned_cols=51  Identities=6%  Similarity=0.080  Sum_probs=35.0

Q ss_pred             HHHHHhCC--CCHHHHHHHhCCCHHHHHHHHcCCC-C-CCHHHHHHHHHHhCCCC
Q 038591           26 QRARLGKK--MSQPDLANQINQRPQVVSEYENGKA-V-PNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        26 k~~r~~~g--~s~~elA~~~gis~~~i~~~e~g~~-~-p~~~~~~~la~~lgv~~   76 (82)
                      ..+|+..+  .|..++++.+||+...|.+|..-.+ . .....+..-|+--|.++
T Consensus        37 ~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~CE~CG~~I   91 (137)
T TIGR03826        37 KFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPCERCGTSI   91 (137)
T ss_pred             HHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcccccCCcC
Confidence            44677777  8999999999999999999986422 1 22234444555555444

This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.

>PRK11557 putative DNA-binding transcriptional regulator; Provisional

Probab=88.58  E-value=1.4  Score=29.01  Aligned_cols=36  Identities=14%  Similarity=0.186  Sum_probs=27.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      -+-..+|..+||+.+|+|++||.++-+--..-....
T Consensus        26 ~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~e   61 (278)
T PRK11557         26 DTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPA   61 (278)
T ss_pred             HHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHH
Confidence            344579999999999999999999987533333333

>PRK14845 translation initiation factor IF-2; Provisional

Probab=88.52  E-value=1.3  Score=34.94  Aligned_cols=50  Identities=20%  Similarity=0.326  Sum_probs=42.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      ...|+.+|...++|+.|++.    +.++++.||+ ...|+.+.+..+..+|.-..
T Consensus       324 ~~el~~lr~~~~lt~~e~~~----~~~~Y~~~e~-~~~~s~~~l~~~l~~~~~~~  373 (1049)
T PRK14845        324 NEELKRLRLLFGFTRNELSS----NIPFYSKYES-EEAPSYEILMEILNSIERGS  373 (1049)
T ss_pred             HHHHHHHHHhcCcchhhccc----cchhhhhhhc-ccCCCHHHHHHHHHHHHhcC
Confidence            55789999999999988775    7899999999 88999999988888776433

>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=88.48  E-value=1.4  Score=23.19  Aligned_cols=33  Identities=9%  Similarity=0.074  Sum_probs=23.2

Q ss_pred             HHHHHHHHhCCC--CHHHHHHHhCCC-HHHHHHHHc
Q 038591           23 RQIQRARLGKKM--SQPDLANQINQR-PQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~--s~~elA~~~gis-~~~i~~~e~   55 (82)
                      ..|.....+.|+  |..|+|+.+|++ +++|.....
T Consensus        13 ~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen   13 EFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             HHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            345555555555  779999999996 888887653

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=88.43  E-value=1.4  Score=28.97  Aligned_cols=28  Identities=4%  Similarity=0.112  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..++|..+|+|.++|.+...
T Consensus       223 l~~~~~~s~~eIA~~lgis~~tV~~~~~  250 (268)
T PRK06288        223 LYYYEDLTLKEIGKVLGVTESRISQLHT  250 (268)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445699999999999999999998764

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=88.40  E-value=1.5  Score=27.09  Aligned_cols=28  Identities=7%  Similarity=-0.065  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+++|+.+|+|..+|.....
T Consensus       142 l~~~~~~s~~eIA~~lgis~~tV~~~l~  169 (189)
T PRK12515        142 LVYYHEKSVEEVGEIVGIPESTVKTRMF  169 (189)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3456799999999999999999987764

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=88.39  E-value=0.71  Score=28.04  Aligned_cols=26  Identities=12%  Similarity=0.018  Sum_probs=22.4

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .-.|+|.+++|+.+|+|.++|.....
T Consensus       139 ~~~g~s~~eIA~~l~is~~~V~~~l~  164 (176)
T PRK09638        139 HYYGYTYEEIAKMLNIPEGTVKSRVH  164 (176)
T ss_pred             hhcCCCHHHHHHHHCCChhHHHHHHH
Confidence            34699999999999999999987763

>cd08804 Death_ank2 Death domain of Ankyrin-2

Probab=88.35  E-value=2.5  Score=23.29  Aligned_cols=34  Identities=9%  Similarity=0.075  Sum_probs=29.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+|..+....|..=++||+.+|+|..-|.+++..
T Consensus         5 ~~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~   38 (84)
T cd08804           5 ERLAVIADHLGFSWTELARELDFTEEQIHQIRIE   38 (84)
T ss_pred             hHHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHH
Confidence            3567778888888899999999999999999875

Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=88.34  E-value=0.94  Score=28.20  Aligned_cols=28  Identities=11%  Similarity=0.033  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|++.+|+|..+|+|..+|.....
T Consensus       139 l~~~~g~s~~EIA~~lgis~~tV~~~l~  166 (188)
T PRK12517        139 LQVIGGFSGEEIAEILDLNKNTVMTRLF  166 (188)
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445699999999999999999988764

>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=88.33  E-value=0.96  Score=25.07  Aligned_cols=48  Identities=10%  Similarity=0.078  Sum_probs=28.7

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591           26 QRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG   73 (82)
Q Consensus        26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg   73 (82)
                      -....+.+.|..+.|...|||.+||.+-..-. ..++......+-.+|.
T Consensus        12 ~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~eV~~vL~   60 (82)
T PF12116_consen   12 ANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAREVRKVLD   60 (82)
T ss_dssp             HHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            34455668999999999999999999877642 2334444444444443

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.

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=88.32  E-value=0.88  Score=28.66  Aligned_cols=33  Identities=9%  Similarity=0.002  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+..+....-++..+||+.+|+|..||.+=.+
T Consensus        11 ~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~   43 (185)
T PRK04424         11 ALQELIEENPFITDEELAEKFGVSIQTIRLDRM   43 (185)
T ss_pred             HHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence            344556666678999999999999999988654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=88.30  E-value=1.4  Score=27.34  Aligned_cols=28  Identities=7%  Similarity=-0.001  Sum_probs=24.1

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|..+|..+..
T Consensus       153 l~~~~~~s~~EIA~~Lgis~~tVk~~l~  180 (194)
T PRK09646        153 LAYYGGLTYREVAERLAVPLGTVKTRMR  180 (194)
T ss_pred             HHHHcCCCHHHHHHHhCCChHhHHHHHH
Confidence            3445799999999999999999988764

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=88.30  E-value=1.1  Score=33.09  Aligned_cols=34  Identities=9%  Similarity=-0.093  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus       593 ~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk  626 (638)
T PRK11388        593 KEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMK  626 (638)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4557777788899999999999999999998765

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=88.29  E-value=0.99  Score=27.92  Aligned_cols=27  Identities=11%  Similarity=0.046  Sum_probs=23.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|++..|+|..+|+|..+|.....
T Consensus       118 ~~~~g~~~~EIA~~lgis~~tV~~~l~  144 (181)
T PRK09637        118 TELEGLSQKEIAEKLGLSLSGAKSRVQ  144 (181)
T ss_pred             HHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            445799999999999999999987764

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=88.29  E-value=1.2  Score=24.62  Aligned_cols=33  Identities=15%  Similarity=0.119  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhC-CCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQIN-QRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~g-is~~~i~~~e~   55 (82)
                      -.+-.++...|+|..++|+.+| .+.+||+...+
T Consensus        34 ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~   67 (90)
T cd06571          34 IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVR   67 (90)
T ss_pred             HHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHH
Confidence            3345567788999999999999 99999887543

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.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=88.24  E-value=1  Score=28.17  Aligned_cols=28  Identities=14%  Similarity=-0.028  Sum_probs=24.1

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..|+|+.+|+|..+|.....
T Consensus       124 L~~~~g~s~~EIA~~LgiS~~tVk~~l~  151 (188)
T PRK12546        124 LVGASGFSYEEAAEMCGVAVGTVKSRAN  151 (188)
T ss_pred             hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455799999999999999999988765

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=88.20  E-value=0.97  Score=27.49  Aligned_cols=27  Identities=15%  Similarity=0.032  Sum_probs=23.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.....
T Consensus       131 ~~~~~~s~~EIA~~lgis~~tV~~~l~  157 (173)
T PRK12522        131 YYYEQYSYKEMSEILNIPIGTVKYRLN  157 (173)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            344699999999999999999988754

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=88.16  E-value=1.6  Score=27.01  Aligned_cols=27  Identities=4%  Similarity=-0.021  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|.+|+|+.+|+|.+||.....
T Consensus       143 ~~~~g~s~~EIA~~lgis~~tV~~~l~  169 (191)
T PRK12520        143 REWLELETEEICQELQITATNAWVLLY  169 (191)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344699999999999999999988754

>PRK15482 transcriptional regulator MurR; Provisional

Probab=88.11  E-value=1.5  Score=29.11  Aligned_cols=38  Identities=16%  Similarity=0.146  Sum_probs=29.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA   66 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~   66 (82)
                      -....+|..+||+.+|+|++||.++-+--..-.+..+.
T Consensus        30 ~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk   67 (285)
T PRK15482         30 SELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELR   67 (285)
T ss_pred             HHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHH
Confidence            34457999999999999999999998754444544443

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=88.07  E-value=1.6  Score=27.07  Aligned_cols=27  Identities=7%  Similarity=0.059  Sum_probs=23.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.....
T Consensus       143 ~~~~g~s~~EIAe~lgis~~~V~~~l~  169 (189)
T PRK06811        143 RYLLGEKIEEIAKKLGLTRSAIDNRLS  169 (189)
T ss_pred             HHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence            345699999999999999999988764

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=87.94  E-value=0.69  Score=31.67  Aligned_cols=24  Identities=8%  Similarity=0.086  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+|..++|+.+|||+..|+++|..
T Consensus       282 ~~Tl~eIa~~lgvS~eRVrQIe~~  305 (324)
T PRK07921        282 PRTLDQIGKLFGLSRERVRQIERE  305 (324)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHH
Confidence            379999999999999999999974

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=87.93  E-value=0.72  Score=23.92  Aligned_cols=35  Identities=6%  Similarity=0.095  Sum_probs=24.7

Q ss_pred             HHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHcCC
Q 038591           23 RQIQRARLGKKM--------SQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        23 ~~lk~~r~~~g~--------s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..|...-+..|+        ...+||..+|++...|.-|.++.
T Consensus        14 ~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~   56 (58)
T TIGR01565        14 EKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN   56 (58)
T ss_pred             HHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence            344455556677        66888888888888887777653

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=87.93  E-value=0.67  Score=32.16  Aligned_cols=24  Identities=4%  Similarity=0.095  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++|..++|+.+|||+..|++++..
T Consensus       325 ~~tl~EIa~~lgvs~erVrQi~~~  348 (367)
T PRK09210        325 TRTLEEVGKVFGVTRERIRQIEAK  348 (367)
T ss_pred             CccHHHHHHHHCCCHHHHHHHHHH
Confidence            489999999999999999999864

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=87.91  E-value=1.1  Score=27.70  Aligned_cols=27  Identities=15%  Similarity=-0.054  Sum_probs=23.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +-..|+|..|+|+.+|+|..+|.....
T Consensus       123 ~~~~g~s~~EIA~~Lgis~~tV~~~l~  149 (182)
T PRK12540        123 VGASGFSYEDAAAICGCAVGTIKSRVN  149 (182)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            445799999999999999999988765

>PF00046 Homeobox: Homeobox domain not present here

Probab=87.82  E-value=0.86  Score=22.71  Aligned_cols=21  Identities=14%  Similarity=0.306  Sum_probs=18.4

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|...
T Consensus        30 ~~~la~~l~l~~~~V~~WF~n   50 (57)
T PF00046_consen   30 REELAKELGLTERQVKNWFQN   50 (57)
T ss_dssp             HHHHHHHHTSSHHHHHHHHHH
T ss_pred             cccccccccccccccccCHHH
Confidence            378999999999999999764

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=87.81  E-value=1.2  Score=26.73  Aligned_cols=28  Identities=14%  Similarity=-0.094  Sum_probs=23.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|..++|+.+|+|..+|.....
T Consensus       123 l~~~~~~s~~eIA~~lgis~~tv~~~l~  150 (161)
T PRK12541        123 LRDYYGFSYKEIAEMTGLSLAKVKIELH  150 (161)
T ss_pred             hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455799999999999999999987654

>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional

Probab=87.75  E-value=1.2  Score=29.52  Aligned_cols=36  Identities=8%  Similarity=0.108  Sum_probs=28.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA   66 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~   66 (82)
                      -..+|..+||+.+|+|+.||.++-+.-..-+...+.
T Consensus        44 v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk   79 (292)
T PRK11337         44 SEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLR   79 (292)
T ss_pred             HHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHH
Confidence            457899999999999999999998765555554443

>TIGR03454 partition_RepB plasmid partitioning protein RepB

Probab=87.75  E-value=1.3  Score=30.48  Aligned_cols=39  Identities=3%  Similarity=0.034  Sum_probs=28.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      ...|+++.++|..+|++.++|+++..=-..++.+.+..|
T Consensus       174 ~~~G~~~~~ia~~Lg~~ks~vSr~lsl~~~lP~~li~~i  212 (325)
T TIGR03454       174 EDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAI  212 (325)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHh
Confidence            468999999999999999999999873222333443333

Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=87.74  E-value=1.3  Score=29.38  Aligned_cols=33  Identities=9%  Similarity=0.075  Sum_probs=25.4

Q ss_pred             HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+.+-+ ..++|..|||+.+|++++|++++.+
T Consensus        32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~   65 (274)
T PRK11569         32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLT   65 (274)
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            33444433 4579999999999999999999854

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=87.70  E-value=0.8  Score=28.58  Aligned_cols=26  Identities=12%  Similarity=0.156  Sum_probs=22.4

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      --.|+|.+|+|+.+|+|+++|.....
T Consensus       167 ~~e~~s~~EIA~~lgis~~tV~~~l~  192 (208)
T PRK08295        167 YLDGKSYQEIAEELNRHVKSIDNALQ  192 (208)
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHH
Confidence            34699999999999999999987654

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=87.67  E-value=0.73  Score=31.48  Aligned_cols=25  Identities=16%  Similarity=0.155  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|.+++|..+|+|..+|.+++.
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~  304 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQV  304 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4589999999999999999999986

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=87.66  E-value=1  Score=27.54  Aligned_cols=27  Identities=19%  Similarity=0.041  Sum_probs=23.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|..+|.....
T Consensus       150 ~~~~~~s~~EIA~~lgis~~tv~~~l~  176 (190)
T TIGR02939       150 RELEGLSYEDIARIMDCPVGTVRSRIF  176 (190)
T ss_pred             hhhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345699999999999999999988764

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.

>COG1737 RpiR Transcriptional regulators [Transcription]

Probab=87.60  E-value=1.2  Score=29.71  Aligned_cols=28  Identities=18%  Similarity=0.200  Sum_probs=23.9

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ....+|..+||+.+|||++||.++-+--
T Consensus        33 ~~~~~si~elA~~a~VS~aTv~Rf~~kL   60 (281)
T COG1737          33 EVALLSIAELAERAGVSPATVVRFARKL   60 (281)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            3456899999999999999999998753

>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional

Probab=87.59  E-value=1.3  Score=29.34  Aligned_cols=37  Identities=27%  Similarity=0.423  Sum_probs=29.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      --|....|+.+|+|+++||+           .+..|.+.||+++-+|+
T Consensus        28 ~gs~s~AA~~L~iSQpavS~-----------~I~~LE~~lG~~LF~R~   64 (311)
T PRK10086         28 HQSFALAADELSLTPSAVSH-----------RINQLEEELGIKLFVRS   64 (311)
T ss_pred             cCCHHHHHHHHCCCHHHHHH-----------HHHHHHHHhCCeeEEEc
Confidence            34667799999999999998           46778888888887765

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=87.57  E-value=1.4  Score=29.22  Aligned_cols=33  Identities=12%  Similarity=0.062  Sum_probs=25.6

Q ss_pred             HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+-. ..++|..|+|+.+|++++|++++.+
T Consensus        29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~   62 (271)
T PRK10163         29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLK   62 (271)
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44444433 3579999999999999999999854

>PRK03601 transcriptional regulator HdfR; Provisional

Probab=87.47  E-value=1.3  Score=28.81  Aligned_cols=37  Identities=19%  Similarity=0.193  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      --|....|+.+|+|+++||+.           +..|...||+++-+|.
T Consensus        15 ~gs~s~AA~~L~isqpavS~~-----------I~~LE~~lG~~LF~R~   51 (275)
T PRK03601         15 TRHFGRAAESLYLTQSAVSFR-----------IRQLENQLGVNLFTRH   51 (275)
T ss_pred             cCCHHHHHHHhCCChHHHHHH-----------HHHHHHHhCCceEEEC
Confidence            346677999999999999984           5677888888876664

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=87.42  E-value=1.8  Score=26.52  Aligned_cols=28  Identities=18%  Similarity=0.108  Sum_probs=23.6

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|..+|.....
T Consensus       128 l~~~e~~s~~EIA~~lgis~~tV~~~l~  155 (179)
T PRK12543        128 LRYLHDYSQEEIAQLLQIPIGTVKSRIH  155 (179)
T ss_pred             HHHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455799999999999999999887754

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=87.41  E-value=1.4  Score=27.12  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .-....++|..++|++++++.+.+
T Consensus        23 ~~~~~~diA~~L~Vsp~sVt~ml~   46 (154)
T COG1321          23 GFARTKDIAERLKVSPPSVTEMLK   46 (154)
T ss_pred             CcccHHHHHHHhCCCcHHHHHHHH
Confidence            347889999999999999988754

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=87.41  E-value=1.1  Score=27.43  Aligned_cols=27  Identities=11%  Similarity=0.044  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|..+|.....
T Consensus       139 ~~~~g~s~~EIA~~l~is~~tv~~~l~  165 (179)
T PRK09415        139 FYYEELSIKEIAEVTGVNENTVKTRLK  165 (179)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344699999999999999999988764

>PRK10870 transcriptional repressor MprA; Provisional

Probab=87.41  E-value=0.86  Score=28.40  Aligned_cols=32  Identities=3%  Similarity=0.076  Sum_probs=24.3

Q ss_pred             HHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARL--GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+..  ..++++.+||+.++++++++++..
T Consensus        59 ~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v   92 (176)
T PRK10870         59 MALITLESQENHSIQPSELSCALGSSRTNATRIA   92 (176)
T ss_pred             HHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            44455543  246899999999999999998764

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=87.37  E-value=0.78  Score=31.22  Aligned_cols=25  Identities=12%  Similarity=0.278  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|.+|+|+.+|+|+.+|.+++..
T Consensus       275 ~~~Tl~EIa~~lgiS~erVRqi~~r  299 (317)
T PRK07405        275 QPLTLAKIGERLNISRERVRQIERE  299 (317)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            5689999999999999999999864

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=87.37  E-value=1.7  Score=28.26  Aligned_cols=28  Identities=7%  Similarity=0.188  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|.+|+|..+|+|..+|.....
T Consensus       212 l~~~~~~s~~EIA~~lgis~~tV~~~~~  239 (251)
T PRK07670        212 LFYKEELTLTEIGQVLNLSTSRISQIHS  239 (251)
T ss_pred             HHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445699999999999999999988764

>PF14174 YycC: YycC-like protein

Probab=87.35  E-value=0.57  Score=23.62  Aligned_cols=20  Identities=25%  Similarity=0.327  Sum_probs=17.3

Q ss_pred             CCCHHHHHHHHHHhCCCCcc
Q 038591           59 VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        59 ~p~~~~~~~la~~lgv~~~e   78 (82)
                      .++.++..+|++.|||+++.
T Consensus         5 qIS~eTA~kLs~~L~vPlE~   24 (53)
T PF14174_consen    5 QISPETAVKLSKKLGVPLEQ   24 (53)
T ss_pred             ccCHHHHHHHHHHHCCcHHH
Confidence            47899999999999999863

>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]

Probab=87.33  E-value=3.3  Score=23.18  Aligned_cols=30  Identities=13%  Similarity=0.202  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      .+++..++|..+|+|+.++.+........+
T Consensus        35 ~~~~l~~la~~~g~S~~~l~r~f~~~~g~s   64 (127)
T COG2207          35 EPLTLEDLARRLGMSRRTLSRLFKKETGTS   64 (127)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
Confidence            458999999999999999999887433333

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=87.26  E-value=1.1  Score=26.99  Aligned_cols=27  Identities=4%  Similarity=-0.080  Sum_probs=23.4

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|..+|+|..+|..+..
T Consensus       120 ~~~~g~s~~eIA~~lgis~~tv~~~l~  146 (165)
T PRK09644        120 CDVHELTYEEAASVLDLKLNTYKSHLF  146 (165)
T ss_pred             HHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence            345699999999999999999988764

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=87.21  E-value=1.7  Score=27.02  Aligned_cols=26  Identities=8%  Similarity=0.020  Sum_probs=22.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +--.|+|.+|+|+.+|+|.++|....
T Consensus       153 ~~~eg~s~~EIA~~lgis~~tVk~rl  178 (194)
T PRK12531        153 VYLEELPHQQVAEMFDIPLGTVKSRL  178 (194)
T ss_pred             HHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence            44569999999999999999997654

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=87.20  E-value=1.1  Score=29.20  Aligned_cols=27  Identities=15%  Similarity=-0.028  Sum_probs=22.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ++.-.|+|.+|+|+.+|+|.++|....
T Consensus       127 L~~~eg~S~~EIAe~LgiS~~tVksrL  153 (228)
T PRK06704        127 LKDVFQYSIADIAKVCSVSEGAVKASL  153 (228)
T ss_pred             hHHhhCCCHHHHHHHHCcCHHHHHHHH
Confidence            344569999999999999999998764

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=87.09  E-value=1.5  Score=31.78  Aligned_cols=33  Identities=12%  Similarity=0.092  Sum_probs=25.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+ +..++|+.+|||++|+++-.+
T Consensus       476 ~~~i~~~l~~~~-~~~~aA~~LGisr~tL~rkl~  508 (520)
T PRK10820        476 RSVLTRLYRNYP-STRKLAKRLGVSHTAIANKLR  508 (520)
T ss_pred             HHHHHHHHHHCC-CHHHHHHHhCCCHHHHHHHHH
Confidence            344555555566 888999999999999998765

>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages

Probab=87.03  E-value=1.5  Score=24.62  Aligned_cols=28  Identities=18%  Similarity=0.345  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      -+|...||+.+|.++++|..+-.....|
T Consensus        12 ~v~~~~FA~~IGKt~sAVr~Mi~~gKLP   39 (87)
T PF10743_consen   12 AVTYEKFAEYIGKTPSAVRKMIKAGKLP   39 (87)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence            5788999999999999999886544444

The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=87.02  E-value=0.68  Score=25.18  Aligned_cols=22  Identities=14%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..++|+.+++++.++.++.+
T Consensus        26 ~s~~eiA~~~~i~~~~l~kil~   47 (83)
T PF02082_consen   26 VSSKEIAERLGISPSYLRKILQ   47 (83)
T ss_dssp             BEHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            8999999999999999999864

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

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

Probab=87.01  E-value=2  Score=26.63  Aligned_cols=28  Identities=4%  Similarity=-0.024  Sum_probs=23.4

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.++|.....
T Consensus       142 l~~~~g~s~~EIA~~lgis~~tvk~rl~  169 (188)
T TIGR02943       142 MREVLGFESDEICQELEISTSNCHVLLY  169 (188)
T ss_pred             HHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445699999999999999999987754

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.

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=87.00  E-value=1.5  Score=26.72  Aligned_cols=27  Identities=11%  Similarity=0.199  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|..|+|+.+|+|.++|.....
T Consensus       131 ~~~~g~s~~EIA~~lgis~~tV~~~l~  157 (172)
T PRK09651        131 SQLDGLTYSEIAHKLGVSVSSVKKYVA  157 (172)
T ss_pred             hhccCCCHHHHHHHhCCCHHHHHHHHH
Confidence            344699999999999999999988764

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=86.82  E-value=1.9  Score=26.58  Aligned_cols=27  Identities=11%  Similarity=-0.028  Sum_probs=23.4

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|..+|.....
T Consensus       143 ~~~~g~s~~eIA~~lgis~~tV~~~l~  169 (184)
T PRK12539        143 VKLEGLSVAEAATRSGMSESAVKVSVH  169 (184)
T ss_pred             HHHcCCcHHHHHHHHCcCHHHHHHHHH
Confidence            445699999999999999999988764

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=86.79  E-value=2  Score=26.30  Aligned_cols=27  Identities=11%  Similarity=-0.060  Sum_probs=23.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|..+|.....
T Consensus       143 ~~~~g~s~~eIA~~l~is~~tV~~~l~  169 (184)
T PRK12512        143 ISVEGASIKETAAKLSMSEGAVRVALH  169 (184)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            344699999999999999999988764

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=86.74  E-value=1.5  Score=31.94  Aligned_cols=25  Identities=4%  Similarity=0.109  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|+.++|+.+|||+..|+++|..
T Consensus       466 e~~TL~EIa~~lGVSrERVRQIe~k  490 (509)
T PRK05901        466 QPKTLDEIGQVYGVTRERIRQIESK  490 (509)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4699999999999999999999974

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=86.68  E-value=1.8  Score=26.89  Aligned_cols=27  Identities=19%  Similarity=-0.025  Sum_probs=22.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ++--.|+|.+|+|..+|+|.++|..-.
T Consensus       145 l~~~~g~s~~EIA~~lg~s~~tV~~rl  171 (192)
T PRK09643        145 AVDMQGYSVADAARMLGVAEGTVKSRC  171 (192)
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            455679999999999999999997654

>PRK13756 tetracycline repressor protein TetR; Provisional

Probab=86.57  E-value=0.62  Score=29.72  Aligned_cols=36  Identities=8%  Similarity=0.078  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      ++|..+||+++|+++.+++++..++...-...+..+
T Consensus        24 ~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~~~~~   59 (205)
T PRK13756         24 GLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEI   59 (205)
T ss_pred             cCCHHHHHHHhCCCchHHHHHcCCHHHHHHHHHHHH
Confidence            579999999999999999999876544333333333

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=86.50  E-value=1  Score=28.98  Aligned_cols=25  Identities=12%  Similarity=0.113  Sum_probs=22.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|+|.+++|+.+|+|.++|.....
T Consensus       163 ~~g~s~~EIAe~lgis~~tVk~~l~  187 (231)
T PRK11922        163 VEELSVEETAQALGLPEETVKTRLH  187 (231)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4599999999999999999988764

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=86.45  E-value=1.6  Score=28.27  Aligned_cols=28  Identities=14%  Similarity=0.198  Sum_probs=24.1

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++.-.|+|.+|+|+.+|+|..+|.....
T Consensus       182 L~~~eg~s~~EIA~~Lgis~~tVk~~l~  209 (233)
T PRK12538        182 LSYHENMSNGEIAEVMDTTVAAVESLLK  209 (233)
T ss_pred             hHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455799999999999999999988765

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=86.43  E-value=1.6  Score=29.53  Aligned_cols=32  Identities=9%  Similarity=0.026  Sum_probs=25.2

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+......+..+||+.+|+|+++|++..
T Consensus         8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l   39 (319)
T PRK11886          8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHI   39 (319)
T ss_pred             HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34455555667899999999999999997753

>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional

Probab=86.42  E-value=1.9  Score=28.70  Aligned_cols=35  Identities=31%  Similarity=0.316  Sum_probs=27.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+++|+++||+.           +..|.+.||+++-+|.
T Consensus        24 s~t~AA~~L~iSQpavS~~-----------I~~LE~~lg~~LF~R~   58 (319)
T PRK10216         24 SVTKAAKRMNVTPSAVSKS-----------LAKLRAWFDDPLFVNT   58 (319)
T ss_pred             CHHHHHHHhCCCHHHHHHH-----------HHHHHHHhCCceEEec
Confidence            6777999999999999984           5667777777766553

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=86.41  E-value=1.3  Score=27.75  Aligned_cols=27  Identities=7%  Similarity=-0.065  Sum_probs=23.4

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.-.|+|.+|+|+.+|+|..+|.....
T Consensus       145 ~~~~g~s~~EIAe~lgis~~tV~~~l~  171 (196)
T PRK12535        145 TQVLGYTYEEAAKIADVRVGTIRSRVA  171 (196)
T ss_pred             HHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            445699999999999999999988764

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=86.40  E-value=2.8  Score=25.03  Aligned_cols=27  Identities=15%  Similarity=0.199  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      -..|++.+++|+.+++|..||..+...
T Consensus       161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~  187 (211)
T PRK15369        161 ITEGYTNRDIAEQLSISIKTVETHRLN  187 (211)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            357899999999999999999988754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	82
1x57_A	91	Solution Structures Of The Hth Domain Of Human Edf-		7e-13
2jvl_A	107	Nmr Structure Of The C-Terminal Domain Of Mbf1 Of T		6e-06

>pdb|1X57|A Chain A, Solution Structures Of The Hth Domain Of Human Edf-1 Protein Length = 91

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 45/55 (81%)
Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79
          IQ+ R  K ++Q DLA +IN++PQV+++YE+G+A+PN  VL K+E+AIG+KLR K
Sbjct: 18 IQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGK 72

>pdb|2JVL|A Chain A, Nmr Structure Of The C-Terminal Domain Of Mbf1 Of Trichoderm Length = 107

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 31/51 (60%)
Query: 27 RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          R +    M+Q +L  +I +    V+ YE G A P+Q +L+KME+ + VKLR
Sbjct: 43 RQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKLR 93
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	82
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	4e-16
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	2e-15
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	1e-08
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	2e-08
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	7e-08
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	2e-07
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	3e-07
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	4e-07
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	7e-07
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	8e-07
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	2e-06
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	4e-06
3ivp_A	126	Putative transposon-related DNA-binding protein; A	5e-06
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	5e-06
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	6e-06
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	3e-05
3mlf_A	111	Transcriptional regulator; structural genomics, he	4e-05
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	4e-05
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	5e-05
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	5e-05
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	6e-05
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	7e-05
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	8e-05
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	3e-04
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	5e-04
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	7e-04
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	7e-04
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	7e-04
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	8e-04

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Length = 91

 Score = 65.6 bits (160), Expect = 4e-16
 Identities = 29/59 (49%), Positives = 46/59 (77%)

Query: 19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
           +  + IQ+ R  K ++Q DLA +IN++PQV+++YE+G+A+PN  VL K+E+AIG+KLR
Sbjct: 12 LEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLR 70

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Length = 107

 Score = 64.5 bits (157), Expect = 2e-15
 Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 10/88 (11%)

Query: 2  KTAGAVINMRKLDEGTEPDTPRQI----------QRARLGKKMSQPDLANQINQRPQVVS 51
                  + K+D   +   P+ +           R +    M+Q +L  +I +    V+
Sbjct: 8  AGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVA 67

Query: 52 EYENGKAVPNQTVLAKMEKAIGVKLRVK 79
           YE G A P+Q +L+KME+ + VKLR  
Sbjct: 68 SYERGTATPDQNILSKMERVLNVKLRGA 95

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 76

 Score = 46.1 bits (110), Expect = 1e-08
 Identities = 12/51 (23%), Positives = 22/51 (43%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
          +I+  R   K+ Q  L   +      +S++E  +  PN   L  + KA+  
Sbjct: 9  RIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59

>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 Length = 68

 Score = 45.2 bits (108), Expect = 2e-08
 Identities = 12/51 (23%), Positives = 22/51 (43%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
          +I+  R   K+ Q  L   +      +S++E  +  PN   L  + KA+  
Sbjct: 9  RIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94

 Score = 44.3 bits (105), Expect = 7e-08
 Identities = 8/53 (15%), Positives = 19/53 (35%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +       + +Q ++A  I   PQ  + +  G A+P    +  +     +  
Sbjct: 13 NLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINK 65

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73

 Score = 42.7 bits (101), Expect = 2e-07
 Identities = 9/54 (16%), Positives = 23/54 (42%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          +++     K  +   L   +++    VS++      P+   L  + +A+ V +R
Sbjct: 12 RLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVR 65

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae} Length = 158

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 10/51 (19%), Positives = 22/51 (43%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
           I+  R    ++Q + A  +      +S YENG +  +  ++  + +   V
Sbjct: 5  NIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNV 55

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis} Length = 76

 Score = 42.3 bits (100), Expect = 4e-07
 Identities = 12/54 (22%), Positives = 27/54 (50%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          +I+     K+ +   LA Q+ +    +S + + K+ P+  +L K+ + + V  R
Sbjct: 14 RIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPR 67

>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* Length = 88

 Score = 41.7 bits (98), Expect = 7e-07
 Identities = 11/59 (18%), Positives = 26/59 (44%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
           ++  R     +Q +LA +I  +   +S +EN       T   K+ +++ + + +   K
Sbjct: 16 AMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK 74

>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} Length = 114

 Score = 42.1 bits (99), Expect = 8e-07
 Identities = 8/45 (17%), Positives = 21/45 (46%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM 68
           + R +    +    +A  +N + + V+ Y +G+  P+   L ++
Sbjct: 13 NLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRL 57

>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 Length = 69

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
          ++  R+   ++Q +LA ++    Q + + ENGK       L ++  A+GV
Sbjct: 6  VKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASALGV 54

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141

 Score = 41.0 bits (96), Expect = 4e-06
 Identities = 17/76 (22%), Positives = 26/76 (34%)

Query: 1   KKTAGAVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60
           +K A      R  D+             R+ K  +Q +LA         +S  EN K   
Sbjct: 49  RKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSL 108

Query: 61  NQTVLAKMEKAIGVKL 76
               + K+  A+GV  
Sbjct: 109 QDKTVQKLANALGVSP 124

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile} Length = 126

 Score = 40.2 bits (94), Expect = 5e-06
 Identities = 11/54 (20%), Positives = 24/54 (44%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            I+ AR  + +++  +   I   P+ ++  EN    P+  VL  +   + V +
Sbjct: 15 LAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSV 68

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646} Length = 293

 Score = 41.3 bits (96), Expect = 5e-06
 Identities = 11/53 (20%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77
          I++ R+ + ++Q  L+  I  + + VS  E+G   P+  +L  +   + + + 
Sbjct: 10 IKKIRVLRGLTQKQLSENICHQSE-VSRIESGAVYPSMDILQGIAAKLQIPII 61

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L* Length = 71

 Score = 38.8 bits (91), Expect = 6e-06
 Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
          +++ R+  KM+Q +LA +   + Q +   E G     +  L ++  A+  
Sbjct: 8  LKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMALNC 56

>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 Length = 133

 Score = 38.2 bits (88), Expect = 3e-05
 Identities = 12/64 (18%), Positives = 23/64 (35%)

Query: 6   AVINMRKLDEGTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL 65
           A +   +     E   P  I + R    ++Q + +          S YE G A P+ + +
Sbjct: 57  AQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTI 116

Query: 66  AKME 69
             + 
Sbjct: 117 KLLR 120

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp} Length = 111

 Score = 37.7 bits (87), Expect = 4e-05
 Identities = 9/54 (16%), Positives = 21/54 (38%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
          + ++  R    ++Q +L +      + +   E        ++L+K   A  VK 
Sbjct: 26 KTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKY 79

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A Length = 98

 Score = 37.6 bits (87), Expect = 4e-05
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 22 PRQIQRARLGKKMSQPDLANQINQRPQV----VSEYENGKAVPNQTVLAKMEKAIGV 74
           R+++ ARL   +SQ  L              +++YE GK  P+  +  ++ K + +
Sbjct: 3  IRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKI 59

>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 Length = 198

 Score = 38.3 bits (89), Expect = 5e-05
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP-NQTVLAKMEKAIGVKL 76
            ++  R   KM    LA+ + + P+ V+ +ENG+      T L ++   +G  +
Sbjct: 13 ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSI 67

>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} Length = 83

 Score = 37.0 bits (86), Expect = 5e-05
 Identities = 11/54 (20%), Positives = 22/54 (40%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            +  AR    ++Q +LA ++ +    VS+ EN +   +        + IG   
Sbjct: 17 DLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDP 70

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3 Length = 74

 Score = 36.5 bits (85), Expect = 6e-05
 Identities = 11/54 (20%), Positives = 23/54 (42%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
          ++++  R  K +SQ  LA         V   E G+   +   + K+  A+ ++ 
Sbjct: 16 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 69

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236

 Score = 38.0 bits (88), Expect = 7e-05
 Identities = 10/50 (20%), Positives = 20/50 (40%)

Query: 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74
           ++ +    +SQ  +A+++      V    NG    N    A + K + V
Sbjct: 22 YEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKV 71

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2} Length = 84

 Score = 36.7 bits (85), Expect = 8e-05
 Identities = 9/60 (15%), Positives = 27/60 (45%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKIRK 82
          + + + R    +SQ +LA  +      +S+ E+ +   +   L ++ + +  +L + +  
Sbjct: 13 QLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGLPMDI 72

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A Length = 117

 Score = 35.8 bits (82), Expect = 3e-04
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            ++  R  K ++  +LA      P  +SE E G+   +  +LA +  A+G  +
Sbjct: 31 AALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASV 84

>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 Length = 99

 Score = 34.6 bits (79), Expect = 5e-04
 Identities = 9/51 (17%), Positives = 24/51 (47%)

Query: 18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM 68
                +I+  R   K++Q + + + +     + ++E G++ P+Q   A +
Sbjct: 28 SAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYL 78

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 Length = 77

 Score = 33.8 bits (78), Expect = 7e-04
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
          R +++ R  K +SQ +LA+        +SE E G    +   + K+  A+ +  
Sbjct: 13 RTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor} Length = 71

 Score = 33.6 bits (77), Expect = 7e-04
 Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 23 RQIQRARLGKKMSQPDLANQINQR--PQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +++  R  + +S   +  +   R    VV  YE G        LA++    GV +
Sbjct: 11 AKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPV 66

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} PDB: 3clc_A* Length = 82

 Score = 33.8 bits (78), Expect = 7e-04
 Identities = 15/54 (27%), Positives = 22/54 (40%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            I++ RL K M+Q DLA + N     +S  E          L  + K + V  
Sbjct: 14 FVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSD 67

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A Length = 99

 Score = 34.3 bits (79), Expect = 8e-04
 Identities = 15/54 (27%), Positives = 22/54 (40%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
            I++ RL K M+Q DLA + N     +S  E          L  + K + V  
Sbjct: 31 FVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSD 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	82
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	99.75
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	99.75
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	99.73
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	99.73
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	99.73
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	99.73
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	99.73
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	99.73
3t76_A	88	VANU, transcriptional regulator vanug; structural	99.73
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	99.72
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	99.71
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	99.71
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	99.71
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	99.71
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	99.71
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	99.7
3ivp_A	126	Putative transposon-related DNA-binding protein; A	99.7
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	99.7
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	99.7
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	99.7
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	99.69
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	99.69
3trb_A	104	Virulence-associated protein I; mobIle and extrach	99.69
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	99.69
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	99.69
3mlf_A	111	Transcriptional regulator; structural genomics, he	99.69
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	99.68
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	99.68
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	99.68
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	99.68
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	99.68
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	99.67
3cec_A	104	Putative antidote protein of plasmid maintenance;	99.66
1b0n_A	111	Protein (SINR protein); transcription regulator, a	99.65
4ghj_A	101	Probable transcriptional regulator; structural gen	99.64
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	99.64
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	99.64
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	99.63
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	99.63
2wus_R	112	RODZ, putative uncharacterized protein; structural	99.63
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	99.63
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	99.62
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	99.62
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	99.61
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	99.61
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	99.61
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	99.59
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	99.59
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	99.56
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	99.56
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.54
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	99.54
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	99.51
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	99.48
2awi_A	317	PRGX; repressor, pheromone, DNA binding, regulator	99.47
4ich_A	311	Transcriptional regulator; structural genomics, PS	99.45
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	99.45
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	99.42
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	99.4
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.4
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	99.4
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	99.28
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	99.19
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	99.02
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	99.01
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	98.92
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	98.82
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	98.74
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	98.68
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	98.66
1s4k_A	120	Putative cytoplasmic protein YDIL; structural geno	98.64
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.61
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	98.54
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.5
2hin_A	71	GP39, repressor protein; transcription factor, dim	98.3
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	98.21
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	98.08
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	97.96
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	97.96
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	97.94
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	97.66
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	97.57
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	97.55
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	97.52
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	97.48
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.36
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	97.32
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	97.26
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	97.25
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	97.03
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	97.02
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	96.97
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	96.87
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	96.77
2csf_A	101	DNA-binding protein SATB2; CUT domain, special AT-	96.76
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	96.73
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	96.59
3e3m_A	355	Transcriptional regulator, LACI family; structural	96.57
3jvd_A	333	Transcriptional regulators; structural genomics, P	96.57
3me5_A	482	Cytosine-specific methyltransferase; structural ge	96.52
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	96.49
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	96.48
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	96.48
1jye_A	349	Lactose operon repressor; gene regulation, protein	96.47
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.44
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	96.4
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.36
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.27
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	96.22
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	96.21
3bil_A	348	Probable LACI-family transcriptional regulator; st	96.14
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	96.11
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	96.1
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	96.09
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	96.08
1e3o_C	160	Octamer-binding transcription factor 1; transcript	96.05
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	96.04
2jml_A	81	DNA binding domain/transcriptional regulator; anti	96.0
1u78_A	141	TC3 transposase, transposable element TC3 transpos	95.99
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.97
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.91
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	95.88
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	95.86
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	95.86
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	95.86
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	95.85
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	95.83
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	95.81
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	95.81
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	95.8
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	95.78
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	95.78
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.71
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	95.71
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	95.67
2ox6_A	166	Hypothetical protein SO3848; structural genomics,	95.66
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	95.65
1x2l_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, hu	95.64
1wh6_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, st	95.59
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	95.53
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	95.49
2o4a_A	93	DNA-binding protein SATB1; protein-DNA complex, tr	95.46
1eto_A	98	FIS, factor for inversion stimulation; transcripti	95.44
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	95.39
1sfx_A	109	Conserved hypothetical protein AF2008; structural	95.37
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	95.37
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	95.33
2k27_A	159	Paired box protein PAX-8; paired domain, solution	95.3
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	95.3
3r0a_A	123	Putative transcriptional regulator; structural gen	95.29
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.25
3c57_A	95	Two component transcriptional regulatory protein;	95.17
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	95.16
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.15
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	95.04
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	94.99
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.98
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	94.97
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	94.93
1wiz_A	101	DNA-binding protein SATB2; helix bundle, KIAA1034	94.92
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	94.92
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	94.92
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.89
2w25_A	150	Probable transcriptional regulatory protein; trans	94.84
3frw_A	107	Putative Trp repressor protein; structural genomic	94.8
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	94.79
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.78
2pg4_A	95	Uncharacterized protein; structural genomics, join	94.71
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.71
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	94.71
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.7
1q06_A	135	Transcriptional regulator CUER; MERR family transc	94.69
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	94.66
1y0u_A	96	Arsenical resistance operon repressor, putative; s	94.6
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	94.56
3hh0_A	146	Transcriptional regulator, MERR family; protein st	94.52
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	94.52
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.51
3iwf_A	107	Transcription regulator RPIR family; transcription	94.5
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.47
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.47
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.44
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	94.38
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	94.38
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.38
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	94.37
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.36
2nnn_A	140	Probable transcriptional regulator; structural gen	94.34
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.33
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	94.29
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	94.28
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	94.26
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.25
3gp4_A	142	Transcriptional regulator, MERR family; structural	94.25
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	94.23
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	94.22
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	94.22
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	94.14
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.13
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.1
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	94.05
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	94.04
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.03
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	94.03
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	94.02
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	94.0
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	93.97
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	93.95
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	93.92
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	93.91
2eth_A	154	Transcriptional regulator, putative, MAR family; M	93.88
2f07_A	197	YVDT; helix-turn-helix, transcription; HET: BTB; 2	93.83
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	93.83
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	93.82
3s2w_A	159	Transcriptional regulator, MARR family; structural	93.82
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	93.81
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	93.8
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	93.75
3b02_A	195	Transcriptional regulator, CRP family; structural	93.71
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	93.71
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	93.7
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	93.68
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	93.68
3mn2_A	108	Probable ARAC family transcriptional regulator; st	93.66
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	93.65
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	93.6
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	93.6
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	93.58
1ft9_A	222	Carbon monoxide oxidation system transcription reg	93.58
1wh8_A	111	CUT-like 2, homeobox protein CUX-2; CUT domain, st	93.55
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.51
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	93.5
1z05_A	429	Transcriptional regulator, ROK family; structural	93.49
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	93.46
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	93.45
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	93.45
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	93.42
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	93.42
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	93.4
3bqz_B	194	HTH-type transcriptional regulator QACR; multidrug	93.39
3gpv_A	148	Transcriptional regulator, MERR family; protein st	93.37
2pex_A	153	Transcriptional regulator OHRR; transcription regu	93.36
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	93.35
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.35
3lsg_A	103	Two-component response regulator YESN; structural	93.33
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	93.32
1u8b_A	133	ADA polyprotein; protein-DNA complex, methylation,	93.31
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	93.27
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	93.27
2gxg_A	146	146AA long hypothetical transcriptional regulator;	93.27
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	93.27
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	93.26
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	93.23
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.23
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	93.21
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	93.2
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	93.18
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	93.17
2d6y_A	202	Putative TETR family regulatory protein; helix-tur	93.14
3egq_A	170	TETR family transcriptional regulator; DNA-binding	93.14
3ppb_A	195	Putative TETR family transcription regulator; DNA-	93.13
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	93.13
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	93.13
3on4_A	191	Transcriptional regulator, TETR family; structural	93.12
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	93.12
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	93.1
3lwj_A	202	Putative TETR-family transcriptional regulator; st	93.09
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	93.09
3vpr_A	190	Transcriptional regulator, TETR family; all alpha,	93.09
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	93.09
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	93.03
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	92.99
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	92.96
2rae_A	207	Transcriptional regulator, ACRR family protein; TE	92.95
3anp_C	204	Transcriptional repressor, TETR family; all alpha	92.93
2qtq_A	213	Transcriptional regulator, TETR family; transcript	92.92
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	92.9
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	92.88
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	92.87
2v57_A	190	TETR family transcriptional repressor LFRR; DNA-bi	92.85
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	92.83
2h09_A	155	Transcriptional regulator MNTR; transcription regu	92.81
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	92.79
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	92.78
3jth_A	98	Transcription activator HLYU; transcription factor	92.76
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	92.76
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	92.75
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	92.73
2zcm_A	192	Biofilm operon icaabcd HTH-type negative transcri	92.72
3qbm_A	199	TETR transcriptional regulator; DNA/RNA-binding th	92.69
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	92.69
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	92.68
2kko_A	108	Possible transcriptional regulatory protein (possi	92.66
3ljl_A	156	Transcriptional regulator LUXT; structural genomic	92.65
4aci_A	191	HTH-type transcriptional repressor ACNR; aconitase	92.61
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	92.59
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	92.59
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	92.59
1ku9_A	152	Hypothetical protein MJ223; putative transcription	92.58
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	92.54
1yse_A	141	DNA-binding protein SATB1; all helical, DNA-bindin	92.54
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	92.53
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	92.5
1z91_A	147	Organic hydroperoxide resistance transcriptional;	92.46
3bni_A	229	Putative TETR-family transcriptional regulator; st	92.45
2dg6_A	222	Putative transcriptional regulator; winged-helix m	92.44
4fx0_A	148	Probable transcriptional repressor protein; helix-	92.43
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	92.43
2eh3_A	179	Transcriptional regulator; all alpha proteins, tet	92.41
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	92.4
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	92.39
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	92.35
3o60_A	185	LIN0861 protein; PSI, MCSG, structural genomics, m	92.31
3bru_A	222	Regulatory protein, TETR family; structural genomi	92.31
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	92.3
3vib_A	210	MTRR; helix-turn-helix motif, DNA binding, DNA bin	92.26
3gzi_A	218	Transcriptional regulator, TETR family; TETR famil	92.25
3bhq_A	211	Transcriptional regulator; bacterial RE proteins,	92.24
3dew_A	206	Transcriptional regulator, TETR family; S genomics	92.24
3nqo_A	189	MARR-family transcriptional regulator; structural	92.24
2jj7_A	186	Hemolysin II regulatory protein; DNA-binding prote	92.23
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	92.22
1u78_A	141	TC3 transposase, transposable element TC3 transpos	92.19
3f0c_A	216	TETR-molecule A, transcriptional regulator; MCSG,P	92.16
3frq_A	195	Repressor protein MPHR(A); macrolide antibiotic. r	92.11
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	92.11
3loc_A	212	HTH-type transcriptional regulator RUTR; helix-tur	92.11
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	92.1
2yve_A	185	Transcriptional regulator; helix-turn-helix, TETR-	92.09
3pas_A	195	TETR family transcription regulator; structural ge	92.09
3rh2_A	212	Hypothetical TETR-like transcriptional regulator;	92.08
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	92.07
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	92.0
2kfs_A	148	Conserved hypothetical regulatory protein; WHTH, D	91.97
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	91.96
3mnl_A	203	KSTR, transcriptional regulatory protein (probably	91.96
3f3x_A	144	Transcriptional regulator, MARR family, putative;	91.92
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	91.89
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	91.88
3c2b_A	221	Transcriptional regulator, TETR family; structural	91.87
2qwt_A	196	Transcriptional regulator, TETR family; structural	91.86
3e7q_A	215	Transcriptional regulator; structural genomics, PS	91.85
2ibd_A	204	Possible transcriptional regulator; probable trans	91.83
2fxa_A	207	Protease production regulatory protein HPR; protea	91.81
3cjd_A	198	Transcriptional regulator, TETR family; YP_510936.	91.8
2nx4_A	194	Transcriptional regulator, TETR family protein; HT	91.8
3dn7_A	194	Cyclic nucleotide binding regulatory protein; stru	91.8
2oer_A	214	Probable transcriptional regulator; helix-turn-hel	91.79
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	91.76
1vi0_A	206	Transcriptional regulator; structural genomics; HE	91.73
2hku_A	215	A putative transcriptional regulator; structural g	91.71
3nxc_A	212	HTH-type protein SLMA; nucleoid occlusion, cell di	91.69
2g3b_A	208	Putative TETR-family transcriptional regulator; tr	91.68
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	91.67
2zb9_A	214	Putative transcriptional regulator; transcription	91.67
2rek_A	199	Putative TETR-family transcriptional regulator; su	91.61
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	91.57
2o7t_A	199	Transcriptional regulator; transcription regulator	91.54
2wui_A	210	MEXZ, transcriptional regulator; gene regulation,	91.53
2gen_A	197	Probable transcriptional regulator; APC6095, TETR	91.53
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	91.49
2i10_A	202	Putative TETR transcriptional regulator; structura	91.48
3mvp_A	217	TETR/ACRR transcriptional regulator; PSI, MCSG, st	91.47
3g7r_A	221	Putative transcriptional regulator; TETR, all-heli	91.47
1okr_A	123	MECI, methicillin resistance regulatory protein ME	91.47
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	91.45
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.42
2hyt_A	197	TETR-family transcriptional regulator; structural	91.4
3bja_A	139	Transcriptional regulator, MARR family, putative;	91.39
2q0o_A	236	Probable transcriptional activator protein TRAR; h	91.39
2qib_A	231	TETR-family transcriptional regulator; HTH DNA bin	91.34
3nnr_A	228	Transcriptional regulator, TETR family; TETR-famil	91.26
2np5_A	203	Transcriptional regulator; TETR family, structural	91.26
3col_A	196	Putative transcription regulator; structural genom	91.25
3rd3_A	197	Probable transcriptional regulator; 2.40A {Pseudom	91.19
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	91.16
3q0w_A	236	HTH-type transcriptional regulator EThr; TETR fami	91.16
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	91.16
3v6g_A	208	Probable transcriptional regulatory protein (PROB	91.15
1mkm_A	249	ICLR transcriptional regulator; structural genomic	91.14
3bjb_A	207	Probable transcriptional regulator, TETR family P;	91.13
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	91.12
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.11
3rqi_A	184	Response regulator protein; structural genomics, s	91.09
3crj_A	199	Transcription regulator; APC88200, TETR, structura	91.08
1rkt_A	205	Protein YFIR; transcription regulator, structural	91.02
2id3_A	225	Putative transcriptional regulator; structural gen	90.96
3s5r_A	216	Transcriptional regulator TETR family; DNA/RNA-bin	90.96
2pz9_A	226	Putative regulatory protein; structural genomics,	90.85
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	90.83
1zk8_A	183	Transcriptional regulator, TETR family; TETR membe	90.83
2guh_A	214	Putative TETR-family transcriptional regulator; he	90.8
2gfn_A	209	HTH-type transcriptional regulator PKSA related P;	90.76
2zcx_A	231	SCO7815, TETR-family transcriptional regulator; he	90.76
3npi_A	251	TETR family regulatory protein; structural genomic	90.73
2q24_A	194	Putative TETR family transcriptional regulator; st	90.67
2o0m_A	345	Transcriptional regulator, SORC family; structural	90.67
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	90.65
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	90.63
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	90.59
1ui5_A	215	A-factor receptor homolog; helix-turn-helix, alpha	90.58
3he0_A	196	Transcriptional regulator, TETR family; ACRR, vibr	90.58
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	90.56
3eup_A	204	Transcriptional regulator, TETR family; structural	90.56
2w53_A	219	Repressor, SMet; antibiotic resistance, multi-drug	90.53
2obp_A	96	Putative DNA-binding protein; structural genomics,	90.4
2id6_A	202	Transcriptional regulator, TETR family; 1.75A {The	90.37
3g1o_A	255	Transcriptional regulatory repressor protein (TETR	90.34
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	90.29
1p6r_A	82	Penicillinase repressor; transcription regulation,	90.28
3geu_A	189	Intercellular adhesion protein R; TETR family, int	90.22
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	90.21
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	89.98
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	89.97
3jsj_A	190	Putative TETR-family transcriptional regulator; DN	89.97
1t33_A	224	Putative transcriptional repressor (TETR/ACRR FAM;	89.93
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	89.85
2ras_A	212	Transcriptional regulator, TETR family; bacterial	89.84
1bl0_A	129	Protein (multiple antibiotic resistance protein),	89.79
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	89.75
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	89.73
2oi8_A	216	Putative regulatory protein SCO4313; TETR, structu	89.72
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	89.69
3bqy_A	209	Putative TETR family transcriptional regulator; st	89.66
2of7_A	260	Putative TETR-family transcriptional regulator; AP	89.65
2iai_A	230	Putative transcriptional regulator SCO3833; struct	89.61
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	89.59
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	89.58
3c07_A	273	Putative TETR-family transcriptional regulator; AP	89.57
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	89.57
1sgm_A	191	Putative HTH-type transcriptional regulator YXAF;	89.5
1ixc_A	294	CBNR, LYSR-type regulatory protein; long alpha hel	89.42
3cdl_A	203	Transcriptional regulator AEFR; APC88582, TETR, ps	89.39
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	89.39
3hta_A	217	EBRA repressor; TETR family, DNA binding protein,	89.37
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	89.36
2esn_A	310	Probable transcriptional regulator; PA0477, APC582	89.27
1y6u_A	70	XIS, excisionase from transposon TN916; structure,	89.27
3hhg_A	306	Transcriptional regulator, LYSR family; transcript	89.21
2xpw_A	207	Tetracycline repressor protein class D; transcript	89.16
2opt_A	234	Actii protein; helical protein, TETR family, APO-p	89.15
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	89.09
2fbq_A	235	Probable transcriptional regulator; PA3006, APC589	88.88
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	88.83
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	88.69
2hyj_A	200	Putative TETR-family transcriptional regulator; HT	88.64
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	88.62
2hxi_A	241	Putative transcriptional regulator; structural gen	88.39
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	88.35
1u3e_M	174	HNH homing endonuclease; HNH catalytic motif, heli	88.24
4ich_A	311	Transcriptional regulator; structural genomics, PS	88.18
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	88.18
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	88.14
3cta_A	230	Riboflavin kinase; structural genomics, transferas	88.11
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	87.91
2g7g_A	213	RHA04620, putative transcriptional regulator; heli	87.9
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	87.85
3fxq_A	305	LYSR type regulator of TSAMBCD; transcriptional re	87.74
3aqt_A	245	Bacterial regulatory proteins, TETR family; helix-	87.74
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.67
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	87.65
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	87.64
1z0x_A	220	Transcriptional regulator, TETR family; structural	87.58
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	87.48
4hku_A	178	LMO2814 protein, TETR transcriptional regulator; s	87.31
1rr7_A	129	Middle operon regulator; MOR, transcription; 2.20A	87.3
2qko_A	215	Possible transcriptional regulator, TETR family P;	87.27
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	87.25
2iu5_A	195	DHAS, YCEG, HTH-type dhaklm operon transcriptional	87.24
2og0_A	52	Excisionase; protein-DNA complex, DNA architectura	87.0
3ni7_A	213	Bacterial regulatory proteins, TETR family; transc	86.94
3him_A	211	Probable transcriptional regulator; TETR, bacteria	86.78
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	86.75
2y2z_A	267	SIM16, SIMR, putative repressor simreg2; transcrip	86.7
3nrg_A	217	TETR family transcriptional regulator; structural	86.64
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	86.62
3ccy_A	203	Putative TETR-family transcriptional regulator; AP	86.56
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	86.53
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	86.48
2g7u_A	257	Transcriptional regulator; ICLR family, structural	86.4
2g7l_A	243	TETR-family transcriptional regulator; APC6062, pr	86.21
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	86.21
2np3_A	212	Putative TETR-family regulator; transcriptional re	86.08
2fd5_A	180	Transcriptional regulator; DNA-binding protein, st	86.07
3on2_A	199	Probable transcriptional regulator; protein struct	85.97
3fiw_A	211	Putative TETR-family transcriptional regulator; TE	85.96
2vn2_A	128	DNAD, chromosome replication initiation protein; D	85.96
3isp_A	303	HTH-type transcriptional regulator RV1985C/MT2039;	85.84
3lsj_A	220	DEST; transcriptional repressor, TETR family, DNA-	85.83
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	85.83
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	85.8
2vpr_A	207	Tetracycline resistance repressor protein; transcr	85.66
4ac0_A	202	Tetracycline repressor protein class B from trans	85.65
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	85.43
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	85.27
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	85.27
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	85.26
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	85.15
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	84.87
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	84.83

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=99.75  E-value=7.4e-18  Score=96.74  Aligned_cols=76  Identities=30%  Similarity=0.488  Sum_probs=66.7

Q ss_pred             chhhhhhhccCCCCCCC--------HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591            5 GAVINMRKLDEGTEPDT--------PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus         5 ~~~~~~~~~~~~~~~~~--------~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      ..+++..+++.....+.        +.+|+.+|.  ..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||
T Consensus        11 ~~~~~~~~~d~~~~~~~~~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v   90 (107)
T 2jvl_A           11 TEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNV   90 (107)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTTTCSCCCHHHHHHHHHTTTC
T ss_pred             CcccccccccccccccCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCc
Confidence            34566666666555432        899999999  99999999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 038591           75 KLRVKI   80 (82)
Q Consensus        75 ~~~e~~   80 (82)
                      ++++.+
T Consensus        91 ~~~e~~   96 (107)
T 2jvl_A           91 KLRGAN   96 (107)
T ss_dssp             BSSSSS
T ss_pred             CHhhhc
Confidence            999865

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=99.75  E-value=1.1e-17  Score=88.81  Aligned_cols=59  Identities=19%  Similarity=0.259  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQIN--QRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|..+|+||.+||+.+|  +|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus         9 ~g~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~g~~~~~~~~l~~la~~l~v~~~~l   69 (71)
T 2ewt_A            9 LGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPVQEL   69 (71)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHHTCSCCCHHHHHHHHHHHTSCGGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            389999999999999999999999  99999999999999999999999999999999863

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=99.73  E-value=1.3e-17  Score=90.74  Aligned_cols=59  Identities=20%  Similarity=0.265  Sum_probs=56.3

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .++.+|+.+|+.+||||.+||+.+|||+++|++||+| ...|+.+.+.+||++|||++++
T Consensus        10 ~~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~G~~~~p~~~~l~~ia~~l~v~~~~   69 (78)
T 3qq6_A           10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHT   69 (78)
T ss_dssp             THHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSCCCCBHHHHHHHHHHHTCCHHH
T ss_pred             CccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            3499999999999999999999999999999999999 8999999999999999999865

>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=99.73  E-value=1.2e-17  Score=91.08  Aligned_cols=58  Identities=28%  Similarity=0.233  Sum_probs=55.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus        12 ~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~v~~~~   69 (82)
T 3s8q_A           12 VSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVV   69 (82)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4899999999999999999999999999999999999999999999999999999875

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=99.73  E-value=4.1e-18  Score=91.24  Aligned_cols=59  Identities=15%  Similarity=0.211  Sum_probs=56.0

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus         9 ~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~l   67 (73)
T 3omt_A            9 IFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVREL   67 (73)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            36789999999999999999999999999999999999999999999999999999864

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=99.73  E-value=1.6e-17  Score=90.43  Aligned_cols=58  Identities=16%  Similarity=0.114  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        14 ~~~l~~~r~~~gltq~~lA~~~gvs~~~is~~e~g~~~~~~~~~~~ia~~l~v~~~~l   71 (80)
T 3kz3_A           14 KAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEF   71 (80)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHH
Confidence            7889999999999999999999999999999999999999999999999999999864

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=99.73  E-value=2.4e-18  Score=97.70  Aligned_cols=59  Identities=27%  Similarity=0.232  Sum_probs=56.5

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..|.+|+.+|+..|+||.+||+.+||++++|++||+|...|+.+.+.+||++|||++++
T Consensus        28 ~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l~v~~~~   86 (99)
T 3g5g_A           28 KVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVV   86 (99)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            34999999999999999999999999999999999999999999999999999999875

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=99.73  E-value=2.9e-17  Score=87.55  Aligned_cols=59  Identities=20%  Similarity=0.197  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++.
T Consensus        14 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~l~~~l~~~~~~l   72 (74)
T 1y7y_A           14 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPREL   72 (74)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHH
Confidence            38999999999999999999999999999999999999999999999999999999763

>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=99.72  E-value=1.8e-17  Score=90.52  Aligned_cols=58  Identities=19%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||++++
T Consensus        15 ~~~~l~~~R~~~gltq~elA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~~   72 (83)
T 3f6w_A           15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYA   72 (83)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHHH
Confidence            3899999999999999999999999999999999999999999999999999999875

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=99.71  E-value=4e-17  Score=91.94  Aligned_cols=59  Identities=22%  Similarity=0.356  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHH----HHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQV----VSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~----i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|...|+||.+||+.+|+|+++    |++||+|...|+.+.+.+||++|||++++.
T Consensus         2 ~g~~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l~v~~~~l   64 (98)
T 3lfp_A            2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYL   64 (98)
T ss_dssp             CHHHHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHTSCGGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            48899999999999999999999999999    999999999999999999999999999763

>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=99.71  E-value=2.4e-17  Score=86.55  Aligned_cols=58  Identities=21%  Similarity=0.277  Sum_probs=55.7

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++
T Consensus         6 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~   63 (68)
T 2r1j_L            6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY   63 (68)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            4899999999999999999999999999999999999999999999999999999875

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=99.71  E-value=1.8e-17  Score=89.62  Aligned_cols=58  Identities=14%  Similarity=0.260  Sum_probs=55.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|..+|+||.+||+.+|||+++|++||+|...|+.+.+.+||++|||++++
T Consensus         3 ~~~~lk~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~   60 (77)
T 2k9q_A            3 LSNELKVERIRLSLTAKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSKGVDLNA   60 (77)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTCCSCCHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHH
Confidence            3789999999999999999999999999999999999999999999999999999875

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=99.71  E-value=4.9e-17  Score=87.54  Aligned_cols=58  Identities=12%  Similarity=0.214  Sum_probs=55.6

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||++++
T Consensus         8 ~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~g~~~~~~~~~l~~ia~~l~~~~~~   66 (78)
T 3b7h_A            8 VSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVHD   66 (78)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHCTTCCCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCHHH
Confidence            48899999999999999999999999999999999998 99999999999999999875

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=99.71  E-value=4.1e-17  Score=87.67  Aligned_cols=58  Identities=22%  Similarity=0.257  Sum_probs=55.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||.+||+++++
T Consensus        11 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~la~~l~~~~~~   68 (77)
T 2b5a_A           11 FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAST   68 (77)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            3889999999999999999999999999999999999999999999999999999865

>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=99.70  E-value=2.9e-17  Score=94.57  Aligned_cols=60  Identities=13%  Similarity=0.284  Sum_probs=57.0

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ...|.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus         8 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l~v~~~~   67 (114)
T 3op9_A            8 HQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDE   67 (114)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            345999999999999999999999999999999999999999999999999999999875

>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=99.70  E-value=6.1e-17  Score=94.72  Aligned_cols=58  Identities=19%  Similarity=0.277  Sum_probs=56.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|..+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||.+|||++++
T Consensus        13 ~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~   70 (126)
T 3ivp_A           13 LGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDE   70 (126)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHHTCCSHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4999999999999999999999999999999999999999999999999999999875

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=99.70  E-value=9.1e-17  Score=89.25  Aligned_cols=59  Identities=51%  Similarity=0.858  Sum_probs=57.0

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||++++.
T Consensus        14 ~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l   72 (91)
T 1x57_A           14 VGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGK   72 (91)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSST
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            49999999999999999999999999999999999999999999999999999999884

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=99.70  E-value=4.6e-17  Score=87.18  Aligned_cols=58  Identities=21%  Similarity=0.277  Sum_probs=55.7

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus         6 ~~~~l~~~r~~~gls~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~~   63 (76)
T 1adr_A            6 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY   63 (76)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4899999999999999999999999999999999999999999999999999999865

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=99.70  E-value=7.2e-17  Score=90.28  Aligned_cols=59  Identities=14%  Similarity=0.209  Sum_probs=56.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        10 ~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~G~~~p~~~~l~~ia~~l~v~~~~l   68 (94)
T 2kpj_A           10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDL   68 (94)
T ss_dssp             HHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            38999999999999999999999999999999999999999999999999999998753

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=99.69  E-value=6.5e-17  Score=93.40  Aligned_cols=59  Identities=25%  Similarity=0.196  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        22 ~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~~~l   80 (114)
T 3vk0_A           22 LAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGVAAYQL   80 (114)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHTTTCCCCCHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHH
Confidence            39999999999999999999999999999999999999999999999999999998753

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=99.69  E-value=9.2e-17  Score=88.75  Aligned_cols=57  Identities=21%  Similarity=0.213  Sum_probs=54.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .+.+|+.+|+..||||.+||+.+|+|+++|++||+|...|+.+.+.+||++||++..
T Consensus        15 ~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~~   71 (86)
T 3eus_A           15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACEGLDV   71 (86)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHTTCGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcH
Confidence            489999999999999999999999999999999999999999999999999999653

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=99.69  E-value=1.1e-16  Score=91.75  Aligned_cols=58  Identities=17%  Similarity=0.174  Sum_probs=55.1

Q ss_pred             CCHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           20 DTPRQIQR-ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        20 ~~~~~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ..|..|+. +|+..|+||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        13 ~pG~~Lk~~lr~~~gltq~eLA~~lGis~~~is~ie~G~~~~s~~~~~kla~~lgvs~~   71 (104)
T 3trb_A           13 HPGEILAEELGFLDKMSANQLAKHLAIPTNRVTAILNGARSITADTALRLAKFFGTTPE   71 (104)
T ss_dssp             CHHHHHHHHHHHTTSCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            34999996 89999999999999999999999999999999999999999999999975

>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=99.69  E-value=2.6e-17  Score=85.96  Aligned_cols=57  Identities=23%  Similarity=0.257  Sum_probs=54.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++
T Consensus         3 ~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~   59 (66)
T 2xi8_A            3 INNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLED   59 (66)
T ss_dssp             EECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            456899999999999999999999999999999999999999999999999999865

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=99.69  E-value=5.3e-17  Score=87.04  Aligned_cols=59  Identities=20%  Similarity=0.262  Sum_probs=56.3

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++.
T Consensus        11 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~~l   69 (76)
T 3bs3_A           11 MLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQL   69 (76)
T ss_dssp             CCBCHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            57889999999999999999999999999999999999999999999999999999764

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=99.69  E-value=7e-17  Score=93.24  Aligned_cols=59  Identities=15%  Similarity=0.237  Sum_probs=56.6

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        24 ~g~~Lk~~R~~~gltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l~v~~~~l   82 (111)
T 3mlf_A           24 AMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDDI   82 (111)
T ss_dssp             SCEEHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHHTCCGGGE
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHH
Confidence            48999999999999999999999999999999999999999999999999999999863

>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=99.68  E-value=1.5e-16  Score=88.31  Aligned_cols=58  Identities=17%  Similarity=0.122  Sum_probs=54.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +..|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        19 ~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~l   76 (92)
T 1lmb_3           19 KAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEF   76 (92)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHH
Confidence            6778888999999999999999999999999999999999999999999999998763

>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=99.68  E-value=8.1e-17  Score=88.53  Aligned_cols=59  Identities=17%  Similarity=0.289  Sum_probs=56.3

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        13 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~l   71 (88)
T 2wiu_B           13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLC   71 (88)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHTTCEEEEE
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHh
Confidence            38999999999999999999999999999999999999999999999999999998764

>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=99.68  E-value=1.1e-16  Score=86.13  Aligned_cols=61  Identities=20%  Similarity=0.337  Sum_probs=56.5

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ..+.|.+|+.+|+..|+||.+||+.+|||+++|++||+|...|+...+ .++.+|+++++..
T Consensus         9 ~~~~g~~lr~~R~~~gltq~elA~~~gvs~~tis~~E~G~~~p~~~~~-~l~~~l~~~p~~l   69 (73)
T 3fmy_A            9 ETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI-KLLRVLDKHPELL   69 (73)
T ss_dssp             CCCCHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHTTSSCCCHHHH-HHHHHHHHCGGGH
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHH-HHHHHHCCCHHHH
Confidence            456799999999999999999999999999999999999999999987 9999999988754

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=99.68  E-value=1.1e-16  Score=92.47  Aligned_cols=57  Identities=23%  Similarity=0.313  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus        30 g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~~~~~~l~~la~~l~v~~~~   86 (117)
T 3f52_A           30 GAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVAD   86 (117)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            999999999999999999999999999999999999999999999999999999864

>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=99.68  E-value=2.4e-16  Score=86.44  Aligned_cols=57  Identities=21%  Similarity=0.215  Sum_probs=54.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|...|+||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||+++.
T Consensus        20 ~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~~~~~~~~l~~la~~l~~~~~~   77 (83)
T 2a6c_A           20 LIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVEI   77 (83)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCCC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCeEE
Confidence            8999999999999999999999999999999999998 59999999999999999874

>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=99.67  E-value=1.4e-16  Score=83.86  Aligned_cols=56  Identities=23%  Similarity=0.436  Sum_probs=52.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.. +.+||++|||++++
T Consensus         3 ~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~la~~l~~~~~~   58 (69)
T 1r69_A            3 SSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRF-LPELASALGVSVDW   58 (69)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCSSCTT-HHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCchH-HHHHHHHHCcCHHH
Confidence            689999999999999999999999999999999998888877 99999999999865

>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=99.66  E-value=3.7e-16  Score=88.69  Aligned_cols=60  Identities=17%  Similarity=0.192  Sum_probs=56.5

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ...|.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++.
T Consensus        17 ~~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~v~~~~   76 (104)
T 3cec_A           17 IHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKALGNGPRL   76 (104)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCHHH
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCcCCCHHHHHHHHHHHCcCHHH
Confidence            345999999999999999999999999999999999999999999999999999999863

>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=99.65  E-value=5.1e-16  Score=88.54  Aligned_cols=58  Identities=21%  Similarity=0.287  Sum_probs=55.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|...|+||.+||+.+|+|+++|++||+| ...|+.+.+.+||.+|||++++
T Consensus         2 ~~~~l~~~r~~~gltq~~lA~~~gis~~~i~~~e~g~~~~p~~~~l~~ia~~l~v~~~~   60 (111)
T 1b0n_A            2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHT   60 (111)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHHH
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            478999999999999999999999999999999999 8999999999999999999865

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=99.64  E-value=8.8e-16  Score=87.63  Aligned_cols=54  Identities=19%  Similarity=0.319  Sum_probs=50.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      |.+|+.+|+.+||||.+||+.+|||+++|++||+|+  ++++.+.+||.+||+++.
T Consensus        38 G~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~--~~~~~l~~i~~aL~~~~~   91 (101)
T 4ghj_A           38 GDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGK--VQLDIMIAILMALDLTEQ   91 (101)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC--CBHHHHHHHHHHTTCCGG
T ss_pred             HHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCC--CCHHHHHHHHHHcCCCcc
Confidence            999999999999999999999999999999999996  567889999999999753

>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=99.64  E-value=7.8e-16  Score=85.87  Aligned_cols=58  Identities=21%  Similarity=0.213  Sum_probs=55.6

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ..|.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++
T Consensus         8 ~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~~~~i~~~l~v~~~   65 (94)
T 2ict_A            8 RPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   65 (94)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             ChhHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            3599999999999999999999999999999999999999999999999999999986

>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=99.64  E-value=4.4e-16  Score=82.31  Aligned_cols=57  Identities=19%  Similarity=0.285  Sum_probs=52.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|.. .+.+||++|||++++
T Consensus         4 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~-~l~~i~~~l~~~~~~   60 (71)
T 1zug_A            4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPR-FLFEIAMALNCDPVW   60 (71)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSCS-THHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCChH-HHHHHHHHHCCCHHH
Confidence            478999999999999999999999999999999999877654 499999999999865

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=99.63  E-value=4.4e-16  Score=92.14  Aligned_cols=58  Identities=10%  Similarity=0.145  Sum_probs=53.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ------TVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~------~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+|+||.|||+.+|+|+++|++||+|...|+.      ..+.+||++||+++++
T Consensus         4 ~G~~lr~~R~~~gltq~elA~~~gis~~~is~iE~g~~~~~~~~~~~~~~l~~ia~~L~v~~~~   67 (130)
T 3fym_A            4 VGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGFIRKYASVVNIEPNQ   67 (130)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHTTCGGGSSSGGGHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCchhhhHHHHHHHHHHHhCCCHHH
Confidence            489999999999999999999999999999999999877766      6799999999999875

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=99.63  E-value=1.4e-15  Score=82.78  Aligned_cols=57  Identities=16%  Similarity=0.204  Sum_probs=50.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH----HHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAK----MEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~----la~~lgv~~~e   78 (82)
                      +.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+..    |+.+|||++++
T Consensus        12 ~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~~~~~l~~~~~v~~~~   72 (84)
T 2ef8_A           12 VQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGLPMDI   72 (84)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCBHHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHccccCCCHHH
Confidence            8999999999999999999999999999999999999999765555    55556999865

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=99.63  E-value=6.2e-16  Score=89.63  Aligned_cols=58  Identities=10%  Similarity=0.156  Sum_probs=52.6

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP------NQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p------~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+|+||.+||+.+||++++|++||+|...|      ....+.+||++|||++++
T Consensus         8 lG~~Lr~~R~~~glSq~eLA~~~gis~~~is~iE~G~~~~~p~~~~~~~~l~~iA~~Lgv~~~~   71 (112)
T 2wus_R            8 LGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFLELSPDE   71 (112)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHSSCCHHHHHHHHHTCCTTSSCHHHHHHHHHHHHHHSSCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCcchhHHHHHHHHHHHHhCcCHHH
Confidence            3899999999999999999999999999999999998754      356789999999999875

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=99.63  E-value=7.9e-16  Score=86.34  Aligned_cols=58  Identities=19%  Similarity=0.230  Sum_probs=55.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH--hCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKA--IGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~--lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++  |+|+++.
T Consensus         5 ~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~~~v~~~~   64 (99)
T 2l49_A            5 ISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTLW   64 (99)
T ss_dssp             TTHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSSSSSSSSSST
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCHHH
Confidence            489999999999999999999999999999999999999999999999999  8888765

>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=99.62  E-value=1.2e-15  Score=89.30  Aligned_cols=57  Identities=16%  Similarity=0.105  Sum_probs=54.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      +.+|+.+|+..||||.+||+.+|+|+++|++||+|.. .|+.+.+.+||.+|||+++.
T Consensus        42 g~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~G~~~~~s~~~l~~ia~~Lgv~~~~   99 (120)
T 2o38_A           42 AYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVEI   99 (120)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEEE
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCcEE
Confidence            7899999999999999999999999999999999997 99999999999999999864

>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=99.62  E-value=4e-16  Score=88.07  Aligned_cols=57  Identities=19%  Similarity=0.274  Sum_probs=53.2

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|+..|+||.+||+.+|||+++|++||+|...|+.. +.+||++||++++.
T Consensus        31 ~~~~lk~~R~~~glsq~elA~~lgvs~~~is~~E~G~~~p~~~-~~~l~~~l~~~~~~   87 (99)
T 2ppx_A           31 RMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP-ARAYLKIIAVDPEG   87 (99)
T ss_dssp             -CCHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH-HHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHH-HHHHHHHHCcCHHH
Confidence            3779999999999999999999999999999999999999988 79999999998865

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=99.61  E-value=1.1e-15  Score=87.79  Aligned_cols=59  Identities=10%  Similarity=0.054  Sum_probs=55.8

Q ss_pred             CCHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQR-ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..|.+|+. +|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++.
T Consensus        10 ~~g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~la~~l~~~~~~   69 (113)
T 2eby_A           10 TPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDF   69 (113)
T ss_dssp             CHHHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHH
T ss_pred             ChHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            35999998 999999999999999999999999999999999999999999999999863

>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=99.61  E-value=3.1e-15  Score=92.60  Aligned_cols=59  Identities=15%  Similarity=0.236  Sum_probs=56.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        12 ~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~~l   70 (192)
T 1y9q_A           12 IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAF   70 (192)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            38999999999999999999999999999999999999999999999999999999764

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=99.61  E-value=7e-16  Score=92.43  Aligned_cols=57  Identities=23%  Similarity=0.275  Sum_probs=54.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++
T Consensus        70 g~~L~~~R~~~glTq~elA~~lGis~s~is~~E~G~~~ps~~~l~~la~~lgv~~~~  126 (141)
T 3kxa_A           70 GETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLE  126 (141)
T ss_dssp             SCCHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHTCSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            567889999999999999999999999999999999999999999999999999875

>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=99.59  E-value=5e-15  Score=91.83  Aligned_cols=59  Identities=22%  Similarity=0.386  Sum_probs=56.3

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|+.+|+||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||++++.
T Consensus        11 ~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l~~~~~~l   70 (198)
T 2bnm_A           11 FAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGAL   70 (198)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHE
Confidence            38999999999999999999999999999999999999 999999999999999998764

>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=99.59  E-value=3.7e-15  Score=81.72  Aligned_cols=56  Identities=16%  Similarity=0.194  Sum_probs=52.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+..  ||.+||+.+|||+++|++||+|.. .|+.+.+.+||++|||++++
T Consensus        17 ~g~~l~~~R~~~--sq~~lA~~~gis~~~is~~E~g~~~~p~~~~l~~ia~~l~v~~~~   73 (86)
T 2ofy_A           17 LGELLRSARGDM--SMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLDD   73 (86)
T ss_dssp             HHHHHHHHHTTS--CHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHC--CHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            389999999988  999999999999999999999998 89999999999999999865

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=99.56  E-value=2e-15  Score=81.90  Aligned_cols=55  Identities=22%  Similarity=0.200  Sum_probs=50.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCccc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG--VKLRVK   79 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg--v~~~e~   79 (82)
                      .+|+.+|+..| ||.+||+.+|||+++|++||+|...| .+.+.+||++||  |++++.
T Consensus         2 ~~l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~p-~~~l~~ia~~l~~~v~~~~l   58 (79)
T 3bd1_A            2 NAIDIAINKLG-SVSALAASLGVRQSAISNWRARGRVP-AERCIDIERVTNGAVICREL   58 (79)
T ss_dssp             CHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCCC-GGGHHHHHHHTTTSSCHHHH
T ss_pred             hHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCcHHHh
Confidence            36899999999 99999999999999999999998877 999999999999  887654

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=99.56  E-value=1.2e-14  Score=86.62  Aligned_cols=58  Identities=10%  Similarity=0.178  Sum_probs=54.3

Q ss_pred             CHHHHHHHHH------hCCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARL------GKKMSQPDLANQIN-----QRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~------~~g~s~~elA~~~g-----is~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|+      ..++||.+||+.+|     +|+++|++||+|++ .|+.+.+.+||++|||+++.
T Consensus         8 ~~~RL~~L~~~~~~~~~~~~T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f~V~~~y   77 (135)
T 3r1f_A            8 FAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAY   77 (135)
T ss_dssp             HHHHHHHHHHHCCCTTSCCCCHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHHTSCTHH
T ss_pred             HHHHHHHHHHhhcccCCCCCCHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            4899999999      47899999999999     99999999999987 89999999999999999864

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=99.54  E-value=1.6e-14  Score=92.89  Aligned_cols=58  Identities=19%  Similarity=0.308  Sum_probs=55.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|+.+|+||.+||+.+ +|+++|++||+|...|+.+.+.+||+.|||++++.
T Consensus         6 ~g~~i~~~R~~~~~tq~~la~~~-~s~~~~s~~e~g~~~~~~~~l~~i~~~l~~~~~~~   63 (293)
T 3u3w_A            6 LGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHF   63 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHh-CCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHH
Confidence            48999999999999999999999 99999999999999999999999999999999753

>3qwg_A ESX-1 secretion-associated regulator ESPR; N-terminal helix-turn-helix motif, transcription factor, transcription; 1.99A {Mycobacterium tuberculosis} PDB: 3qf3_A 3qyx_A

Probab=99.54  E-value=2.5e-14  Score=84.10  Aligned_cols=58  Identities=10%  Similarity=0.178  Sum_probs=54.1

Q ss_pred             CHHHHHHHHH------hCCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARL------GKKMSQPDLANQIN-----QRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~------~~g~s~~elA~~~g-----is~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+++|..+++      ..++||.+||+.+|     +|+++|++||+|.+ .|+.+.+.+||++|||+++.
T Consensus         6 ~a~RL~~L~~~~~~~~~~~lT~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f~V~~~y   75 (123)
T 3qwg_A            6 FAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAY   75 (123)
T ss_dssp             HHHHHHHHHHHSSCTTTCSCCHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHTTSCTHH
T ss_pred             HHHHHHHHHHhhccCCCCCCCHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            4789999999      66899999999998     99999999999987 89999999999999999864

>3pxp_A Helix-turn-helix domain protein; DNA-binding, basic helix-loop-helix motif, BHLH motif, lambd repressor-like DNA-binding fold; HET: MSE MYR; 2.30A {Chloroflexus aurantiacus}

Probab=99.51  E-value=3.2e-14  Score=93.99  Aligned_cols=60  Identities=17%  Similarity=0.241  Sum_probs=57.2

Q ss_pred             CHHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLG------KKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~------~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      .|.+|+.+|+.      .|+||.|||+.+|||.++|++||+|+. .|+.+.+.+||++|+++++|++
T Consensus         7 lG~~Lr~lR~~~~~~~~~gLtqeelA~~~gvS~~~is~iE~G~~~~ps~~~l~~lA~aL~v~~~er~   73 (292)
T 3pxp_A            7 FGKLVQALRREHRDEKGRVWTQEVLAERTQLPKRTIERIENGSLAHLDADILLRLADALELTIGERR   73 (292)
T ss_dssp             HHHHHHHHHHTCBCTTSCBCCHHHHHHHHTCCHHHHHHHHHTCCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHccCccCcCCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHhcCCCHHHHH
Confidence            38999999999      999999999999999999999999996 9999999999999999998864

>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=99.48  E-value=6.1e-14  Score=82.61  Aligned_cols=60  Identities=20%  Similarity=0.325  Sum_probs=53.9

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..+.+.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+... ..|++.++++++.
T Consensus        69 ~~~~~~~l~~~R~~~glsq~~la~~~g~s~~~i~~~E~g~~~p~~~~-~~l~~~~~~~p~~  128 (133)
T 3o9x_A           69 ETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPST-IKLLRVLDKHPEL  128 (133)
T ss_dssp             TTCCHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHHTSSCCCHHH-HHHHHHHHHCGGG
T ss_pred             cCCCHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH-HHHHHHHccCHHH
Confidence            44568999999999999999999999999999999999999998876 7788888887764

>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain, transcription; 2.25A {Enterococcus faecalis} SCOP: a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A 2grl_A 2grm_A

Probab=99.47  E-value=6.7e-14  Score=92.75  Aligned_cols=57  Identities=19%  Similarity=0.167  Sum_probs=55.0

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+|+||.+||+.+ +|+++|++||+|...|+.+.+.+||+.|||++++
T Consensus         4 ig~~lk~~R~~~gltq~~la~~~-is~~~is~~E~g~~~~~~~~l~~i~~~l~v~~~~   60 (317)
T 2awi_A            4 IGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFFE   60 (317)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHh-cCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHHH
Confidence            48999999999999999999999 9999999999999999999999999999999875

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=99.45  E-value=5.9e-15  Score=96.55  Aligned_cols=59  Identities=17%  Similarity=0.196  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..+.+|+.+|+.+|+||.+||+.+|||+++|++||+|...|+.+.+.+||++|||++++
T Consensus        30 ~~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~~~l~~ia~~l~~~~~~   88 (311)
T 4ich_A           30 ELRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSPHELVRIAEHSGVTVNW   88 (311)
T ss_dssp             -----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCCChhh
Confidence            35899999999999999999999999999999999999999999999999999999865

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=99.45  E-value=3.5e-13  Score=72.87  Aligned_cols=59  Identities=14%  Similarity=0.055  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ...+..+|+.++..+|+|+.+||+.+|+|+++|++|+++   |.+.....||++|||++++.
T Consensus         7 ~~~~~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~~---~~p~~~~~IA~aLgv~~~~L   65 (74)
T 1neq_A            7 RDWHRADVIAGLKKRKLSLSALSRQFGYAPTTLANALER---HWPKGEQIIANALETKPEVI   65 (74)
T ss_dssp             SSCCHHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTTS---SCHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC---CCccHHHHHHHHHCcCHHHH
Confidence            355688999999999999999999999999999999997   33444456999999999763

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=99.42  E-value=1.3e-14  Score=87.91  Aligned_cols=58  Identities=17%  Similarity=0.269  Sum_probs=0.0

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|...|+||.+||+.+|+|+++|++||+|...|+.+.+.+||+.||+++++
T Consensus         2 ig~~lk~~R~~~gltq~elA~~lgis~~~vs~~e~G~~~~~~~~~~~la~~~~v~~~~   59 (158)
T 2p5t_A            2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVD   59 (158)
T ss_dssp             ----------------------------------------------------------
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            3678999999999999999999999999999999999999999999999999999764

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=99.40  E-value=1.8e-13  Score=86.71  Aligned_cols=59  Identities=17%  Similarity=0.112  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .+.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++.
T Consensus        18 ~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~g~~~p~~~~l~~ia~~l~v~~~~l   76 (236)
T 3bdn_A           18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEF   76 (236)
T ss_dssp             HHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTTTSCCCHHHHHHTTTTTTSCGGGT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHHh
Confidence            38899999999999999999999999999999999999999999999999999998653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.40  E-value=6.7e-14  Score=90.01  Aligned_cols=57  Identities=19%  Similarity=0.333  Sum_probs=54.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+|+||.+||+.+ +|+++|++||+|...|+.+.+.+||+.||+++++
T Consensus         6 ~g~~i~~~r~~~~~tq~~la~~~-~s~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~~   62 (293)
T 2qfc_A            6 LGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIH   62 (293)
T ss_dssp             HHHHHHHHHHHHTCCTTTTTTTT-SCHHHHHHHHTSSSCCCHHHHHHHTTTSCCCTHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHH-cCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            48999999999999999999999 9999999999999999999999999999999865

>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=99.40  E-value=2.4e-13  Score=74.17  Aligned_cols=49  Identities=18%  Similarity=0.182  Sum_probs=45.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      ...|+.++.  |++|.+||+.+|||++||+.+|+|+..|++.  .+||++||.
T Consensus        23 ~~kLK~il~--GikQ~eLAK~iGIsqsTLSaIenG~~~PsL~--~kIAk~fg~   71 (83)
T 2l1p_A           23 RNALKDLLK--DMNQSSLAKECPLSQSMISSIVNSTYYANVS--AAKCQEFGR   71 (83)
T ss_dssp             HHHHHHHHT--TSCHHHHHHHSSSCHHHHHHHHTCSSCCCCC--SHHHHHHHH
T ss_pred             HHHHHHHHH--hcCHHHHHHHcCCCHHHHHHHHcCCCCCCch--HHHHHHHHH
Confidence            678888888  9999999999999999999999999999998  899999974

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=99.28  E-value=7.4e-12  Score=77.05  Aligned_cols=54  Identities=19%  Similarity=0.097  Sum_probs=49.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +++|+.+|...  ||.+||+.+|+|+++|++||+|...| .+.+.+||++||++++.
T Consensus        11 ~~rl~~~r~~~--tq~elA~~~Gis~~~i~~~e~g~~~p-~~~l~~ia~~~~v~~~~   64 (189)
T 2fjr_A           11 LDRICEAYGFS--QKIQLANHFDIASSSLSNRYTRGAIS-YDFAAHCALETGANLQW   64 (189)
T ss_dssp             HHHHHHHHTCS--SHHHHHHHTTCCHHHHHHHHHSSSCC-HHHHHHHHHHHCCCHHH
T ss_pred             HHHHHHHHhhc--CHHHHHHHhCcCHHHHHHHHhCCCCC-HHHHHHHHHHHCCCHHH
Confidence            67888888766  99999999999999999999999989 99999999999998753

>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=99.19  E-value=8.9e-11  Score=72.26  Aligned_cols=47  Identities=13%  Similarity=0.119  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL   65 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~   65 (82)
                      .....+|+.+|+..|+||+++|+.+|||+++|++||+|.+.|+...+
T Consensus        89 ~~s~~~lk~lR~~~glTQ~elA~~LGvsr~tis~yE~G~r~iP~~~~  135 (170)
T 2auw_A           89 EVSHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIW  135 (170)
T ss_dssp             CCCHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHH
T ss_pred             CCCcHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Confidence            45588999999999999999999999999999999999987777664

>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI, protei structure initiative, midwest center for structural genomic; HET: SO4; 1.65A {Escherichia coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A 2iu7_A 2iv1_A 2iuo_A 2ivg_A

Probab=99.02  E-value=7.8e-10  Score=67.09  Aligned_cols=58  Identities=10%  Similarity=0.064  Sum_probs=54.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ...|..+|..+|+|..++|+.+|+|+..+..++.|+..|+.+.+.+|+++||++.++.
T Consensus        15 ~~~I~~AK~~KGLTwe~IAe~iG~S~v~vtaa~lGQ~~ls~e~A~kLa~~LgL~~e~~   72 (156)
T 1dw9_A           15 ADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSI   72 (156)
T ss_dssp             HHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHHH
Confidence            6889999999999999999999999999999999999999999999999999987653

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=99.01  E-value=2.4e-13  Score=79.47  Aligned_cols=49  Identities=20%  Similarity=0.245  Sum_probs=45.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC------CCCCCHHHHHHHHHHhCCCCcc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENG------KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g------~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |+ +||||.+||+.+|+|+++|++||+|      ...|+...+.+||..|++++++
T Consensus         2 R~-~glTQ~eLA~~~Gvs~~~is~~E~G~~~~~~~~~p~~~~l~~la~~l~v~~~~   56 (122)
T 1nr3_A            2 RE-RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPVRILCRR   56 (122)
T ss_dssp             CC-CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCEEEEECC
T ss_pred             cc-cCCCHHHHHHHhCCCHHHHHHHHcCCCccchhcccCHHHHHHHHHHHcccccc
Confidence            55 8999999999999999999999999      8899999999999999998864

>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=98.92  E-value=2.8e-09  Score=55.20  Aligned_cols=48  Identities=15%  Similarity=0.086  Sum_probs=37.6

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           26 QRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      +.+.+. ++||.+||+.+|||+++|++|| +  .++...+..|++++|..+.
T Consensus         4 ~~~i~~-~~tq~~lA~~lGvs~~~Vs~we-~--~~p~~~~~~i~~~~~g~v~   51 (61)
T 1rzs_A            4 KDVIDH-FGTQRAVAKALGISDAAVSQWK-E--VIPEKDAYRLEIVTAGALK   51 (61)
T ss_dssp             HHHHHH-HSSHHHHHHHHTCCHHHHHHCC-S--BCCHHHHHHHHHHTTSCSC
T ss_pred             HHHHHH-cCCHHHHHHHhCCCHHHHHHHH-h--hCCHHHHHHHHHHHCCCce
Confidence            344443 4599999999999999999999 3  3444666799999997664

>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=98.82  E-value=1.3e-08  Score=53.50  Aligned_cols=46  Identities=17%  Similarity=0.126  Sum_probs=37.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHHH---HHHHhCCCCccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA---VPNQTVLAK---MEKAIGVKLRVK   79 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~---~p~~~~~~~---la~~lgv~~~e~   79 (82)
                      +|+.|||+.+|+|++||+++++|..   .++.++..+   +++.||..++..
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~~~~~vs~et~~rI~~aa~~lgY~pn~~   52 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAV   52 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCTTTTTCTTHHHHHHHHHHHHHTCCCC--
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHhCCCccHH
Confidence            5899999999999999999999988   788776665   555799887653

>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=98.74  E-value=3.5e-08  Score=52.14  Aligned_cols=46  Identities=15%  Similarity=0.106  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .+|+.|+|+.+|||++||+++++|...++.+.   +..+++.||..++.
T Consensus         9 ~~t~~diA~~aGVS~sTVSr~ln~~~~vs~~t~~rV~~~a~~lgY~pn~   57 (67)
T 2l8n_A            9 AATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQP   57 (67)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHTTTCCCCSCHHHHHHHHHHHHHHCCCC--
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCccH
Confidence            57999999999999999999999988888877   55668889988764

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=98.68  E-value=7.6e-09  Score=64.74  Aligned_cols=56  Identities=14%  Similarity=0.185  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH----------------HcCCCCCCHHHHHHHHHHh---CCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY----------------ENGKAVPNQTVLAKMEKAI---GVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~----------------e~g~~~p~~~~~~~la~~l---gv~~~e   78 (82)
                      |.++..+ ...|+||.++|+.+|||+++|+++                ++|...|+...+.+++..|   ++++++
T Consensus        14 G~ria~~-y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~~~ls~p~~~~L~k~~~~l~~~~~~l~e   88 (192)
T 1zx4_A           14 GLRLMRM-KNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQ   88 (192)
T ss_dssp             HHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCGGGCCHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHH-HHcCCCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCcccCccchHHHHHHHHHHhhhcCCCHHH
Confidence            7888888 779999999999999999999998                6888899999999999999   655443

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=98.66  E-value=5e-08  Score=65.54  Aligned_cols=57  Identities=18%  Similarity=0.182  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      +..|+.+|...|+||.+||+..||++..|+.+|+|+. .+..+.+..|+++||++...
T Consensus       232 gv~LR~ar~ReglTQ~~LAe~TGIPq~hISeMenGKr~~IGkdeaR~LA~ALnvDYRv  289 (443)
T 3g7d_A          232 GSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRV  289 (443)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCTTSHHHHHHHHHHHHHHTCCGGG
T ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHhcCCcCCccHHHHHHHHHHhCCCchh
Confidence            8889999999999999999999999999999999998 67999999999999998643

>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, PROT structure initiative; 1.90A {Salmonella typhimurium} SCOP: a.35.1.6

Probab=98.64  E-value=2.8e-07  Score=53.34  Aligned_cols=51  Identities=14%  Similarity=0.176  Sum_probs=45.5

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQIN--QRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      ..+..|+.+|...|+|+.|.|..+|  ++..|..+||+|...++.+.+..+..
T Consensus         3 Mn~~ELkalR~ilgLt~~EaA~~i~~~vs~rtWQqWE~G~~~IP~~i~e~~~~   55 (120)
T 1s4k_A            3 MNALELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLKE   55 (120)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCCHHHHHHHHhccCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            4578899999999999999999998  89999999999999999888666553

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.61  E-value=1.7e-07  Score=59.66  Aligned_cols=48  Identities=10%  Similarity=0.064  Sum_probs=42.2

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      .+..|+.+|...|+||.+||+.+|||+++|++||++....+...+..+
T Consensus        32 ~~~~Ik~~r~~~gltQ~evA~~tGISqS~ISq~e~~g~~~t~~k~a~~   79 (221)
T 2h8r_A           32 AAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQKRAAL   79 (221)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCchhHHHHHHH
Confidence            367899999999999999999999999999999997777777766544

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=98.54  E-value=1.1e-07  Score=49.34  Aligned_cols=38  Identities=11%  Similarity=0.079  Sum_probs=34.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ   62 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~   62 (82)
                      +|+.++...| |+.++|+.+|+|+++|++|++|...|++
T Consensus         5 ~l~~~~~~~g-s~~~~A~~lgis~~~vs~~~~~~~~~~l   42 (67)
T 2pij_A            5 PLSKYLEEHG-TQSALAAALGVNQSAISQMVRAGRSIEI   42 (67)
T ss_dssp             EHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHcCCCCCCe
Confidence            5788999999 9999999999999999999999877653

>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=98.50  E-value=2.1e-07  Score=58.27  Aligned_cols=49  Identities=8%  Similarity=0.010  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAK   67 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~   67 (82)
                      ...+..|+.++...|+||.+||+.+|+|.++|++|++|...++......
T Consensus        29 ~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kraa   77 (194)
T 1ic8_A           29 WRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAA   77 (194)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCcccccccccc
Confidence            3347899999999999999999999999999999999877777665433

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=98.30  E-value=1.6e-06  Score=46.24  Aligned_cols=49  Identities=12%  Similarity=0.022  Sum_probs=37.9

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      .+.+..| +|.+||+.||||+++|++|++|. .++...+..|..+-+-.+.
T Consensus         5 ~ai~~~G-~~~~lA~~lGVs~~aVs~W~~g~-~iP~~~~~~Ie~~T~G~vk   53 (71)
T 2hin_A            5 ELVRHFG-DVEKAAVGVGVTPGAVYQWLQAG-EIPPLRQSDIEVRTAYKLK   53 (71)
T ss_dssp             HHHHHHS-SHHHHHHHHTSCHHHHHHHHHHT-SCCHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHC-CHHHHHHHHCCCHHHHHHHHhCC-CCCHHHHHHHHHHhCCcch
Confidence            3333344 69999999999999999999884 4567778888888876553

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=98.21  E-value=1.2e-06  Score=48.92  Aligned_cols=54  Identities=9%  Similarity=0.076  Sum_probs=45.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~   76 (82)
                      ..|..+....++|..++|+.+|+|.+||+++.++. ..++.++..++.++||..+
T Consensus        10 ~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~~~~~Vs~~tr~rV~~algY~~   64 (93)
T 2l0k_A           10 IKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTERLPEINPDLANEVKEILDYHK   64 (93)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTTHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCH
Confidence            34555556667999999999999999999999996 7789999999988877643

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=98.08  E-value=6e-06  Score=43.25  Aligned_cols=36  Identities=11%  Similarity=0.055  Sum_probs=29.8

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      .|+.++...  ||.++|+.+|+|+++||+|+++...+.
T Consensus         6 ~Lk~l~~~~--sq~~~A~~Lgvsq~aVS~~~~~~r~i~   41 (65)
T 2cw1_A            6 DLKKFVEDK--NQEYAARALGLSQKLIEEVLKRGLPVY   41 (65)
T ss_dssp             CHHHHHTTS--CHHHHHHHSSSCHHHHHHHHHTTCCCB
T ss_pred             HHHHHHHHc--CHHHHHHHhCCCHHHHHHHHHhcCCce
Confidence            377777765  999999999999999999998765443

>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=97.96  E-value=1.1e-05  Score=44.19  Aligned_cols=43  Identities=5%  Similarity=0.033  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .-++|..+|+.+|++.++||+|.+|.    ++.+..|..+||..+..
T Consensus        23 a~~gQ~~vAe~~GvdeStISR~k~~~----~~~~~~lLa~Lglkvv~   65 (83)
T 1zs4_A           23 AMLGTEKTAEAVGVDKSQISRWKRDW----IPKFSMLLAVLEWGVVD   65 (83)
T ss_dssp             HHHCHHHHHHHHTSCHHHHHHHHHHT----HHHHHHHHHHHTTCCCH
T ss_pred             HHHhhHHHHHHhCCCHHHHhhhhhhH----HHHHHHHHHHhccCCCc
Confidence            45789999999999999999999974    56777778888887743

>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=97.96  E-value=8.7e-06  Score=50.34  Aligned_cols=34  Identities=18%  Similarity=0.230  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhCCC--CHHHHHHHhCCC-HHHHHHHHc
Q 038591           22 PRQIQRARLGKKM--SQPDLANQINQR-PQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~--s~~elA~~~gis-~~~i~~~e~   55 (82)
                      .++|+.+|+..|+  ||.+||+.+|++ +++|++|++
T Consensus        12 ~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~   48 (202)
T 1jhf_A           12 FDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   48 (202)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHH
Confidence            7899999999999  999999999999 999999987

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=97.94  E-value=6.2e-07  Score=50.53  Aligned_cols=48  Identities=13%  Similarity=0.121  Sum_probs=34.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..-.+++|..||+.+||+.++||+|++|. .+....+..+. .|+|+++|
T Consensus        19 ~~la~~gq~~vA~~iGV~~StISR~k~~~-~~~~~~lLa~l-~l~v~~~e   66 (97)
T 1xwr_A           19 NKIAMLGTEKTAEAVGVDKSQISRWKRDW-IPKFSMLLAVL-EWGVVDDD   66 (97)
T ss_dssp             HHHHHHCHHHHHHHHTCCTTTHHHHHHHH-HHHHHHHHHHH-HHCCCHHH
T ss_pred             HHHHHHhHHHHHHHhCCCHHHHHHHHhhh-HHHHHHHHHHH-hcCCChHH
Confidence            34467899999999999999999999974 22333333333 67777654

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=97.66  E-value=4.5e-05  Score=46.18  Aligned_cols=38  Identities=13%  Similarity=0.242  Sum_probs=32.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHHHh
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQ-TVLAKMEKAI   72 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~-~~~~~la~~l   72 (82)
                      |+|+.++|+.+|||++|+++|.+.  .|.. +.+..++..|
T Consensus        48 ~lTv~eIA~~LGIS~~TLyrW~k~--~p~~~~~l~~vad~~   86 (155)
T 2ao9_A           48 KRTQDEMANELGINRTTLWEWRTK--NQDFIAFKSEVADSF   86 (155)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHH--CHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHc--CcchHHHHHHHHHHH
Confidence            799999999999999999999985  5664 6777777765

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=97.57  E-value=0.0002  Score=35.34  Aligned_cols=31  Identities=13%  Similarity=0.141  Sum_probs=25.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+..+ ...|+|+.++|+.+|+|++||++|.+
T Consensus        23 ~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           23 VAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34444 46899999999999999999999975

>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=97.55  E-value=0.00028  Score=45.80  Aligned_cols=46  Identities=15%  Similarity=0.193  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      ..|.+|+|+.+|||.+|||+..||...++.++   +...++.||..++.
T Consensus         2 ~~ti~dvA~~agVS~~TVSrvln~~~~vs~~tr~rV~~aa~~lgY~pn~   50 (332)
T 2hsg_A            2 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNA   50 (332)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCSCH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            36899999999999999999999987777666   55567788887653

>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=97.52  E-value=0.00028  Score=45.97  Aligned_cols=45  Identities=16%  Similarity=0.080  Sum_probs=37.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .|.+|+|+.+|||.+|||+..||...++.++   +...++.||..++.
T Consensus         1 ~ti~diA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~   48 (340)
T 1qpz_A            1 ATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA   48 (340)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCCCH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCcCCCCHHHHHHHHHHHHHhCCCCCH
Confidence            4789999999999999999999987787765   55567778887653

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=97.48  E-value=0.00029  Score=45.97  Aligned_cols=48  Identities=10%  Similarity=0.112  Sum_probs=38.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .+..|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++.
T Consensus         8 ~~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~pn~   58 (344)
T 3kjx_A            8 KRPLTLRDVSEASGVSEMTVSRVLRNRGDVSDATRARVLAAAKELGYVPNK   58 (344)
T ss_dssp             --CCCHHHHHHHHCCCSHHHHHHHTTCSCCCHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence            3468999999999999999999999988777666   55567778887754

>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=97.36  E-value=0.00035  Score=33.03  Aligned_cols=26  Identities=12%  Similarity=0.222  Sum_probs=23.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..|+|..++|+.+|+|++||.+|...
T Consensus        19 ~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C           19 LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            57999999999999999999999864

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=97.32  E-value=0.00043  Score=39.07  Aligned_cols=41  Identities=17%  Similarity=0.191  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      .+||.|+|+.+|+|.+||+++-+.-...+...-..|...++
T Consensus        58 e~TQREIA~~lGiS~stISRi~r~L~~l~~~~k~~l~~~l~   98 (101)
T 1jhg_A           58 EMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL   98 (101)
T ss_dssp             CSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHCCChhhhhHHHHHHHHccHHHHHHHHHHhc
Confidence            39999999999999999999965444455566566666554

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=97.26  E-value=0.00033  Score=46.10  Aligned_cols=47  Identities=11%  Similarity=0.075  Sum_probs=36.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCC-Cc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVK-LR   77 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~-~~   77 (82)
                      ....|.+|+|+.+|||.+|||+..||...++.++   +...++.||.. ++
T Consensus         7 ~~~~Ti~diA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~~lgY~~pn   57 (366)
T 3h5t_A            7 QQYGTLASIAAKLGISRTTVSNAYNRPEQLSAELRQRILDTAEDMGYLGPD   57 (366)
T ss_dssp             CCTTHHHHHHHHHTSCHHHHHHHHHCGGGSCHHHHHHHHHHHHHTTC----
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCC
Confidence            3567899999999999999999999977676655   66677788876 54

>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=97.25  E-value=0.00053  Score=32.82  Aligned_cols=32  Identities=22%  Similarity=0.140  Sum_probs=26.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+..+. ..|+|..++|+.+|||++||++|.+.
T Consensus        13 ~i~~l~-~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           13 QISRLL-EKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             HHHHHH-HTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            343443 46899999999999999999999865

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=97.03  E-value=0.00062  Score=38.41  Aligned_cols=27  Identities=19%  Similarity=0.116  Sum_probs=23.9

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      --..|+||.++|+.+|+|+++|+++..
T Consensus        30 yYv~g~tQ~eIA~~lGiSR~~VsrlL~   56 (101)
T 2w7n_A           30 VLVDGKPQATFATSLGLTRGAVSQAVH   56 (101)
T ss_dssp             HHTTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345799999999999999999999864

>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=97.02  E-value=0.0007  Score=35.28  Aligned_cols=32  Identities=9%  Similarity=0.145  Sum_probs=25.5

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      |+.+....  |+.++|+.||||+++||+|.++.+
T Consensus         7 L~~~~~~~--s~t~aA~~L~vtQ~AVS~~ir~~r   38 (66)
T 2ovg_A            7 LKDYAMRF--GQTKTAKDLGVYPSSINQAIHAGR   38 (66)
T ss_dssp             HHHHHHHH--CHHHHHHHHTSCHHHHHHHHHHTC
T ss_pred             HHHHHHHC--CHHHHHHHhCCCHHHHHHHHHhCC
Confidence            55555544  899999999999999999986543

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=96.97  E-value=0.00012  Score=47.66  Aligned_cols=46  Identities=15%  Similarity=0.109  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      ...|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++
T Consensus         4 ~~~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~pn   52 (332)
T 2o20_A            4 STTTIYDVARVAGVSMATVSRVVNGNANVKEKTRQKVLEAIAELDYRPN   52 (332)
T ss_dssp             -------------------------------------------------
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            457999999999999999999999976565554   5556677887664

>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=96.87  E-value=0.00069  Score=35.10  Aligned_cols=23  Identities=9%  Similarity=0.303  Sum_probs=21.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+|||++||.+|...
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            67899999999999999999864

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=96.77  E-value=0.00021  Score=46.48  Aligned_cols=45  Identities=13%  Similarity=0.115  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCCc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQT---VLAKMEKAIGVKLR   77 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~---~~~~la~~lgv~~~   77 (82)
                      -.|.+|+|+.+|||.+|||+..||...++.+   .+...++.+|..++
T Consensus         3 ~~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~pn   50 (338)
T 3dbi_A            3 LTTMLEVAKRAGVSKATVSRVLSGNGYVSQETKDRVFQAVEESGYRPN   50 (338)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            3588999999999999999999997655544   46667777777664

>2csf_A DNA-binding protein SATB2; CUT domain, special AT-rich sequence-binding protein 2, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=96.76  E-value=0.0046  Score=34.60  Aligned_cols=59  Identities=19%  Similarity=0.134  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQI-NQRPQVVSEYENGKAVPN------QTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e~g~~~p~------~~~~~~la~~lgv~~~e~~   80 (82)
                      ...|....+..+++|.-||+.+ +-|+.+++.+.+-+..|.      .+.+..+-+.|+.+..+|+
T Consensus        23 ~~~I~~ELK~~~IsQa~FAk~vlnRsQGtLSelLR~~enPkP~~~~lW~~Lk~m~nWL~Lpe~eR~   88 (101)
T 2csf_A           23 YDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQHERD   88 (101)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHhchhHHHHHHhcccCCCcchhhHHHHHHHHHHHHcCCHHHHH
Confidence            7888888999999999999976 899999999998444443      4777888899998887765

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=96.73  E-value=0.00024  Score=46.32  Aligned_cols=46  Identities=13%  Similarity=0.073  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      +..|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++
T Consensus         3 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~pn   51 (339)
T 3h5o_A            3 LGVTMHDVAKAAGVSAITVSRVLNQPQQVSEQLREKVMQAVDALAYVPS   51 (339)
T ss_dssp             -------------------------------------------------
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            357899999999999999999999976555444   5566667777654

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=96.59  E-value=0.0096  Score=30.98  Aligned_cols=46  Identities=15%  Similarity=0.154  Sum_probs=37.3

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv~~   76 (82)
                      ..|+|..++|+.+|+|..+|..+...    -...+...+..++..+|++.
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~~~l~~~~~~~g~~~   78 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLVRMALAGGFGP   78 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTCCC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence            68999999999999999999987643    34567777888888888764

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=96.57  E-value=0.00035  Score=45.83  Aligned_cols=47  Identities=13%  Similarity=0.082  Sum_probs=0.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      .+-.|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++
T Consensus        10 ~~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn   59 (355)
T 3e3m_A           10 HRPVTMRDVAKAAGVSRMTVSRALKKDSPISSETRERILKVVKDMNYVPD   59 (355)
T ss_dssp             --------------------------------------------------
T ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            3457899999999999999999999876655444   6666777777665

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=96.57  E-value=0.00035  Score=45.56  Aligned_cols=47  Identities=15%  Similarity=0.064  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      ...|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++.
T Consensus         5 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~   54 (333)
T 3jvd_A            5 AKSSLKEVAELAGVGYATASRALSGKGYVSPQTREKVQAAAKELNYVPNQ   54 (333)
T ss_dssp             --------------------------------------------------
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            457899999999999999999999876655544   56667777776653

>3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A

Probab=96.52  E-value=0.0049  Score=43.10  Aligned_cols=52  Identities=6%  Similarity=0.031  Sum_probs=34.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHh------CCCHHHHHHHHcCCCCC---CHHHHHHHHHHhCCCC
Q 038591           23 RQIQRARLGKKMSQPDLANQI------NQRPQVVSEYENGKAVP---NQTVLAKMEKAIGVKL   76 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~------gis~~~i~~~e~g~~~p---~~~~~~~la~~lgv~~   76 (82)
                      ..|++++.  -+||++||+.|      ++|..+|.+||+|...|   +...+..|-..+-.++
T Consensus        21 ~~~~~~~~--~~~~~~~a~~l~~~~~~~~~~~~~~rw~~~~~~~~~~~~~~~~~l~~~~~~~p   81 (482)
T 3me5_A           21 AMLEKLLQ--IYDVKMLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPKPP   81 (482)
T ss_dssp             HHHHHHHT--TSCHHHHHHHHHHTCSSCCCHHHHHHHHC-------CCTHHHHHHHTTSCCCC
T ss_pred             HHHHHHHH--HcCHHHHHHHHHhhccCCCCHHHHHHHHcCCCCCccccHHHHHHHHhhCCCCC
Confidence            34455444  68999999999      89999999999996655   4445566655555543

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=96.49  E-value=0.00043  Score=44.91  Aligned_cols=44  Identities=11%  Similarity=0.109  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      .|.+|+|+.+|||.+|||+..||...++.++   +...++.||..++
T Consensus         3 ~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~~~~lgY~pn   49 (330)
T 3ctp_A            3 ANIREIAKRAGISIATVSRHLNNTGYVSEDAREKIQKVVDELNYTPN   49 (330)
T ss_dssp             -----------------------------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            5889999999999999999999976555544   5556677777664

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=96.48  E-value=0.0082  Score=30.53  Aligned_cols=34  Identities=9%  Similarity=-0.105  Sum_probs=29.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|++++..
T Consensus        21 ~~~i~~aL~~~~gn~~~aA~~LGisr~tL~rklk   54 (63)
T 3e7l_A           21 KIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIK   54 (63)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            5667788888999999999999999999998864

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=96.48  E-value=0.0029  Score=34.58  Aligned_cols=23  Identities=13%  Similarity=0.147  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+|..++|..+|||++||++|..
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~   45 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWII   45 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CChHHHHHHHHCcCHHHHHHHHH
Confidence            89999999999999999999974

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=96.47  E-value=0.00045  Score=45.28  Aligned_cols=45  Identities=13%  Similarity=0.014  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCCc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQT---VLAKMEKAIGVKLR   77 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~---~~~~la~~lgv~~~   77 (82)
                      ..|.+|+|+.+|||.+|||+..||...++.+   .+...++.+|..++
T Consensus         3 ~~ti~diA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn   50 (349)
T 1jye_A            3 PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN   50 (349)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            3689999999999999999999997655544   45666777777664

>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=96.44  E-value=0.0048  Score=32.84  Aligned_cols=32  Identities=9%  Similarity=0.080  Sum_probs=26.6

Q ss_pred             HHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGK---KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~---g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..++..-   ++|..+||+.+|++.++|.+..
T Consensus        18 ~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L   52 (77)
T 1qgp_A           18 RILKFLEELGEGKATTAHDLSGKLGTPKKEINRVL   52 (77)
T ss_dssp             HHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            4456667776   7999999999999999998874

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=96.40  E-value=0.0053  Score=33.10  Aligned_cols=24  Identities=13%  Similarity=0.165  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|.|..++|+.+||+++||++|..
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            589999999999999999999974

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.36  E-value=0.0085  Score=31.70  Aligned_cols=32  Identities=6%  Similarity=-0.037  Sum_probs=26.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+.....+|..|+|+.+|+|++++++..+
T Consensus         5 Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~   36 (81)
T 2htj_A            5 ILEFLNRHNGGKTAEIAEALAVTDYQARYYLL   36 (81)
T ss_dssp             HHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34555555679999999999999999998754

>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=96.27  E-value=0.01  Score=31.94  Aligned_cols=32  Identities=9%  Similarity=0.080  Sum_probs=26.4

Q ss_pred             HHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGK---KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~---g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..++...   .+|..+||+.+|+|+.+|.+..
T Consensus        14 ~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L   48 (81)
T 1qbj_A           14 RILKFLEELGEGKATTAHDLSGKLGTPKKEINRVL   48 (81)
T ss_dssp             HHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            4556667666   7999999999999999988764

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=96.21  E-value=0.0089  Score=29.85  Aligned_cols=25  Identities=12%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             hCCCC----HHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMS----QPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s----~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|.|    ..++|..+||++++|.+|..
T Consensus        19 ~~g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A           19 RNDNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             HHCTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HcCCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            35778    99999999999999999975

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=96.14  E-value=0.00087  Score=43.94  Aligned_cols=45  Identities=11%  Similarity=0.160  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      ..|.+|+|+.+|||.+|||+..||...++.++   +...++.+|..++
T Consensus         8 ~~ti~dvA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~aa~~lgY~pn   55 (348)
T 3bil_A            8 RPTLKDVARQAGVSIATASRALADNPAVAASTRERIQQLASDLGYRAN   55 (348)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            36899999999999999999999976555544   5566677777665

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=96.11  E-value=0.0021  Score=33.15  Aligned_cols=29  Identities=3%  Similarity=0.015  Sum_probs=24.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      =++..|+|+.+|+|++||++|.+....|.
T Consensus        10 ~l~~~eva~~lgvsrstiy~~~~~g~fP~   38 (66)
T 1z4h_A           10 LVDLKFIMADTGFGKTFIYDRIKSGDLPK   38 (66)
T ss_dssp             EECHHHHHHHHSSCHHHHHHHHHHHHCCC
T ss_pred             ccCHHHHHHHHCcCHHHHHHHHHCCCCCC
Confidence            36889999999999999999997544443

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=96.10  E-value=0.0081  Score=30.43  Aligned_cols=33  Identities=9%  Similarity=0.040  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.... .+..+.|+.+|||++|+++...
T Consensus        23 r~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklk   55 (61)
T 1g2h_A           23 AQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             HHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHH
Confidence            56777777777 7999999999999999998875

>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=96.09  E-value=0.012  Score=33.51  Aligned_cols=35  Identities=23%  Similarity=0.332  Sum_probs=25.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.+..+.+.-..++.++|+.+||+++||++|.++.
T Consensus        15 ~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~   49 (131)
T 1hlv_A           15 RIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNK   49 (131)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             HHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhch
Confidence            34444444334455699999999999999998873

>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=96.08  E-value=0.0072  Score=30.88  Aligned_cols=24  Identities=8%  Similarity=0.221  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+|+|+.+|+|.++|..+..
T Consensus        24 ~g~s~~eIA~~lgis~~tV~~~~~   47 (68)
T 2p7v_B           24 TDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            599999999999999999999864

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=96.05  E-value=0.023  Score=34.07  Aligned_cols=45  Identities=13%  Similarity=0.245  Sum_probs=37.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQ------RPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gi------s~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      +..++..|...|+||.+++..+|.      |.++|+++|.-  ..+...+.++
T Consensus        13 ~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l--~lS~knm~kl   63 (160)
T 1e3o_C           13 AKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMSKL   63 (160)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHT--CSCHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHhhccccCCCcCcccccccccc--CCChHHHHhc
Confidence            788899999999999999999998      99999999974  4455554443

>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=96.04  E-value=0.014  Score=32.48  Aligned_cols=25  Identities=16%  Similarity=0.126  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|..++|+.+|+|++||++|..
T Consensus        31 ~~g~s~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           31 ADGIRPCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4799999999999999999999964

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=96.00  E-value=0.0048  Score=32.86  Aligned_cols=23  Identities=13%  Similarity=0.232  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -++..|+|+.+|||+.||..||.
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~   27 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWER   27 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            47889999999999999999987

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=95.99  E-value=0.014  Score=33.23  Aligned_cols=25  Identities=12%  Similarity=0.230  Sum_probs=23.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|..++|+.+|+|++||++|.+
T Consensus        20 ~~G~s~~~ia~~lgis~~Tv~r~~~   44 (141)
T 1u78_A           20 LLNVSLHEMSRKISRSRHCIRVYLK   44 (141)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            5799999999999999999999974

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=95.97  E-value=0.012  Score=30.35  Aligned_cols=33  Identities=6%  Similarity=-0.009  Sum_probs=26.0

Q ss_pred             HHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+... ..+|..+||+.+|+|+++|.+..+
T Consensus        14 ~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~   47 (67)
T 2heo_A           14 KILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLY   47 (67)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            345555554 469999999999999999998754

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=95.91  E-value=0.022  Score=28.77  Aligned_cols=28  Identities=11%  Similarity=-0.123  Sum_probs=24.4

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..++|+.+|+|+++|.++..
T Consensus        26 l~~~~g~s~~eIA~~lgis~~tv~~~~~   53 (70)
T 2o8x_A           26 LTQLLGLSYADAAAVCGCPVGTIRSRVA   53 (70)
T ss_dssp             HHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3446899999999999999999998765

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=95.88  E-value=0.0067  Score=30.11  Aligned_cols=44  Identities=9%  Similarity=0.132  Sum_probs=31.0

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      -..|+|.+|+|+.+|+|++||..+...    -...+...+..++...|
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~l~~~~~~~g   57 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTELLNCARRMR   57 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHCSC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            467999999999999999999987653    12334445555554443

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=95.86  E-value=0.03  Score=33.85  Aligned_cols=46  Identities=13%  Similarity=0.259  Sum_probs=37.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQ------RPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gi------s~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      +..++..|...|+||.+++..+|.      |.++|+++|+-  ..+...+.++-
T Consensus        19 a~~fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l--~ls~kn~~klk   70 (164)
T 2xsd_C           19 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEAL--QLSFKNMCKLK   70 (164)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTT--CSBHHHHHHHH
T ss_pred             HHHHHHHHhhcCCcccccccccccccCCCcCcchhhhhhcc--CCCHHHHHHcc
Confidence            778888899999999999999986      99999999974  44555554443

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=95.86  E-value=0.022  Score=33.78  Aligned_cols=46  Identities=11%  Similarity=0.199  Sum_probs=36.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQ------RPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gi------s~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      +...+.-|...|+||.+++..+|.      |.+||+++|+-  ..+...+.+|-
T Consensus         9 a~~~k~~ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l--~ls~knm~kLk   60 (146)
T 1au7_A            9 ANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENL--QLSFKNACKLK   60 (146)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTT--CSBHHHHHHHH
T ss_pred             HHHHHHHHHhccCcHHhhhhhcchhccCCCCcchHHHHhcc--CCChHHHHhcc
Confidence            566788888999999999999986      99999999974  45555555543

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=95.86  E-value=0.019  Score=35.21  Aligned_cols=33  Identities=21%  Similarity=0.312  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..++.+.. .|+|+.++|..+|+|+++|+++..
T Consensus        42 A~a~~~L~~-~G~t~eeiA~~lG~s~s~V~~~Lr   74 (178)
T 1r71_A           42 ADFIGRELA-KGKKKGDIAKEIGKSPAFITQHVT   74 (178)
T ss_dssp             HHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            455555555 499999999999999999999975

>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=95.85  E-value=0.031  Score=29.62  Aligned_cols=43  Identities=7%  Similarity=0.009  Sum_probs=31.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||..+...    -...+...+..++...|
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l~~~a~~~g   80 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER   80 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence            68999999999999999999887642    22334445555554444

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=95.83  E-value=0.021  Score=30.76  Aligned_cols=29  Identities=10%  Similarity=0.080  Sum_probs=25.3

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++-..|+|..|+|+.+|+|..||..+..
T Consensus        47 ~l~~~~g~s~~eIA~~lgis~~tV~~~l~   75 (92)
T 3hug_A           47 QRSYYRGWSTAQIATDLGIAEGTVKSRLH   75 (92)
T ss_dssp             HHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34567899999999999999999998875

>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=95.81  E-value=0.013  Score=31.93  Aligned_cols=34  Identities=6%  Similarity=-0.026  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++...
T Consensus        53 ~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rklk   86 (91)
T 1ntc_A           53 RTLLTTALRHTQGHKQEAARLLGWGAATLTAKLK   86 (91)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            5667777888899999999999999999988754

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=95.81  E-value=0.0084  Score=33.64  Aligned_cols=23  Identities=13%  Similarity=0.208  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|..|+|+.+|||+.||..||.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~   23 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDD   23 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999985

>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=95.80  E-value=0.019  Score=33.36  Aligned_cols=25  Identities=16%  Similarity=0.158  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|..++|+.+|+|++||++|.+
T Consensus        46 ~~G~s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           46 HQGVRPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4799999999999999999999964

>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=95.78  E-value=0.012  Score=32.32  Aligned_cols=34  Identities=12%  Similarity=-0.040  Sum_probs=28.5

Q ss_pred             HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...++.+..  ..|++|++||..++++..+|+++..
T Consensus        23 ~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk   58 (91)
T 2dk5_A           23 KLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILK   58 (91)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            456677777  5599999999999999999998764

>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=95.78  E-value=0.026  Score=29.07  Aligned_cols=24  Identities=8%  Similarity=0.207  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|..|+|+.+|+|.++|..+..
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~   52 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIEN   52 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            699999999999999999999875

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=95.71  E-value=0.022  Score=30.43  Aligned_cols=32  Identities=9%  Similarity=0.180  Sum_probs=26.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+..+.+...++..|||+.+++|+.||.+..
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL   37 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLNTPQPMINAML   37 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence            34556667778999999999999999998754

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=95.71  E-value=0.017  Score=37.82  Aligned_cols=33  Identities=15%  Similarity=0.226  Sum_probs=28.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++..+....++||.|||+.+|+|+.||++..+
T Consensus        11 ~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~   43 (315)
T 2w48_A           11 VKIAQLYYEQDMTQAQIARELGIYRTTISRLLK   43 (315)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            456667788899999999999999999999854

>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=95.67  E-value=0.038  Score=30.01  Aligned_cols=24  Identities=8%  Similarity=0.198  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|.+|+|+.+|+|..||..+..
T Consensus        43 ~G~s~~eIA~~L~iS~~TV~~~~~   66 (90)
T 3ulq_B           43 KGFTNQEIADALHLSKRSIEYSLT   66 (90)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            899999999999999999988765

>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, Pro structure initiative; 1.70A {Shewanella oneidensis} SCOP: a.35.1.6

Probab=95.66  E-value=0.15  Score=29.93  Aligned_cols=45  Identities=13%  Similarity=0.136  Sum_probs=39.6

Q ss_pred             CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 038591           19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQT   63 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~   63 (82)
                      .+++-.++.+|...|+|..++|+..+.|..-|-.||.|....+.-
T Consensus         6 glnaie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~l   50 (166)
T 2ox6_A            6 GLNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPEL   50 (166)
T ss_dssp             CCCHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH
T ss_pred             ccchHhHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCcch
Confidence            456788999999999999999999999999999999997765543

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=95.65  E-value=0.022  Score=36.07  Aligned_cols=34  Identities=15%  Similarity=0.138  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +..++.+. ..|+|+.++|+.+|+|+++|+++..=
T Consensus       124 a~~~~~l~-~~g~t~~~iA~~lG~s~~~V~~~l~l  157 (230)
T 1vz0_A          124 ARGYQALL-EMGLTQEEVARRVGKARSTVANALRL  157 (230)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             HHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45556666 78999999999999999999998753

>1x2l_A CUT-like 2, homeobox protein CUX-2; CUT domain, human homeobox protein CUX-2, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=95.64  E-value=0.032  Score=31.37  Aligned_cols=53  Identities=15%  Similarity=0.129  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENGKAV------PNQTVLAKMEKAIGV   74 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g~~~------p~~~~~~~la~~lgv   74 (82)
                      ...|++.....+++|..||+. +|.++.+++.+.+.-..      ..-+...++-..|..
T Consensus        23 ~~~ike~L~~~~isQ~~FA~~VLgrsQgtlS~lL~~PkpW~~L~~~Gre~yiRM~nWL~~   82 (101)
T 1x2l_A           23 AFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLSD   82 (101)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCCCCGGGCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHccccchHHHHhcCCCCHHHHhHhhhHHHHHHHHHccC
Confidence            788899999999999999998 89999999999986221      124456666666664

>1wh6_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=95.59  E-value=0.076  Score=29.80  Aligned_cols=59  Identities=12%  Similarity=0.112  Sum_probs=47.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCC---CCC---HHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKA---VPN---QTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~---~p~---~~~~~~la~~lgv~~~e~~   80 (82)
                      ...|+..+...+++|..||+ -+|.++.+++.+.+.-.   ..+   -+...++-..|..+.+++.
T Consensus        23 ~~~ike~L~~~~isQ~~FA~~ILgrsqgtlSdlL~~PKpW~~L~~~Gre~fiRM~nWL~l~e~qr~   88 (101)
T 1wh6_A           23 TRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQLGQAV   88 (101)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTTCSCC
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHccCcCcHHHHhcCCCCHHHHhHHhHHHHHHHHHHhCCcHHHHH
Confidence            78899999999999999999 67999999999998622   222   5677888888887777653

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=95.53  E-value=0.016  Score=29.56  Aligned_cols=43  Identities=9%  Similarity=0.078  Sum_probs=30.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|..++|+.+|+|+++|+.+...    -...+...+...+...|
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~~~~~~~~~g   70 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMG   70 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhC
Confidence            67999999999999999999987653    12334444444444443

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=95.49  E-value=0.031  Score=32.31  Aligned_cols=26  Identities=4%  Similarity=0.118  Sum_probs=23.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..|+|+.++|+.+|+|..||+++-+.
T Consensus        73 ~~G~syreIA~~~g~S~aTIsRv~r~   98 (119)
T 3kor_A           73 KQGYTYATIEQESGASTATISRVKRS   98 (119)
T ss_dssp             HHTCCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            46899999999999999999988654

>2o4a_A DNA-binding protein SATB1; protein-DNA complex, transcription, transcription/DNA complex; HET: DNA; 1.75A {Homo sapiens} SCOP: a.35.1.7 PDB: 2o49_A*

Probab=95.46  E-value=0.019  Score=31.84  Aligned_cols=60  Identities=15%  Similarity=0.086  Sum_probs=48.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKAVP------NQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~~p------~~~~~~~la~~lgv~~~e~~   80 (82)
                      ....|+......++||.-||+ -+|.++.+++.+.+.-..|      ..+.+.++-..|+.+-++++
T Consensus        12 I~~~ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lL~~Pkdpw~~l~~Gre~f~rM~nWL~l~e~eR~   78 (93)
T 2o4a_A           12 IYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPEAERD   78 (93)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHhhhHHHHHHcCCCCcHHHHHHHHHHHHHHHHHhCCCHHHHH
Confidence            478899999999999999999 5699999999999754312      24558888889998877764

>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=95.44  E-value=0.038  Score=30.70  Aligned_cols=34  Identities=6%  Similarity=-0.141  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++...|+.+|||++|+++...
T Consensus        60 r~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkLk   93 (98)
T 1eto_A           60 QPLLDMVMQYTLGNQTRAALMMGINRGTLRKKLK   93 (98)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4566777888899999999999999999998764

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=95.39  E-value=0.041  Score=29.42  Aligned_cols=24  Identities=13%  Similarity=0.166  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|+|..++|+.+|+|..+|..+..
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            689999999999999999999875

>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=95.37  E-value=0.037  Score=29.82  Aligned_cols=34  Identities=12%  Similarity=0.091  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|+++++|++..+
T Consensus        23 ~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~   56 (109)
T 1sfx_A           23 VRIYSLLLERGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456666667889999999999999999998754

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=95.37  E-value=0.02  Score=32.03  Aligned_cols=22  Identities=14%  Similarity=0.216  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|..|+|+.+|||+.||..||.
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~   24 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDN   24 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999986

>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=95.33  E-value=0.022  Score=30.88  Aligned_cols=32  Identities=13%  Similarity=0.125  Sum_probs=25.5

Q ss_pred             HHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+.. ..++|+.+||+.+|+|+++++++.+
T Consensus        26 ~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~   58 (109)
T 2d1h_A           26 VLLKMVEIEKPITSEELADIFKLSKTTVENSLK   58 (109)
T ss_dssp             HHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444444 6789999999999999999998743

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=95.30  E-value=0.019  Score=33.85  Aligned_cols=25  Identities=16%  Similarity=0.158  Sum_probs=23.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|..++|+.+|+|++||++|.+
T Consensus        39 ~~G~s~~~IA~~lgis~~TV~rwl~   63 (159)
T 2k27_A           39 HQGVRPCDISRQLRVSHGCVSKILG   63 (159)
T ss_dssp             HHTCCHHHHHHHHTCCSHHHHHHHC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4699999999999999999999975

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=95.30  E-value=0.004  Score=34.59  Aligned_cols=22  Identities=14%  Similarity=0.235  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..++|..+||+++||++|..
T Consensus        31 ~s~~~va~~~gIs~~tl~~W~~   52 (108)
T 2rn7_A           31 ATICSIAPKIGCTPETLRVWVR   52 (108)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH
Confidence            7999999999999999999964

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=95.29  E-value=0.023  Score=32.39  Aligned_cols=33  Identities=6%  Similarity=0.005  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKK--MSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....+  +|+.+||+.+|++++||++..
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L   63 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSV   63 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            455666666666  899999999999999999874

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.25  E-value=0.019  Score=31.13  Aligned_cols=31  Identities=16%  Similarity=0.155  Sum_probs=24.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..++ ..|+|..+||+.+|+|+++|.+..
T Consensus        21 ~IL~lL~-~~g~sa~eLAk~LgiSk~aVr~~L   51 (82)
T 1oyi_A           21 EAIKTIG-IEGATAAQLTRQLNMEKREVNKAL   51 (82)
T ss_dssp             HHHHHHS-SSTEEHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3444444 678999999999999999988764

>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=95.17  E-value=0.05  Score=29.61  Aligned_cols=25  Identities=12%  Similarity=0.323  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|+|.+|+|+.+|+|..||..+..
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~   64 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVS   64 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            7899999999999999999998764

>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=95.16  E-value=0.052  Score=30.74  Aligned_cols=28  Identities=14%  Similarity=0.163  Sum_probs=24.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..|+|+.+|+|++||+.+..
T Consensus        33 l~y~~g~s~~EIA~~lgiS~~tV~~~l~   60 (113)
T 1s7o_A           33 LYYADDYSLAEIADEFGVSRQAVYDNIK   60 (113)
T ss_dssp             HHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3446899999999999999999998865

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=95.15  E-value=0.028  Score=30.74  Aligned_cols=32  Identities=9%  Similarity=0.148  Sum_probs=26.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+..+.+...++..|||+.+++|+.||.+..
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL   37 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARLQTPQPLIDAML   37 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence            44566677778999999999999999998764

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

Probab=95.04  E-value=0.019  Score=30.81  Aligned_cols=32  Identities=9%  Similarity=-0.076  Sum_probs=24.8

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+....++|..++|+.+|+|++++++..+
T Consensus        29 il~~l~~~~~~s~~ela~~l~is~~tvs~~l~   60 (99)
T 3cuo_A           29 ILCMLSGSPGTSAGELTRITGLSASATSQHLA   60 (99)
T ss_dssp             HHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34444444479999999999999999998753

>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=94.99  E-value=0.058  Score=30.39  Aligned_cols=35  Identities=9%  Similarity=0.009  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA   66 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~   66 (82)
                      ..+|..+||+.+|+|++||.++-+--..-....+.
T Consensus        38 ~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~efk   72 (111)
T 2o3f_A           38 IESTVNEISALANSSDAAVIRLCXSLGLKGFQDLX   72 (111)
T ss_dssp             HTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHH
T ss_pred             HhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHH
Confidence            58999999999999999999999865555544433

>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=94.98  E-value=0.049  Score=31.60  Aligned_cols=32  Identities=22%  Similarity=0.346  Sum_probs=27.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+.....+|..+||+.+|+|++++++..
T Consensus         9 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   40 (144)
T 2cfx_A            9 NIIEELKKDSRLSMRELGRKIKLSPPSVTERV   40 (144)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            45677777778999999999999999998864

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=94.97  E-value=0.21  Score=29.50  Aligned_cols=45  Identities=13%  Similarity=0.263  Sum_probs=36.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQ------RPQVVSEYENGKAVPNQTVLAKM   68 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gi------s~~~i~~~e~g~~~p~~~~~~~l   68 (82)
                      +...+.-|...|+||.+++..+|.      |.++|+++|.-.  .+...+.++
T Consensus        10 a~~f~~~ri~lg~tQ~~vg~al~~l~g~~~Sqsti~rfe~l~--ls~kn~~kl   60 (151)
T 3d1n_I           10 AKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLD--ITPKSAQKL   60 (151)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHSCSSSCCCCHHHHHHHHTTC--SCHHHHHHH
T ss_pred             HHHHHHHHhhcCCCcccHHHhhccccCCCCCccccccccCCC--CChhHHHHh
Confidence            566788889999999999999996      999999999754  355554443

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=94.93  E-value=0.037  Score=29.77  Aligned_cols=43  Identities=14%  Similarity=0.061  Sum_probs=30.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||..+...    -...+...+..++...|
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l~~~a~~~g   88 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQAVIYAFQHN   88 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSSHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            68999999999999999999887643    22334444555555554

>1wiz_A DNA-binding protein SATB2; helix bundle, KIAA1034 protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=94.92  E-value=0.047  Score=30.67  Aligned_cols=60  Identities=15%  Similarity=0.078  Sum_probs=48.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKAV------PNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~~------p~~~~~~~la~~lgv~~~e~~   80 (82)
                      ....|+...+..+++|.-||+ -+|.++.+++.+.+.-..      +..+.+.++-..|..+-++|+
T Consensus        22 I~~~Ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lLr~P~kPW~~L~~Gre~f~RM~nWL~l~e~eR~   88 (101)
T 1wiz_A           22 IYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEEDPRTASQSLLVNLRAMQNFLNLPEVERD   88 (101)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHTCCCTTTCCHHHHHHHHHHHHHTTSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHhhhHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence            378999999999999999999 569999999999985421      235668888888888877764

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=94.92  E-value=0.16  Score=30.20  Aligned_cols=46  Identities=13%  Similarity=0.233  Sum_probs=36.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      +..++.-|...|+||.+++..+|      .|.+||.++|.-  ..+...+-+|-
T Consensus        16 a~~fk~~ri~lg~tq~~vg~al~~l~G~~~Sqtti~rfE~l--~ls~~nm~kLk   67 (155)
T 3l1p_A           16 AKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEAL--QLSLKNMSKLR   67 (155)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTT--CSCHHHHHHHH
T ss_pred             HHHHHhhhheecccHHHHHHHHHhhcCcccccccccccccc--cCChhhHhhcc
Confidence            56778888999999999999865      789999999984  44555554443

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=94.92  E-value=0.075  Score=29.37  Aligned_cols=44  Identities=14%  Similarity=0.260  Sum_probs=33.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv   74 (82)
                      ..|+|.+|+|+.+|+|..||..+...    -...+...+..+|...|+
T Consensus        47 ~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~~r~elv~~a~~~gl   94 (99)
T 1p4w_A           47 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSM   94 (99)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcCC
Confidence            46999999999999999999888653    223455566666666665

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=94.89  E-value=0.044  Score=29.17  Aligned_cols=24  Identities=17%  Similarity=0.141  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..|+|+.+|+|..||.+..+
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L~   46 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYLE   46 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            567899999999999999988753

>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=94.84  E-value=0.054  Score=31.54  Aligned_cols=33  Identities=9%  Similarity=0.062  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        10 ~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l   42 (150)
T 2w25_A           10 RILVRELAADGRATLSELATRAGLSVSAVQSRV   42 (150)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            355677777778999999999999999998864

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=94.80  E-value=0.086  Score=29.90  Aligned_cols=34  Identities=15%  Similarity=0.273  Sum_probs=26.0

Q ss_pred             HHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +.+++-++ -..|+|+.++|+.+|+|..||+++-+
T Consensus        46 aqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv~r   80 (107)
T 3frw_A           46 SQRFEVAKMLTDKRTYLDISEKTGASTATISRVNR   80 (107)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHHHH
Confidence            33443332 34689999999999999999998765

>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=94.79  E-value=0.069  Score=26.48  Aligned_cols=27  Identities=15%  Similarity=0.120  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHh-----CCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQI-----NQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~-----gis~~~i~~~e~   55 (82)
                      .....+|..||++.+     ++|..||++..+
T Consensus        15 ~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A           15 TSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            345679999999999     999999999876

>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=94.78  E-value=0.056  Score=31.57  Aligned_cols=33  Identities=12%  Similarity=0.138  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        11 ~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   43 (152)
T 2cg4_A           11 RGILEALMGNARTAYAELAKQFGVSPETIHVRV   43 (152)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            456677777788999999999999999998864

>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=94.71  E-value=0.047  Score=29.42  Aligned_cols=29  Identities=3%  Similarity=-0.049  Sum_probs=22.6

Q ss_pred             HHHHHhC-CCCHHHHHHHhCCCHHH-HHHHH
Q 038591           26 QRARLGK-KMSQPDLANQINQRPQV-VSEYE   54 (82)
Q Consensus        26 k~~r~~~-g~s~~elA~~~gis~~~-i~~~e   54 (82)
                      ..+.... ++|+.+||+.+|+++++ +++..
T Consensus        22 ~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l   52 (95)
T 2pg4_A           22 LEFEKKGYEPSLAEIVKASGVSEKTFFMGLK   52 (95)
T ss_dssp             HHHHHTTCCCCHHHHHHHHCCCHHHHHTTHH
T ss_pred             HHHHhcCCCCCHHHHHHHHCCCchHHHHHHH
Confidence            3344444 79999999999999999 77654

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=94.71  E-value=0.06  Score=31.79  Aligned_cols=33  Identities=9%  Similarity=0.157  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        13 ~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   45 (162)
T 2p5v_A           13 IKILQVLQENGRLTNVELSERVALSPSPCLRRL   45 (162)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            456677777778999999999999999988864

>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=94.71  E-value=0.035  Score=29.73  Aligned_cols=32  Identities=6%  Similarity=0.008  Sum_probs=25.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+....++|..++|+.+|++++++++..+
T Consensus        21 iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~   52 (100)
T 1ub9_A           21 IMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIR   52 (100)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44555556789999999999999999998643

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=94.70  E-value=0.06  Score=31.35  Aligned_cols=33  Identities=12%  Similarity=0.165  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        12 ~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   44 (151)
T 2dbb_A           12 MQLVKILSENSRLTYRELADILNTTRQRIARRI   44 (151)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            355677777788999999999999999998764

>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=94.69  E-value=0.047  Score=31.77  Aligned_cols=23  Identities=22%  Similarity=0.316  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|+|+.+|||+.||..||.-
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~~   23 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEEK   23 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

>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=94.66  E-value=0.076  Score=29.95  Aligned_cols=28  Identities=18%  Similarity=0.112  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..|+|+.+|+|.+||..+..
T Consensus        36 l~~~~g~s~~EIA~~lgiS~~tV~~~l~   63 (113)
T 1xsv_A           36 LFYLEDYSLSEIADTFNVSRQAVYDNIR   63 (113)
T ss_dssp             HHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3446899999999999999999998764

>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=94.60  E-value=0.079  Score=28.57  Aligned_cols=30  Identities=7%  Similarity=0.065  Sum_probs=24.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+  ...++..+||+.+|+|+++|++..+
T Consensus        36 Il~~L--~~~~~~~eLa~~l~is~~tv~~~L~   65 (96)
T 1y0u_A           36 ILRML--DKGRSEEEIMQTLSLSKKQLDYHLK   65 (96)
T ss_dssp             HHHHH--HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHH--cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34444  5779999999999999999998653

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

Probab=94.56  E-value=0.068  Score=30.06  Aligned_cols=34  Identities=12%  Similarity=0.069  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        32 ~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~   65 (138)
T 3bpv_A           32 VACLLRIHREPGIKQDELATFFHVDKGTIARTLR   65 (138)
T ss_dssp             HHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456666677889999999999999999998753

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=94.52  E-value=0.045  Score=32.35  Aligned_cols=25  Identities=8%  Similarity=0.015  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+|..|+|+.+|||+.||..||.-
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~~   27 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDKI   27 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHC
Confidence            3589999999999999999999963

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

Probab=94.52  E-value=0.078  Score=29.88  Aligned_cols=34  Identities=12%  Similarity=0.042  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        34 ~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~   67 (142)
T 3bdd_A           34 YSILQTLLKDAPLHQLALQERLQIDRAAVTRHLK   67 (142)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3456666677789999999999999999998743

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

Probab=94.51  E-value=0.066  Score=30.56  Aligned_cols=34  Identities=15%  Similarity=0.056  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        43 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~   76 (148)
T 3nrv_A           43 WRIISVLSSASDCSVQKISDILGLDKAAVSRTVK   76 (148)
T ss_dssp             HHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4556666676789999999999999999998743

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=94.50  E-value=0.051  Score=30.56  Aligned_cols=37  Identities=11%  Similarity=0.103  Sum_probs=28.5

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      ...-..+|..+||+.+|+|++||.++-+--..-+...
T Consensus        30 ~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~e   66 (107)
T 3iwf_A           30 PHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNE   66 (107)
T ss_dssp             HHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHH
T ss_pred             HHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHH
Confidence            3445689999999999999999999987544444444

>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=94.47  E-value=0.046  Score=31.16  Aligned_cols=33  Identities=9%  Similarity=0.136  Sum_probs=24.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...-++|+.+||+.+|++++++++..
T Consensus        40 ~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   72 (142)
T 3ech_A           40 VHVLKLIDEQRGLNLQDLGRQMCRDKALITRKI   72 (142)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHC---CHHHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            455666777779999999999999999999874

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

Probab=94.47  E-value=0.08  Score=30.15  Aligned_cols=34  Identities=12%  Similarity=-0.014  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        34 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~   67 (145)
T 3g3z_A           34 FAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCK   67 (145)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4556667777789999999999999999998743

>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=94.44  E-value=0.078  Score=30.92  Aligned_cols=33  Identities=9%  Similarity=0.051  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        10 ~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   42 (151)
T 2cyy_A           10 KKIIKILQNDGKAPLREISKITGLAESTIHERI   42 (151)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            355666777778999999999999999998864

>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=94.38  E-value=0.051  Score=31.57  Aligned_cols=32  Identities=19%  Similarity=0.161  Sum_probs=25.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+.....+|..++|+.+|+|++++++..
T Consensus         7 ~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l   38 (150)
T 2pn6_A            7 RILKILQYNAKYSLDEIAREIRIPKATLSYRI   38 (150)
T ss_dssp             HHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34555666667999999999999999998864

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=94.38  E-value=0.089  Score=28.92  Aligned_cols=31  Identities=16%  Similarity=0.090  Sum_probs=24.7

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+. ..+++..++|+.+|+|+++|++..+
T Consensus        31 IL~~L~-~~~~~~~ela~~l~is~stvs~~L~   61 (106)
T 1r1u_A           31 IMELLS-VSEASVGHISHQLNLSQSNVSHQLK   61 (106)
T ss_dssp             HHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444 6778999999999999999998743

>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=94.37  E-value=0.042  Score=30.54  Aligned_cols=25  Identities=8%  Similarity=0.198  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..|+|+.+|+|.++|.+++..
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~r   62 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAK   62 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5799999999999999999998753

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.36  E-value=0.079  Score=31.84  Aligned_cols=33  Identities=6%  Similarity=0.143  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.....+|..+||+.+|+|++++++..
T Consensus        20 ~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l   52 (171)
T 2ia0_A           20 RNILRLLKKDARLTISELSEQLKKPESTIHFRI   52 (171)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            456677777778999999999999999998764

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

Probab=94.34  E-value=0.085  Score=29.64  Aligned_cols=34  Identities=9%  Similarity=-0.037  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        41 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~   74 (140)
T 2nnn_A           41 WAALVRLGETGPCPQNQLGRLTAMDAATIKGVVE   74 (140)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455666666799999999999999999998753

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=94.33  E-value=0.055  Score=30.69  Aligned_cols=32  Identities=13%  Similarity=-0.026  Sum_probs=25.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+....+++..++|+.+|+|++++++..+
T Consensus        47 IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~   78 (122)
T 1u2w_A           47 ITYALCQDEELCVCDIANILGVTIANASHHLR   78 (122)
T ss_dssp             HHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34445545679999999999999999998753

>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=94.29  E-value=0.045  Score=31.49  Aligned_cols=27  Identities=11%  Similarity=0.119  Sum_probs=23.9

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|..|+|+.+|+|.++|.....
T Consensus       120 ~~~~g~s~~EIA~~lgis~~tV~~~~~  146 (164)
T 3mzy_A          120 YLIRGYSYREIATILSKNLKSIDNTIQ  146 (164)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345799999999999999999998875

>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=94.28  E-value=0.091  Score=30.07  Aligned_cols=32  Identities=6%  Similarity=0.067  Sum_probs=26.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+.....+|..+||+.+|+|++++++..
T Consensus         8 ~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l   39 (141)
T 1i1g_A            8 IILEILEKDARTPFTEIAKKLGISETAVRKRV   39 (141)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            45666666677999999999999999998753

>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=94.26  E-value=0.087  Score=29.97  Aligned_cols=34  Identities=12%  Similarity=0.101  Sum_probs=27.8

Q ss_pred             HHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.. ..++|+.++|+.+|++++++++..+
T Consensus        38 ~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~   72 (147)
T 2hr3_A           38 LVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLR   72 (147)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHH
Confidence            345666666 6789999999999999999988743

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

Probab=94.25  E-value=0.062  Score=30.55  Aligned_cols=33  Identities=12%  Similarity=0.089  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.+||+.+|++++++++..
T Consensus        40 ~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   72 (143)
T 3oop_A           40 WSVLEGIEANEPISQKEIALWTKKDTPTVNRIV   72 (143)
T ss_dssp             HHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHH
Confidence            455666777789999999999999999999874

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=94.25  E-value=0.037  Score=32.57  Aligned_cols=23  Identities=9%  Similarity=0.238  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++..|+|+.+|||+.||..||.
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~   24 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYER   24 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999986

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=94.23  E-value=0.082  Score=33.75  Aligned_cols=33  Identities=9%  Similarity=0.060  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.+||+.+|++++|+++..
T Consensus       155 ~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L  187 (244)
T 2wte_A          155 MKLLNVLYETKGTGITELAKMLDKSEKTLINKI  187 (244)
T ss_dssp             HHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            345566667789999999999999999999884

>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=94.22  E-value=0.041  Score=32.88  Aligned_cols=23  Identities=9%  Similarity=0.253  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~  186 (207)
T 2oz6_A          164 KITRQEIGRIVGCSREMVGRVLK  186 (207)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHH
Confidence            48999999999999999998864

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

Probab=94.22  E-value=0.083  Score=29.04  Aligned_cols=32  Identities=16%  Similarity=0.125  Sum_probs=25.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+ ...+++..+||+.+|+++++|++..+
T Consensus        25 ~IL~~L-~~~~~~~~ela~~l~is~~tv~~~l~   56 (114)
T 2oqg_A           25 EILTEL-GRADQSASSLATRLPVSRQAIAKHLN   56 (114)
T ss_dssp             HHHHHH-HHSCBCHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344555 56789999999999999999998743

>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=94.14  E-value=0.11  Score=29.44  Aligned_cols=34  Identities=9%  Similarity=0.036  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        36 ~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~   69 (145)
T 2a61_A           36 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVK   69 (145)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHH
Confidence            4455666667789999999999999999998753

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

Probab=94.13  E-value=0.1  Score=29.73  Aligned_cols=34  Identities=9%  Similarity=0.052  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        45 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~   78 (150)
T 2rdp_A           45 FVALQWLLEEGDLTVGELSNKMYLACSTTTDLVD   78 (150)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHH
Confidence            4556666667789999999999999999998743

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.10  E-value=0.12  Score=28.75  Aligned_cols=30  Identities=23%  Similarity=0.226  Sum_probs=24.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+.. ..+|..++|+.+|+++++|++..
T Consensus        37 il~~L~~-~~~s~~ela~~l~is~stvsr~l   66 (119)
T 2lkp_A           37 ILTQLRN-GPLPVTDLAEAIGMEQSAVSHQL   66 (119)
T ss_dssp             HHHHHHH-CCCCHHHHHHHHSSCHHHHHHHH
T ss_pred             HHHHHHH-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            3444444 67999999999999999999864

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

Probab=94.05  E-value=0.11  Score=30.08  Aligned_cols=34  Identities=18%  Similarity=0.042  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++++.+||+.+|+++++|++..+
T Consensus        52 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~   85 (162)
T 2fa5_A           52 WRVITILALYPGSSASEVSDRTAMDKVAVSRAVA   85 (162)
T ss_dssp             HHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455666666789999999999999999988743

>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=94.04  E-value=0.048  Score=32.64  Aligned_cols=23  Identities=9%  Similarity=0.241  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.++++..+
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l~  189 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRILK  189 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCHHHHHHHhCCcHHHHHHHHH
Confidence            57999999999999999999864

>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=94.03  E-value=0.1  Score=29.85  Aligned_cols=26  Identities=15%  Similarity=0.185  Sum_probs=22.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ....++|+.+||+.+|+++++|++..
T Consensus        18 ~~~~~~~~~ela~~l~vs~~tvs~~l   43 (142)
T 1on2_A           18 EEKGYARVSDIAEALAVHPSSVTKMV   43 (142)
T ss_dssp             HHHSSCCHHHHHHHHTSCHHHHHHHH
T ss_pred             hhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            34578999999999999999998874

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=94.03  E-value=0.083  Score=28.81  Aligned_cols=29  Identities=10%  Similarity=0.029  Sum_probs=24.2

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+....+++..++|+.+|+|++++++..+
T Consensus        35 ~l~~~~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           35 ELYKHKALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             HHHHHSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44455679999999999999999998754

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=94.02  E-value=0.092  Score=32.60  Aligned_cols=35  Identities=11%  Similarity=0.039  Sum_probs=26.9

Q ss_pred             HHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARLG-KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |.....+... ...+|++||+.+|+|++.|+++.+-
T Consensus        30 g~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~   65 (189)
T 3mky_B           30 GQRYASRLQNEFAGNISALADAENISRKIITRCINT   65 (189)
T ss_dssp             HHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHH
Confidence            4444444433 4689999999999999999999864

>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=94.00  E-value=0.11  Score=29.22  Aligned_cols=33  Identities=15%  Similarity=0.129  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGK--KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~--g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....  ++|+.+||+.+|++++++++..
T Consensus        37 ~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l   71 (141)
T 3bro_A           37 MTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLL   71 (141)
T ss_dssp             HHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHH
Confidence            34556666655  7999999999999999998874

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=93.97  E-value=0.051  Score=32.58  Aligned_cols=23  Identities=17%  Similarity=0.267  Sum_probs=20.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       146 ~~t~~~lA~~lg~sr~tvsR~l~  168 (202)
T 2zcw_A          146 KATHDELAAAVGSVRETVTKVIG  168 (202)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            38999999999999999998754

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

Probab=93.95  E-value=0.068  Score=30.77  Aligned_cols=34  Identities=0%  Similarity=-0.037  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.+||+.+|+++++++++.+
T Consensus        44 ~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~   77 (149)
T 4hbl_A           44 YLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLK   77 (149)
T ss_dssp             HHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4556667777899999999999999999998753

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

Probab=93.92  E-value=0.079  Score=29.86  Aligned_cols=34  Identities=24%  Similarity=0.071  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        39 ~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~   72 (142)
T 2fbi_A           39 WRVIRILRQQGEMESYQLANQACILRPSMTGVLA   72 (142)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHH
Confidence            4456666777789999999999999999988753

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

Probab=93.91  E-value=0.083  Score=29.91  Aligned_cols=34  Identities=12%  Similarity=0.086  Sum_probs=27.9

Q ss_pred             HHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRA-RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~-r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+ ....++|+.+||+.+|++++++++..+
T Consensus        40 ~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~   74 (146)
T 2fbh_A           40 WLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLD   74 (146)
T ss_dssp             HHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHH
Confidence            4566666 566789999999999999999998743

>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=93.88  E-value=0.12  Score=29.83  Aligned_cols=33  Identities=9%  Similarity=-0.029  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.++|+.+|++++++++..
T Consensus        47 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   79 (154)
T 2eth_A           47 LYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   79 (154)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            345666666678999999999999999999874

>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp}

Probab=93.83  E-value=0.085  Score=31.33  Aligned_cols=34  Identities=15%  Similarity=0.122  Sum_probs=27.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL   65 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~   65 (82)
                      .+.|..++|+.+|||+.+++.+-.++...=...+
T Consensus        29 ~~~s~~~Ia~~Agvskgt~Y~yF~sKe~L~~~~~   62 (197)
T 2f07_A           29 DKASISDIVKKAGTAQGTFYLYFSSKNALIPAIA   62 (197)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSSTTHHHHHH
T ss_pred             ccCCHHHHHHHhCCCchHHHHhCCCHHHHHHHHH
Confidence            4679999999999999999999887765443333

>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=93.83  E-value=0.13  Score=28.91  Aligned_cols=34  Identities=6%  Similarity=0.066  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.++|+.+|++++++++..+
T Consensus        37 ~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~   70 (138)
T 1jgs_A           37 FKVLCSIRCAACITPVELKKVLSVDLGALTRMLD   70 (138)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHH
Confidence            4456666667789999999999999999998743

>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=93.82  E-value=0.097  Score=31.78  Aligned_cols=31  Identities=16%  Similarity=0.183  Sum_probs=23.9

Q ss_pred             HHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLG-KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+... ..+|..+||+.+|+|++||.+..
T Consensus        26 Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi   57 (187)
T 1j5y_A           26 IVRILERSKEPVSGAQLAEELSVSRQVIVQDI   57 (187)
T ss_dssp             HHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            34445544 34999999999999999998864

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

Probab=93.82  E-value=0.075  Score=30.87  Aligned_cols=33  Identities=9%  Similarity=0.010  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.+||+.+|+++++++++.
T Consensus        53 ~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   85 (159)
T 3s2w_A           53 FPFLMRLYREDGINQESLSDYLKIDKGTTARAI   85 (159)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            566777777788999999999999999999874

>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=93.81  E-value=0.079  Score=29.90  Aligned_cols=33  Identities=15%  Similarity=0.175  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGK--KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~--g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....  ++|+.+||+.+|++++++++..
T Consensus        34 ~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l   68 (139)
T 3eco_A           34 GHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLL   68 (139)
T ss_dssp             HHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHH
Confidence            44556666554  8999999999999999999874

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=93.80  E-value=0.061  Score=32.42  Aligned_cols=23  Identities=17%  Similarity=0.416  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.++++..+
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~  191 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLR  191 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            78999999999999999999864

>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=93.75  E-value=0.058  Score=32.74  Aligned_cols=22  Identities=14%  Similarity=0.214  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|+.++|..+|+|+.+|++..+
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~  209 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLK  209 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHhCCcHHHHHHHHH
Confidence            7999999999999999999865

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=93.71  E-value=0.049  Score=32.54  Aligned_cols=23  Identities=17%  Similarity=0.202  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       139 ~~t~~~lA~~lg~sr~tvsR~l~  161 (195)
T 3b02_A          139 TVSHEEIADATASIRESVSKVLA  161 (195)
T ss_dssp             ECCHHHHHHTTTSCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            37999999999999999998754

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=93.71  E-value=0.059  Score=32.84  Aligned_cols=24  Identities=13%  Similarity=0.173  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       174 ~~~t~~~iA~~lg~sr~tvsR~l~  197 (231)
T 3e97_A          174 LPLGTQDIMARTSSSRETVSRVLK  197 (231)
T ss_dssp             ECCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCcHHHHHHHHH
Confidence            358999999999999999999754

>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=0.076  Score=31.51  Aligned_cols=32  Identities=9%  Similarity=0.098  Sum_probs=26.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+.+...+|..+||+.+|+|++++.+-.
T Consensus         7 ~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl   38 (162)
T 3i4p_A            7 KILRILQEDSTLAVADLAKKVGLSTTPCWRRI   38 (162)
T ss_dssp             HHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            45677777788999999999999999987753

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=93.68  E-value=0.035  Score=32.16  Aligned_cols=40  Identities=13%  Similarity=0.082  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI   72 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l   72 (82)
                      ++|..++|+.+|||++|++++-.++...-...+..+...+
T Consensus        32 ~~tv~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~   71 (177)
T 3kkc_A           32 KITVQDVIGLANVGRSTFYSHYESKEVLLKELCEDLFHHL   71 (177)
T ss_dssp             TCCHHHHHHHHCCCHHHHTTTCSSTHHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHhCCcHhhHHHHcCCHHHHHHHHHHHHHHHH
Confidence            4699999999999999999987765444333444443333

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

Probab=93.68  E-value=0.083  Score=30.33  Aligned_cols=34  Identities=12%  Similarity=0.022  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.+||+.+|+++++++++.+
T Consensus        44 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~   77 (154)
T 2qww_A           44 LAMINVIYSTPGISVADLTKRLIITGSSAAANVD   77 (154)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3456666666789999999999999999998753

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=93.66  E-value=0.14  Score=28.09  Aligned_cols=31  Identities=3%  Similarity=-0.082  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQ   62 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~   62 (82)
                      ..+|..+||+.+|+|+.++++..+.....++
T Consensus        17 ~~~~~~~lA~~~~~s~~~l~r~fk~~~G~s~   47 (108)
T 3mn2_A           17 RPITIEKLTALTGISSRGIFKAFQRSRGYSP   47 (108)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHTSSCH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHhCcCH
Confidence            4689999999999999999999875433343

>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=93.65  E-value=0.067  Score=32.41  Aligned_cols=24  Identities=21%  Similarity=0.188  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.++++..+
T Consensus       166 ~~~t~~~lA~~lg~sr~tvsR~l~  189 (220)
T 2fmy_A          166 LGLNTEEIALMLGTTRQTVSVLLN  189 (220)
T ss_dssp             CSSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCCHHHHHHHhCCcHHHHHHHHH
Confidence            468999999999999999998754

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=93.60  E-value=0.063  Score=32.27  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       163 ~~t~~~lA~~lg~sr~tvsR~l~  185 (216)
T 4ev0_A          163 QIRHHELAALAGTSRETVSRVLH  185 (216)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            47999999999999999999853

>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=93.60  E-value=0.089  Score=29.81  Aligned_cols=33  Identities=12%  Similarity=-0.002  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...-++|+.++|+.+|++++++++..
T Consensus        32 ~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l   64 (144)
T 1lj9_A           32 YLYLVRVCENPGIIQEKIAELIKVDRTTAARAI   64 (144)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHH
Confidence            456666767678999999999999999999874

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=93.58  E-value=0.073  Score=32.33  Aligned_cols=23  Identities=13%  Similarity=0.264  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       177 ~~t~~~lA~~lg~sr~tvsR~l~  199 (227)
T 3d0s_A          177 DLTQEEIAQLVGASRETVNKALA  199 (227)
T ss_dssp             CCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHH
Confidence            58999999999999999998754

>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=93.58  E-value=0.069  Score=32.45  Aligned_cols=22  Identities=23%  Similarity=0.229  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .+|+.++|..+|+|+.+|++..
T Consensus       163 ~~t~~~lA~~lG~sr~tvsR~l  184 (222)
T 1ft9_A          163 DFTVEEIANLIGSSRQTTSTAL  184 (222)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCcHHHHHHHH
Confidence            3899999999999999999874

>1wh8_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=93.55  E-value=0.18  Score=28.76  Aligned_cols=55  Identities=7%  Similarity=0.079  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCC---CC---CHHHHHHHHHHhCCCC
Q 038591           22 PRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKA---VP---NQTVLAKMEKAIGVKL   76 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~---~p---~~~~~~~la~~lgv~~   76 (82)
                      ...|++.....+++|.-||+ -+|.++.+|+.+.+.-.   ..   .-+...++-..|..+-
T Consensus        33 ~~~ikewL~~~~isQ~~FA~~ILgrsQgtlSdlL~~PkpW~~L~~~GRe~yiRM~nWL~l~e   94 (111)
T 1wh8_A           33 TKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLNDPH   94 (111)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTSCHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHCCCcHHHHHHHHhccCcCcHHHHHcCCCCHHHHhHhhhHHHHHHHHHhcChH
Confidence            78889999999999999999 77999999999997522   11   2455666666666553

>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=93.51  E-value=0.068  Score=30.74  Aligned_cols=33  Identities=6%  Similarity=0.022  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+ ...++|+.+||+.+|++++++++..+
T Consensus        41 ~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~   73 (151)
T 3kp7_A           41 SHVLNML-SIEALTVGQITEKQGVNKAAVSRRVK   73 (151)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHH
T ss_pred             HHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            4556777 78899999999999999999998753

>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=93.50  E-value=0.057  Score=29.14  Aligned_cols=22  Identities=14%  Similarity=0.022  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +|+.+||+.+|+++++++++.+
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l~   52 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLIIK   52 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            9999999999999999998753

>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=93.49  E-value=0.13  Score=34.88  Aligned_cols=34  Identities=15%  Similarity=0.190  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|+.++....+|..|||+.+|+|++||+++.+
T Consensus        42 ~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v~   75 (429)
T 1z05_A           42 GRVYKLIDQKGPISRIDLSKESELAPASITKITR   75 (429)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            3457788888899999999999999999999743

>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=93.46  E-value=0.08  Score=30.89  Aligned_cols=33  Identities=15%  Similarity=0.124  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...-++|+.+||+.+|+++++++++.
T Consensus        49 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   81 (162)
T 3k0l_A           49 FTALSVLAAKPNLSNAKLAERSFIKPQSANKIL   81 (162)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            355666666678999999999999999998874

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=93.45  E-value=0.04  Score=31.99  Aligned_cols=26  Identities=23%  Similarity=0.248  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        28 ~~ti~~Ia~~agvs~~t~Y~~F~sK~   53 (188)
T 3qkx_A           28 QLSMLKLAKEANVAAGTIYLYFKNKD   53 (188)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHSSSHH
T ss_pred             cCCHHHHHHHhCCCcchHHHHcCCHH
Confidence            58999999999999999999876543

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=93.45  E-value=0.092  Score=31.25  Aligned_cols=24  Identities=13%  Similarity=0.199  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|..++|+.+|||+.||..||.
T Consensus        10 ~~~~i~e~A~~~gvs~~TLR~ye~   33 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVSALHFYES   33 (154)
T ss_dssp             CCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999985

>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=93.42  E-value=0.11  Score=34.90  Aligned_cols=33  Identities=12%  Similarity=0.049  Sum_probs=28.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|+.++....+|..|||+.+|+|++||+++.
T Consensus        19 ~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v   51 (406)
T 1z6r_A           19 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIV   51 (406)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            345777888889999999999999999999974

>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=93.42  E-value=0.15  Score=28.07  Aligned_cols=33  Identities=18%  Similarity=0.129  Sum_probs=25.4

Q ss_pred             HHHHHHHHHhC-CCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGK-KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~-g~s~~elA~~~gis~~~i~~~e   54 (82)
                      -..|..+...- .+|..+||+.+|+|+++|++..
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L   54 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKL   54 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34555554433 6999999999999999999864

>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=93.40  E-value=0.22  Score=30.63  Aligned_cols=28  Identities=14%  Similarity=0.213  Sum_probs=25.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..|+|..++|+.+|+|++|+++|.+...
T Consensus       173 ~~G~s~~~Ia~~l~is~~tv~r~l~~~~  200 (209)
T 2r0q_C          173 EEGQAISKIAKEVNITRQTVYRIKHDNG  200 (209)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhccc
Confidence            4799999999999999999999987543

>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=93.39  E-value=0.043  Score=32.09  Aligned_cols=27  Identities=4%  Similarity=-0.074  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+++++++-.++.
T Consensus        21 ~~~ti~~Ia~~agvs~~t~Y~~F~sK~   47 (194)
T 3bqz_B           21 NATTTGEIVKLSESSKGNLYYHFKTKE   47 (194)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHTSSHH
T ss_pred             ccCCHHHHHHHhCCCchhHHHhCCCHH
Confidence            468999999999999999999977643

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=93.37  E-value=0.1  Score=30.85  Aligned_cols=25  Identities=8%  Similarity=0.046  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..++..|+|+.+|||+.||..||.-
T Consensus        15 ~~~~I~evA~~~gvs~~tLR~Ye~~   39 (148)
T 3gpv_A           15 MYYTIGQVAKMQHLTISQIRYYDKQ   39 (148)
T ss_dssp             CCBCHHHHHHHTTCCHHHHHHHHHT
T ss_pred             CceeHHHHHHHHCcCHHHHHHHHHC
Confidence            3589999999999999999999863

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

Probab=93.36  E-value=0.1  Score=29.99  Aligned_cols=34  Identities=3%  Similarity=-0.042  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|+++++++++.+
T Consensus        50 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~   83 (153)
T 2pex_A           50 YLVMLVLWETDERSVSEIGERLYLDSATLTPLLK   83 (153)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHH
Confidence            3455666666789999999999999999998753

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=93.35  E-value=0.071  Score=32.71  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|++..+
T Consensus       186 ~~t~~~lA~~lG~sr~tvsR~l~  208 (232)
T 1zyb_A          186 KVKMDDLARCLDDTRLNISKTLN  208 (232)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHHH
Confidence            37999999999999999998864

>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=93.35  E-value=0.1  Score=29.82  Aligned_cols=34  Identities=15%  Similarity=0.216  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        43 ~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~   76 (152)
T 3bj6_A           43 RAILEGLSLTPGATAPQLGAALQMKRQYISRILQ   76 (152)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3455666666789999999999999999998743

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=93.33  E-value=0.11  Score=28.25  Aligned_cols=25  Identities=8%  Similarity=0.098  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++..++|+.+|+|+.++++.....
T Consensus        19 ~~~~~~lA~~~~~S~~~l~r~fk~~   43 (103)
T 3lsg_A           19 QFTLSVLSEKLDLSSGYLSIMFKKN   43 (103)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            7899999999999999999997654

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

Probab=93.32  E-value=0.11  Score=30.54  Aligned_cols=34  Identities=12%  Similarity=0.117  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        48 ~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~   81 (168)
T 2nyx_A           48 FRTLVILSNHGPINLATLATLLGVQPSATGRMVD   81 (168)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4556666666789999999999999999998743

>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A

Probab=93.31  E-value=0.18  Score=28.74  Aligned_cols=34  Identities=12%  Similarity=0.102  Sum_probs=27.3

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      ...+|..++|..+|+|+++++++.+.....++..
T Consensus        91 ~~~~sl~~lA~~~g~S~~~f~r~Fk~~~G~tp~~  124 (133)
T 1u8b_A           91 ETPVTLEALADQVAMSPFHLHRLFKATTGMTPKA  124 (133)
T ss_dssp             SSCCCHHHHHHHHTSCHHHHHHHHHHHTSSCHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH
Confidence            4579999999999999999999987544444444

>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=93.27  E-value=0.11  Score=34.68  Aligned_cols=30  Identities=20%  Similarity=0.287  Sum_probs=27.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|+.++ ...+|..|||+.+|+|++||+++.
T Consensus        25 il~~l~-~~~~sr~~la~~~gls~~tv~~~v   54 (380)
T 2hoe_A           25 ILKRIM-KSPVSRVELAEELGLTKTTVGEIA   54 (380)
T ss_dssp             SHHHHH-HSCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHH-cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            477888 889999999999999999999974

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=93.27  E-value=0.16  Score=28.02  Aligned_cols=31  Identities=10%  Similarity=0.024  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQ   62 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~   62 (82)
                      ..++..+||+.+|+|+.++++........++
T Consensus        22 ~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~   52 (113)
T 3oio_A           22 EPLSTDDIAYYVGVSRRQLERLFKQYLGTVP   52 (113)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHTSSCH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence            4689999999999999999999875444443

>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=93.27  E-value=0.12  Score=29.31  Aligned_cols=32  Identities=9%  Similarity=-0.011  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+. ..++|+.+||+.+|++++++++..
T Consensus        40 ~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l   71 (146)
T 2gxg_A           40 FLVLRATS-DGPKTMAYLANRYFVTQSAITASV   71 (146)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHH
Confidence            34455555 778999999999999999998874

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=93.27  E-value=0.24  Score=27.07  Aligned_cols=26  Identities=12%  Similarity=0.189  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..++..++|+.+|+|+.++++.....
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~~   44 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQQ   44 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            46899999999999999999997643

>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=93.26  E-value=0.17  Score=29.96  Aligned_cols=28  Identities=14%  Similarity=-0.014  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|.++|.....
T Consensus       151 l~~~~g~s~~EIA~~lgis~~tV~~~l~  178 (194)
T 1or7_A          151 LRELDGLSYEEIAAIMDCPVGTVRSRIF  178 (194)
T ss_dssp             HHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445799999999999999999998875

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=93.23  E-value=0.078  Score=32.82  Aligned_cols=24  Identities=21%  Similarity=0.246  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       192 ~~lt~~~lA~~lG~sr~tvsR~l~  215 (243)
T 3la7_A          192 LKLSHQAIAEAIGSTRVTVTRLLG  215 (243)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCCHHHHHHHHCCcHHHHHHHHH
Confidence            468999999999999999999864

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

Probab=93.23  E-value=0.11  Score=30.17  Aligned_cols=34  Identities=9%  Similarity=-0.053  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|++++++++..+
T Consensus        55 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~   88 (162)
T 3cjn_A           55 MRALAILSAKDGLPIGTLGIFAVVEQSTLSRALD   88 (162)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHH
Confidence            3455666666789999999999999999998753

>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=93.21  E-value=0.14  Score=30.76  Aligned_cols=34  Identities=9%  Similarity=0.110  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ...|..+. ..|+|..++|+.+|+|++||++|.+.
T Consensus       148 ~~~i~~~~-~~G~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          148 RDAVLNMW-QQGLGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            45565544 47999999999999999999999764

>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=93.20  E-value=0.17  Score=30.86  Aligned_cols=28  Identities=11%  Similarity=0.158  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++-..|+|..|+|+.+|+|.++|.++..
T Consensus       198 l~~~~g~s~~EIA~~lgis~~~V~~~~~  225 (239)
T 1rp3_A          198 LIFYEELPAKEVAKILETSVSRVSQLKA  225 (239)
T ss_dssp             HHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445799999999999999999998875

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=93.18  E-value=0.058  Score=32.68  Aligned_cols=24  Identities=13%  Similarity=0.236  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       177 ~~~t~~~lA~~lg~sr~tvsR~l~  200 (227)
T 3dkw_A          177 IPVAKQLVAGHLSIQPETFSRIMH  200 (227)
T ss_dssp             CCSCTHHHHHHTTSCHHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHHH
Confidence            357999999999999999999864

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

Probab=93.17  E-value=0.12  Score=29.36  Aligned_cols=33  Identities=12%  Similarity=0.182  Sum_probs=25.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.. .++|+.+||+.+|++++++++..+
T Consensus        41 ~~iL~~l~~-~~~t~~eLa~~l~~s~~tvs~~l~   73 (146)
T 3tgn_A           41 EHILMLLSE-ESLTNSELARRLNVSQAAVTKAIK   73 (146)
T ss_dssp             HHHHHHHTT-CCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344444444 449999999999999999998753

>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=93.14  E-value=0.059  Score=32.24  Aligned_cols=28  Identities=14%  Similarity=0.143  Sum_probs=24.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      +.|..++|+.+|||+.+|+++..++...
T Consensus        28 ~~s~~~IA~~aGvs~~tiY~~F~sKe~L   55 (202)
T 2d6y_A           28 GARIDRIAAEARANKQLIYAYYGNKGEL   55 (202)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHSSHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence            6799999999999999999998765433

>3egq_A TETR family transcriptional regulator; DNA-binding, transcription regulation, bacterial regulatory DNA/RNA-binding 3-helical bundle fold; HET: MSE PE8; 2.55A {Archaeoglobus fulgidus}

Probab=93.14  E-value=0.039  Score=31.85  Aligned_cols=26  Identities=12%  Similarity=0.105  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        24 ~~t~~~Ia~~agvs~~t~Y~~F~sK~   49 (170)
T 3egq_A           24 EVSIEEIAREAKVSKSLIFYHFESKQ   49 (170)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             cCcHHHHHHHhCCCchhHHHHcCCHH
Confidence            47999999999999999999976654

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=93.13  E-value=0.045  Score=31.88  Aligned_cols=26  Identities=12%  Similarity=0.010  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+++++++-.++.
T Consensus        29 ~~tv~~Ia~~agvs~~t~Y~~F~sK~   54 (195)
T 3ppb_A           29 GTSTATIAREAGVATGTLFHHFPSKE   54 (195)
T ss_dssp             TSCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHcCCHH
Confidence            57999999999999999999976543

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=93.13  E-value=0.092  Score=31.99  Aligned_cols=24  Identities=17%  Similarity=0.026  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       179 ~~~t~~~lA~~lg~sr~tvsR~l~  202 (232)
T 2gau_A          179 IYLSREELATLSNMTVSNAIRTLS  202 (232)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHHH
Confidence            468999999999999999998754

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

Probab=93.13  E-value=0.19  Score=28.53  Aligned_cols=25  Identities=20%  Similarity=0.246  Sum_probs=21.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..++|+.++|+.+|+++++|++..+
T Consensus        29 ~~~~s~~ela~~l~is~~tv~~~l~   53 (139)
T 2x4h_A           29 GEGAKINRIAKDLKIAPSSVFEEVS   53 (139)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCcCHHHHHHHhCCChHHHHHHHH
Confidence            4578999999999999999988643

>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp}

Probab=93.12  E-value=0.04  Score=32.09  Aligned_cols=27  Identities=22%  Similarity=0.193  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++-.++.
T Consensus        29 ~~~t~~~IA~~agvs~~t~Y~~F~sK~   55 (191)
T 3on4_A           29 NAFSFKDIATAINIKTASIHYHFPSKE   55 (191)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCcchhhhcCCCHH
Confidence            368999999999999999999976543

>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=93.12  E-value=0.097  Score=30.03  Aligned_cols=34  Identities=9%  Similarity=0.209  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++|+.+||+.+|+++++|++..+
T Consensus        40 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~   73 (155)
T 1s3j_A           40 LFVLASLKKHGSLKVSEIAERMEVKPSAVTLMAD   73 (155)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455666666789999999999999999998753

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=93.10  E-value=0.15  Score=33.05  Aligned_cols=34  Identities=12%  Similarity=-0.010  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+.++.+.|+.+|||++|+++..+
T Consensus       270 ~~~i~~~l~~~~gn~~~aA~~Lgi~r~tl~~kl~  303 (304)
T 1ojl_A          270 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  303 (304)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            4567777888899999999999999999998653

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=93.09  E-value=0.046  Score=32.21  Aligned_cols=25  Identities=16%  Similarity=0.058  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++-.++
T Consensus        32 ~~t~~~Ia~~agvs~~t~Y~~F~sK   56 (202)
T 3lwj_A           32 NTSIRDIIALSEVGTGTFYNYFVDK   56 (202)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHCSSH
T ss_pred             cCCHHHHHHHhCCCchhHHHHcCCH
Confidence            6899999999999999999987654

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=93.09  E-value=0.084  Score=32.69  Aligned_cols=24  Identities=17%  Similarity=0.086  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       176 ~~~t~~~iA~~lG~sr~tvsR~l~  199 (250)
T 3e6c_C          176 MPLSQKSIGEITGVHHVTVSRVLA  199 (250)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHHH
Confidence            468999999999999999999853

>3vpr_A Transcriptional regulator, TETR family; all alpha, helix-turn-helix, transcriptional repressor, DNA protein; 2.27A {Thermus thermophilus}

Probab=93.09  E-value=0.086  Score=30.95  Aligned_cols=27  Identities=19%  Similarity=0.140  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.|++.+-.++.
T Consensus        22 ~~~s~~~IA~~agvsk~t~Y~~F~sK~   48 (190)
T 3vpr_A           22 EATSVQDLAQALGLSKAALYHHFGSKE   48 (190)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            467999999999999999999987643

>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=93.09  E-value=0.077  Score=31.01  Aligned_cols=26  Identities=8%  Similarity=-0.026  Sum_probs=24.0

Q ss_pred             hCCCCHHHHHHHhCC-CHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQ-RPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gi-s~~~i~~~e~g   56 (82)
                      ..|.|..++|...|| |.+||++|.+-
T Consensus        26 ~~G~sl~~i~~~~~~ps~~T~~~W~~~   52 (140)
T 4dyq_A           26 SSGESLLKVCKRPGMPDKSTVFRWLAK   52 (140)
T ss_dssp             HTTCCHHHHHTSTTCCCHHHHHHHHHH
T ss_pred             HCCCcHHHHHhcCCCCCHHHHHHHHHc
Confidence            479999999999999 99999999874

>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=93.03  E-value=0.13  Score=28.23  Aligned_cols=26  Identities=15%  Similarity=0.165  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..++..++|+.+|+|+.++++.....
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~fk~~   45 (108)
T 3oou_A           20 EGMSLKTLGNDFHINAVYLGQLFQKE   45 (108)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            47999999999999999999998654

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

Probab=92.99  E-value=0.1  Score=30.39  Aligned_cols=32  Identities=13%  Similarity=-0.015  Sum_probs=26.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+...-++|+.+||+.+|++++++++..
T Consensus        57 ~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   88 (161)
T 3e6m_A           57 RLLSSLSAYGELTVGQLATLGVMEQSTTSRTV   88 (161)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            45556666678999999999999999999874

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=92.96  E-value=0.066  Score=32.74  Aligned_cols=24  Identities=13%  Similarity=0.171  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.++|..+|+|+.+|++..+
T Consensus       177 l~~t~~~iA~~lg~sr~tvsR~l~  200 (237)
T 3fx3_A          177 LPYDKMLIAGRLGMKPESLSRAFS  200 (237)
T ss_dssp             CCSCTHHHHHHTTCCHHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHHH
Confidence            357899999999999999999864

>2rae_A Transcriptional regulator, ACRR family protein; TETR/ACRR family transcriptional regulator, structural genom 2, RHA08332, MCSG; 2.20A {Rhodococcus SP}

Probab=92.95  E-value=0.078  Score=31.40  Aligned_cols=29  Identities=14%  Similarity=0.083  Sum_probs=25.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .++|..++|+.+|||+.+++++..++...
T Consensus        36 ~~~ti~~Ia~~agvs~~t~Y~~F~sK~~L   64 (207)
T 2rae_A           36 DATSVDEVAEASGIARRTLFRYFPSKNAI   64 (207)
T ss_dssp             TTSCHHHHHHHTTSCHHHHHHHCSSTTTG
T ss_pred             ccCCHHHHHHHhCCCcchHhhhCCCHHHH
Confidence            36899999999999999999998776543

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=92.93  E-value=0.076  Score=31.55  Aligned_cols=28  Identities=11%  Similarity=0.127  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .+.|..++|+.+|||+.|++++-.++..
T Consensus        28 ~~~t~~~Ia~~Agvs~gt~Y~yF~sKe~   55 (204)
T 3anp_C           28 QETTATEIAKAAHVSRGTFFNYYPYKEA   55 (204)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSTHH
T ss_pred             ccccHHHHHHHcCCchHHHHHHcCCHHH
Confidence            3579999999999999999999876543

>2qtq_A Transcriptional regulator, TETR family; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: MSE; 1.85A {Novosphingobium aromaticivorans} PDB: 2rha_A*

Probab=92.92  E-value=0.069  Score=31.57  Aligned_cols=26  Identities=23%  Similarity=0.267  Sum_probs=23.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        36 ~~t~~~Ia~~agvs~~t~Y~~F~sK~   61 (213)
T 2qtq_A           36 DISLSELSLRSGLNSALVKYYFGNKA   61 (213)
T ss_dssp             CCCHHHHHHHHCCCHHHHHHHHSSHH
T ss_pred             cccHHHHHHHhCCChhhHhHhcCCHH
Confidence            68999999999999999999987654

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=92.90  E-value=0.049  Score=31.98  Aligned_cols=26  Identities=15%  Similarity=0.155  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        34 ~~ti~~Ia~~agvs~~t~Y~~F~sK~   59 (203)
T 3f1b_A           34 ETSMDAIAAKAEISKPMLYLYYGSKD   59 (203)
T ss_dssp             TCCHHHHHHHTTSCHHHHHHHCCSHH
T ss_pred             cccHHHHHHHhCCchHHHHHHhCCHH
Confidence            68999999999999999999976543

>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A

Probab=92.88  E-value=0.053  Score=32.14  Aligned_cols=27  Identities=15%  Similarity=0.051  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        33 ~~~ti~~Ia~~agvs~~t~Y~~F~sK~   59 (220)
T 3lhq_A           33 SATSLAEIANAAGVTRGAIYWHFKNKS   59 (220)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCceeehhhcCCHH
Confidence            358999999999999999999976643

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=92.87  E-value=0.093  Score=32.87  Aligned_cols=23  Identities=9%  Similarity=0.241  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.+|+++.+
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l~  239 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRILK  239 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            47999999999999999999864

>2v57_A TETR family transcriptional repressor LFRR; DNA-binding, transcription regulation; HET: PRL; 1.90A {Mycobacterium smegmatis} PDB: 2wgb_A

Probab=92.85  E-value=0.054  Score=31.67  Aligned_cols=27  Identities=15%  Similarity=0.160  Sum_probs=24.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++++..++.
T Consensus        31 ~~~t~~~Ia~~agvs~~t~Y~~F~sK~   57 (190)
T 2v57_A           31 PTAALGDIAAAAGVGRSTVHRYYPERT   57 (190)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            889999999999999999999976543

>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=92.83  E-value=0.16  Score=30.95  Aligned_cols=31  Identities=13%  Similarity=-0.033  Sum_probs=23.4

Q ss_pred             HHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKK--MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |.......|  .|+.|||+.+|++.++++++.+
T Consensus        14 I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~   46 (196)
T 3k2z_A           14 IEEFIEKNGYPPSVREIARRFRITPRGALLHLI   46 (196)
T ss_dssp             HHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHH
Confidence            444434444  8999999999999999888653

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

Probab=92.81  E-value=0.25  Score=28.59  Aligned_cols=27  Identities=19%  Similarity=0.160  Sum_probs=23.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +....++++.++|+.+|+|+++|++..
T Consensus        49 l~~~~~~~~~~la~~l~vs~~tvs~~l   75 (155)
T 2h09_A           49 IREVGEARQVDMAARLGVSQPTVAKML   75 (155)
T ss_dssp             HHHHSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHhCCCcCHHHHHHHhCcCHHHHHHHH
Confidence            344567999999999999999999874

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=92.79  E-value=0.055  Score=32.07  Aligned_cols=27  Identities=7%  Similarity=0.041  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        33 ~~~ti~~IA~~agvs~~t~Y~~F~sK~   59 (212)
T 3knw_A           33 VGVGLQEILKTSGVPKGSFYHYFESKE   59 (212)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCChHHHHHHCCCHH
Confidence            368999999999999999999976643

>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=92.78  E-value=0.072  Score=31.46  Aligned_cols=25  Identities=8%  Similarity=0.149  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+.|..++|+.+|||+.||+++-.+
T Consensus        31 ~~~t~~~IA~~agvsk~tlY~~F~s   55 (192)
T 2fq4_A           31 KAVTVDKIAERAKVSKATIYKWWPN   55 (192)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             ccccHHHHHHHcCCCHHHHHHHCCC
Confidence            3679999999999999999998654

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=92.76  E-value=0.079  Score=28.56  Aligned_cols=23  Identities=13%  Similarity=0.226  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..++..+||+.+|+|++++++..
T Consensus        35 ~~~~~~ela~~l~is~~tvs~~L   57 (98)
T 3jth_A           35 QELSVGELCAKLQLSQSALSQHL   57 (98)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHH
Confidence            67899999999999999999874

>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=92.76  E-value=0.069  Score=30.22  Aligned_cols=34  Identities=15%  Similarity=0.095  Sum_probs=27.1

Q ss_pred             HHHHHHHHHh--CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLG--KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~--~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...  .++|+.+||+.++++++++++..+
T Consensus        40 ~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~   75 (127)
T 2frh_A           40 FAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVK   75 (127)
T ss_dssp             HHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            3455666665  689999999999999999998743

>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=92.75  E-value=0.089  Score=30.11  Aligned_cols=33  Identities=21%  Similarity=0.163  Sum_probs=21.1

Q ss_pred             HHHHHHHHHh--CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLG--KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~--~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...  .++|+.+||+.+|++++++++..
T Consensus        44 ~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l   78 (148)
T 3jw4_A           44 GRMIGYIYENQESGIIQKDLAQFFGRRGASITSML   78 (148)
T ss_dssp             HHHHHHHHHHTTTCCCHHHHHHC------CHHHHH
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHH
Confidence            3456666665  79999999999999999998874

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=92.73  E-value=0.057  Score=32.09  Aligned_cols=26  Identities=23%  Similarity=0.261  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        51 ~~tv~~Ia~~agvs~~t~Y~~F~sK~   76 (218)
T 3dcf_A           51 ATSLDDIADRIGFTKPAIYYYFKSKE   76 (218)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCcHHHHHHHhCCCHHHHHHHcCCHH
Confidence            47999999999999999999876543

>2zcm_A Biofilm operon icaabcd HTH-type negative transcri regulator ICAR; helix-turn-helix, TETR family, repressor; 1.33A {Staphylococcus epidermidis} PDB: 2zcn_A

Probab=92.72  E-value=0.064  Score=31.53  Aligned_cols=27  Identities=11%  Similarity=0.145  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++++-.++.
T Consensus        26 ~~~t~~~IA~~agvs~~tlY~~F~sK~   52 (192)
T 2zcm_A           26 DGTTLDDISKSVNIKKASLYYHYDNKE   52 (192)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHTCCHH
T ss_pred             ccCCHHHHHHHhCCChHHHHHHCCCHH
Confidence            468999999999999999999876543

>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}

Probab=92.69  E-value=0.038  Score=32.40  Aligned_cols=27  Identities=7%  Similarity=-0.028  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++++-.++.
T Consensus        26 ~~~t~~~IA~~agvs~~t~Y~~F~sK~   52 (199)
T 3qbm_A           26 AGTAISDIMAATGLEKGGIYRHFESKE   52 (199)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHTTCSSHH
T ss_pred             CcCCHHHHHHHhCCCccHHHHhCCCHH
Confidence            468999999999999999999866543

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=92.69  E-value=0.31  Score=27.19  Aligned_cols=30  Identities=7%  Similarity=0.146  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQ   62 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~   62 (82)
                      ..++..+||+.+|+|+.++++..... ..++
T Consensus        22 ~~~~~~~lA~~~~~S~~~l~r~fk~~-G~s~   51 (120)
T 3mkl_A           22 HEWTLARIASELLMSPSLLKKKLREE-ETSY   51 (120)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHT-TCCH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHc-CCCH
Confidence            37899999999999999999997654 4444

>2g7s_A Transcriptional regulator, TETR family; APC5906, PSI, protein structure initiat midwest center for structural genomics, MCSG; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: a.4.1.9 a.121.1.1

Probab=92.68  E-value=0.051  Score=31.64  Aligned_cols=27  Identities=15%  Similarity=0.203  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+++++++-.++.
T Consensus        27 ~~~ti~~Ia~~agvs~~t~Y~~F~sK~   53 (194)
T 2g7s_A           27 NSFSYADISQVVGIRNASIHHHFPSKS   53 (194)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCchHHHHHcCCHH
Confidence            468999999999999999999876543

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=92.66  E-value=0.13  Score=28.40  Aligned_cols=32  Identities=6%  Similarity=-0.033  Sum_probs=25.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+. ..+++..+||+.+|+++++|++..+
T Consensus        29 ~IL~~L~-~~~~s~~eLa~~lgis~stvs~~L~   60 (108)
T 2kko_A           29 QILDLLA-QGERAVEAIATATGMNLTTASANLQ   60 (108)
T ss_dssp             HHHHHHT-TCCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4455554 4678999999999999999998753

>3ljl_A Transcriptional regulator LUXT; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MES; 3.20A {Vibrio parahaemolyticus}

Probab=92.65  E-value=0.079  Score=30.50  Aligned_cols=26  Identities=27%  Similarity=0.155  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        34 ~~ti~~Ia~~agvs~~t~Y~~F~sK~   59 (156)
T 3ljl_A           34 KMSYTTLSQQTGVSRTGISHHFPKKT   59 (156)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHCSSTH
T ss_pred             hcCHHHHHHHHCCCHHHHHHHCCCHH
Confidence            57999999999999999999987653

>4aci_A HTH-type transcriptional repressor ACNR; aconitase, citrate, TETR superfamily; HET: CIT; 1.65A {Corynebacterium glutamicum} PDB: 4ac6_A*

Probab=92.61  E-value=0.055  Score=31.65  Aligned_cols=26  Identities=8%  Similarity=-0.006  Sum_probs=23.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        34 ~~t~~~IA~~agvs~~t~Y~~F~sK~   59 (191)
T 4aci_A           34 GATVRRLEEATGKSRGAIFHHFGDKE   59 (191)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             cCCHHHHHHHHCCCchHHHHHCCCHH
Confidence            58999999999999999999987643

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

Probab=92.59  E-value=0.12  Score=29.79  Aligned_cols=32  Identities=13%  Similarity=-0.031  Sum_probs=25.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+...-++|+.+||+.+|++++++++..
T Consensus        47 ~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l   78 (155)
T 3cdh_A           47 RVLACLVDNDAMMITRLAKLSLMEQSRMTRIV   78 (155)
T ss_dssp             HHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34455555567999999999999999999874

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=92.59  E-value=0.061  Score=31.53  Aligned_cols=27  Identities=11%  Similarity=-0.050  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        27 ~~~t~~~IA~~Agvs~~tly~~F~sK~   53 (194)
T 3dpj_A           27 AQTSFVDISAAVGISRGNFYYHFKTKD   53 (194)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHHCCChHHHHHHcCCHH
Confidence            468999999999999999999976543

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=92.59  E-value=0.094  Score=30.86  Aligned_cols=26  Identities=15%  Similarity=0.187  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        27 ~~t~~~Ia~~agvs~~t~Y~~F~sK~   52 (195)
T 2dg7_A           27 NVTVTDIAERAGLTRRSYFRYFPDKR   52 (195)
T ss_dssp             GCCHHHHHHHTTCCHHHHHHHCSSTT
T ss_pred             ccCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            48999999999999999999987654

>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=92.58  E-value=0.13  Score=29.12  Aligned_cols=31  Identities=13%  Similarity=0.020  Sum_probs=24.4

Q ss_pred             HHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRAR-LGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+. ...++|+.++|+.+|++++++++..
T Consensus        31 il~~L~~~~~~~t~~ela~~l~~~~stvs~~l   62 (152)
T 1ku9_A           31 VYAILYLSDKPLTISDIMEELKISKGNVSMSL   62 (152)
T ss_dssp             HHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            344443 3468999999999999999999874

>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=92.54  E-value=0.25  Score=27.68  Aligned_cols=28  Identities=0%  Similarity=0.001  Sum_probs=25.0

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .....++|..|.|++.+||+++|.+|+.
T Consensus        45 ~v~~g~lS~~EAa~ry~Is~~ei~~W~r   72 (101)
T 2oa4_A           45 GVIYGLITLAEAKQTYGLSDEEFNSWVS   72 (101)
T ss_dssp             HHHHTTCCHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3456799999999999999999999985

>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell development; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=92.54  E-value=0.081  Score=31.38  Aligned_cols=59  Identities=14%  Similarity=0.043  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCCCCcccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENGKAV------PNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g~~~------p~~~~~~~la~~lgv~~~e~~   80 (82)
                      ...|+...+..+++|.-||+. +|.++.+++.+.+.-..      ...+.+.++-..|..+-++|+
T Consensus        27 ~~~Ik~eLk~~~IsQ~~FA~~VL~rsQGtLS~LLr~PkdPW~~LksGRE~fiRM~NWL~Lpe~eR~   92 (141)
T 1yse_A           27 YQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPEAERD   92 (141)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHCCSCTTHHHHHHHHCCCGGGCCHHHHHHHHHHHHHHHSCHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHHHcCCCCcHHHHHHHHHHHHHHHHHhcCCHHHHH
Confidence            788999999999999999995 58999999999875332      235667788888887776654

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=92.53  E-value=0.28  Score=27.02  Aligned_cols=26  Identities=0%  Similarity=0.111  Sum_probs=23.3

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..-++|..|+|++.|||++.|..|..
T Consensus        46 ~~g~~s~~e~arry~Is~s~i~~W~r   71 (95)
T 2jrt_A           46 IHGLITEREALDRYSLSEEEFALWRS   71 (95)
T ss_dssp             HTTSSCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34678999999999999999999974

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=92.50  E-value=0.062  Score=31.57  Aligned_cols=25  Identities=16%  Similarity=0.166  Sum_probs=22.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++.+..++
T Consensus        37 ~~s~~~Ia~~agvs~~t~Y~~F~sK   61 (206)
T 3kz9_A           37 RGGHADIAEIAQVSVATVFNYFPTR   61 (206)
T ss_dssp             SCCHHHHHHHHTSCHHHHHHHCCSH
T ss_pred             cccHHHHHHHhCCCHHHHHHHcCCH
Confidence            4789999999999999999997654

>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=92.46  E-value=0.11  Score=29.44  Aligned_cols=34  Identities=3%  Similarity=-0.028  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|+++++|++..+
T Consensus        43 ~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~   76 (147)
T 1z91_A           43 YLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLK   76 (147)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHH
Confidence            4456666666789999999999999999998743

>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3}

Probab=92.45  E-value=0.064  Score=32.70  Aligned_cols=26  Identities=15%  Similarity=0.092  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++.+..++.
T Consensus        63 ~~tv~~IA~~AGvs~~t~Y~~F~sKe   88 (229)
T 3bni_A           63 ALSTRAVALRADVPIGSVYRFFGNKR   88 (229)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             hccHHHHHHHHCCCchhHHHHcCCHH
Confidence            68999999999999999999976643

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=92.44  E-value=0.12  Score=32.72  Aligned_cols=22  Identities=18%  Similarity=0.267  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..|+|+.+|+|..||..||+
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~   22 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLR   22 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=92.43  E-value=0.12  Score=30.07  Aligned_cols=23  Identities=13%  Similarity=0.252  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|+.+||+.++++++++++..+
T Consensus        52 ~~t~~eLa~~l~~~~~tvsr~v~   74 (148)
T 4fx0_A           52 DLTMSELAARIGVERTTLTRNLE   74 (148)
T ss_dssp             --CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHH
Confidence            48999999999999999998753

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=92.43  E-value=0.066  Score=31.73  Aligned_cols=25  Identities=4%  Similarity=0.032  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+++++.+-.++
T Consensus        32 ~~ti~~Ia~~agvs~~t~Y~~F~~K   56 (189)
T 3vp5_A           32 EAKIMHIVKALDIPRGSFYQYFEDL   56 (189)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccHHHHHHHhCCChHHHHHHCCCH
Confidence            5699999999999999999986654

>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin repressor-like, C-terminal D homeodomain-like, DNA/RNA-binding 3-helical bundle; 1.55A {Aquifex aeolicus}

Probab=92.41  E-value=0.072  Score=31.06  Aligned_cols=27  Identities=11%  Similarity=0.005  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+-.++.
T Consensus        21 ~~~s~~~Ia~~agvskgtlY~~F~sKe   47 (179)
T 2eh3_A           21 QGTSVEEIVKRANLSKGAFYFHFKSKE   47 (179)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCcHHHHHHcCCHH
Confidence            367999999999999999999976543

>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=92.40  E-value=0.2  Score=28.63  Aligned_cols=34  Identities=12%  Similarity=0.081  Sum_probs=25.6

Q ss_pred             HHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+... .++|+.+||+.++++++++++..+
T Consensus        42 ~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~   76 (150)
T 3fm5_A           42 YSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVD   76 (150)
T ss_dssp             HHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHH
Confidence            3444555443 368999999999999999998743

>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=92.39  E-value=0.055  Score=30.83  Aligned_cols=32  Identities=6%  Similarity=0.049  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+....++|+.+||+.+++++++++++.
T Consensus        40 ~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   71 (140)
T 3hsr_A           40 IVLMAIENDEKLNIKKLGERVFLDSGTLTPLL   71 (140)
T ss_dssp             HHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCChhhHHHHH
Confidence            34444555668999999999999999999874

>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=92.35  E-value=0.1  Score=28.10  Aligned_cols=33  Identities=6%  Similarity=0.005  Sum_probs=26.0

Q ss_pred             HHHHHHHHhCCCCHHHH----HHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDL----ANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~el----A~~~gis~~~i~~~e~   55 (82)
                      ..|..+....++++.+|    |+.++++++++++..+
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~   48 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKK   48 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            44555555568999999    8999999999998743

>3o60_A LIN0861 protein; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative, unknown function; 2.80A {Listeria innocua}

Probab=92.31  E-value=0.11  Score=31.10  Aligned_cols=26  Identities=15%  Similarity=0.075  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+++++.+-.++.
T Consensus        40 ~~tv~~Ia~~Agvs~~t~Y~~F~~K~   65 (185)
T 3o60_A           40 SISIKDLCEQARVSRATFYRHHKEII   65 (185)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHCSSTH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            57999999999999999999987653

>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structur initiative; 2.30A {Rhodobacter sphaeroides 2}

Probab=92.31  E-value=0.069  Score=31.92  Aligned_cols=26  Identities=12%  Similarity=0.106  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        50 ~~t~~~IA~~aGvs~~t~Y~~F~sK~   75 (222)
T 3bru_A           50 SVGVDEILKAARVPKGSFYHYFRNKA   75 (222)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCcHHHHHHHhCCCcchhhhhCCCHH
Confidence            57999999999999999999976543

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=92.30  E-value=0.068  Score=31.67  Aligned_cols=27  Identities=11%  Similarity=0.011  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        37 ~~~s~~~Ia~~agvs~~t~Y~~F~sK~   63 (212)
T 1pb6_A           37 HGTRLEQIAELAGVSKTNLLYYFPSKE   63 (212)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHSSSHH
T ss_pred             chhhHHHHHHHHCCChhHHHHhCCCHH
Confidence            468999999999999999999976643

>3vib_A MTRR; helix-turn-helix motif, DNA binding, DNA binding protein; HET: CXS; 2.40A {Neisseria gonorrhoeae}

Probab=92.26  E-value=0.069  Score=31.89  Aligned_cols=27  Identities=11%  Similarity=0.024  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+..++.
T Consensus        29 ~~~s~~~IA~~aGvs~~t~Y~~F~sKe   55 (210)
T 3vib_A           29 ARTSLNEIAQAAGVTRDALYWHFKNKE   55 (210)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCCCHH
Confidence            467999999999999999999876543

>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4}

Probab=92.25  E-value=0.07  Score=31.80  Aligned_cols=26  Identities=19%  Similarity=0.328  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      +.|..++|+.+|||+.+|+++..++.
T Consensus        37 ~~t~~~IA~~agvs~~t~Y~~F~sK~   62 (218)
T 3gzi_A           37 QVSIREIASLAGTDPGLIRYYFGSKE   62 (218)
T ss_dssp             CCCHHHHHHHHTSCTHHHHHHHSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            47999999999999999999987654

>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=92.24  E-value=0.093  Score=31.38  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .+.|..++|+.+|||+.+|+++-.++..
T Consensus        31 ~~ts~~~IA~~aGvsk~tlY~~F~sKe~   58 (211)
T 3bhq_A           31 DGTSMEEIATKAGASKQTVYKHFTDKET   58 (211)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHCSHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence            4689999999999999999999876543

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=92.24  E-value=0.12  Score=30.19  Aligned_cols=26  Identities=23%  Similarity=0.189  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        28 ~~t~~~Ia~~agvs~~t~Y~~F~sK~   53 (206)
T 3dew_A           28 GVSIRELAQAAGASISMISYHFGGKE   53 (206)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHSCHHH
T ss_pred             cCcHHHHHHHhCCCHHHHHHHcCCHH
Confidence            68999999999999999999976543

>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=92.24  E-value=0.23  Score=29.88  Aligned_cols=34  Identities=9%  Similarity=0.066  Sum_probs=26.7

Q ss_pred             HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+..  ..++|+.+||+.+|++++++++..+
T Consensus        44 ~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~   79 (189)
T 3nqo_A           44 YMTILSILHLPEEETTLNNIARKMGTSKQNINRLVA   79 (189)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            344555554  4589999999999999999998753

>2jj7_A Hemolysin II regulatory protein; DNA-binding protein, transcription regulation, DNA-binding, family, transcription, transcriptional regulator; 2.10A {Bacillus cereus} PDB: 2wv1_A 2jk3_A 2fx0_A

Probab=92.23  E-value=0.084  Score=30.78  Aligned_cols=25  Identities=28%  Similarity=0.325  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++..++
T Consensus        27 ~~t~~~IA~~agvs~~tlY~~F~sK   51 (186)
T 2jj7_A           27 GTSIQEIAKEAKVNVAMASYYFNGK   51 (186)
T ss_dssp             HCCHHHHHHHHTSCHHHHHHHHSSH
T ss_pred             cCCHHHHHHHhCCChhhhhhhcCCH
Confidence            5899999999999999999998654

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=92.22  E-value=0.21  Score=26.02  Aligned_cols=33  Identities=15%  Similarity=0.127  Sum_probs=25.3

Q ss_pred             HHHHHHHHh--CCCCHHHHHHHh-----CCCHHHHHHHHc
Q 038591           23 RQIQRARLG--KKMSQPDLANQI-----NQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~--~g~s~~elA~~~-----gis~~~i~~~e~   55 (82)
                      ..|..+...  ..+|..||++.+     ++|.+||++..+
T Consensus        21 ~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~   60 (83)
T 2fu4_A           21 KILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLN   60 (83)
T ss_dssp             HHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHH
Confidence            344445443  579999999999     999999998753

>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=92.19  E-value=0.35  Score=27.23  Aligned_cols=32  Identities=13%  Similarity=0.193  Sum_probs=26.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQIN--QRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~   55 (82)
                      .|..+.....+|..++|..+|  +|.+||++|..
T Consensus        68 ~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~  101 (141)
T 1u78_A           68 NVIRAASNSCKTARDIRNELQLSASKRTILNVIK  101 (141)
T ss_dssp             HHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHH
T ss_pred             HHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHH
Confidence            344445667799999999999  89999999985

>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD, structural genomics, protein structure initiative; 2.96A {Cytophaga hutchinsonii}

Probab=92.16  E-value=0.073  Score=31.68  Aligned_cols=26  Identities=15%  Similarity=0.195  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        31 ~~ti~~Ia~~agvs~~t~Y~~F~sK~   56 (216)
T 3f0c_A           31 KTTMNEIASDVGMGKASLYYYFPDKE   56 (216)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            68999999999999999999976543

>3frq_A Repressor protein MPHR(A); macrolide antibiotic. repressor, biosensor, erythromycin, STRPTOMYCES, natural products, biosynthesis, DNA-binding; HET: ERY; 1.76A {Escherichia coli} PDB: 3g56_A

Probab=92.11  E-value=0.07  Score=31.43  Aligned_cols=27  Identities=4%  Similarity=0.099  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        27 ~~~t~~~IA~~agvs~~t~Y~~F~sK~   53 (195)
T 3frq_A           27 IEFTLSGVAKEVGLSRAALIQRFTNRD   53 (195)
T ss_dssp             HHCCHHHHHHHHTCCHHHHHHHHCSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            367999999999999999999987653

>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=92.11  E-value=0.4  Score=29.98  Aligned_cols=43  Identities=12%  Similarity=0.001  Sum_probs=31.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||......    -...+...+..+|..+|
T Consensus       188 ~~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~~~~a~~~g  234 (237)
T 3szt_A          188 AVGKTYGEIGLILSIDQRTVKFHIVNAMRKLNSSNKAEATMKAYAIG  234 (237)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence            68999999999999999999887653    22345555555555554

>3loc_A HTH-type transcriptional regulator RUTR; helix-turn-helix, putative transcriptional regulator, dimer, structural genomics, PSI; HET: MSE; 2.50A {Escherichia coli}

Probab=92.11  E-value=0.053  Score=32.07  Aligned_cols=26  Identities=12%  Similarity=0.011  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++..++
T Consensus        37 ~~~s~~~IA~~aGvs~~tlY~~F~sK   62 (212)
T 3loc_A           37 HGTRLEQIAELAGVSKTNLLYYFPSK   62 (212)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHSSSH
T ss_pred             ccCCHHHHHHHHCcCHHHHhhhCCCH
Confidence            46899999999999999999998765

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=92.10  E-value=0.26  Score=30.32  Aligned_cols=38  Identities=11%  Similarity=0.080  Sum_probs=28.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPN   61 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~   61 (82)
                      .+..+++..-+|..|||+.+|+|.+||.+=..--..|.
T Consensus        17 i~~~l~~~~~~~~~~la~~~~vs~~TiRrDl~eL~~~~   54 (190)
T 4a0z_A           17 IRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPE   54 (190)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHCCCEeHHHHHHHHCCCHHHHHHHHHHhcCcc
Confidence            34555555668999999999999999988655434444

>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A*

Probab=92.09  E-value=0.078  Score=31.24  Aligned_cols=25  Identities=12%  Similarity=-0.024  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++..++
T Consensus        24 ~~t~~~Ia~~agvs~~t~Y~~F~sK   48 (185)
T 2yve_A           24 TLSYDSLAEATGLSKSGLIYHFPSR   48 (185)
T ss_dssp             TCCHHHHHHHHCCCHHHHHHHCSSH
T ss_pred             hccHHHHHHHhCCChHHHHHhCcCH
Confidence            5799999999999999999987654

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=92.09  E-value=0.052  Score=31.61  Aligned_cols=27  Identities=19%  Similarity=0.202  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++-.++.
T Consensus        27 ~~~t~~~Ia~~agvs~~t~Y~~F~sK~   53 (195)
T 3pas_A           27 SATSVGKIAKAAGLSPATLYIYYEDKE   53 (195)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             HhcCHHHHHHHhCCCchHHHHHcCCHH
Confidence            368999999999999999999976643

>3rh2_A Hypothetical TETR-like transcriptional regulator; DNA/RNA-binding 3-helical bundle, structural genomics, joint for structural genomics; 2.42A {Shewanella amazonensis}

Probab=92.08  E-value=0.065  Score=31.98  Aligned_cols=27  Identities=11%  Similarity=0.183  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++-.++.
T Consensus        22 ~~~s~~~IA~~Agvs~~t~Y~~F~sK~   48 (212)
T 3rh2_A           22 RTITTNHIAAHLDISPGNLYYHFRNKE   48 (212)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            358999999999999999999876543

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=92.07  E-value=0.77  Score=28.93  Aligned_cols=43  Identities=14%  Similarity=0.161  Sum_probs=32.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||......    -+..+...+..+|...|
T Consensus       210 ~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~~~~~~~~~~a~~~g  256 (258)
T 3clo_A          210 RKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMK  256 (258)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence            68999999999999999999887643    23445666666666555

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=92.00  E-value=0.18  Score=29.69  Aligned_cols=33  Identities=15%  Similarity=0.013  Sum_probs=26.2

Q ss_pred             HHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARL-GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+.. .-++|+.+||+.++++++++++..
T Consensus        56 ~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l   89 (166)
T 3deu_A           56 WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTL   89 (166)
T ss_dssp             HHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHH
Confidence            344555555 457999999999999999999874

>2kfs_A Conserved hypothetical regulatory protein; WHTH, DNA binding, phosphorylation, DNA-binding protein; NMR {Mycobacterium tuberculosis}

Probab=91.97  E-value=0.13  Score=30.74  Aligned_cols=29  Identities=10%  Similarity=0.069  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .=+|..|+|+.+||+.++|+++.+....+
T Consensus        30 ~~LTv~EVAe~LgVs~srV~~LIr~G~L~   58 (148)
T 2kfs_A           30 PTYDLPRVAELLGVPVSKVAQQLREGHLV   58 (148)
T ss_dssp             CEEEHHHHHHHHTCCHHHHHHHHHTTSCC
T ss_pred             ceEcHHHHHHHhCCCHHHHHHHHHCCCce
Confidence            45799999999999999999998765443

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=91.96  E-value=0.42  Score=28.44  Aligned_cols=53  Identities=11%  Similarity=0.113  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCC-----CCCHHHHHHHHHHhCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQI-NQRPQVVSEYENGKA-----VPNQTVLAKMEKAIGV   74 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e~g~~-----~p~~~~~~~la~~lgv   74 (82)
                      ...|+..+...+++|..||+.+ |+++.+++.+.+.-.     ....+....+-..|..
T Consensus        10 ~~~i~~~l~~~~i~q~~fa~~ilg~sq~~ls~~l~~pkpw~~l~~g~~~y~rm~~WL~~   68 (164)
T 2d5v_A           10 AQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQE   68 (164)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCCHHHHHHHHHSCCCGGGCSTTHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCchHHHHHHHhcCCchhHHHHcCCCCCHHHHcccchHHHHHHHHHhc
Confidence            6788999999999999999965 999999999997421     1233444445555543

>3mnl_A KSTR, transcriptional regulatory protein (probably TETR; TETR family of transcriptional regulator, all-helical; 1.80A {Mycobacterium tuberculosis}

Probab=91.96  E-value=0.057  Score=31.79  Aligned_cols=26  Identities=12%  Similarity=0.138  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        40 ~~t~~~Ia~~agvs~~t~Y~~F~~K~   65 (203)
T 3mnl_A           40 AVQMRAVADRADVAVGTLYRYFPSKV   65 (203)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHcCCChhHHHHHcCCHH
Confidence            68999999999999999999976644

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

Probab=91.92  E-value=0.2  Score=28.42  Aligned_cols=33  Identities=12%  Similarity=0.026  Sum_probs=25.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+ |+.+||+.+|++++++++..+
T Consensus        40 ~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~l~   72 (144)
T 3f3x_A           40 FSILKATSEEPR-SMVYLANRYFVTQSAITAAVD   72 (144)
T ss_dssp             HHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCC-CHHHHHHHHCCChhHHHHHHH
Confidence            345555655556 999999999999999998753

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=91.89  E-value=0.14  Score=29.95  Aligned_cols=28  Identities=18%  Similarity=0.045  Sum_probs=23.9

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++--.|+|.+|+|+.+|+|..||.....
T Consensus       104 L~~~~g~s~~EIA~~lgis~~tV~~~l~  131 (157)
T 2lfw_A          104 LTAMEGFSPEDAAYLIEVDTSEVETLVT  131 (157)
T ss_dssp             TTSSSCCCHHHHHHTTTSCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4456799999999999999999988754

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=91.88  E-value=0.06  Score=31.68  Aligned_cols=26  Identities=12%  Similarity=0.309  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++-.++
T Consensus        36 ~~~ti~~Ia~~agvs~~t~Y~~F~sK   61 (208)
T 3cwr_A           36 AAMTMEGVASEAGIAKKTLYRFASGR   61 (208)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             HhccHHHHHHHhCCCHHHHHHHcCCH
Confidence            46899999999999999999997654

>3c2b_A Transcriptional regulator, TETR family; structural genomics, APC5923, PSI-2, PR structure initiative; 2.10A {Agrobacterium tumefaciens str}

Probab=91.87  E-value=0.12  Score=30.88  Aligned_cols=27  Identities=15%  Similarity=0.234  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+|+++..++.
T Consensus        34 ~~~s~~~IA~~agvs~~t~Y~~F~sKe   60 (221)
T 3c2b_A           34 KALTTSGLARAANCSKESLYKWFGDRD   60 (221)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHhCCCHH
Confidence            368999999999999999999987643

>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1}

Probab=91.86  E-value=0.077  Score=31.50  Aligned_cols=26  Identities=12%  Similarity=0.029  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        32 ~~t~~~IA~~agvs~~tlY~~F~sK~   57 (196)
T 2qwt_A           32 GVPMDEIARRAGVGAGTVYRHFPTKQ   57 (196)
T ss_dssp             TSCHHHHHHHTTSCHHHHHHHCSSHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            68999999999999999999976543

>3e7q_A Transcriptional regulator; structural genomics, PSI, MCSG, P structure initiative, midwest center for structural genomic binding; 2.20A {Pseudomonas aeruginosa}

Probab=91.85  E-value=0.059  Score=31.87  Aligned_cols=27  Identities=11%  Similarity=0.160  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++.+..++.
T Consensus        33 ~~~t~~~Ia~~agvs~~t~Y~~F~sK~   59 (215)
T 3e7q_A           33 QGASVRKICAEAGVSVGLINHHYDGKD   59 (215)
T ss_dssp             HHCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            368999999999999999999976543

>2ibd_A Possible transcriptional regulator; probable transcriptional regulatory protein, rhodococcus SP. structural genomics, PSI-2; 1.50A {Rhodococcus SP}

Probab=91.83  E-value=0.088  Score=31.33  Aligned_cols=27  Identities=11%  Similarity=0.084  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+-.++.
T Consensus        33 ~~~s~~~IA~~agvs~~tlY~~F~sKe   59 (204)
T 2ibd_A           33 RATTVRDIADAAGILSGSLYHHFDSKE   59 (204)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHCSCHH
T ss_pred             hhcCHHHHHHHhCCCchhHHHhcCCHH
Confidence            468999999999999999999976643

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

Probab=91.81  E-value=0.21  Score=30.66  Aligned_cols=34  Identities=9%  Similarity=-0.082  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+++++++++++.+
T Consensus        51 ~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~   84 (207)
T 2fxa_A           51 HHILWIAYQLNGASISEIAKFGVMHVSTAFNFSK   84 (207)
T ss_dssp             HHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            4556666666799999999999999999988753

>3cjd_A Transcriptional regulator, TETR family; YP_510936.1, putative TETR transcriptional regulator, struct genomics; HET: STE; 1.79A {Jannaschia SP}

Probab=91.80  E-value=0.071  Score=31.80  Aligned_cols=27  Identities=11%  Similarity=0.032  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++.+-.++.
T Consensus        31 ~~~s~~~IA~~agvs~~t~Y~hF~~Ke   57 (198)
T 3cjd_A           31 ASLRARELARQADCAVGAIYTHFQDLN   57 (198)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             hhcCHHHHHHHhCCCccHHHHHhCCHH
Confidence            368999999999999999999876643

>2nx4_A Transcriptional regulator, TETR family protein; HTH DNA binding motif, structural genomics, PSI-2, Pro structure initiative; 1.70A {Rhodococcus SP}

Probab=91.80  E-value=0.092  Score=31.09  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+.+..++.
T Consensus        29 ~~~s~~~IA~~aGvs~gtlY~yF~sKe   55 (194)
T 2nx4_A           29 EAANMRDIATEAGYTNGALSHYFAGKD   55 (194)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCcchHHHhCcCHH
Confidence            468999999999999999999976543

>3dn7_A Cyclic nucleotide binding regulatory protein; structural genomics, APC88869, cyclic nucleotide binding REG protein, PSI-2; 1.80A {Cytophaga hutchinsonii}

Probab=91.80  E-value=0.031  Score=33.22  Aligned_cols=25  Identities=24%  Similarity=0.263  Sum_probs=0.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+|++++|..+|+++.+++++.+
T Consensus       166 ~~~~t~~~iA~~lG~sretlsR~l~  190 (194)
T 3dn7_A          166 IQRVPQYLLASYLGFTPEYLSEIRK  190 (194)
T ss_dssp             -------------------------
T ss_pred             HHHCCHHHHHHHhCCCHHHHHHHHH
Confidence            3478999999999999999999865

>2oer_A Probable transcriptional regulator; helix-turn-helix, alpha-beta, structural genomics, PSI-2, protein structure initiative; 2.00A {Pseudomonas aeruginosa}

Probab=91.79  E-value=0.087  Score=31.70  Aligned_cols=26  Identities=15%  Similarity=0.211  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      +.|..++|+.+|||+.+|+++..++.
T Consensus        44 ~~s~~~IA~~aGvskgtlY~yF~sKe   69 (214)
T 2oer_A           44 RFTTARVAERAGVSIGSLYQYFPNKA   69 (214)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cccHHHHHHHhCCCCchHHHhCCCHH
Confidence            68999999999999999999976643

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=91.76  E-value=0.056  Score=31.92  Aligned_cols=26  Identities=12%  Similarity=0.080  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+++++.+..++.
T Consensus        29 ~~ti~~IA~~agvs~~t~Y~~F~sK~   54 (193)
T 2dg8_A           29 RVSHRRIAQRAGVPLGSMTYHFTGIE   54 (193)
T ss_dssp             GCCHHHHHHHHTSCTHHHHHHCSSHH
T ss_pred             hccHHHHHHHhCCCchhhheeCCCHH
Confidence            58999999999999999999876543

>1vi0_A Transcriptional regulator; structural genomics; HET: MSE DCC; 1.65A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=91.73  E-value=0.073  Score=31.90  Aligned_cols=27  Identities=15%  Similarity=0.144  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+++-.++.
T Consensus        27 ~~~s~~~IA~~AGvs~gt~Y~yF~sKe   53 (206)
T 1vi0_A           27 HQSQVSKIAKQAGVADGTIYLYFKNKE   53 (206)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCChhHHHHHcCCHH
Confidence            367999999999999999999976643

>2hku_A A putative transcriptional regulator; structural genomics, APC6040, TET rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.71  E-value=0.11  Score=31.04  Aligned_cols=27  Identities=15%  Similarity=0.275  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+|+.+..++.
T Consensus        38 ~~~s~~~IA~~aGvs~~tlY~~F~sK~   64 (215)
T 2hku_A           38 EGVPITQICAAAGAHPNQVTYYYGSKE   64 (215)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            579999999999999999999987643

>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}

Probab=91.69  E-value=0.052  Score=32.19  Aligned_cols=27  Identities=11%  Similarity=0.175  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++.+-.++.
T Consensus        44 ~~~t~~~Ia~~agvs~~t~Y~~F~sK~   70 (212)
T 3nxc_A           44 QRITTAKLAASVGVSEAALYRHFPSKT   70 (212)
T ss_dssp             --CCHHHHHHHTTSCHHHHHTTCSSHH
T ss_pred             hhcCHHHHHHHhCCChhHHHHHCCCHH
Confidence            358999999999999999999876543

>2g3b_A Putative TETR-family transcriptional regulator; transcription regulator, structural genomics, P protein structure initiative; HET: MSE; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.68  E-value=0.08  Score=31.83  Aligned_cols=29  Identities=10%  Similarity=0.056  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      .+.|..++|+.+|||+.+|+.+..++...
T Consensus        22 ~~~s~~~IA~~AGvskgtlY~hF~sKe~L   50 (208)
T 2g3b_A           22 RGLRVNDVAEVAGVSPGLLYYHFKDRIGL   50 (208)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHHCSHHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCCCHHHH
Confidence            46899999999999999999998765443

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=91.67  E-value=0.059  Score=31.70  Aligned_cols=26  Identities=12%  Similarity=0.165  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+++++-.++
T Consensus        30 ~~~s~~~Ia~~agvs~~t~Y~~F~sK   55 (203)
T 3b81_A           30 ENTTLAFIINKLGISKGALYHYFSSK   55 (203)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHTTCSSH
T ss_pred             ccCcHHHHHHHhCCCchhHHHHcCCH
Confidence            36899999999999999999986553

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=91.67  E-value=0.078  Score=31.68  Aligned_cols=26  Identities=8%  Similarity=0.077  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        43 ~~t~~~IA~~agvs~~t~Y~~F~sK~   68 (214)
T 2zb9_A           43 QLTFERVARVSGVSKTTLYKWWPSKG   68 (214)
T ss_dssp             GCCHHHHHHHHCCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHCCCHH
Confidence            68999999999999999999976643

>2rek_A Putative TETR-family transcriptional regulator; sulfur, SAD, structural genomics, PSI-2, protein structure initiative; 1.86A {Streptomyces coelicolor A3}

Probab=91.61  E-value=0.079  Score=31.28  Aligned_cols=25  Identities=8%  Similarity=0.069  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..++|+.+|||+.+++++..++
T Consensus        35 ~~s~~~Ia~~agvs~~t~Y~~F~sK   59 (199)
T 2rek_A           35 DASLEEIARRAGVGSATLHRHFPSR   59 (199)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             CCCHHHHHHHhCCchHHHHHHCCCH
Confidence            6899999999999999999997654

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

Probab=91.57  E-value=0.19  Score=29.31  Aligned_cols=33  Identities=15%  Similarity=0.054  Sum_probs=25.4

Q ss_pred             HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+-. ..+.+|.+||+.+|+++++++++.+
T Consensus        35 ~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~   68 (151)
T 4aik_A           35 VTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLD   68 (151)
T ss_dssp             HHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            34455533 4678999999999999999998753

>2o7t_A Transcriptional regulator; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1

Probab=91.54  E-value=0.082  Score=31.29  Aligned_cols=26  Identities=8%  Similarity=0.049  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        28 ~~t~~~IA~~agvs~~tlY~~F~sK~   53 (199)
T 2o7t_A           28 SLTMENIAEQAGVGVATLYRNFPDRF   53 (199)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            57999999999999999999976543

>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription regulation, TETR, DNA-binding transcription; 2.90A {Pseudomonas aeruginosa}

Probab=91.53  E-value=0.12  Score=30.92  Aligned_cols=26  Identities=19%  Similarity=0.107  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+.+..++
T Consensus        30 ~~~s~~~IA~~aGvskgtlY~~F~sK   55 (210)
T 2wui_A           30 GTTAMADLADAAGVSRGAVYGHYKNK   55 (210)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHcCCH
Confidence            35799999999999999999986543

>2gen_A Probable transcriptional regulator; APC6095, TETR family, structural genomics, PSI, protein structure initiative; 1.70A {Pseudomonas aeruginosa PAO1} SCOP: a.4.1.9 a.121.1.1

Probab=91.53  E-value=0.11  Score=30.85  Aligned_cols=27  Identities=4%  Similarity=-0.080  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++++-.++.
T Consensus        26 ~~ts~~~IA~~aGvs~gtlY~~F~sKe   52 (197)
T 2gen_A           26 DATTIEMIRDRSGASIGSLYHHFGNKE   52 (197)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHTCSHH
T ss_pred             ccCCHHHHHHHHCCChHHHHHHCCCHH
Confidence            357999999999999999999976543

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=91.49  E-value=0.27  Score=27.86  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=21.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+++..++|+.+|+|++++++..
T Consensus        57 ~~~~s~~ela~~lgis~stvs~~L   80 (122)
T 1r1t_A           57 RSELCVGDLAQAIGVSESAVSHQL   80 (122)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHH
Confidence            346899999999999999999864

>2i10_A Putative TETR transcriptional regulator; structural genomics, APC5890, TETR family, PSI-2, protein ST initiative; HET: MSE NPO PGE; 2.05A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.48  E-value=0.18  Score=30.08  Aligned_cols=26  Identities=19%  Similarity=0.202  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++-.++
T Consensus        30 ~~ts~~~IA~~aGvsk~tlY~~F~sK   55 (202)
T 2i10_A           30 EGTSITDLTKALGINPPSLYAAFGSK   55 (202)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHCSH
T ss_pred             ccCCHHHHHHHhCCChHHHHHHhCCH
Confidence            46899999999999999999997654

>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans}

Probab=91.47  E-value=0.081  Score=31.35  Aligned_cols=26  Identities=12%  Similarity=0.222  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        46 ~~t~~~Ia~~agvs~~t~Y~~F~sK~   71 (217)
T 3mvp_A           46 NVTTNEIAKKADVSVGTLYAYFASKE   71 (217)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccCHHHHHHHhCCChhHHHHHcCCHH
Confidence            68999999999999999999976643

>3g7r_A Putative transcriptional regulator; TETR, all-helical, structural genomics, PSI-2, protein structure initiative; 1.38A {Streptomyces coelicolor A3}

Probab=91.47  E-value=0.094  Score=31.70  Aligned_cols=26  Identities=8%  Similarity=0.075  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      +.|..++|+.+|||+.+|+.+..++.
T Consensus        55 ~~t~~~IA~~AGvs~~tlY~~F~sKe   80 (221)
T 3g7r_A           55 SVGIDRITAEAQVTRATLYRHFSGKD   80 (221)
T ss_dssp             TSCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            58999999999999999999976643

>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=91.47  E-value=0.19  Score=27.86  Aligned_cols=33  Identities=12%  Similarity=0.136  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC----CCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN----QRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g----is~~~i~~~e   54 (82)
                      ...|..+....++|+.+||+.++    ++++||+++.
T Consensus        13 ~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l   49 (123)
T 1okr_A           13 WEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLI   49 (123)
T ss_dssp             HHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHH
Confidence            34556666678999999999999    8999999874

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

Probab=91.45  E-value=0.25  Score=27.90  Aligned_cols=33  Identities=15%  Similarity=0.031  Sum_probs=28.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh--CCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQI--NQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~--gis~~~i~~~e   54 (82)
                      ...|..++..-.+|..+||+.+  |+|+++|++..
T Consensus        16 ~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL   50 (111)
T 3b73_A           16 DRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRL   50 (111)
T ss_dssp             HHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHH
Confidence            5567777777899999999999  99999999864

>2hyt_A TETR-family transcriptional regulator; structural genomics, center for structural genomics, JCSG, protein structure INI PSI-2; HET: MSE; 1.64A {Pectobacterium atrosepticum}

Probab=91.40  E-value=0.083  Score=31.32  Aligned_cols=27  Identities=19%  Similarity=0.073  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+-.++.
T Consensus        31 ~~~s~~~IA~~aGvs~~tlY~~F~sKe   57 (197)
T 2hyt_A           31 ADTSMDDLTAQASLTRGALYHHFGDKK   57 (197)
T ss_dssp             TTCCHHHHHHHHTCCTTHHHHHHSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            367999999999999999999987654

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

Probab=91.39  E-value=0.085  Score=29.61  Aligned_cols=33  Identities=18%  Similarity=0.100  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.++|+.+|++++++++..
T Consensus        36 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l   68 (139)
T 3bja_A           36 FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMI   68 (139)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHH
Confidence            445566666678999999999999999988874

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=91.39  E-value=0.39  Score=29.82  Aligned_cols=43  Identities=19%  Similarity=0.171  Sum_probs=31.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||......    -...+...+..+|..+|
T Consensus       188 ~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~~~~a~~~g  234 (236)
T 2q0o_A          188 SKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRG  234 (236)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence            58999999999999999999887653    12345555566665555

>2qib_A TETR-family transcriptional regulator; HTH DNA binding, STRU genomics, MCSG, PSI-2, protein structure initiative; HET: P6G; 1.70A {Streptomyces coelicolor A3}

Probab=91.34  E-value=0.084  Score=32.20  Aligned_cols=26  Identities=23%  Similarity=0.293  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        33 ~~tv~~IA~~agvs~~t~Y~~F~sK~   58 (231)
T 2qib_A           33 EVSIDEIASAAGISRPLVYHYFPGKL   58 (231)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             hcCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            47999999999999999999976543

>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei}

Probab=91.26  E-value=0.089  Score=31.79  Aligned_cols=26  Identities=12%  Similarity=0.147  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        25 ~~t~~~IA~~Agvs~~t~Y~~F~sK~   50 (228)
T 3nnr_A           25 NITTNHIAAHLAISPGNLYYHFRNKS   50 (228)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             hcCHHHHHHHhCCCCccchhcCCCHH
Confidence            58999999999999999999876643

>2np5_A Transcriptional regulator; TETR family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE LMT NDS; 1.80A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.26  E-value=0.09  Score=31.36  Aligned_cols=27  Identities=15%  Similarity=0.044  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+++..++.
T Consensus        28 ~~~s~~~IA~~AGvs~gtlY~~F~sKe   54 (203)
T 2np5_A           28 EGASVREVAKRAGVSIGAVQHHFSTKD   54 (203)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             hhccHHHHHHHhCCCHHHHHHHcCCHH
Confidence            368999999999999999999876543

>3col_A Putative transcription regulator; structural genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Lactobacillus plantarum WCFS1}

Probab=91.25  E-value=0.046  Score=31.86  Aligned_cols=25  Identities=20%  Similarity=0.210  Sum_probs=22.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++-.++
T Consensus        30 ~~ti~~Ia~~agvs~~t~Y~~F~sK   54 (196)
T 3col_A           30 GVSTTKVAKRVGIAQSNVYLYFKNK   54 (196)
T ss_dssp             GCCHHHHHHHHTSCHHHHHTTCSSH
T ss_pred             cCCHHHHHHHhCCcHHHHHHHhCCH
Confidence            5899999999999999999986654

>3rd3_A Probable transcriptional regulator; 2.40A {Pseudomonas aeruginosa}

Probab=91.19  E-value=0.056  Score=31.59  Aligned_cols=25  Identities=8%  Similarity=0.070  Sum_probs=22.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++-.++
T Consensus        30 ~~t~~~IA~~agvs~~tlY~~F~sK   54 (197)
T 3rd3_A           30 GVGLNEILQSAGVPKGSFYHYFKSK   54 (197)
T ss_dssp             TCCHHHHHHHHTCCHHHHTTTCSCH
T ss_pred             cCCHHHHHHHhCCChhhHHHHcCCH
Confidence            5799999999999999999986554

>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=91.16  E-value=0.29  Score=29.99  Aligned_cols=31  Identities=19%  Similarity=0.345  Sum_probs=25.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+. ...+|..+||+.+|+|++++++..
T Consensus        24 ~IL~~L~-~~~~s~~eLA~~lglS~stv~~~l   54 (192)
T 1uly_A           24 KILKLLR-NKEMTISQLSEILGKTPQTIYHHI   54 (192)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3455555 578999999999999999998864

>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=91.16  E-value=0.092  Score=32.07  Aligned_cols=26  Identities=23%  Similarity=0.146  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        64 ~~t~~~IA~~aGvs~~tlY~~F~sK~   89 (236)
T 3q0w_A           64 DISVDDLAKGAGISRPTFYFYFPSKE   89 (236)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCcHHHHHHHCCCHH
Confidence            46999999999999999999977643

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=91.16  E-value=0.14  Score=31.48  Aligned_cols=22  Identities=14%  Similarity=0.120  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCH-HHHHHHH
Q 038591           33 KMSQPDLANQINQRP-QVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~-~~i~~~e   54 (82)
                      .+|+.+||..+|+|+ .+|++..
T Consensus       169 ~~t~~~lA~~lG~sr~etvsR~l  191 (238)
T 2bgc_A          169 NLTMQELGYSSGIAHSSAVSRII  191 (238)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCChHHHHHHHH
Confidence            789999999999999 6999874

>3v6g_A Probable transcriptional regulatory protein (PROB family); helix-turn-helix DNA binding domain; 1.82A {Mycobacterium tuberculosis}

Probab=91.15  E-value=0.11  Score=31.45  Aligned_cols=27  Identities=19%  Similarity=0.118  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+.+..++.
T Consensus        33 ~~~s~~~IA~~AGvs~~tlY~~F~sKe   59 (208)
T 3v6g_A           33 GGLSHRRVAAEANVPVGSTTYYFNDLD   59 (208)
T ss_dssp             TCCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCchhHHHHcCCHH
Confidence            468999999999999999999976543

>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=91.14  E-value=0.34  Score=30.53  Aligned_cols=32  Identities=13%  Similarity=0.104  Sum_probs=25.0

Q ss_pred             HHHHHHHhC-CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGK-KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~-g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+.... ++|..|||+.+|++++|++++.+
T Consensus        13 iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~   45 (249)
T 1mkm_A           13 ILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMV   45 (249)
T ss_dssp             HHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444433 69999999999999999999753

>3bjb_A Probable transcriptional regulator, TETR family P; APC7331, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.50A {Rhodococcus SP}

Probab=91.13  E-value=0.12  Score=30.98  Aligned_cols=25  Identities=12%  Similarity=0.167  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..++|+.+|||+.+++++..++
T Consensus        42 ~~s~~~IA~~AGVsk~tlY~~F~sK   66 (207)
T 3bjb_A           42 RVQMHEVAKRAGVAIGTLYRYFPSK   66 (207)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHCCCH
Confidence            4789999999999999999986553

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=91.12  E-value=0.47  Score=32.25  Aligned_cols=58  Identities=10%  Similarity=0.118  Sum_probs=45.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .-+|--.+..+.+|..|+|...|+...-+.++..+. ..|....+..||..|+|.+...
T Consensus         5 ~frl~hwmnark~t~~e~~~~~~~~~~~~~~~l~~~~~e~~~~~~~~l~~~l~v~~~qi   63 (443)
T 3g7d_A            5 PFKLAHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEALSVEPSQL   63 (443)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHC--------CHHHHHHHHHTTCCGGGT
T ss_pred             hhhHHHhhhhhccccHHHHhhcCCCHHHHHHHhcCcccCCCHHHHHHHHHHhcCChHHh
Confidence            345677788899999999999999999999999875 4688889999999999998653

>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=91.11  E-value=0.2  Score=26.74  Aligned_cols=33  Identities=12%  Similarity=-0.042  Sum_probs=25.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHH-HHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQ-VVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~-~i~~~e   54 (82)
                      ...|..+...-+.|..++|+.+||+.. +|.+..
T Consensus        14 ~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL   47 (79)
T 1xmk_A           14 EKICDYLFNVSDSSALNLAKNIGLTKARDINAVL   47 (79)
T ss_dssp             HHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHH
Confidence            345566667778999999999999998 777654

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=91.09  E-value=0.53  Score=27.63  Aligned_cols=36  Identities=17%  Similarity=0.092  Sum_probs=30.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ...+..+....|.+..++|+.+|+|+.|++++.+..
T Consensus       145 ~~~~~~~~~~~~~~~~~ia~~l~is~~tv~~~l~~~  180 (184)
T 3rqi_A          145 WEHIQRVLAENNNNISATARALNMHRRTLQRKLAKK  180 (184)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHCC-
T ss_pred             HHHHHHHHHhccccHHHHHHHcCCcHHHHHHHHHhc
Confidence            566777777889999999999999999999998753

>3crj_A Transcription regulator; APC88200, TETR, structura genomics, PSI-2, protein structure initiative; HET: MSE; 2.60A {Haloarcula marismortui atcc 43049}

Probab=91.08  E-value=0.072  Score=31.76  Aligned_cols=26  Identities=15%  Similarity=0.284  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+.+..++
T Consensus        33 ~~~s~~~IA~~agvsk~tlY~yF~sK   58 (199)
T 3crj_A           33 ADLTIQRIADEYGKSTAAVHYYYDTK   58 (199)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTCSSH
T ss_pred             ccCCHHHHHHHhCCChhHHhhhcCCH
Confidence            46899999999999999999986554

>1rkt_A Protein YFIR; transcription regulator, structural genomics, PSI, protein S initiative, midwest center for structural genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=91.02  E-value=0.08  Score=31.53  Aligned_cols=27  Identities=11%  Similarity=0.030  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+++..++.
T Consensus        31 ~~ts~~~IA~~agvs~gtlY~yF~sKe   57 (205)
T 1rkt_A           31 ELTTMKDVVEESGFSRGGVYLYFSSTE   57 (205)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTCSCHH
T ss_pred             ccCCHHHHHHHHCCCcchhhhhCCCHH
Confidence            468999999999999999999876543

>2id3_A Putative transcriptional regulator; structural genomics, PSI-2, prote structure initiative; 1.70A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=90.96  E-value=0.11  Score=31.48  Aligned_cols=38  Identities=13%  Similarity=0.081  Sum_probs=28.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      ++|..++|+.+|||+.+|+.+..++...-...+..+..
T Consensus        60 ~~t~~~IA~~Agvs~~t~Y~~F~sK~~L~~~v~~~~~~   97 (225)
T 2id3_A           60 ALDLGEIARRAGVGKTTVYRRWGTPGGLAADLLADMAE   97 (225)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHHCSHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            58999999999999999999987654433333333333

>3s5r_A Transcriptional regulator TETR family; DNA/RNA-binding 3-helical bundle, tetracyclin repressor-like structural genomics; 2.60A {Syntrophus aciditrophicus}

Probab=90.96  E-value=0.074  Score=31.57  Aligned_cols=26  Identities=12%  Similarity=0.322  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        29 ~~~ti~~Ia~~agvs~~t~Y~~F~sK   54 (216)
T 3s5r_A           29 AATTMAEIAASVGVNPAMIHYYFKTR   54 (216)
T ss_dssp             TTCCHHHHHHTTTCCHHHHHHHCSSH
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHcCCH
Confidence            46899999999999999999997654

>2pz9_A Putative regulatory protein; structural genomics, transcriptional regulator, PSI, protein structure initiative; 2.80A {Streptomyces coelicolor A3}

Probab=90.85  E-value=0.08  Score=32.14  Aligned_cols=27  Identities=19%  Similarity=0.144  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+|+++..++.
T Consensus        49 ~~~s~~~IA~~aGvs~~tlY~~F~sK~   75 (226)
T 2pz9_A           49 AGARVDRIAKQARTSKERVYAYFRSKE   75 (226)
T ss_dssp             HHCCHHHHHHHTTSCHHHHHHHCSSHH
T ss_pred             ccCcHHHHHHHHCCChHHHHHHcCCHH
Confidence            368999999999999999999976643

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=90.83  E-value=0.53  Score=27.95  Aligned_cols=33  Identities=18%  Similarity=0.174  Sum_probs=27.1

Q ss_pred             HHHHHH-HHhCCCCHHHHHHHh-----CCCHHHHHHHHc
Q 038591           23 RQIQRA-RLGKKMSQPDLANQI-----NQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~-r~~~g~s~~elA~~~-----gis~~~i~~~e~   55 (82)
                      ..|+++ .+..-.||.||++.+     ++|+.||++..+
T Consensus         8 ~~I~~li~~~~~~tq~eL~~~L~~~G~~VtqaTisRDL~   46 (149)
T 1b4a_A            8 IKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIK   46 (149)
T ss_dssp             HHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccHHHHHHHHHHcCCCcCHHHHHHHHH
Confidence            445555 556678999999999     999999999976

>1zk8_A Transcriptional regulator, TETR family; TETR member,transcriptional regulator, STRU genomics, PSI, protein structure initiative; 2.15A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1

Probab=90.83  E-value=0.051  Score=31.64  Aligned_cols=25  Identities=16%  Similarity=0.244  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++.+-.++
T Consensus        28 ~~t~~~Ia~~agvs~~t~Y~~F~sK   52 (183)
T 1zk8_A           28 EVTLASLAQTLGVRSPSLYNHVKGL   52 (183)
T ss_dssp             GCCHHHHHHHHTSCHHHHTTTCSSH
T ss_pred             ccCHHHHHHHcCCCchHHHHHcCCH
Confidence            5899999999999999999986654

>2guh_A Putative TETR-family transcriptional regulator; helix-turn-helix, TETR fold, structural genomics, PSI, prote structure initiative; HET: MSE; 1.52A {Rhodococcus SP}

Probab=90.80  E-value=0.17  Score=30.61  Aligned_cols=25  Identities=16%  Similarity=0.333  Sum_probs=22.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+|+.+..++
T Consensus        59 ~~tv~~IA~~AGvs~~tlY~~F~sK   83 (214)
T 2guh_A           59 EITLKDIAEDAGVSAPLIIKYFGSK   83 (214)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHHSSH
T ss_pred             hcCHHHHHHHhCCCHHHHHHHcCCH
Confidence            4799999999999999999997654

>2gfn_A HTH-type transcriptional regulator PKSA related P; transcriptional regulato PSI-2, regulatory protein, structural genomics, protein STR initiative; 1.90A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=90.76  E-value=0.11  Score=31.16  Aligned_cols=27  Identities=11%  Similarity=0.203  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+.+..++.
T Consensus        28 ~~~s~~~IA~~aGvs~gtlY~yF~sKe   54 (209)
T 2gfn_A           28 SAVTTRAVAEESGWSTGVLNHYFGSRH   54 (209)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHTSSHH
T ss_pred             ccCCHHHHHHHHCCCcchHHhcCCCHH
Confidence            468999999999999999999976543

>2zcx_A SCO7815, TETR-family transcriptional regulator; helix-turn-helix, DNA-binding, transcription regulation; 2.22A {Streptomyces coelicolor}

Probab=90.76  E-value=0.12  Score=31.74  Aligned_cols=26  Identities=12%  Similarity=0.291  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+.+..++.
T Consensus        43 ~~s~~~IA~~agvs~~tlY~~F~sKe   68 (231)
T 2zcx_A           43 EITLTDIAATVGMHKSALLRYFETRE   68 (231)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHhCCCHH
Confidence            68999999999999999999976543

>3npi_A TETR family regulatory protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; 2.96A {Corynebacterium diphtheriae}

Probab=90.73  E-value=0.11  Score=32.02  Aligned_cols=39  Identities=8%  Similarity=-0.014  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      .+.|..++|+.+|||+.+|+++..++...=...+..+..
T Consensus        37 ~~~t~~~IA~~aGvs~~tlY~~F~sKe~Ll~av~~~~~~   75 (251)
T 3npi_A           37 SDAKLEAIAKKSGMSKRMIHYHFGDKRGLYICCLEEAVR   75 (251)
T ss_dssp             HHCCHHHHHHHHCCCHHHHHHHHCSHHHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHCCCHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            368999999999999999999987764443334444333

>2q24_A Putative TETR family transcriptional regulator; structural genomics, PSI, protein structure initiative; 1.80A {Streptomyces coelicolor A3}

Probab=90.67  E-value=0.12  Score=30.42  Aligned_cols=26  Identities=4%  Similarity=-0.041  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..|..++|+.+|||+.+|+++..++.
T Consensus        34 ~~s~~~IA~~agvs~~tlY~~F~sK~   59 (194)
T 2q24_A           34 DAHLERIAREAGVGSGTLYRNFPTRE   59 (194)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHCCSHH
T ss_pred             CCCHHHHHHHhCCChHHHHHHcCCHH
Confidence            37999999999999999999976543

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

Probab=90.67  E-value=0.047  Score=36.25  Aligned_cols=34  Identities=6%  Similarity=0.106  Sum_probs=0.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....++||.+||+.+|+|++||++..+
T Consensus        23 ~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~   56 (345)
T 2o0m_A           23 FQILRNIYWMQPIGRRSLSETMGITERVLRTETD   56 (345)
T ss_dssp             ----------------------------------
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3456666777899999999999999999998854

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=90.65  E-value=0.12  Score=27.47  Aligned_cols=27  Identities=7%  Similarity=0.099  Sum_probs=21.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ......|..++|+++|++.+.|.++..
T Consensus        25 ~~~~~~Ta~~IAkkLg~sK~~vNr~LY   51 (75)
T 1sfu_A           25 NTNDYTTAISLSNRLKINKKKINQQLY   51 (75)
T ss_dssp             CTTCEECHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHCCCHHHHHHHHH
Confidence            334447889999999999999988753

>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=90.63  E-value=0.51  Score=29.27  Aligned_cols=43  Identities=9%  Similarity=-0.021  Sum_probs=31.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ..|+|.+|+|+.+|+|..||......    -...+...+..+|..+|
T Consensus       186 ~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~~~~a~~~g  232 (234)
T 1l3l_A          186 AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRK  232 (234)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence            58999999999999999999887643    12345555556655554

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=90.59  E-value=0.048  Score=33.18  Aligned_cols=28  Identities=7%  Similarity=0.048  Sum_probs=0.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..|+|..++|+.+|||++|+++|.+...
T Consensus       156 ~~G~s~~~Ia~~l~vs~~Tvyr~l~~~~  183 (193)
T 3uj3_X          156 AQGIPRKQVALIYDVALSTLYKKHPAKR  183 (193)
T ss_dssp             ----------------------------
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHhh
Confidence            3689999999999999999999987643

>1ui5_A A-factor receptor homolog; helix-turn-helix, alpha-helix-bundle, antibiotic; 2.40A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 PDB: 1ui6_A

Probab=90.58  E-value=0.14  Score=30.87  Aligned_cols=27  Identities=4%  Similarity=-0.032  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+..++.
T Consensus        28 ~~ts~~~IA~~AGvskgtlY~~F~sKe   54 (215)
T 1ui5_A           28 ESTTLSEIVAHAGVTKGALYFHFAAKE   54 (215)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCchhhHhhCCCHH
Confidence            467999999999999999999876543

>3he0_A Transcriptional regulator, TETR family; ACRR, vibrio parahaemolytic structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.20A {Vibrio parahaemolyticus}

Probab=90.58  E-value=0.086  Score=30.81  Aligned_cols=26  Identities=23%  Similarity=0.298  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++-.++
T Consensus        30 ~~~tv~~Ia~~agvs~~t~Y~~F~sK   55 (196)
T 3he0_A           30 QGLSMQKLANEAGVAAGTIYRYFSDK   55 (196)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTCSSH
T ss_pred             ccCCHHHHHHHhCCCcchHHHhcCCH
Confidence            46899999999999999999976554

>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=90.56  E-value=0.11  Score=29.39  Aligned_cols=33  Identities=6%  Similarity=-0.080  Sum_probs=26.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....++|+.++|+.+|++++++++..
T Consensus        40 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l   72 (142)
T 2bv6_A           40 FLVLTILWDESPVNVKKVVTELALDTGTVSPLL   72 (142)
T ss_dssp             HHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHH
Confidence            345556666667999999999999999988874

>3eup_A Transcriptional regulator, TETR family; structural genomics, MCSG, protein structure initiative, midwest center for STRU genomics; 1.99A {Cytophaga hutchinsonii}

Probab=90.56  E-value=0.048  Score=32.05  Aligned_cols=27  Identities=19%  Similarity=0.089  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++-.++.
T Consensus        30 ~~~ti~~IA~~agvs~~t~Y~~F~sK~   56 (204)
T 3eup_A           30 AGTSLTDLTEATNLTKGSIYGNFENKE   56 (204)
T ss_dssp             HHCCHHHHHHHHTCCHHHHTTTSSSHH
T ss_pred             ccCCHHHHHHHhCCCcHHHHHhCCCHH
Confidence            368999999999999999999866543

>2w53_A Repressor, SMet; antibiotic resistance, multi-drug efflux pump, transcription regulation, transcriptional repressor, DNA binding; 2.00A {Stenotrophomonas maltophilia} PDB: 3p9t_A*

Probab=90.53  E-value=0.086  Score=31.66  Aligned_cols=27  Identities=7%  Similarity=-0.058  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+++..++.
T Consensus        30 ~~~s~~~IA~~aGvskgtlY~~F~sKe   56 (219)
T 2w53_A           30 ARTTLEMIGARAGYTRGAVYWHFKNKS   56 (219)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTCSSHH
T ss_pred             ccCCHHHHHHHhCCCchHHhhcCCCHH
Confidence            468999999999999999999876543

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=90.40  E-value=0.72  Score=25.43  Aligned_cols=32  Identities=16%  Similarity=0.114  Sum_probs=25.6

Q ss_pred             HHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLG------KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~------~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+...      ..+++.+||+.++++++++++..
T Consensus        20 ~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l   57 (96)
T 2obp_A           20 EVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVL   57 (96)
T ss_dssp             HHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHH
Confidence            445556555      56999999999999999998864

>2id6_A Transcriptional regulator, TETR family; 1.75A {Thermotoga maritima} SCOP: a.4.1.9 a.121.1.1 PDB: 3ih2_A 3ih3_A 3ih4_A 1zkg_A* 2iek_A* 1z77_A*

Probab=90.37  E-value=0.1  Score=31.08  Aligned_cols=27  Identities=11%  Similarity=0.252  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+++.+-.++.
T Consensus        24 ~~~s~~~IA~~AgvskgtlY~yF~sKe   50 (202)
T 2id6_A           24 DRATTDEIAEKAGVAKGLIFHYFKNKE   50 (202)
T ss_dssp             HHCCHHHHHHHHTCCTHHHHHHHSSHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            368999999999999999999987643

>3g1o_A Transcriptional regulatory repressor protein (TETR-family) EThr; TERT family, transcriptional repressor, DNA-binding; HET: RF1; 1.85A {Mycobacterium tuberculosis}

Probab=90.34  E-value=0.12  Score=31.91  Aligned_cols=26  Identities=23%  Similarity=0.146  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        63 ~~t~~~IA~~aGvs~~tlY~~F~sK~   88 (255)
T 3g1o_A           63 DISVDDLAKGAGISRPTFYFYFPSKE   88 (255)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCcHHHHHHHhCCCHHHHHHHcCCHH
Confidence            47999999999999999999976643

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=90.29  E-value=0.36  Score=30.85  Aligned_cols=24  Identities=17%  Similarity=0.306  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|..+||+.+|||+.||..||.
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~   25 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDK   25 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            358999999999999999999986

>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=90.28  E-value=0.24  Score=25.82  Aligned_cols=34  Identities=3%  Similarity=0.088  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC----CCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN----QRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g----is~~~i~~~e~   55 (82)
                      ...|..+....++|+.|||+.++    ++++||+...+
T Consensus        12 ~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~   49 (82)
T 1p6r_A           12 LEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLL   49 (82)
T ss_dssp             HHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHH
Confidence            34566666667899999999996    78999988754

>3geu_A Intercellular adhesion protein R; TETR family, intercellular adhesion regulator, IDP00851, DNA repressor, transcription; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=90.22  E-value=0.05  Score=31.84  Aligned_cols=26  Identities=15%  Similarity=0.152  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+++++++-.++
T Consensus        22 ~~~ti~~IA~~agvs~~t~Y~~F~sK   47 (189)
T 3geu_A           22 DGTTLDDIAKSVNIKKASLYYHFDSK   47 (189)
T ss_dssp             HHCCHHHHHHHTTCCHHHHTTTCSSH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHhCCH
Confidence            36899999999999999999986554

>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=90.21  E-value=0.59  Score=25.81  Aligned_cols=32  Identities=6%  Similarity=0.045  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQI-NQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e   54 (82)
                      ...|..+. ..++++.+||+.+ |++++++++..
T Consensus        25 ~~IL~~L~-~~~~~~~eLa~~l~~is~~tvs~~L   57 (112)
T 1z7u_A           25 LSLMDELF-QGTKRNGELMRALDGITQRVLTDRL   57 (112)
T ss_dssp             HHHHHHHH-HSCBCHHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHhccCCHHHHHHHH
Confidence            34555555 4689999999999 99999999864

>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=89.98  E-value=0.39  Score=25.95  Aligned_cols=30  Identities=17%  Similarity=0.134  Sum_probs=23.6

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+ ....++..+||+.+|+|+++|++..
T Consensus        28 Il~~L-~~~~~~~~ela~~l~is~~tvs~~L   57 (102)
T 3pqk_A           28 LVCTL-VEGEFSVGELEQQIGIGQPTLSQQL   57 (102)
T ss_dssp             HHHHH-HTCCBCHHHHHHHHTCCTTHHHHHH
T ss_pred             HHHHH-HhCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34444 3456999999999999999998864

>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=89.97  E-value=0.53  Score=31.11  Aligned_cols=32  Identities=19%  Similarity=0.135  Sum_probs=25.6

Q ss_pred             HHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGK--KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~--g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|+.+++..  -+|..+||+.+|+|+++|.+..
T Consensus         7 ~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i   40 (323)
T 3rkx_A            7 DVLQLLYKNKPNYISGQSIAESLNISRTAVKKVI   40 (323)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHH
Confidence            4566666543  5899999999999999998874

>3jsj_A Putative TETR-family transcriptional regulator; DNA-binding, transcription regulation; 2.10A {Streptomyces avermitilis ma-4680}

Probab=89.97  E-value=0.16  Score=29.66  Aligned_cols=25  Identities=8%  Similarity=0.072  Sum_probs=22.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .|..++|+.+|||+.+|+++..++.
T Consensus        29 ~t~~~IA~~aGvs~~tly~~F~sK~   53 (190)
T 3jsj_A           29 IGVEALCKAAGVSKRSMYQLFESKD   53 (190)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHCSCHH
T ss_pred             ccHHHHHHHhCCCHHHHHHHcCCHH
Confidence            7999999999999999999976543

>1t33_A Putative transcriptional repressor (TETR/ACRR FAM; structural genomics, TETR/CCRR FA helix turn helix DNA binding domain, PSI; 2.20A {Salmonella typhimurium} SCOP: a.4.1.9 a.121.1.1

Probab=89.93  E-value=0.24  Score=29.54  Aligned_cols=26  Identities=19%  Similarity=0.190  Sum_probs=23.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .|..++|+.+|||+.+|+++..++..
T Consensus        32 ~s~~~IA~~agvs~~tiY~~F~sK~~   57 (224)
T 1t33_A           32 ATTRDIAALAGQNIAAITYYFGSKED   57 (224)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHSSHHH
T ss_pred             ccHHHHHHHhCCCHHHHHHhcCCHHH
Confidence            89999999999999999999876543

>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=89.85  E-value=0.084  Score=31.49  Aligned_cols=26  Identities=15%  Similarity=0.072  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++-.++
T Consensus        30 ~~~s~~~IA~~aGvskgtlY~~F~sK   55 (210)
T 2xdn_A           30 ARTTLADIAELAGVTRGAIYWHFNNK   55 (210)
T ss_dssp             TTCCHHHHHHHHTCCTTHHHHHCSSH
T ss_pred             ccCcHHHHHHHHCCChHHHHHHhCCH
Confidence            46899999999999999999987654

>2ras_A Transcriptional regulator, TETR family; bacterial regulatory proteins, DNA-binding, DNA binding 3-helical bundle fold; 1.80A {Novosphingobium aromaticivorans}

Probab=89.84  E-value=0.11  Score=30.95  Aligned_cols=26  Identities=15%  Similarity=0.227  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++..++
T Consensus        30 ~~~s~~~IA~~agvs~~t~Y~~F~sK   55 (212)
T 2ras_A           30 AGLTLSELAARAGISQANLSRYFETR   55 (212)
T ss_dssp             SCCCHHHHHHHHTSCHHHHTTTCSSH
T ss_pred             ccCcHHHHHHHhCCCHHHHHHHcCCH
Confidence            46899999999999999999986543

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=89.79  E-value=0.25  Score=27.94  Aligned_cols=25  Identities=4%  Similarity=-0.015  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++..++|+.+|+|+.++++.....
T Consensus        27 ~~sl~~lA~~~~~S~~~l~r~fk~~   51 (129)
T 1bl0_A           27 PLSLEKVSERSGYSKWHLQRMFKKE   51 (129)
T ss_dssp             CCCCHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5899999999999999999997643

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B

Probab=89.75  E-value=0.74  Score=28.20  Aligned_cols=35  Identities=9%  Similarity=0.160  Sum_probs=29.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++||+           .+..|.+.||+++-+|.
T Consensus        17 s~t~AA~~L~isq~avS~-----------~i~~LE~~lg~~Lf~R~   51 (291)
T 3szp_A           17 SYTSTSKKTMIPVATITR-----------RIQALEDSLNLRLLNRH   51 (291)
T ss_dssp             SHHHHHHHHTCCHHHHHH-----------HHHHHHHHHTCCCEEEE
T ss_pred             CHHHHHHHhCCCHHHHHH-----------HHHHHHHHhCCceEeec
Confidence            566699999999999998           46788888998887765

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=89.73  E-value=0.062  Score=32.55  Aligned_cols=25  Identities=8%  Similarity=0.023  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+|+.++|..+|+|+.+|++..+.
T Consensus       163 ~~~t~~~lA~~lg~sr~tvsR~l~~  187 (213)
T 1o5l_A          163 LPVTLEELSRLFGCARPALSRVFQE  187 (213)
T ss_dssp             -------------------------
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            4689999999999999999998764

>2oi8_A Putative regulatory protein SCO4313; TETR, structural genomics, PSI-2, P structure initiative; 2.50A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=89.72  E-value=0.11  Score=31.65  Aligned_cols=26  Identities=15%  Similarity=0.323  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        35 ~~~s~~~IA~~agvs~~t~Y~~F~~K   60 (216)
T 2oi8_A           35 SALSLNAIAKRMGMSGPALYRYFDGR   60 (216)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTTCSSH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCH
Confidence            46899999999999999999986654

>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=89.69  E-value=0.48  Score=25.99  Aligned_cols=30  Identities=10%  Similarity=0.138  Sum_probs=24.2

Q ss_pred             HHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQI-NQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e   54 (82)
                      .|..+. .-.+++.+||+.+ |++++++++..
T Consensus        19 IL~~L~-~~~~~~~eLa~~l~~is~~tls~~L   49 (107)
T 2hzt_A           19 ILXHLT-HGKKRTSELKRLMPNITQKMLTQQL   49 (107)
T ss_dssp             HHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHhcCCCHHHHHHHH
Confidence            445554 5679999999999 99999999864

>3bqy_A Putative TETR family transcriptional regulator; structural genomics, strept coelicolor, PSI-2, protein structure initiative; 1.95A {Streptomyces coelicolor A3}

Probab=89.66  E-value=0.19  Score=30.62  Aligned_cols=26  Identities=15%  Similarity=0.275  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++-.++
T Consensus        21 ~~~s~~~IA~~aGvs~~tlY~hf~~K   46 (209)
T 3bqy_A           21 DTLTMRRLAQAMDVQAGALYRYFAAK   46 (209)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHCSSH
T ss_pred             ccCCHHHHHHHhCCCcchHHhhcCCH
Confidence            36899999999999999999987654

>2of7_A Putative TETR-family transcriptional regulator; APC7240, streptomyces coelicolor A3, structural genomics, PSI-2; 2.30A {Streptomyces coelicolor}

Probab=89.65  E-value=0.32  Score=30.17  Aligned_cols=25  Identities=16%  Similarity=0.242  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..++|+.+|||+.+|+.+..+
T Consensus        67 ~~~Ti~~IA~~AGvs~~t~Y~yF~s   91 (260)
T 2of7_A           67 EATTVEQIAERAEVSPSTVLRYFPT   91 (260)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             ccccHHHHHHHhCCChHHHHHHcCC
Confidence            3689999999999999999998654

>2iai_A Putative transcriptional regulator SCO3833; structural genomics, TETR, unknow function, PSI-2, protein structure initiative; 1.65A {Streptomyces coelicolor}

Probab=89.61  E-value=0.087  Score=32.05  Aligned_cols=26  Identities=15%  Similarity=0.124  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        49 ~~~t~~~IA~~Agvs~~t~Y~~F~sK   74 (230)
T 2iai_A           49 DGTSMEHLSKAAGISKSSIYHHVTGK   74 (230)
T ss_dssp             TTCCHHHHHHHHTSCHHHHTTTCSSH
T ss_pred             cccCHHHHHHHHCCChhHHHHhCCCH
Confidence            46899999999999999999987654

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=89.59  E-value=0.27  Score=27.48  Aligned_cols=29  Identities=10%  Similarity=0.059  Sum_probs=23.6

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      |..+. ...++..+||+.+|+|++++++..
T Consensus        24 l~~L~-~~~~~~~eLa~~l~is~~tvs~hL   52 (118)
T 3f6o_A           24 LGRLS-RGPATVSELAKPFDMALPSFMKHI   52 (118)
T ss_dssp             HHHHH-TCCEEHHHHHTTCCSCHHHHHHHH
T ss_pred             HHHHH-hCCCCHHHHHHHhCcCHHHHHHHH
Confidence            34444 567899999999999999999874

>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=89.58  E-value=0.32  Score=30.56  Aligned_cols=31  Identities=13%  Similarity=0.105  Sum_probs=24.6

Q ss_pred             HHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+... .++|..|+|+.+|++++|++++.+
T Consensus        12 L~~l~~~~~~~s~~ela~~~gl~~stv~r~l~   43 (241)
T 2xrn_A           12 MRALGSHPHGLSLAAIAQLVGLPRSTVQRIIN   43 (241)
T ss_dssp             HHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4444433 369999999999999999999854

>3c07_A Putative TETR-family transcriptional regulator; APC6322, structural GEN PSI-2, protein structure initiative; 2.70A {Streptomyces coelicolor A3} SCOP: a.4.1.9 a.121.1.1 PDB: 2ofl_A*

Probab=89.57  E-value=0.17  Score=31.99  Aligned_cols=26  Identities=15%  Similarity=0.141  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++.+..++.
T Consensus        61 ~~S~~~IA~~AGVs~~tlY~hF~sKe   86 (273)
T 3c07_A           61 RTTMRAIAQEAGVSVGNAYYYFAGKE   86 (273)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccCHHHHHHHHCCCHHHHHHHcCCHH
Confidence            57999999999999999999976543

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

Probab=89.57  E-value=0.17  Score=29.25  Aligned_cols=23  Identities=9%  Similarity=0.299  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|+.+||+.+++++++++++.+
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~   73 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVD   73 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            58999999999999999998753

>1sgm_A Putative HTH-type transcriptional regulator YXAF; structural genomics, PSI, protein structure initiative; 2.00A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=89.50  E-value=0.079  Score=30.78  Aligned_cols=25  Identities=0%  Similarity=-0.001  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..++|+.+|||+.+++++-.+
T Consensus        25 ~~~t~~~Ia~~agvs~~t~Y~~F~~   49 (191)
T 1sgm_A           25 HATGLNQIVKESGAPKGSLYHFFPN   49 (191)
T ss_dssp             TTCCHHHHHHHHCCCSCHHHHSTTT
T ss_pred             cccCHHHHHHHHCCCchhHHHHccc
Confidence            3689999999999999999998763

>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domai binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A

Probab=89.42  E-value=0.79  Score=28.30  Aligned_cols=35  Identities=14%  Similarity=0.257  Sum_probs=27.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++||+           .+.+|.+.||+++-+|.
T Consensus        17 s~s~AA~~L~isq~avS~-----------~i~~LE~~lg~~Lf~R~   51 (294)
T 1ixc_A           17 NMAAAAKRLHVSQPPITR-----------QMQALEADLGVVLLERS   51 (294)
T ss_dssp             SHHHHHHHHTCCHHHHHH-----------HHHHHHHHHTSCCBC--
T ss_pred             CHHHHHHHhCCCcchHHH-----------HHHHHHHHHCCEEEEeC
Confidence            667799999999999998           45677788888876664

>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=89.39  E-value=0.16  Score=30.23  Aligned_cols=26  Identities=15%  Similarity=0.046  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++..++
T Consensus        28 ~~~s~~~IA~~aGvsk~tlY~~F~sK   53 (203)
T 3cdl_A           28 EITSMDRIAARAEVSKRTVYNHFPSK   53 (203)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHTTSSSH
T ss_pred             hhcCHHHHHHHhCCCHHHHHHHCCCH
Confidence            46799999999999999999986554

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=89.39  E-value=0.2  Score=31.76  Aligned_cols=25  Identities=12%  Similarity=0.100  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .-+|..++|+.+|||..||..||.-
T Consensus         4 ~~~~i~e~a~~~gvs~~tlr~y~~~   28 (278)
T 1r8e_A            4 SYYSIGEVSKLANVSIKALRYYDKI   28 (278)
T ss_dssp             CEEEHHHHHHHHTCCHHHHHHHHHT
T ss_pred             CcEeHHHHHHHHCcCHHHHHHHHHC
Confidence            3478899999999999999999863

>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=89.37  E-value=0.12  Score=31.16  Aligned_cols=25  Identities=8%  Similarity=-0.081  Sum_probs=22.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+|+.+..++
T Consensus        48 ~~t~~~IA~~aGvs~~tlY~~F~sK   72 (217)
T 3hta_A           48 GLSHRTVAAEADVPLGSTTYHFATL   72 (217)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cCCHHHHHHHcCCCcchhhhcCCCH
Confidence            5799999999999999999987654

>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=89.36  E-value=0.74  Score=26.78  Aligned_cols=31  Identities=3%  Similarity=-0.015  Sum_probs=24.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+. .-.+++.+|++.+|++++++++..
T Consensus        28 ~IL~~L~-~g~~~~~eLa~~lgis~~tls~~L   58 (146)
T 2f2e_A           28 LIVRDAF-EGLTRFGEFQKSLGLAKNILAARL   58 (146)
T ss_dssp             HHHHHHH-TTCCSHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Confidence            3455554 456999999999999999998864

>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1

Probab=89.27  E-value=0.8  Score=28.62  Aligned_cols=35  Identities=11%  Similarity=0.215  Sum_probs=29.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++||+           .+..|.+.||+++-+|.
T Consensus        26 s~s~AA~~L~isq~avS~-----------~I~~LE~~lg~~Lf~R~   60 (310)
T 2esn_A           26 NVGTAASELAISASAFSH-----------ALGRLRQGLDDELFLRQ   60 (310)
T ss_dssp             SHHHHHHHHTCCHHHHHH-----------HHHHHHHHHTSCCEEEE
T ss_pred             CHHHHHHHhCCChHHHHH-----------HHHHHHHhhCCcceeec
Confidence            566799999999999998           46788888888887664

>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis}

Probab=89.27  E-value=0.24  Score=25.78  Aligned_cols=26  Identities=0%  Similarity=-0.003  Sum_probs=22.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..-+|.+|.|+.+||+.+++.++-+.
T Consensus        14 K~~LTi~EaAeylgIg~~~l~~L~~~   39 (70)
T 1y6u_A           14 RYTLTIEEASKYFRIGENKLRRLAEE   39 (70)
T ss_dssp             SSEEEHHHHHHHTCSCHHHHHHHHHH
T ss_pred             cceeCHHHHHHHHCcCHHHHHHHHHc
Confidence            35679999999999999999999754

>3hhg_A Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B}

Probab=89.21  E-value=0.84  Score=28.34  Aligned_cols=36  Identities=25%  Similarity=0.344  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      -|....|+.+|+|+++||+           .+..|.+.||+++-+|.
T Consensus        18 gs~t~AA~~L~isq~avS~-----------~i~~LE~~lg~~Lf~R~   53 (306)
T 3hhg_A           18 GSFSRAAEQLAMANSAVSR-----------IVKRLEEKLGVNLLNRT   53 (306)
T ss_dssp             SSHHHHHHHHTCCHHHHHH-----------HHHHHHHHHTSCCEETT
T ss_pred             CCHHHHHHHhCCCHHHHHH-----------HHHHHHHHhCCeeEeec
Confidence            3777899999999999998           45778888888887764

>2xpw_A Tetracycline repressor protein class D; transcription, transcription regulator, helix-turn-helix, ME coordination; HET: OTC MES; 1.44A {Escherichia coli} PDB: 1bjy_A* 1bj0_A 1du7_A* 1ork_A* 2fj1_A* 1bjz_A* 2o7o_A* 2x6o_A* 2x9d_A* 2xps_A* 2xpt_A* 2vke_A* 2xpu_A* 2xpv_A* 2tct_A* 2xb5_A* 2trt_A* 2xrl_A* 1qpi_A* 1a6i_A ...

Probab=89.16  E-value=0.19  Score=30.58  Aligned_cols=27  Identities=11%  Similarity=0.102  Sum_probs=23.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      ++|..++|+.+|||+.+++++..++..
T Consensus        23 ~~s~~~IA~~~Gvs~~slY~hF~~K~~   49 (207)
T 2xpw_A           23 GLTTRKLAQKLGIEQPTLYWHVKNKRA   49 (207)
T ss_dssp             HCCHHHHHHHHTCCHHHHHHHCCCHHH
T ss_pred             cCCHHHHHHHhCCCcchHHHhcCCHHH
Confidence            689999999999999999999776543

>2opt_A Actii protein; helical protein, TETR family, APO-protein, transcriptional R transcription; 2.05A {Streptomyces coelicolor} PDB: 3b6a_A* 3b6c_A*

Probab=89.15  E-value=0.28  Score=30.54  Aligned_cols=26  Identities=12%  Similarity=0.137  Sum_probs=23.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        26 ~~S~r~IA~~aGvs~~tlY~hF~~K~   51 (234)
T 2opt_A           26 ALSMRRLAQELKTGHASLYAHVGNRD   51 (234)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHHCSHH
T ss_pred             ccCHHHHHHHHCCChhHHHHHcCCHH
Confidence            58999999999999999999987653

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

Probab=89.09  E-value=0.4  Score=29.66  Aligned_cols=24  Identities=21%  Similarity=0.434  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++++.+||+.+|++++++++..+
T Consensus        19 ~~~~~~~lA~~l~vs~~tvs~~l~   42 (214)
T 3hrs_A           19 NKITNKEIAQLMQVSPPAVTEMMK   42 (214)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhHHHHHHH
Confidence            468999999999999999998753

>2fbq_A Probable transcriptional regulator; PA3006, APC5893, structural genom protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.1.9 a.121.1.1

Probab=88.88  E-value=0.23  Score=30.31  Aligned_cols=27  Identities=11%  Similarity=-0.037  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.|..++|+.+|||+.+|+.+..++.
T Consensus        26 ~~ts~~~IA~~AGvs~~tlY~hF~sKe   52 (235)
T 2fbq_A           26 AETSLRLITSKAGVNLAAVNYHFGSKK   52 (235)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHTCSHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            367999999999999999999876543

>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=88.83  E-value=1.1  Score=28.61  Aligned_cols=44  Identities=11%  Similarity=0.070  Sum_probs=32.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv   74 (82)
                      ..|+|.+|+|+.+|+|..||......    -...+...+..+|..+|+
T Consensus       210 ~~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~~~~~~~~~~a~~~gl  257 (265)
T 3qp6_A          210 SRGKTNWEIATILNISERTVKFHVANVIRKLNANNRTHAIVLGMHLAM  257 (265)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHHHHHTHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcCC
Confidence            58999999999999999999887653    223455555555555554

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=88.69  E-value=0.71  Score=31.95  Aligned_cols=25  Identities=8%  Similarity=0.185  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..|+|+.+|||+.+|.+++..
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~R  418 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENK  418 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5799999999999999999999863

>2hyj_A Putative TETR-family transcriptional regulator; HTH DNA binding motif, structural genomics, PSI-2, Pro structure initiative; 2.19A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=88.64  E-value=0.13  Score=30.65  Aligned_cols=26  Identities=15%  Similarity=0.107  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+.+..++
T Consensus        31 ~~~s~~~IA~~aGvsk~tlY~hF~sK   56 (200)
T 2hyj_A           31 DGITIGRLAEELEMSKSGVHKHFGTK   56 (200)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHTTCSSH
T ss_pred             ccCCHHHHHHHhCCChHHHHHHcCCH
Confidence            46899999999999999999876543

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

Probab=88.62  E-value=0.13  Score=29.75  Aligned_cols=33  Identities=15%  Similarity=0.070  Sum_probs=25.6

Q ss_pred             HHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRA-RLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~-r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+ ....++++.+||+.+|++++++++..
T Consensus        50 ~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l   83 (160)
T 3boq_A           50 FDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLV   83 (160)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHH
Confidence            3455556 45568999999999999998888774

>2hxi_A Putative transcriptional regulator; structural genomics, APC6293, TET streptomyces coelicolor A3(2), PSI-2; 1.70A {Streptomyces coelicolor}

Probab=88.39  E-value=0.32  Score=30.28  Aligned_cols=26  Identities=15%  Similarity=0.124  Sum_probs=23.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        49 ~~s~~~IA~~aGvs~~tlY~hF~~K~   74 (241)
T 2hxi_A           49 TFSVRKLAASLGTDSSSLYRHFRNKT   74 (241)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHTSSHH
T ss_pred             cCCHHHHHHHhCcCHHHHHHHcCCHH
Confidence            58999999999999999999977653

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

Probab=88.35  E-value=0.24  Score=28.97  Aligned_cols=34  Identities=12%  Similarity=0.169  Sum_probs=23.3

Q ss_pred             HHHHHHHHHh--CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLG--KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~--~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...  .++|+.+||+.+++++++|+++.+
T Consensus        49 ~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~   84 (168)
T 3u2r_A           49 YNTLRLLRSVHPEGMATLQIADRLISRAPDITRLID   84 (168)
T ss_dssp             HHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHH
T ss_pred             HHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHH
Confidence            3455556553  589999999999999999988743

>1u3e_M HNH homing endonuclease; HNH catalytic motif, helix-turn-helix DNA binding domain, PR complex, DNA binding protein-DNA complex; 2.92A {Bacillus phage SPO1} SCOP: d.4.1.3 d.285.1.1

Probab=88.24  E-value=0.52  Score=28.26  Aligned_cols=25  Identities=12%  Similarity=0.093  Sum_probs=22.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      -|+.++|+.+|++.++|+.+.+|+.
T Consensus       136 ~s~~eAa~~~Gvs~~tIs~~~~gk~  160 (174)
T 1u3e_M          136 PSTKCACEELGLTRGKVTDVLKGHR  160 (174)
T ss_dssp             SCHHHHHHHHTCCHHHHHHHHHTSS
T ss_pred             CCHHHHHHHHCcCHhHhHHHHcCCC
Confidence            4899999999999999999999864

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=88.18  E-value=0.21  Score=32.00  Aligned_cols=27  Identities=11%  Similarity=0.133  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus       139 ~~~T~~~IA~~AGvs~gtlY~yF~sKe  165 (311)
T 4ich_A          139 HNVRIHDIASELGTSNATIHYHFPSKK  165 (311)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccCCHHHHHHHhCCCchhHHHhCCCHH
Confidence            357999999999999999999976643

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=88.18  E-value=1  Score=26.21  Aligned_cols=35  Identities=3%  Similarity=-0.038  Sum_probs=28.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++|++           .+..|.+.||+++-++.
T Consensus        40 S~s~AA~~L~iSqsavS~-----------~I~~LE~~lG~~Lf~R~   74 (135)
T 2ijl_A           40 SISAAGRAMDMSYRRAWL-----------LVDALNHMFRQPVICSQ   74 (135)
T ss_dssp             CHHHHHHHTTCCHHHHHH-----------HHHHHHHHBSSCSEEEC
T ss_pred             CHHHHHHHHCcCHHHHHH-----------HHHHHHHHHCCeeEEec
Confidence            667799999999999998           45677788888876664

>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=88.14  E-value=0.12  Score=30.28  Aligned_cols=26  Identities=19%  Similarity=0.247  Sum_probs=22.2

Q ss_pred             hCCCCHHHHHH----Hh--CCCHHHHHHHHcC
Q 038591           31 GKKMSQPDLAN----QI--NQRPQVVSEYENG   56 (82)
Q Consensus        31 ~~g~s~~elA~----~~--gis~~~i~~~e~g   56 (82)
                      .-+++|.+||.    ..  +++++||++|.+.
T Consensus        28 ~~~~~q~~la~wa~~~f~~~is~stis~ilk~   59 (144)
T 1iuf_A           28 QNRSGQQDLIEWFREKFGKDISQPSVSQILSS   59 (144)
T ss_dssp             SSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhh
Confidence            36799999999    88  8999999998653

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=88.11  E-value=0.38  Score=29.88  Aligned_cols=23  Identities=17%  Similarity=0.147  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|..++|+.+|+|+++|++..+
T Consensus        27 ~~s~s~aA~~L~isq~avSr~I~   49 (230)
T 3cta_A           27 YLTSSKLADMLGISQQSASRIII   49 (230)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            47899999999999999998743

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=87.91  E-value=0.65  Score=25.55  Aligned_cols=34  Identities=9%  Similarity=-0.112  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC----CCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN----QRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g----is~~~i~~~e~   55 (82)
                      ...|..+...-++|+.||++.++    ++++||+.+.+
T Consensus        38 ~~VL~~L~~~~~~t~~eL~~~l~~~~~~s~sTVt~~L~   75 (99)
T 2k4b_A           38 LIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLG   75 (99)
T ss_dssp             SHHHHHHHHHSCEEHHHHHHTCCGGGCCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHhcccCCCHhhHHHHHH
Confidence            46677777777999999999997    57888887753

>2g7g_A RHA04620, putative transcriptional regulator; helix-turn-helix, structural genomics, PSI, protein structur initiative; 2.01A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=87.90  E-value=0.32  Score=29.54  Aligned_cols=25  Identities=24%  Similarity=0.462  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++..++
T Consensus        29 ~~s~~~IA~~aGvs~~tlY~hF~~K   53 (213)
T 2g7g_A           29 DFRMPDLARHLNVQVSSIYHHAKGR   53 (213)
T ss_dssp             SCCHHHHHHHTTSCHHHHHTTSCHH
T ss_pred             CCCHHHHHHHhCCCHhHHHHHcCCH
Confidence            8999999999999999999986543

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=87.85  E-value=0.53  Score=26.10  Aligned_cols=33  Identities=9%  Similarity=0.018  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC----CCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN----QRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g----is~~~i~~~e   54 (82)
                      ...|..+...-++|+.+||+.++    ++++||+.+.
T Consensus        13 ~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l   49 (126)
T 1sd4_A           13 WDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLI   49 (126)
T ss_dssp             HHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHH
Confidence            45677777777899999999997    5899988874

>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- transcription, transcription regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A 3n6t_A 3n6u_A*

Probab=87.74  E-value=1.2  Score=27.89  Aligned_cols=35  Identities=17%  Similarity=0.242  Sum_probs=29.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+++|+|+++||+           .+..|.+.||+++-+|.
T Consensus        18 s~t~AA~~L~isq~avS~-----------~i~~LE~~lg~~Lf~R~   52 (305)
T 3fxq_A           18 SLRAAAQLLHLSQPALSA-----------AIQQLEDELKAPLLVRT   52 (305)
T ss_dssp             CHHHHHHHTTCCHHHHHH-----------HHHHHHHHHTSCSEEEC
T ss_pred             CHHHHHHHhCCCHHHHHH-----------HHHHHHHHhCCeeEEec
Confidence            666799999999999998           46778888888887664

>3aqt_A Bacterial regulatory proteins, TETR family; helix-turn-helix, all alpha, transcription, transcription RE transcription regulator; 2.50A {Corynebacterium glutamicum} PDB: 3aqs_A

Probab=87.74  E-value=0.055  Score=33.39  Aligned_cols=26  Identities=8%  Similarity=0.147  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+|+++..++.
T Consensus        66 ~~t~~~IA~~aGvs~~t~Y~~F~sKe   91 (245)
T 3aqt_A           66 NVGIAEITEGANIGTGTFYNYFPDRE   91 (245)
T ss_dssp             GCCHHHHHHHTTSCGGGGGGTCSSHH
T ss_pred             cCcHHHHHHHhCCChHHHHHHcCCHH
Confidence            58999999999999999999876643

>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=87.67  E-value=0.57  Score=30.76  Aligned_cols=31  Identities=13%  Similarity=0.074  Sum_probs=24.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..+.....+|..+||+.+|+|+.||.+-.
T Consensus        10 Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l   40 (321)
T 1bia_A           10 LIALLANGEFHSGEQLGETLGMSRAAINKHI   40 (321)
T ss_dssp             HHHHHTTSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            3454544456999999999999999998854

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=87.65  E-value=0.1  Score=31.78  Aligned_cols=27  Identities=22%  Similarity=0.295  Sum_probs=0.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +--.|+|.+|+|+.+|+|..+|.++..
T Consensus       210 ~~~~g~s~~EIA~~lgis~~tV~~~~~  236 (243)
T 1l0o_C          210 RYYKDQTQSEVASRLGISQVQMSRLEK  236 (243)
T ss_dssp             ---------------------------
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345699999999999999999998765

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=87.64  E-value=0.28  Score=26.70  Aligned_cols=21  Identities=24%  Similarity=0.194  Sum_probs=19.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 038591           35 SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~   55 (82)
                      |..+||+.+|+|+++|++...
T Consensus        37 s~~eLa~~~~vSr~tvr~al~   57 (102)
T 1v4r_A           37 SVADIRAQFGVAAKTVSRALA   57 (102)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            899999999999999998754

>1z0x_A Transcriptional regulator, TETR family; structural genomics, PSI, P structure initiative; 2.40A {Enterococcus faecalis} SCOP: a.4.1.9 a.121.1.1

Probab=87.58  E-value=0.2  Score=30.55  Aligned_cols=26  Identities=19%  Similarity=0.274  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        26 ~~s~~~IA~~aGvs~~tlY~~F~sK~   51 (220)
T 1z0x_A           26 QLSMRKVAKQLGVQAPAIYWYFKNKQ   51 (220)
T ss_dssp             GCCHHHHHHHHTSCHHHHHTTCSSHH
T ss_pred             cCCHHHHHHHcCCCHHHHHHhcCCHH
Confidence            57999999999999999999876543

>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=87.48  E-value=0.59  Score=25.75  Aligned_cols=19  Identities=11%  Similarity=0.239  Sum_probs=17.8

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q 038591           35 SQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~   53 (82)
                      |..+||+.+|+|+++|.+.
T Consensus        45 s~~eLa~~lgVSr~tVr~a   63 (102)
T 2b0l_A           45 VASKIADRVGITRSVIVNA   63 (102)
T ss_dssp             CHHHHHHHHTCCHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHH
Confidence            9999999999999999876

>4hku_A LMO2814 protein, TETR transcriptional regulator; structural genomics, PSI-biology; 2.30A {Listeria monocytogenes}

Probab=87.31  E-value=0.076  Score=31.13  Aligned_cols=26  Identities=19%  Similarity=0.206  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+|+++..++
T Consensus        26 ~~~s~~~IA~~aGvs~~tlY~~F~sK   51 (178)
T 4hku_A           26 EKTTLYDIASNLNVTHAALYKHYRNK   51 (178)
T ss_dssp             GGCCHHHHHHHTTSCGGGGGGTCSSH
T ss_pred             ccccHHHHHHHhCcCHhHHHHHCCCH
Confidence            36799999999999999999986554

>1rr7_A Middle operon regulator; MOR, transcription; 2.20A {Enterobacteria phage MU} SCOP: a.4.1.14

Probab=87.30  E-value=0.84  Score=26.37  Aligned_cols=25  Identities=8%  Similarity=-0.065  Sum_probs=22.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.|.+..+||++.|+|..+|.++..
T Consensus        90 f~G~n~~eLArkYgLSer~I~~Ii~  114 (129)
T 1rr7_A           90 FNGRNVSELTTRYGVTFNTVYKAIR  114 (129)
T ss_dssp             CCSSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3689999999999999999999975

>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP}

Probab=87.27  E-value=0.21  Score=29.80  Aligned_cols=24  Identities=13%  Similarity=0.086  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ++|..++|+.+|||+.+++.+..+
T Consensus        48 ~~tv~~IA~~agvs~~t~Y~~F~s   71 (215)
T 2qko_A           48 GLTFRAVDVEANVPKGTASNYFPS   71 (215)
T ss_dssp             TCCHHHHHHHSSSTTTCHHHHCSC
T ss_pred             hccHHHHHHHcCCCcchHHHhCCC
Confidence            589999999999999999998654

>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=87.25  E-value=1.6  Score=24.96  Aligned_cols=34  Identities=6%  Similarity=0.120  Sum_probs=26.4

Q ss_pred             HHHHHHH-HhCCCCHHHHHHHh--------C--CCHHHHHHHHcC
Q 038591           23 RQIQRAR-LGKKMSQPDLANQI--------N--QRPQVVSEYENG   56 (82)
Q Consensus        23 ~~lk~~r-~~~g~s~~elA~~~--------g--is~~~i~~~e~g   56 (82)
                      ..|..+. +...+|..+++..+        |  +|.+||.+|...
T Consensus        97 ~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~  141 (149)
T 1k78_A           97 EKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRT  141 (149)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHC
T ss_pred             HHHHHHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHH
Confidence            3454444 44679999999988        7  899999999875

>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=87.24  E-value=0.08  Score=31.27  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.|++++-.++.
T Consensus        33 ~~tv~~Ia~~agvs~~t~Y~~F~sK~   58 (195)
T 2iu5_A           33 QISVSDIMQTAKIRRQTFYNYFQNQE   58 (195)
T ss_dssp             GCCHHHHHHHHTSCGGGGGGTCSSHH
T ss_pred             eeCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            47999999999999999999876543

>2og0_A Excisionase; protein-DNA complex, DNA architectural protein, 'winged'HELI protein, phage excision; 1.90A {Enterobacteria phage lambda} SCOP: a.6.1.7 PDB: 1lx8_A 1rh6_A 2ief_A

Probab=87.00  E-value=0.43  Score=23.45  Aligned_cols=25  Identities=4%  Similarity=0.110  Sum_probs=21.0

Q ss_pred             CCHHHHHHHh--CCCHHHHHHHHcCCC
Q 038591           34 MSQPDLANQI--NQRPQVVSEYENGKA   58 (82)
Q Consensus        34 ~s~~elA~~~--gis~~~i~~~e~g~~   58 (82)
                      +|..|+|+.+  .+|.+|+.+|-+...
T Consensus         3 ltl~EwA~~~~~~~s~~Tl~r~ar~G~   29 (52)
T 2og0_A            3 LTLQEWNARQRRPRSLETVRRWVRESR   29 (52)
T ss_dssp             EEHHHHHHTSSSCCCHHHHHHHHHTTC
T ss_pred             eeHHHHHHHhcCCCCHHHHHHHHHCCC
Confidence            5788999999  689999999987543

>3ni7_A Bacterial regulatory proteins, TETR family; transcriptional regulator, structural genomics, PSI-2, structure initiative; HET: MSE; 2.78A {Nitrosomonas europaea}

Probab=86.94  E-value=0.31  Score=29.54  Aligned_cols=25  Identities=16%  Similarity=0.157  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..++|+.+|||+.+++.+..++
T Consensus        27 ~~tv~~Ia~~agvs~~t~y~~F~~K   51 (213)
T 3ni7_A           27 AVRLYDIAARLAVSLDEIRLYFREK   51 (213)
T ss_dssp             TCCHHHHHHHTTSCHHHHHHHCSSH
T ss_pred             ccCHHHHHHHhCCCHHHHHHHCCCH
Confidence            4789999999999999999997654

>3him_A Probable transcriptional regulator; TETR, bacterial, RHA1, PSI-2, MCSG, structural midwest center for structural genomics; 2.20A {Rhodococcus jostii}

Probab=86.78  E-value=0.048  Score=32.16  Aligned_cols=26  Identities=15%  Similarity=0.204  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        35 ~~~t~~~Ia~~agvs~~t~Y~~F~sK   60 (211)
T 3him_A           35 GATTTREIAASLDMSPGAVYPHYKTK   60 (211)
T ss_dssp             TTCCHHHHHHHTTCCTTSSTTTCSSH
T ss_pred             CcCCHHHHHHHhCCCcChhhhcCCCH
Confidence            36899999999999999999886654

>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=86.75  E-value=0.59  Score=26.75  Aligned_cols=19  Identities=32%  Similarity=0.440  Sum_probs=17.5

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q 038591           35 SQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~   53 (82)
                      |..+||+.+|||+.||.+-
T Consensus        40 ser~La~~~gVSr~tVReA   58 (134)
T 4ham_A           40 SIREFASRIGVNPNTVSKA   58 (134)
T ss_dssp             CHHHHHHHHTCCHHHHHHH
T ss_pred             cHHHHHHHHCCCHHHHHHH
Confidence            8899999999999998876

>2y2z_A SIM16, SIMR, putative repressor simreg2; transcription, simocyclinone regulator, TETR-family; 1.95A {Streptomyces antibioticus} PDB: 2y30_A* 2y31_A* 3zql_A

Probab=86.70  E-value=0.29  Score=31.13  Aligned_cols=26  Identities=15%  Similarity=0.132  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..+||+.+||++.+|+.+..++
T Consensus        46 ~~~Smr~IA~~aGVs~~tlY~hF~~K   71 (267)
T 2y2z_A           46 EAASMRRVAAELGAGTMSLYYYVPTK   71 (267)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHTTCCSH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCCH
Confidence            46899999999999999999987654

>3nrg_A TETR family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.56A {Chloroflexus aurantiacus}

Probab=86.64  E-value=0.065  Score=31.85  Aligned_cols=25  Identities=12%  Similarity=0.108  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..++|+.+|||+.+++++-.++
T Consensus        33 ~~t~~~IA~~agvs~~tlY~~F~sK   57 (217)
T 3nrg_A           33 SVSINRITERAGIAKGSFYQYFADK   57 (217)
T ss_dssp             GCCHHHHHHHHTCCTTGGGGTCSSH
T ss_pred             cCCHHHHHHHhCCcHHHHHHHcCCH
Confidence            4899999999999999999986554

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=86.62  E-value=0.59  Score=29.66  Aligned_cols=25  Identities=12%  Similarity=0.013  Sum_probs=22.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..++|..|||+.+|++++|++++.+
T Consensus        36 ~~~~~~~eia~~~gl~kstv~r~l~   60 (260)
T 2o0y_A           36 HPTRSLKELVEGTKLPKTTVVRLVA   60 (260)
T ss_dssp             BSSBCHHHHHHHHCCCHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3579999999999999999999854

>3ccy_A Putative TETR-family transcriptional regulator; APC88698, structural G PSI-2, protein structure initiative; HET: MSE; 2.01A {Bordetella parapertussis 12822}

Probab=86.56  E-value=0.08  Score=31.42  Aligned_cols=25  Identities=20%  Similarity=0.190  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..++|+.+|||+.+++++-.++
T Consensus        34 ~~s~~~Ia~~agvs~~t~Y~yF~sK   58 (203)
T 3ccy_A           34 ETSIGDIARACECSKSRLYHYFDSK   58 (203)
T ss_dssp             TSCHHHHHHHTTCCGGGGTTTCSCH
T ss_pred             cCCHHHHHHHhCCCcCeeeeeeCCH
Confidence            5799999999999999999986554

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

Probab=86.53  E-value=0.7  Score=25.68  Aligned_cols=20  Identities=20%  Similarity=0.207  Sum_probs=18.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHH
Q 038591           35 SQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e   54 (82)
                      |..+||+.+|||+.+|.+..
T Consensus        35 s~~~La~~~~vSr~tvr~al   54 (113)
T 3tqn_A           35 SIRKISTEYQINPLTVSKAY   54 (113)
T ss_dssp             CHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHH
Confidence            89999999999999988763

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

Probab=86.48  E-value=0.79  Score=26.16  Aligned_cols=33  Identities=3%  Similarity=-0.070  Sum_probs=26.6

Q ss_pred             HHHHHHHHH-hCCCCHHHHHHHhC----CCHHHHHHHH
Q 038591           22 PRQIQRARL-GKKMSQPDLANQIN----QRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~-~~g~s~~elA~~~g----is~~~i~~~e   54 (82)
                      ...|..+.. .-++|+.+||+.++    ++++||+.+.
T Consensus        12 ~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l   49 (138)
T 2g9w_A           12 RAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVL   49 (138)
T ss_dssp             HHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHH
Confidence            345666666 46899999999998    8999998874

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=86.40  E-value=0.61  Score=29.51  Aligned_cols=24  Identities=13%  Similarity=0.047  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++|..|||+.+|++++|++++.+
T Consensus        28 ~~~~~~eia~~~gl~~stv~r~l~   51 (257)
T 2g7u_A           28 PNPTLAELATEAGLSRPAVRRILL   51 (257)
T ss_dssp             SSCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            469999999999999999999864

>2g7l_A TETR-family transcriptional regulator; APC6062, protein structure initiativ midwest center for structural genomics, MCSG; 2.10A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=86.21  E-value=0.23  Score=31.03  Aligned_cols=25  Identities=20%  Similarity=0.367  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..+||+.+|||+.+|+.+..++
T Consensus        39 ~~S~~~IA~~aGvs~~tlY~hF~sK   63 (243)
T 2g7l_A           39 KVTMRRLAQELDTGPASLYVYVANT   63 (243)
T ss_dssp             SCCHHHHHHHTTSCHHHHTTTCCSH
T ss_pred             hcCHHHHHHHHCCChhHHHHHcCCH
Confidence            6899999999999999999986554

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

Probab=86.21  E-value=0.38  Score=28.38  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=21.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...++..+||+.+|+++++|++..
T Consensus        69 ~~~~t~~eLa~~lgls~stvs~hL   92 (151)
T 3f6v_A           69 SGEQTVNNLAAHFPASRSAISQHL   92 (151)
T ss_dssp             GCCEEHHHHHTTSSSCHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHH
Confidence            567999999999999999999874

>2np3_A Putative TETR-family regulator; transcriptional regulator, structural genomics, PSI-2, structure initiative; HET: MSE; 2.35A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=86.08  E-value=0.13  Score=30.67  Aligned_cols=27  Identities=15%  Similarity=0.131  Sum_probs=3.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      ++|..++|+.+|||+.+++++..++..
T Consensus        50 ~~ti~~IA~~agvs~~t~Y~~F~sK~~   76 (212)
T 2np3_A           50 ATSLRRIAETAGVDQSLVHHFYGTKEN   76 (212)
T ss_dssp             ---------------------CCC-CH
T ss_pred             cccHHHHHHHcCCCHHHHHHHhCCHHH
Confidence            579999999999999999999876543

>2fd5_A Transcriptional regulator; DNA-binding protein, structural G PSI, protein structure initiative, midwest center for struc genomics, MCSG; 1.70A {Pseudomonas aeruginosa} SCOP: a.4.1.9 a.121.1.1

Probab=86.07  E-value=0.098  Score=30.37  Aligned_cols=26  Identities=8%  Similarity=-0.147  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+.|..++|+.+|||+.+++.+-.++
T Consensus        26 ~~~s~~~IA~~agvs~~tly~~F~sK   51 (180)
T 2fd5_A           26 VEPSVGEVMGAAGLTVGGFYAHFQSK   51 (180)
T ss_dssp             TSCCHHHHHHHTTCCGGGGGGTCSCH
T ss_pred             ccCCHHHHHHHhCCCccHHHHHCCCH
Confidence            36899999999999999999876543

>3on2_A Probable transcriptional regulator; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG; HET: MSE PG6; 1.96A {Rhodococcus jostii}

Probab=85.97  E-value=0.055  Score=31.60  Aligned_cols=25  Identities=16%  Similarity=0.082  Sum_probs=17.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++-.++
T Consensus        32 ~~t~~~IA~~agvs~~t~Y~~F~sK   56 (199)
T 3on2_A           32 GLSLRQLAREAGVSHAAPSKHFRDR   56 (199)
T ss_dssp             GCCHHHHHHHTC-----CCCSSSSH
T ss_pred             hhhHHHHHHHhCCChHHHHHHhCCH
Confidence            5899999999999999999876553

>3fiw_A Putative TETR-family transcriptional regulator; TETR-family transcriptional regulator streptomyces, structur genomics, PSI-2; 2.20A {Streptomyces coelicolor}

Probab=85.96  E-value=0.22  Score=30.36  Aligned_cols=25  Identities=20%  Similarity=0.173  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+|+++..++
T Consensus        45 ~~s~~~IA~~aGvs~~tlY~~F~~K   69 (211)
T 3fiw_A           45 GVSTRRLAKRLGVEQPSLYWYFRTK   69 (211)
T ss_dssp             GCCHHHHHHHHTSCTHHHHTTCSSH
T ss_pred             cCCHHHHHHHhCCChhHHHHHcCCH
Confidence            5899999999999999999986543

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=85.96  E-value=0.64  Score=26.51  Aligned_cols=24  Identities=13%  Similarity=0.075  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+.|+.+||+.+|++..+|.+..+
T Consensus        50 ~~ps~~~LA~~l~~s~~~V~~~l~   73 (128)
T 2vn2_A           50 LFPTPAELAERMTVSAAECMEMVR   73 (128)
T ss_dssp             SSCCHHHHHHTSSSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            348999999999999999877643

>3isp_A HTH-type transcriptional regulator RV1985C/MT2039; ROD shaped structure, DNA binding domain, regulatory domain, DNA-binding; 2.70A {Mycobacterium tuberculosis}

Probab=85.84  E-value=1.1  Score=27.97  Aligned_cols=35  Identities=26%  Similarity=0.380  Sum_probs=29.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++||+           .+..|.+.||+++-+|.
T Consensus        22 s~s~AA~~L~isq~avS~-----------~i~~LE~~lg~~Lf~R~   56 (303)
T 3isp_A           22 SFDAAAERLHVTPSAVSQ-----------RIKSLEQQVGQVLVVRE   56 (303)
T ss_dssp             CHHHHHTTTTCCHHHHHH-----------HHHHHHHHHTSCCEECS
T ss_pred             CHHHHHHHhCCChHHHHH-----------HHHHHHHHhCCeeEEcC
Confidence            566699999999999998           45778888888887764

>3lsj_A DEST; transcriptional repressor, TETR family, DNA-binding, transcription, transcription regulation; HET: PLM COA; 2.30A {Pseudomonas aeruginosa} PDB: 3lsp_A* 3lsr_A*

Probab=85.83  E-value=0.096  Score=31.35  Aligned_cols=25  Identities=8%  Similarity=-0.001  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|||+.+++++..++
T Consensus        32 ~~ti~~Ia~~Agvs~~t~Y~~F~sK   56 (220)
T 3lsj_A           32 SLSLREVTRAAGIVPAGFYRHFSDM   56 (220)
T ss_dssp             GCCHHHHHHHHTSCGGGGTTTCSSH
T ss_pred             cCCHHHHHHHhCCChhHHHHHcCCH
Confidence            5899999999999999999986553

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

Probab=85.83  E-value=0.78  Score=25.98  Aligned_cols=20  Identities=20%  Similarity=0.265  Sum_probs=18.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHH
Q 038591           35 SQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e   54 (82)
                      |..+||+.+|||+.+|.+..
T Consensus        39 s~~~La~~~~vSr~tvr~Al   58 (125)
T 3neu_A           39 SVREMGVKLAVNPNTVSRAY   58 (125)
T ss_dssp             CHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHH
Confidence            79999999999999988763

>2vpr_A Tetracycline resistance repressor protein; transcription, metal-binding, antibiotic resistance, transcr regulator; HET: TDC; 2.49A {Pasteurella multocida}

Probab=85.66  E-value=0.19  Score=30.58  Aligned_cols=26  Identities=15%  Similarity=0.125  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++..++.
T Consensus        24 ~~s~~~IA~~agvs~~tlY~~f~~K~   49 (207)
T 2vpr_A           24 GLTTRKLAQKIGVEQPTLYWHVKNKR   49 (207)
T ss_dssp             HCCHHHHHHHHTCCHHHHTTTCCSHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHcCCHH
Confidence            58999999999999999999876543

>4ac0_A Tetracycline repressor protein class B from trans TN1 0; transcription; HET: MIY; 2.45A {Escherichia coli}

Probab=85.65  E-value=0.19  Score=30.63  Aligned_cols=39  Identities=10%  Similarity=0.063  Sum_probs=28.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKA   71 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~   71 (82)
                      ++|..++|+.+|||+.+++++..++...-...+..+...
T Consensus        23 ~~s~~~IA~~aGvs~~tlY~~F~~K~~Ll~a~~~~~~~~   61 (202)
T 4ac0_A           23 GLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDR   61 (202)
T ss_dssp             HCCHHHHHHHHTSCHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCchhHHhhcCCHHHHHHHHHHHHHHH
Confidence            689999999999999999998766543333333444333

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

Probab=85.43  E-value=0.29  Score=29.02  Aligned_cols=33  Identities=6%  Similarity=-0.110  Sum_probs=24.4

Q ss_pred             HHHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGK---KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~---g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....   ++|+.+||+.+|++++++++..
T Consensus        72 ~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l  107 (181)
T 2fbk_A           72 WDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRI  107 (181)
T ss_dssp             HHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34455555544   3999999999999999877653

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

Probab=85.27  E-value=0.76  Score=25.89  Aligned_cols=23  Identities=13%  Similarity=0.070  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..+|..++|+.+|++++++.++.
T Consensus        25 ~~~s~~ela~~~~i~~~~v~~il   47 (129)
T 2y75_A           25 GPTSLKSIAQTNNLSEHYLEQLV   47 (129)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             CcCCHHHHHHHHCcCHHHHHHHH
Confidence            45899999999999999999985

>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=85.27  E-value=0.84  Score=24.92  Aligned_cols=30  Identities=10%  Similarity=0.087  Sum_probs=23.6

Q ss_pred             HHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQI-NQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e   54 (82)
                      .|..+. ..++++.+||+.+ |++++++++..
T Consensus        30 IL~~L~-~~~~~~~eL~~~l~gis~~~ls~~L   60 (107)
T 2fsw_A           30 IIFQIN-RRIIRYGELKRAIPGISEKMLIDEL   60 (107)
T ss_dssp             HHHHHT-TSCEEHHHHHHHSTTCCHHHHHHHH
T ss_pred             HHHHHH-hCCcCHHHHHHHcccCCHHHHHHHH
Confidence            445554 5569999999999 59999998864

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=85.26  E-value=2.8  Score=26.16  Aligned_cols=31  Identities=3%  Similarity=0.065  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQT   63 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~   63 (82)
                      ..+|..++|+.+|+|+.++++..+. ...++.
T Consensus       184 ~~~sl~~lA~~~~~S~~~l~r~fk~-~G~t~~  214 (276)
T 3gbg_A          184 RNWRWADICGELRTNRMILKKELES-RGVKFR  214 (276)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHT-TTCCHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH-cCCCHH
Confidence            3689999999999999999999874 444443

>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=85.15  E-value=1.2  Score=27.59  Aligned_cols=23  Identities=17%  Similarity=0.289  Sum_probs=20.3

Q ss_pred             CCCCH--HHHHHHhCCCHHHHHHHH
Q 038591           32 KKMSQ--PDLANQINQRPQVVSEYE   54 (82)
Q Consensus        32 ~g~s~--~elA~~~gis~~~i~~~e   54 (82)
                      .|+++  .+||+.+|++++++++..
T Consensus        21 ~~~~~~~~~La~~l~vs~~tvs~~l   45 (230)
T 1fx7_A           21 EGVTPLRARIAERLDQSGPTVSQTV   45 (230)
T ss_dssp             HTSCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCCcHHHHHHHHCcCHHHHHHHH
Confidence            47888  999999999999998874

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=84.87  E-value=0.59  Score=29.99  Aligned_cols=33  Identities=6%  Similarity=0.098  Sum_probs=23.7

Q ss_pred             HHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLG-KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+-.. .++|..|+|+.+|++++|++++.+
T Consensus        34 ~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~   67 (275)
T 3mq0_A           34 RILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLA   67 (275)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHH
T ss_pred             HHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444443 469999999999999999999864

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=84.83  E-value=0.43  Score=30.32  Aligned_cols=24  Identities=13%  Similarity=0.095  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++|..|+|+.+|++++|++++.+
T Consensus        20 ~~lsl~eia~~lgl~ksT~~RlL~   43 (260)
T 3r4k_A           20 LEIGLSDLTRLSGMNKATVYRLMS   43 (260)
T ss_dssp             SEEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            568999999999999999999864

---

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	82
d1y7ya1	69	a.35.1.3 (A:5-73) Restriction-modification control	7e-10
d2b5aa1	77	a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacil	5e-08
d1utxa_	66	a.35.1.3 (A:) Putative transcription regulator Cyl	1e-07
d2r1jl1	66	a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding do	1e-06
d1y9qa1	79	a.35.1.8 (A:4-82) Probable transcriptional regulat	1e-06
d1b0na2	68	a.35.1.3 (A:1-68) SinR repressor, DNA-binding doma	3e-06
d2croa_	65	a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 1	6e-05
d2ppxa1	62	a.35.1.3 (A:30-91) Uncharacterized protein Atu1735	1e-04
d1r69a_	63	a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain	6e-04
d2auwa1	67	a.35.1.10 (A:88-154) Hypothetical protein NE0471 C	8e-04

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]} Length = 69

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]

 Score = 47.8 bits (114), Expect = 7e-10
 Identities = 11/54 (20%), Positives = 23/54 (42%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
          ++++  R  K +SQ  LA         V   E G+   +   + K+  A+ ++ 
Sbjct: 12 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 65

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Length = 77

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]

 Score = 43.3 bits (102), Expect = 5e-08
 Identities = 13/54 (24%), Positives = 25/54 (46%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
          R +++ R  K +SQ +LA+        +SE E G    +   + K+  A+ +  
Sbjct: 13 RTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} Length = 66

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]

 Score = 42.1 bits (99), Expect = 1e-07
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           ++  R  KK+SQ +LA  +    Q ++  E  K  P+  +  K+   +   L
Sbjct: 5  NLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPL 57

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} Length = 66

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]

 Score = 39.4 bits (92), Expect = 1e-06
 Identities = 12/54 (22%), Positives = 22/54 (40%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +I+  R   K+ Q  L   +      +S++E  +  PN   L  + KA+    
Sbjct: 6  ERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSP 59

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]} Length = 79

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]

 Score = 39.9 bits (93), Expect = 1e-06
 Identities = 9/54 (16%), Positives = 20/54 (37%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           Q++  R  + +S    A        ++ + E G++ P    L K+   +    
Sbjct: 11 NQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASF 64

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Length = 68

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]

 Score = 39.0 bits (91), Expect = 3e-06
 Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKL 76
          ++I++ R  K  S  +LA +       +S  E   +  P+   L K+   + V +
Sbjct: 4  QRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSV 58

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]} Length = 65

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]

 Score = 35.2 bits (81), Expect = 6e-05
 Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           ++++ R+  KM+Q +LA +   + Q +   E G     +  L ++  A+    
Sbjct: 6  ERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMALNCDP 58

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Length = 62

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]

 Score = 34.4 bits (79), Expect = 1e-04
 Identities = 9/48 (18%), Positives = 25/48 (52%)

Query: 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKA 71
          +I+  R   K++Q + + + +     + ++E G++ P+Q   A ++  
Sbjct: 3  RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKII 50

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]} Length = 63

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]

 Score = 32.6 bits (74), Expect = 6e-04
 Identities = 13/54 (24%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76
           +++  R+   ++Q +LA ++    Q + + ENGK       L ++  A+GV +
Sbjct: 4  SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSV 56

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Length = 67

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]

 Score = 32.4 bits (74), Expect = 8e-04
 Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 1/47 (2%)

Query: 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLA 66
          +            +S    A  +    ++VS Y    K +P    LA
Sbjct: 2  SHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLA 48

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	82
d1y7ya1	69	Restriction-modification controller protein C.AhdI	99.81
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	99.79
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	99.78
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	99.78
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	99.78
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	99.78
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	99.77
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	99.77
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	99.75
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	99.75
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	99.74
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	99.72
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	99.68
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	99.67
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	99.62
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	99.47
d2bnma1	71	Hydroxypropylphosphonic acid epoxidase Fom4, N-ter	98.63
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	98.53
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	98.45
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	98.4
d1dwka1	86	Cyanase N-terminal domain {Escherichia coli [TaxId	98.26
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	98.23
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	98.04
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	97.92
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.88
d2awia1	65	PrgX {Enterococcus faecalis [TaxId: 1351]}	97.61
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	97.52
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.32
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	97.31
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.3
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	97.23
d1s4ka_	120	Putative cytoplasmic protein YdiL {Salmonella typh	97.17
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	97.08
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.03
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.83
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.71
d2csfa1	88	DNA-binding protein SATB2 {Human (Homo sapiens) [T	96.67
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.61
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	96.59
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	96.59
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	96.58
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.51
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.36
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	96.31
d2o4aa1	83	DNA-binding protein SATB1 {Human (Homo sapiens) [T	96.3
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	96.26
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.24
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	96.23
d2ox6a1	162	Hypothetical protein SO3848 {Shewanella oneidensis	96.21
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	96.17
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.15
d1zyba1	73	Probable transcription regulator BT4300, C-termina	96.14
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.11
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.08
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	96.06
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	96.01
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	96.0
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	95.96
d1s7ea2	80	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	95.9
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	95.87
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	95.65
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	95.62
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	95.54
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	95.53
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	95.44
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.42
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	95.41
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	95.37
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	95.33
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	95.3
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	95.15
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	95.15
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	95.14
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	95.13
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	95.13
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	95.11
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	95.09
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	95.08
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.08
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	95.06
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	95.03
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	95.0
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	94.97
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	94.96
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	94.91
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	94.89
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	94.89
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	94.88
d1x2la1	87	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	94.88
d1wh8a_	111	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	94.88
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	94.85
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	94.83
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	94.82
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	94.8
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	94.73
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	94.73
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.65
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	94.62
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	94.5
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	94.48
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	94.48
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.39
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	94.32
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	94.23
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	94.23
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	94.14
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	94.13
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	94.12
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	94.07
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	94.03
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	94.01
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	94.01
d1zs4a1	78	Regulatory protein cII {Bacteriophage lambda [TaxI	93.94
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	93.8
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	93.76
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	93.71
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	93.69
d1d1la_	61	cro lambda repressor {Bacteriophage lambda [TaxId:	93.67
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	93.65
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	93.62
d1wh6a_	101	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.55
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	93.54
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	93.49
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	93.29
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	93.29
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	93.17
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	93.07
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	92.87
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	92.73
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	92.55
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	92.36
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	92.12
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	92.08
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	92.06
d1tc3c_	51	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	91.9
d2np3a1	65	Putative transcriptional regulator SCO0857 {Strept	91.56
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	91.55
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	91.41
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	91.29
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	91.18
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	91.04
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	90.96
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.93
d2esna1	89	Probable LysR-type transcriptional regulator PA047	90.8
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	90.79
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	90.71
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	90.61
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	90.28
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	89.96
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	89.89
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	89.87
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	89.79
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	89.66
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	89.24
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	88.85
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	88.59
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	88.54
d1bl0a2	62	MarA {Escherichia coli [TaxId: 562]}	88.53
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	88.2
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	87.81
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.79
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	87.62
d2dt5a1	74	Transcriptional repressor Rex, N-terminal domain {	87.57
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	87.54
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	87.35
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	87.08
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	87.07
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	86.71
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	86.71
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	86.67
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	86.51
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	86.03
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	85.68
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	85.61
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	85.3
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	84.67
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	84.65
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	84.65
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	84.37
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	84.05
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	83.91
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	83.81
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	83.78
d1vola1	95	Transcription factor IIB (TFIIB), core domain {Hum	83.57
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	83.47
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	83.26
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	83.22
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	83.09
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	82.88
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	82.56
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	82.37
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	82.32
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	81.78
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	81.22
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	80.67
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	80.54
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	80.02

>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=99.81  E-value=4.9e-20  Score=97.43  Aligned_cols=57  Identities=21%  Similarity=0.229  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|+..||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus        11 g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~   67 (69)
T d1y7ya1          11 GQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE   67 (69)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            899999999999999999999999999999999999999999999999999999987

>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=99.79  E-value=1.5e-19  Score=94.71  Aligned_cols=59  Identities=20%  Similarity=0.250  Sum_probs=56.7

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..|.+|+.+|+.+||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus         3 ~ig~rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~   61 (66)
T d2r1jl1           3 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDY   61 (66)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            45899999999999999999999999999999999999999999999999999999875

>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=99.78  E-value=4.4e-19  Score=95.83  Aligned_cols=60  Identities=50%  Similarity=0.823  Sum_probs=57.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      .|.+|+.+|+.+||||.+||..+|+|.++|++||+|...|+.+.+.+||.+|||++...+
T Consensus         7 iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~G~~~p~~~~l~~la~~l~v~l~~~~   66 (78)
T d1x57a1           7 VGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKD   66 (78)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSSTT
T ss_pred             HHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHccCCCCCHHHHHHHHHHhCCcccccc
Confidence            499999999999999999999999999999999999999999999999999999997654

>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=99.78  E-value=4.3e-19  Score=93.45  Aligned_cols=58  Identities=21%  Similarity=0.262  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|..+||||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||++++
T Consensus         2 ig~~ik~~R~~~gltq~~la~~~gis~~~i~~~E~g~~~~ps~~~l~~ia~~l~v~~~~   60 (68)
T d1b0na2           2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHT   60 (68)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCcHHH
Confidence            48999999999999999999999999999999999964 69999999999999999875

>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=99.78  E-value=6.5e-19  Score=95.08  Aligned_cols=58  Identities=16%  Similarity=0.244  Sum_probs=56.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      |.+|+.+|+.+||||.+||+.+|+++++|++||+|...|+.+.+.+||++|||++++.
T Consensus        10 g~~lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~l   67 (79)
T d1y9qa1          10 ANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAF   67 (79)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSGGG
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHH
Confidence            8999999999999999999999999999999999999999999999999999999864

>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=99.78  E-value=1.9e-19  Score=94.38  Aligned_cols=56  Identities=23%  Similarity=0.277  Sum_probs=54.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+|+.+|..+||||.+||+.+|||+++|++||+|...|+.+.+.+||++|||++++
T Consensus         4 ~ri~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~~   59 (66)
T d1utxa_           4 NNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLED   59 (66)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            47899999999999999999999999999999999999999999999999999876

>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=99.77  E-value=5e-19  Score=95.10  Aligned_cols=58  Identities=22%  Similarity=0.257  Sum_probs=56.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .|.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||.+|||++++
T Consensus        11 ~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~   68 (77)
T d2b5aa1          11 FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAST   68 (77)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            3899999999999999999999999999999999999999999999999999999875

>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=99.77  E-value=3.6e-19  Score=93.03  Aligned_cols=57  Identities=19%  Similarity=0.275  Sum_probs=53.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.+|+.+|+..|+||.+||+.+|+++++|++||+|...|+ +.+.+||++|||++++
T Consensus         4 i~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~g~~~~~-~~l~~ia~~l~v~~~~   60 (65)
T d2croa_           4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRP-RFLFEIAMALNCDPVW   60 (65)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSC-TTHHHHHHHTTSCHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHCCCCCCH-HHHHHHHHHhCCCHHH
Confidence            48999999999999999999999999999999999988776 7899999999999875

>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=99.75  E-value=6.9e-19  Score=91.36  Aligned_cols=56  Identities=23%  Similarity=0.453  Sum_probs=52.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |.+|+.+|+.+||||.|||+.+|+|+++|++||+|+ .|+.+.+.+||++|||++++
T Consensus         3 g~rik~~R~~~g~sq~elA~~~gvs~~~is~~E~g~-~~~~~~l~~ia~~l~v~~~~   58 (63)
T d1r69a_           3 SSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSVDW   58 (63)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTS-CSSCTTHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHhCcCHHHHHHHHCCC-CcCHHHHHHHHHHHCcCHHH
Confidence            789999999999999999999999999999999997 47889999999999999875

>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=99.75  E-value=1.6e-18  Score=95.31  Aligned_cols=57  Identities=21%  Similarity=0.219  Sum_probs=55.1

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      +|++|+++|+.+||||.+||+.+|||+++|++||+|++.|+.+.+.+|+++||++++
T Consensus         2 PGe~lke~r~~~glsq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~lgvs~~   58 (87)
T d2icta1           2 PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   58 (87)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             cHHHHHHHHHHcCCCHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHHCcCHH
Confidence            388999999999999999999999999999999999999999999999999999975

>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=99.74  E-value=5.2e-18  Score=93.19  Aligned_cols=58  Identities=17%  Similarity=0.122  Sum_probs=54.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +..++.+|+..||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus        14 ~~~i~~~R~~~gltq~~lA~~lgis~~~is~~E~g~~~~s~~~l~~ia~~l~v~~~~~   71 (87)
T d1lmb3_          14 KAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEF   71 (87)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHHhccCCCcHHHHHHHHHHHCCCHHHH
Confidence            5667777999999999999999999999999999999999999999999999999875

>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=99.72  E-value=1.4e-17  Score=87.87  Aligned_cols=58  Identities=21%  Similarity=0.219  Sum_probs=55.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      +.+|+.+|+.+||||.+||+.+|+++++|++||+|+ ..|+.+.+.+||.+||++++..
T Consensus         8 ~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~~Lg~~i~~~   66 (69)
T d2a6ca1           8 LIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVEIN   66 (69)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCCCC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHHHhCCCcEee
Confidence            678999999999999999999999999999999997 7899999999999999999754

>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=99.68  E-value=5.8e-17  Score=89.28  Aligned_cols=57  Identities=16%  Similarity=0.112  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e   78 (82)
                      +..|+.+|+.+||||.++|+.+|+++++|++||+|+ ..|+.+.+.+||.+||++++.
T Consensus        13 ~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~Lg~~i~~   70 (89)
T d2o38a1          13 AYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVEI   70 (89)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEEE
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHcCCCHHH
Confidence            789999999999999999999999999999999997 679999999999999999864

>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=99.67  E-value=9.5e-17  Score=87.30  Aligned_cols=57  Identities=19%  Similarity=0.235  Sum_probs=52.7

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      .|.+|+.+|+  ++||.+||+.+|+|+++|++||+|+ ..|+.+.+.+||++|||++++.
T Consensus        15 lG~~ir~~R~--~~t~~eLA~~~Gvs~~~ls~iE~G~~~~ps~~tl~kia~~L~v~~~~L   72 (82)
T d2ofya1          15 LGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLDDV   72 (82)
T ss_dssp             HHHHHHHHHT--TSCHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHH--cCCHHHHHHHHcCCHHHHHHHHcCCcCCCCHHHHHHHHHHHCCCHHHH
Confidence            4899999995  7899999999999999999999997 5899999999999999999864

>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=99.62  E-value=6.9e-16  Score=79.77  Aligned_cols=52  Identities=21%  Similarity=0.367  Sum_probs=45.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL   76 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~   76 (82)
                      +|+.+|+..||||++||+.+|||++||++||+|...|+...+..|+ .++..+
T Consensus         3 ~ik~~R~~~gltQ~elA~~lGvs~~tvs~~E~G~~~P~~~~~~ll~-~l~~~P   54 (62)
T d2ppxa1           3 RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLK-IIAVDP   54 (62)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHH-HHHHCH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHH-HHhcCH
Confidence            6899999999999999999999999999999999999998876664 444444

>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=99.47  E-value=2.3e-13  Score=71.07  Aligned_cols=44  Identities=14%  Similarity=0.158  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      .+++|+.+|+..|+||.+||+.+|||+.+|++||+|...++...
T Consensus         2 s~e~~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~iP~~v   45 (67)
T d2auwa1           2 SHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTI   45 (67)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHH
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Confidence            46899999999999999999999999999999999987765443

>d2bnma1 a.35.1.3 (A:6-76) Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain {Streptomyces wedmorensis [TaxId: 43759]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain
species: Streptomyces wedmorensis [TaxId: 43759]

Probab=98.63  E-value=2.5e-07  Score=46.03  Aligned_cols=56  Identities=23%  Similarity=0.431  Sum_probs=52.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~   77 (82)
                      .++|+..|++..|....||..+|-++.++..||||. ...++..+-+|+.+||.++.
T Consensus         7 ae~lk~rreqvkmdhaalas~lgetpetvaawengeggeltltqlg~ia~~lgtsig   63 (71)
T d2bnma1           7 AELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIG   63 (71)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTG
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHcCCchHHHHhhcCCCceeeHHHHHHHHHHHccccc
Confidence            678999999999999999999999999999999995 57899999999999999874

>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=98.53  E-value=2.6e-07  Score=46.11  Aligned_cols=45  Identities=16%  Similarity=0.197  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR   77 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~   77 (82)
                      ++|.+|+|+.+|+|..|||++.+|...++.++   +..+++.||..++
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~~~~Vs~~tr~rV~~aa~~lgY~pn   48 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPN   48 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCSC
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCCCCcCCHHHHHHHHHHHHHHCcCCC
Confidence            57999999999999999999999988887766   5666777777665

>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=98.45  E-value=3.5e-07  Score=45.92  Aligned_cols=46  Identities=13%  Similarity=0.011  Sum_probs=38.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      .+|..|+|+.+|+|++|||++.+|...++.++   +..+++.+|..++.
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~~~~vs~~tr~rI~~~a~~lgY~pn~   50 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR   50 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTTCSSCCTHHHHHHHHHHHHHTCCCCH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCcCCHHHHHHHHHHHHHHCCCcCH
Confidence            57999999999999999999999987776555   66777788877653

>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=98.40  E-value=7.4e-07  Score=44.42  Aligned_cols=44  Identities=16%  Similarity=0.087  Sum_probs=37.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV   78 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e   78 (82)
                      |.+|+|+.+|+|.+|||++.+|...++.++   +..+++.||..++.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~a~~lgY~pn~   48 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA   48 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHHHHHHCCCCCH
Confidence            789999999999999999999988887666   66667788877653

>d1dwka1 a.35.1.4 (A:1-86) Cyanase 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: Cyanase N-terminal domain
domain: Cyanase N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.26  E-value=1.8e-06  Score=46.23  Aligned_cols=57  Identities=11%  Similarity=0.077  Sum_probs=52.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+.|-..+..+|+|-.++|+.+|+|+..+.....|....+.+.+.++++.||++-+.
T Consensus        15 te~Il~AK~~kgltw~~IA~~iG~s~vwvtaa~lGQ~~l~~~~A~~l~~~L~L~~e~   71 (86)
T d1dwka1          15 ADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDS   71 (86)
T ss_dssp             HHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHH
Confidence            467778899999999999999999999999999999999999999999999987653

>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=98.23  E-value=1.7e-06  Score=43.36  Aligned_cols=45  Identities=16%  Similarity=0.077  Sum_probs=38.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCcc
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA------VPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~------~p~~~~~~~la~~lgv~~~e   78 (82)
                      +|.+|+|+.+|+|.+|||++.||..      .-+.+.+..+++.||..++.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~   51 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNA   51 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGGTTCTTTTHHHHHHHHHHHTCCCCS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCcCcCCHHHHHHHHHHHHHHCCCcCH
Confidence            5889999999999999999999853      23677788999999988764

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.04  E-value=2.1e-05  Score=42.33  Aligned_cols=49  Identities=8%  Similarity=0.047  Sum_probs=41.4

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      ....|+.+...++++|.++|+.+|+|.++||+|.++....+...=..|-
T Consensus        29 v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~~g~~M~~~KR~alY   77 (94)
T d1ic8a2          29 VAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALY   77 (94)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHhCCCCccHHHHHHHH
Confidence            3788999999999999999999999999999999987766655544433

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=97.92  E-value=3.1e-05  Score=40.08  Aligned_cols=59  Identities=14%  Similarity=0.049  Sum_probs=49.1

Q ss_pred             CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591           18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK   79 (82)
Q Consensus        18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~   79 (82)
                      ......-|......+|+|..+|++..|++.+|+.+...   .|....=..||+++|+.+.+.
T Consensus         7 ~dWh~adI~AaL~krG~sLa~lsr~~gls~stl~naL~---rp~pKgEriIA~aLg~~P~eI   65 (74)
T d1nera_           7 RDWHRADVIAGLKKRKLSLSALSRQFGYAPTTLANALE---RHWPKGEQIIANALETKPEVI   65 (74)
T ss_dssp             SSCCHHHHHHHHTTSSCCHHHHHHHHSCCHHHHHHTTT---SSCHHHHHHHHHHTTSCHHHH
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHHHh
Confidence            34456667777788999999999999999999999765   667777788999999998763

>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=97.88  E-value=3.1e-05  Score=36.87  Aligned_cols=36  Identities=14%  Similarity=0.069  Sum_probs=28.2

Q ss_pred             CCHHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           20 DTPRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        20 ~~~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..+.+..+|  ...|.|..++|+.+|||++||++|.-
T Consensus         6 lt~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           6 INKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             SCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhCC
Confidence            3445555543  25799999999999999999999974

>d2awia1 a.35.1.11 (A:2-66) PrgX {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: PrgX N-terminal domain-like
domain: PrgX
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.61  E-value=0.00019  Score=34.80  Aligned_cols=56  Identities=20%  Similarity=0.174  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      |..|+++|++.++-|-+|-.-+ +|.+.+-++|...++++.+.+.++++-||+++-|
T Consensus         4 g~~lkqir~elnyhqidlysgi-msksiyikveadsrpisveel~kfserlginffe   59 (65)
T d2awia1           4 GSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFFE   59 (65)
T ss_dssp             HHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHHH
T ss_pred             chHHHHHHHHhhhhHhHHHhhh-cccceEEEEecCCCcccHHHHHHHHHHhCchHHH
Confidence            7889999999999998876432 6899999999999999999999999999998755

>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Oct-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.52  E-value=0.00034  Score=35.98  Aligned_cols=47  Identities=13%  Similarity=0.233  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      +..++..|...|+||.+++..+|      .|++||+++|+  -..+..++.+|-=
T Consensus        13 a~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~--l~LS~kn~~kLkP   65 (75)
T d1e3oc2          13 AKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEA--LNLSFKNMSKLKP   65 (75)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHH--TCSCHHHHHHHHH
T ss_pred             HHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHH--hccCHHHHHHHHH
Confidence            67788999999999999999986      69999999998  4567777666543

>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Pit-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.32  E-value=0.00055  Score=34.87  Aligned_cols=47  Identities=11%  Similarity=0.198  Sum_probs=38.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEK   70 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~   70 (82)
                      ...++..|...|+||.|++..+|      .|++||+++|+  -..+..++.+|-=
T Consensus         9 a~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~--l~LS~kn~~klkP   61 (72)
T d1au7a2           9 ANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFEN--LQLSFKNACKLKA   61 (72)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHT--TCSBHHHHHHHHH
T ss_pred             HHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHh--cccCHHHHHHHHH
Confidence            56788889999999999999976      79999999997  4567777666543

>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=97.31  E-value=0.00083  Score=31.04  Aligned_cols=36  Identities=8%  Similarity=0.064  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ...+.++.++. .|++..++|+.+||++.+|+++.+.
T Consensus         6 Id~~~V~~L~~-~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           6 IDRDAVLNMWQ-QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             SCHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            34677888874 8999999999999999999999864

>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=97.30  E-value=0.00074  Score=34.07  Aligned_cols=46  Identities=22%  Similarity=0.327  Sum_probs=32.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV   74 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv   74 (82)
                      .|+.+-....++|.|+|..+||+++||+.|...+     +.+..-++.+|.
T Consensus        16 ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK-----~kil~~~~~~g~   61 (66)
T d1hlva1          16 IIQEVEENPDLRKGEIARRFNIPPSTLSTILKNK-----RAILASERKYGV   61 (66)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH-----HHHHHHHHHHGG
T ss_pred             HHHHHHcCCcchHHHHHHHhCCChhHHHHHHHHH-----HHHHHHHHHcCc
Confidence            3444444445899999999999999999999853     455555555553

>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=97.23  E-value=0.00014  Score=38.47  Aligned_cols=34  Identities=9%  Similarity=0.055  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...++......|.|..++|+.+||++++|++|.+
T Consensus        12 ~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1          12 RDAVALYENSDGASLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             HHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            3444444444589999999999999999999974

>d1s4ka_ a.35.1.6 (A:) Putative cytoplasmic protein YdiL {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Putative cytoplasmic protein YdiL
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.17  E-value=0.0023  Score=35.31  Aligned_cols=50  Identities=14%  Similarity=0.172  Sum_probs=43.1

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQIN--QRPQVVSEYENGKAVPNQTVLAKME   69 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~g~~~p~~~~~~~la   69 (82)
                      ..+-.|+.+|.-.-|+..|-|..++  ++..+..+||+|...++.+.+..+.
T Consensus         3 MN~~ELQalR~if~mti~EaA~~I~~~~~s~tWQqWE~Gd~~IP~~Vi~~l~   54 (120)
T d1s4ka_           3 MNALELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLK   54 (120)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhHHHHHHHHhcCccHHHHHHHHcCCCCCCHHHHHHHH
Confidence            3467899999999999999999775  6899999999999999988865554

>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=97.08  E-value=0.00061  Score=36.49  Aligned_cols=33  Identities=15%  Similarity=0.187  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..++.+. +.|+|+.++|+++|.|+++|++...
T Consensus         9 A~a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1           9 ARGYQALL-EMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHH-HcCCCHHHHHHHHccchHHHHHHHH
Confidence            45567776 5899999999999999999999854

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=97.03  E-value=0.00077  Score=34.00  Aligned_cols=34  Identities=15%  Similarity=0.190  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..++..-.+|..|||+.+|+|++||+++.+
T Consensus         9 ~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~   42 (71)
T d1z05a1           9 GRVYKLIDQKGPISRIDLSKESELAPASITKITR   42 (71)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            3567788888899999999999999999998854

>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=96.83  E-value=0.0011  Score=33.46  Aligned_cols=34  Identities=12%  Similarity=0.059  Sum_probs=29.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|+.++..-.+|..|||+.+|+|.+||+++.+
T Consensus         8 ~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~   41 (70)
T d1z6ra1           8 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVH   41 (70)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3567888888999999999999999999999854

>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=96.71  E-value=0.00097  Score=33.08  Aligned_cols=33  Identities=12%  Similarity=0.104  Sum_probs=26.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+....-+|..+||+.+|||+.||.+..+
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~   41 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGMSRAAINKHIQ   41 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHH
Confidence            345555556668999999999999999998753

>d2csfa1 a.35.1.7 (A:8-95) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.002  Score=34.12  Aligned_cols=60  Identities=18%  Similarity=0.135  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKAVPN------QTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~~p~------~~~~~~la~~lgv~~~e~~   80 (82)
                      ...+|++..+..+++|+-||+ -+|.|+.+++.+......|.      ...+.++-++|+.+..+++
T Consensus        15 Ia~~i~~eL~~~~IsQ~~Fak~vL~rSQGtlSdLLrkpkp~~~~~~sg~e~~~rm~~wL~lPe~~R~   81 (88)
T d2csfa1          15 IYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQHERD   81 (88)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCcchhhHHHHHHHHHHHHHHhChHHHHH
Confidence            388999999999999999999 56999999999998644442      4678888999998876665

>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=96.61  E-value=0.0019  Score=32.02  Aligned_cols=32  Identities=19%  Similarity=0.213  Sum_probs=25.5

Q ss_pred             HHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKK-MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+....+ +|..+||+.+|||..||.+..+
T Consensus        12 Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~   44 (65)
T d1j5ya1          12 IVRILERSKEPVSGAQLAEELSVSRQVIVQDIA   44 (65)
T ss_dssp             HHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            3455555554 8999999999999999998754

>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=96.59  E-value=0.0029  Score=30.99  Aligned_cols=34  Identities=15%  Similarity=0.060  Sum_probs=30.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....+..+.+.|+.+|||++|+++-..
T Consensus        22 r~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmk   55 (60)
T d1umqa_          22 WEHIQRIYEMCDRNVSETARRLNMHRRTLQRILA   55 (60)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHH
Confidence            5778888899999999999999999999988764

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.59  E-value=0.0025  Score=34.80  Aligned_cols=33  Identities=21%  Similarity=0.312  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +..++.+.. .|+|+.++|+.+|+|+++|+++..
T Consensus        20 A~a~~~l~~-~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          20 ADFIGRELA-KGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             HHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHHHHHHH-hCCCHHHHHHHHCCcHHHHHHHHH
Confidence            666777754 699999999999999999999976

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.58  E-value=0.0011  Score=33.22  Aligned_cols=23  Identities=9%  Similarity=0.241  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+||.|+|..+|+|+.+|++..+
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L~   51 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRILK   51 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            48999999999999999999865

>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=96.51  E-value=0.0028  Score=31.31  Aligned_cols=32  Identities=22%  Similarity=0.342  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      ...|..+.....+|..++|+.+|+|+++|.+-
T Consensus         8 ~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~R   39 (63)
T d2cfxa1           8 LNIIEELKKDSRLSMRELGRKIKLSPPSVTER   39 (63)
T ss_dssp             HHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            46678888889999999999999999998753

>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=96.36  E-value=0.0029  Score=31.16  Aligned_cols=30  Identities=20%  Similarity=0.306  Sum_probs=25.6

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+.+++ ..+|..|+|+.+|+|++||+++.+
T Consensus         5 l~~i~~-~pisr~eLa~~~gls~~TVs~~v~   34 (62)
T d2hoea1           5 LKRIMK-SPVSRVELAEELGLTKTTVGEIAK   34 (62)
T ss_dssp             HHHHHH-SCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHH-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            667775 579999999999999999998753

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=96.31  E-value=0.0021  Score=32.95  Aligned_cols=24  Identities=17%  Similarity=0.086  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.|||..+|+|+.+++++.+
T Consensus        29 ~~lt~~elA~~~g~sretvsr~l~   52 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVSRVLA   52 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             eCCCHHHHHHHHCCCHHHHHHHHH
Confidence            368999999999999999998864

>d2o4aa1 a.35.1.7 (A:370-452) DNA-binding protein SATB1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.30  E-value=0.0036  Score=32.74  Aligned_cols=60  Identities=15%  Similarity=0.107  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCCCcccc
Q 038591           21 TPRQIQRARLGKKMSQPDLAN-QINQRPQVVSEYENGKAVPN------QTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~-~~gis~~~i~~~e~g~~~p~------~~~~~~la~~lgv~~~e~~   80 (82)
                      ...+|+...+..+++|+-||+ -+|.|+.+++.+...-..++      .+.+.++-.+|+.|-.+++
T Consensus         6 I~~~i~~eL~~~~IsQ~~Fak~vL~rSQgtlSdLL~~pkpw~~ls~sgre~f~Rm~~wL~lP~~~r~   72 (83)
T d2o4aa1           6 IYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPEAERD   72 (83)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCchhhhHHHHHHHHHHHHHHcChHHHHH
Confidence            367899999999999999999 56999999999998644442      3567888888887765543

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=96.26  E-value=0.002  Score=33.02  Aligned_cols=24  Identities=17%  Similarity=0.026  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           32 KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+|+.|||..+|+|+.||++..+
T Consensus        28 ~~lt~~eLA~~~G~sretvsr~L~   51 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAIRTLS   51 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHH
Confidence            468999999999999999998854

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.24  E-value=0.0046  Score=30.40  Aligned_cols=31  Identities=13%  Similarity=0.187  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSE   52 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~   52 (82)
                      ...|..+.....+|..++|+.+|+|.+++..
T Consensus         8 ~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~   38 (63)
T d2cg4a1           8 RGILEALMGNARTAYAELAKQFGVSPETIHV   38 (63)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            5678889999999999999999999998765

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=96.23  E-value=0.0062  Score=31.81  Aligned_cols=60  Identities=13%  Similarity=0.219  Sum_probs=44.3

Q ss_pred             CCCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCCcc
Q 038591           19 PDTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        19 ~~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      .+......-++ -..|++.+++|+.+++|..||..+.+.    -...+...+...|...|+-+-|
T Consensus        22 ~LT~rE~~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~~lv~~a~~~gl~~~~   86 (87)
T d1p4wa_          22 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSMTPVD   86 (87)
T ss_dssp             SCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTCSSCC
T ss_pred             CCCHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCCCC
Confidence            34444443332 356999999999999999999888754    3456778888899999976654

>d2ox6a1 a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Hypothetical protein SO3848
species: Shewanella oneidensis [TaxId: 70863]

Probab=96.21  E-value=0.028  Score=31.51  Aligned_cols=45  Identities=13%  Similarity=0.149  Sum_probs=39.0

Q ss_pred             CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591           20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV   64 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~   64 (82)
                      +++-.++.+|...|+|..++++..+.|..-+-.||.|....+.-.
T Consensus         3 lnaie~~ylr~slglt~aqv~~l~k~se~dv~aweage~~~~~la   47 (162)
T d2ox6a1           3 LNAIEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELA   47 (162)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHH
T ss_pred             chhHHHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCchHH
Confidence            346778999999999999999999999999999999977665433

>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=96.17  E-value=0.0072  Score=29.99  Aligned_cols=32  Identities=16%  Similarity=0.167  Sum_probs=25.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .++-++- ..|+|..++|++++||.+++++|.+
T Consensus        21 ~Riv~~~-~~G~s~r~aA~rf~VS~s~v~k~l~   52 (63)
T d1k78a1          21 QRIVELA-HQGVRPCDISRQLRVSHGCVSKILG   52 (63)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3444443 4799999999999999999999964

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.15  E-value=0.0058  Score=29.76  Aligned_cols=32  Identities=6%  Similarity=0.080  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      -..|..+.....+|..++|+.+|+|++++..-
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~R   37 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRKR   37 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            45677888888999999999999999998764

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=96.14  E-value=0.0026  Score=32.29  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|++++|..+|+|+.+|++..+
T Consensus        27 ~lt~~elA~~lg~sr~tvsr~l~   49 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNISKTLN   49 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHHHHHH
Confidence            58999999999999999998764

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.11  E-value=0.0063  Score=29.56  Aligned_cols=32  Identities=9%  Similarity=0.080  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY   53 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~   53 (82)
                      ...|..+.....+|..++|+.+|+|+++|..-
T Consensus         6 ~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~R   37 (60)
T d2cyya1           6 KKIIKILQNDGKAPLREISKITGLAESTIHER   37 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            45678888889999999999999999988653

>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=96.08  E-value=0.0071  Score=29.90  Aligned_cols=31  Identities=10%  Similarity=0.172  Sum_probs=26.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +=.++--.|+|..|+|+.+|+|+++|.....
T Consensus        29 v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~   59 (71)
T d1rp3a2          29 VIQLIFYEELPAKEVAKILETSVSRVSQLKA   59 (71)
T ss_dssp             HHHHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHhHhCCHHHHHHHHCCCHHHHHHHHH
Confidence            3345667899999999999999999998764

>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=96.06  E-value=0.0026  Score=34.84  Aligned_cols=27  Identities=19%  Similarity=0.350  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH-cCCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYE-NGKAV   59 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e-~g~~~   59 (82)
                      .-||.++|+.+|||+.++++|- +.+..
T Consensus        36 kktqeqiAeelGisr~tLyrWrt~dk~F   63 (120)
T d2ao9a1          36 KRTQDEMANELGINRTTLWEWRTKNQDF   63 (120)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHCHHH
T ss_pred             hhhHHHHHHHhChhHHHHHHHhhcchhH
Confidence            4599999999999999999998 44433

>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=96.01  E-value=0.024  Score=27.88  Aligned_cols=36  Identities=14%  Similarity=0.206  Sum_probs=26.8

Q ss_pred             CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +....++-++ -..|+|..++|+.+|+|+.||..+..
T Consensus         7 LT~rE~~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~   43 (67)
T d1a04a1           7 LTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVK   43 (67)
T ss_dssp             SCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3333343332 35799999999999999999988765

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=96.00  E-value=0.0036  Score=32.02  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+.++|..+|+|+.|+++..+
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~   52 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALN   52 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            68999999999999999998753

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=95.96  E-value=0.0088  Score=31.44  Aligned_cols=34  Identities=3%  Similarity=-0.122  Sum_probs=30.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.+..+..+.+.|+.+||+++|+++..+
T Consensus        51 ~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~klk   84 (89)
T d1etxa_          51 QPLLDMVMQYTRGNATRAALMMGINRGTLRKKLK   84 (89)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHHH
Confidence            5677888899999999999999999999998654

>d1s7ea2 a.35.1.7 (A:6-85) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.90  E-value=0.011  Score=30.64  Aligned_cols=57  Identities=12%  Similarity=0.074  Sum_probs=46.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcC-----CCCCCHHHHHHHHHHhCCCCcc
Q 038591           22 PRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENG-----KAVPNQTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g-----~~~p~~~~~~~la~~lgv~~~e   78 (82)
                      ..+|+...+..+++|.-||+. +|.|+.+++.+.+.     .-.+..+...++-.+++-+-.+
T Consensus         8 ~~~i~~eL~~~~IsQ~~Fa~~vL~rsQGtlSdLL~kPKPW~~l~~gre~y~RM~~wL~~pe~~   70 (80)
T d1s7ea2           8 AQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQ   70 (80)
T ss_dssp             HHHHHHHHTSSCCCHHHHHHHTSSSCSSHHHHHTTSCCTTCCCSSCHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHccChHHHHHHHcCCCChhhhcchhHHHHHHHHHHcCHHHH
Confidence            678899999999999999995 58999999999874     1234678888999988855543

>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=95.65  E-value=0.014  Score=28.75  Aligned_cols=27  Identities=11%  Similarity=0.148  Sum_probs=23.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      -..|+|.+|+|..+|+|..||..+...
T Consensus        16 ~~~G~s~~eIA~~L~is~~TV~~~~~~   42 (67)
T d1fsea_          16 LVQDKTTKEIASELFISEKTVRNHISN   42 (67)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHHH
Confidence            457999999999999999999887653

>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=95.62  E-value=0.016  Score=28.45  Aligned_cols=52  Identities=12%  Similarity=0.084  Sum_probs=34.1

Q ss_pred             HHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591           22 PRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        22 ~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg   73 (82)
                      ...+.-++ -..|+|-+|+|+.+|+|..||..+.+.    -...+...+..+|...|
T Consensus         7 ~rE~~vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~~l~~~a~~~g   63 (65)
T d1l3la1           7 PKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRK   63 (65)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC
Confidence            33344333 457999999999999999999887653    12334444555554444

>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=95.54  E-value=0.0065  Score=32.65  Aligned_cols=38  Identities=16%  Similarity=0.120  Sum_probs=28.2

Q ss_pred             CCCHHHHHHHhCCC-HHHHHHHHc-----C--------CCCCCHHHHHHHHH
Q 038591           33 KMSQPDLANQINQR-PQVVSEYEN-----G--------KAVPNQTVLAKMEK   70 (82)
Q Consensus        33 g~s~~elA~~~gis-~~~i~~~e~-----g--------~~~p~~~~~~~la~   70 (82)
                      .+||.|||..+|+| ++||++..+     |        -..++.+.+..+|.
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~~~~~i~I~D~~~L~~~A~   82 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAP   82 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHCH
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEEcCCEEEEeCHHHHHHHhc
Confidence            58999999999996 899988753     2        11346677777665

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=95.53  E-value=0.019  Score=28.15  Aligned_cols=36  Identities=17%  Similarity=0.306  Sum_probs=27.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg   73 (82)
                      +...+|..+|||+++|++|  |...| .-....|...-+
T Consensus        12 ~~~k~A~algis~~AVsqW--Ge~VP-e~RA~~ie~~T~   47 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW--KEVIP-EKDAYRLEIVTA   47 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC--CSBCC-HHHHHHHHHHTT
T ss_pred             CHHHHHHHhCCCHHHHHHH--hccCc-HHHHHHHHHHhC
Confidence            6778999999999999999  66444 444566665544

>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=95.44  E-value=0.004  Score=31.27  Aligned_cols=27  Identities=11%  Similarity=-0.017  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        23 ~~~s~~~Ia~~agvs~~t~Y~~F~~K~   49 (74)
T d1v7ba1          23 ETLSYDSLAEATGLSKSGLIYHFPSRH   49 (74)
T ss_dssp             TTCCHHHHHHHHCSCHHHHHHHCSSHH
T ss_pred             cccCHHHHHHHhCcCcchHhhhCCCHH
Confidence            468999999999999999999976653

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=95.42  E-value=0.01  Score=31.75  Aligned_cols=34  Identities=12%  Similarity=0.076  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKK-MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....| +|+.+||+.+|+++++|++..+
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~   58 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLSKTTVENSLK   58 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHH
Confidence            445566655555 9999999999999999998743

>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=95.41  E-value=0.0024  Score=31.66  Aligned_cols=32  Identities=22%  Similarity=0.329  Sum_probs=25.7

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .+.+.-++|..++|+.+|||+.+|+.+..++.
T Consensus        13 l~~~~G~~ti~~Ia~~agvs~~~iY~~F~~K~   44 (65)
T d2g7ga1          13 LVDRDGDFRMPDLARHLNVQVSSIYHHAKGRA   44 (65)
T ss_dssp             HHHHHSSCCHHHHHHHTTSCHHHHHTTSCHHH
T ss_pred             HHHHcCCCCHHHHHHHhCccccchhhcCCCHH
Confidence            33344489999999999999999999876553

>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=95.37  E-value=0.0072  Score=33.39  Aligned_cols=22  Identities=23%  Similarity=0.347  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      |+..|||+.+|||+.||..||+
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~   22 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEE   22 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

>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=95.33  E-value=0.021  Score=28.01  Aligned_cols=31  Identities=13%  Similarity=-0.044  Sum_probs=26.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      +=.++--.|+|..|+|+.+|+|.++|.....
T Consensus        26 v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~   56 (68)
T d1or7a1          26 AITLRELDGLSYEEIAAIMDCPVGTVRSRIF   56 (68)
T ss_dssp             HHHHHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3446677899999999999999999988754

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=95.30  E-value=0.0094  Score=29.17  Aligned_cols=39  Identities=8%  Similarity=-0.058  Sum_probs=30.9

Q ss_pred             CCCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           16 GTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        16 ~~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -.+.|-...|..+.+..| +..+.|+.+||+++|+.+-..
T Consensus        17 ~~~~~Er~~I~~aL~~~g-n~~~aA~~Lgisr~tL~rKlk   55 (61)
T d1g2ha_          17 IIGFYEAQVLKLFYAEYP-STRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             SCSHHHHHHHHHHHHHSC-SHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHH
Confidence            334444788888888886 788999999999999988664

>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=95.15  E-value=0.013  Score=28.76  Aligned_cols=25  Identities=12%  Similarity=0.287  Sum_probs=22.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+|..++|+.+|||...|++++.
T Consensus        26 ~~~~tl~eIa~~lgiS~erVrqi~~   50 (61)
T d1ku3a_          26 GREHTLEEVGAYFGVTRERIRQIEN   50 (61)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4568999999999999999999985

>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=95.15  E-value=0.02  Score=29.62  Aligned_cols=38  Identities=8%  Similarity=0.011  Sum_probs=30.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA   66 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~   66 (82)
                      -.-..+|..+||+.+|+|++||.++-+.-..-.+..+.
T Consensus        32 ~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~e~k   69 (83)
T d2o3fa1          32 HKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLK   69 (83)
T ss_dssp             HHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHH
T ss_pred             HHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHH
Confidence            34468999999999999999999998865555555543

>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=95.14  E-value=0.014  Score=31.36  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|..|||+.+|+|+.||.-||.
T Consensus         2 ~ytI~e~A~~~gvs~~tlR~Ye~   24 (109)
T d1r8da_           2 KYQVKQVAEISGVSIRTLHHYDN   24 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999985

>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=95.13  E-value=0.007  Score=30.07  Aligned_cols=26  Identities=4%  Similarity=-0.077  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+++++.+-.++
T Consensus        20 ~~~s~~~Ia~~agvs~~~~y~~F~~K   45 (71)
T d1jt6a1          20 NATTTGEIVKLSESSKGNLYYHFKTK   45 (71)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHHSSH
T ss_pred             cccCHHHHHHHHCcCHhHHHHHCcCH
Confidence            57899999999999999999998764

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=95.13  E-value=0.0027  Score=31.62  Aligned_cols=27  Identities=19%  Similarity=0.278  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+.+++++..++.
T Consensus        22 ~~~t~~~Ia~~agvs~~~iy~hF~~K~   48 (68)
T d1z0xa1          22 EQLSMRKVAKQLGVQAPAIYWYFKNKQ   48 (68)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHTTCSSHH
T ss_pred             cccCHHHHHHHHCcchhHHHHhcCCHH
Confidence            368999999999999999999876544

>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=95.11  E-value=0.0061  Score=30.70  Aligned_cols=22  Identities=9%  Similarity=0.332  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 038591           34 MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++..+||+..|||+.||..|..
T Consensus         3 Vnk~~lA~iFGVS~~TI~~W~~   24 (68)
T d1j9ia_           3 VNKKQLADIFGASIRTIQNWQE   24 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHH
Confidence            5688999999999999999975

>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=95.09  E-value=0.0061  Score=30.88  Aligned_cols=27  Identities=11%  Similarity=-0.037  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+.+++++..++.
T Consensus        23 ~~~ti~~Ia~~agvs~~s~y~~F~~K~   49 (79)
T d2fbqa1          23 AETSLRLITSKAGVNLAAVNYHFGSKK   49 (79)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHTCSHH
T ss_pred             ccccHHHHHHHHCcChhHHHHHCcCHH
Confidence            578999999999999999999976543

>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=95.08  E-value=0.012  Score=32.55  Aligned_cols=24  Identities=13%  Similarity=0.079  Sum_probs=22.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|++..++|+.++||+++|++|.
T Consensus        30 ~~G~s~r~iA~~~~VS~~tV~k~l   53 (123)
T d1pdnc_          30 ADGIRPCVISRQLRVSHGCVSKIL   53 (123)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HhcCCHHHHHHHHCcCHHHHHHHH
Confidence            579999999999999999999995

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=95.08  E-value=0.0088  Score=31.05  Aligned_cols=23  Identities=17%  Similarity=0.147  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ++|+.+||+.+|+++++++++.+
T Consensus        21 ~lt~~eLa~~l~i~~~~vs~~l~   43 (85)
T d3ctaa1          21 YLTSSKLADMLGISQQSASRIII   43 (85)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            68999999999999999998854

>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=95.06  E-value=0.0049  Score=30.94  Aligned_cols=27  Identities=15%  Similarity=0.203  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+++++++..++.
T Consensus        23 ~~~s~~~Ia~~agvs~~~iY~~F~sK~   49 (74)
T d2g7sa1          23 NSFSYADISQVVGIRNASIHHHFPSKS   49 (74)
T ss_dssp             GGCCHHHHHHHHCCCHHHHHHHCSSHH
T ss_pred             cccCHHHHHHHHCcCcchHHHHCcCHH
Confidence            468999999999999999999876543

>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=95.03  E-value=0.014  Score=30.42  Aligned_cols=33  Identities=6%  Similarity=-0.035  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|....+..+..+.+.|+.+||++.|+++-.
T Consensus        53 ~~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Kl   85 (91)
T d1ntca_          53 RTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHCCCHHHHHHHH
Confidence            456788888999999999999999999998754

>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=95.00  E-value=0.012  Score=29.01  Aligned_cols=26  Identities=19%  Similarity=0.202  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+.+++.+..++
T Consensus        19 ~~~ti~~Ia~~agvs~~~~Y~~F~~K   44 (69)
T d2i10a1          19 EGTSITDLTKALGINPPSLYAAFGSK   44 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHCSH
T ss_pred             ccCCHHHHHHHhCCChhHHHHHCcCH
Confidence            57899999999999999999998764

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=94.97  E-value=0.0049  Score=30.00  Aligned_cols=27  Identities=11%  Similarity=0.121  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+.+|+++..++.
T Consensus        18 ~~~s~~~Ia~~agvs~~tiy~~F~~K~   44 (62)
T d2vkva1          18 EGLTTRKLAQKLGVEQPTLYWHVKNKR   44 (62)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHSCCHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            468999999999999999999977643

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.96  E-value=0.0054  Score=30.59  Aligned_cols=26  Identities=23%  Similarity=0.146  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ++|..++|+.+|||+.+++++-.++.
T Consensus        23 ~~t~~~Ia~~agvs~~t~Y~~F~~K~   48 (73)
T d1t56a1          23 DISVDDLAKGAGISRPTFYFYFPSKE   48 (73)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHCcCHH
Confidence            57999999999999999999876543

>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=94.91  E-value=0.033  Score=30.11  Aligned_cols=33  Identities=12%  Similarity=0.106  Sum_probs=27.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+=.++--.|+|..|+|+.+|+|+++|+....
T Consensus        22 R~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~   54 (106)
T d1s7oa_          22 MNYIELYYADDYSLAEIADEFGVSRQAVYDNIK   54 (106)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334456778899999999999999999988764

>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=94.89  E-value=0.029  Score=30.95  Aligned_cols=34  Identities=9%  Similarity=0.036  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+|+++++|+++.+
T Consensus        33 ~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~   66 (139)
T d2a61a1          33 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVK   66 (139)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHH
Confidence            5566777777899999999999999999998864

>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=94.89  E-value=0.026  Score=30.41  Aligned_cols=35  Identities=17%  Similarity=0.198  Sum_probs=27.8

Q ss_pred             HHHHHHHHH-hCC-CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           22 PRQIQRARL-GKK-MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        22 ~~~lk~~r~-~~g-~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +.|+.-++. ..| +|+.++|+.+|+|..||++.-+-
T Consensus        45 a~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~~   81 (101)
T d1jhga_          45 GTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNS   81 (101)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            566766653 356 89999999999999999887653

>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=94.88  E-value=0.012  Score=29.68  Aligned_cols=32  Identities=13%  Similarity=0.078  Sum_probs=25.4

Q ss_pred             HHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .|..+-. ..++|..|+|+.+|+++++++++.+
T Consensus        10 IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~   42 (75)
T d1mkma1          10 ILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMV   42 (75)
T ss_dssp             HHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444433 4689999999999999999999853

>d1x2la1 a.35.1.7 (A:9-95) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.88  E-value=0.032  Score=29.21  Aligned_cols=53  Identities=15%  Similarity=0.118  Sum_probs=41.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENGKAV---PN---QTVLAKMEKAIGV   74 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g~~~---p~---~~~~~~la~~lgv   74 (82)
                      ..+|+...+..+++|.-||+. +|.|+.+++.+.+.-..   .+   -+...++-..|+-
T Consensus        15 ~~~v~~~L~~~~I~Q~~Fa~~VL~rsQGtlSdLL~~PKPW~kl~~~gR~~y~RM~~WL~~   74 (87)
T d1x2la1          15 AFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLSD   74 (87)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCCCCGGGCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHhhChHHHHHHHhCCCChHHhhHHHHHHHHHHHHHhcC
Confidence            788999999999999999995 58999999999985322   22   3556677777664

>d1wh8a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.88  E-value=0.038  Score=30.18  Aligned_cols=55  Identities=7%  Similarity=0.094  Sum_probs=43.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCCCC
Q 038591           22 PRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENGKAV---PN---QTVLAKMEKAIGVKL   76 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g~~~---p~---~~~~~~la~~lgv~~   76 (82)
                      ..+|++..+..+++|.-||+. +|.|+.+++.+.+.-..   .+   .+...++-.+|+-+-
T Consensus        33 a~~v~~~L~~~~I~Q~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gR~~y~RM~~wL~~pe   94 (111)
T d1wh8a_          33 TKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLNDPH   94 (111)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTSCHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHcCchHHHHHHHHHccChHHHHHHHhCCCChhHhhHHHHHHHHHHHHHhcCHH
Confidence            889999999999999999995 58999999999986322   22   356777777777443

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.85  E-value=0.0083  Score=29.64  Aligned_cols=26  Identities=4%  Similarity=-0.083  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+++++++-.++
T Consensus        19 ~~~si~~Ia~~agvs~~t~Y~~F~sK   44 (70)
T d2gena1          19 DATTIEMIRDRSGASIGSLYHHFGNK   44 (70)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHTCSH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCCCH
Confidence            57899999999999999999997654

>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=94.83  E-value=0.015  Score=29.05  Aligned_cols=23  Identities=9%  Similarity=0.229  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|..++|..+|||+..|.++|.
T Consensus        25 ~~tl~eI~~~lgiSrerVrqie~   47 (68)
T d2p7vb1          25 DYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHH
Confidence            37999999999999999999986

>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=94.82  E-value=0.0017  Score=32.23  Aligned_cols=26  Identities=15%  Similarity=0.050  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+++++.+..++
T Consensus        20 ~~~ti~~Ia~~agvs~~~iy~~F~sK   45 (69)
T d2np5a1          20 EGASVREVAKRAGVSIGAVQHHFSTK   45 (69)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCcCH
Confidence            46899999999999999999987554

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=94.80  E-value=0.0067  Score=30.60  Aligned_cols=27  Identities=11%  Similarity=0.203  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+.+++++..++.
T Consensus        25 ~~~s~~~Ia~~agvs~~~lY~~F~~K~   51 (77)
T d2gfna1          25 SAVTTRAVAEESGWSTGVLNHYFGSRH   51 (77)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHTSSHH
T ss_pred             cccCHHHHHHHHCCCHHHHHHHCcCHH
Confidence            467999999999999999999976543

>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=94.73  E-value=0.011  Score=29.22  Aligned_cols=27  Identities=15%  Similarity=0.195  Sum_probs=24.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+++++++..++.
T Consensus        21 ~~~ti~~Ia~~agvs~~~~Y~~F~~K~   47 (68)
T d2d6ya1          21 AGARIDRIAAEARANKQLIYAYYGNKG   47 (68)
T ss_dssp             TSCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             cccCHHHHHHHHCcchhHHHHHCcCHH
Confidence            568999999999999999999987653

>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=94.73  E-value=0.019  Score=28.62  Aligned_cols=26  Identities=8%  Similarity=0.069  Sum_probs=22.9

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      -..|+|..++|..+|+|+.||..+..
T Consensus        24 l~~G~s~~eIA~~l~iS~~TV~~~~~   49 (70)
T d1yioa1          24 TIRGLMNKQIAGELGIAEVTVKVHRH   49 (70)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            35799999999999999999988754

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.65  E-value=0.04  Score=29.43  Aligned_cols=34  Identities=12%  Similarity=0.091  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+..+...-++|+.++|+.+|+++++|+.+.+
T Consensus        23 ~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~   56 (109)
T d1sfxa_          23 VRIYSLLLERGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHH
Confidence            4556667777889999999999999999998753

>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=94.62  E-value=0.0059  Score=30.71  Aligned_cols=27  Identities=11%  Similarity=0.252  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+++|+++..++.
T Consensus        22 ~~~ti~~Ia~~agvs~~~iY~~F~~k~   48 (75)
T d2id6a1          22 DRATTDEIAEKAGVAKGLIFHYFKNKE   48 (75)
T ss_dssp             HHCCHHHHHHHHTCCTHHHHHHHSSHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            478999999999999999999987543

>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=94.50  E-value=0.017  Score=28.86  Aligned_cols=26  Identities=27%  Similarity=0.328  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        23 ~~~si~~Ia~~agvs~~~~Y~~F~~K   48 (73)
T d2fx0a1          23 EGTSIQEIAKEAKVNVAMASYYFNGK   48 (73)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTSH
T ss_pred             ccCcHHHHHHHHCcChhHHHHHCcCH
Confidence            57899999999999999999998765

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=94.48  E-value=0.0083  Score=30.42  Aligned_cols=26  Identities=8%  Similarity=0.084  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||..+++++..++
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~F~sK   51 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRNFPDR   51 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCcCH
Confidence            57899999999999999999986543

>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=94.48  E-value=0.01  Score=32.27  Aligned_cols=23  Identities=13%  Similarity=0.137  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +|..|||+.+|||+.||.-||+-
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~~   26 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDKI   26 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHc
Confidence            57889999999999999999963

>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=94.39  E-value=0.063  Score=26.03  Aligned_cols=27  Identities=15%  Similarity=0.187  Sum_probs=22.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           29 RLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        29 r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+....+..++|+.+|+|+++++...+
T Consensus        17 ~~~~~v~~~~iA~~L~vs~~SVs~mik   43 (61)
T d2ev0a1          17 EEKGYARVSDIAEALAVHPSSVTKMVQ   43 (61)
T ss_dssp             HHHSSCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hcCCCccHHHHHHHhCCCchhHHHHHH
Confidence            345678999999999999999998754

>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=94.32  E-value=0.011  Score=29.10  Aligned_cols=26  Identities=8%  Similarity=0.014  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+.+++++..++
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F~~k   50 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRWGTP   50 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHCSH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCcCH
Confidence            46799999999999999999997654

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=94.23  E-value=0.012  Score=29.35  Aligned_cols=26  Identities=12%  Similarity=0.011  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+++++++..++
T Consensus        23 ~~~ti~~Ia~~agvs~~t~y~~F~~K   48 (72)
T d1pb6a1          23 HGTRLEQIAELAGVSKTNLLYYFPSK   48 (72)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHHSSSH
T ss_pred             cccCHHHHHHHhCCChHHHHHHCcCH
Confidence            57899999999999999999987554

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=94.23  E-value=0.027  Score=27.77  Aligned_cols=25  Identities=8%  Similarity=0.149  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..++|+++|+|+.+++++..+
T Consensus        23 ~~~t~~~Ia~~agvs~~~~y~~F~~   47 (69)
T d2fq4a1          23 KAVTVDKIAERAKVSKATIYKWWPN   47 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCCC
Confidence            5789999999999999999998654

>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=94.14  E-value=0.011  Score=29.39  Aligned_cols=27  Identities=15%  Similarity=0.144  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|||+.+++++..++.
T Consensus        20 ~~~ti~~Ia~~agvs~~~~y~~F~~K~   46 (72)
T d1vi0a1          20 HQSQVSKIAKQAGVADGTIYLYFKNKE   46 (72)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred             ccccHHHHHHHHCcCHHHHHHHCcCHH
Confidence            568999999999999999999876543

>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=94.13  E-value=0.0076  Score=30.54  Aligned_cols=26  Identities=15%  Similarity=0.323  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        28 ~~~t~~~Ia~~agvs~~~~Y~~F~~k   53 (79)
T d2oi8a1          28 SALSLNAIAKRMGMSGPALYRYFDGR   53 (79)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTTCSSH
T ss_pred             cccCHHHHHHHhCCCCCchhhhcCCH
Confidence            46899999999999999999976543

>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=94.12  E-value=0.057  Score=29.11  Aligned_cols=32  Identities=16%  Similarity=0.086  Sum_probs=26.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+=.++--.|+|..|+|+.+|+|+++|.....
T Consensus        25 ~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~   56 (106)
T d1xsva_          25 NYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   56 (106)
T ss_dssp             HHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHH
Confidence            34456778899999999999999999988764

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.07  E-value=0.024  Score=28.03  Aligned_cols=27  Identities=19%  Similarity=0.356  Sum_probs=24.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      -.+.|..++|+.+|||..+++.+..++
T Consensus        18 G~~~t~~~Ia~~agvs~~~~Y~~F~~K   44 (70)
T d2hkua1          18 GEGVPITQICAAAGAHPNQVTYYYGSK   44 (70)
T ss_dssp             CTTSCHHHHHHHHTCCHHHHHHHHSSH
T ss_pred             ccCchHHHHHHHHCCChhhHHhcCCCH
Confidence            357999999999999999999998664

>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=94.03  E-value=0.0072  Score=30.38  Aligned_cols=27  Identities=15%  Similarity=0.103  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .++|..++|+.+|+|+++++.+..++.
T Consensus        24 ~~~t~~~Ia~~agvs~~~~Y~~F~~K~   50 (75)
T d2hyja1          24 DGITIGRLAEELEMSKSGVHKHFGTKE   50 (75)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHTTCSSHH
T ss_pred             ccCcHHHHHHHHCcCHHHHHHHCcCHH
Confidence            468999999999999999999876543

>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=94.01  E-value=0.014  Score=29.08  Aligned_cols=26  Identities=15%  Similarity=0.147  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+.+++++..++
T Consensus        24 ~~~t~~~Ia~~agvs~~~~y~~F~~k   49 (75)
T d3c07a1          24 DRTTMRAIAQEAGVSVGNAYYYFAGK   49 (75)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCcCH
Confidence            46799999999999999999987654

>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=94.01  E-value=0.014  Score=28.92  Aligned_cols=26  Identities=4%  Similarity=-0.033  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+.+++++..++
T Consensus        24 ~~~si~~Ia~~agvs~~~~y~~F~sK   49 (71)
T d1ui5a1          24 ESTTLSEIVAHAGVTKGALYFHFAAK   49 (71)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHHCcCHhHHHHHCcCH
Confidence            57899999999999999999986543

>d1zs4a1 a.35.1.9 (A:4-81) Regulatory protein cII {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Bacteriophage CII protein
domain: Regulatory protein cII
species: Bacteriophage lambda [TaxId: 10710]

Probab=93.94  E-value=0.055  Score=27.34  Aligned_cols=24  Identities=8%  Similarity=0.178  Sum_probs=21.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      +.|..+|..+||..++|++|.+|-
T Consensus        21 ~Gq~k~A~amGv~esqiSRwK~~f   44 (78)
T d1zs4a1          21 LGTEKTAEAVGVDKSQISRWKRDW   44 (78)
T ss_dssp             HCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HcchhHHHHhCCCHHHHHHHHHhh
Confidence            458999999999999999999873

>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=93.80  E-value=0.01  Score=30.19  Aligned_cols=26  Identities=12%  Similarity=0.031  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+++++++..++
T Consensus        30 ~~~ti~~Ia~~agvs~~t~Y~~F~~K   55 (81)
T d1rkta1          30 ELTTMKDVVEESGFSRGGVYLYFSST   55 (81)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTCSCH
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHCcCH
Confidence            57899999999999999999986553

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.76  E-value=0.0003  Score=39.53  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=22.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+|+||+|+|+.+|.|++.|+.+|.
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk   27 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIER   27 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHH
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHH
Confidence            5899999999999999988888875

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=93.71  E-value=0.069  Score=29.08  Aligned_cols=34  Identities=15%  Similarity=0.129  Sum_probs=26.2

Q ss_pred             HHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKK--MSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+....|  +|+.+||+.+++++++++++.+
T Consensus        32 ~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~   67 (135)
T d3broa1          32 MTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQ   67 (135)
T ss_dssp             HHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHH
Confidence            345555655444  9999999999999999998643

>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=93.69  E-value=0.044  Score=30.30  Aligned_cols=34  Identities=9%  Similarity=0.135  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+-...|+|+.+||+.+++++++|++..+
T Consensus        39 ~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~   72 (141)
T d1lnwa_          39 VHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIR   72 (141)
T ss_dssp             HHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHH
Confidence            4566667677789999999999999999999853

>d1d1la_ a.35.1.2 (A:) cro lambda repressor {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: cro lambda repressor
species: Bacteriophage lambda [TaxId: 10710]

Probab=93.67  E-value=0.043  Score=26.72  Aligned_cols=34  Identities=6%  Similarity=0.009  Sum_probs=27.6

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591           25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP   60 (82)
Q Consensus        25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p   60 (82)
                      |..+-.+.|  |...|+.+|+.++.|++.....+++
T Consensus         7 L~dyv~~~G--QaKaA~~LGv~Q~AIsKAira~R~I   40 (61)
T d1d1la_           7 LKDYAMRFG--QTKTAKDLGVYQSAINKAIHAGRKI   40 (61)
T ss_dssp             HHHHHHHHC--HHHHHHHHTCCTHHHHHHHHTTCCE
T ss_pred             HHHHHHHHC--hHHHHHHcCccHHHHHHHHhcCCeE
Confidence            455666677  9999999999999999998765554

>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=93.65  E-value=0.066  Score=29.39  Aligned_cols=34  Identities=9%  Similarity=-0.006  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.++++++++++..+
T Consensus        35 ~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~   68 (140)
T d2etha1          35 LYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVD   68 (140)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3456677778889999999999999999998753

>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=93.62  E-value=0.024  Score=26.52  Aligned_cols=25  Identities=4%  Similarity=-0.029  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+|..+||+.+|+|+.+++++.+.
T Consensus        18 ~~~tl~~lA~~~~~s~~~l~r~Fk~   42 (54)
T d1bl0a1          18 SPLSLEKVSERSGYSKWHLQRMFKK   42 (54)
T ss_dssp             SCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4789999999999999999998764

>d1wh6a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.55  E-value=0.13  Score=27.50  Aligned_cols=58  Identities=12%  Similarity=0.108  Sum_probs=43.5

Q ss_pred             CHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCCCCcc
Q 038591           21 TPRQIQRARLGKKMSQPDLANQ-INQRPQVVSEYENGKAV---PN---QTVLAKMEKAIGVKLRV   78 (82)
Q Consensus        21 ~~~~lk~~r~~~g~s~~elA~~-~gis~~~i~~~e~g~~~---p~---~~~~~~la~~lgv~~~e   78 (82)
                      ...+|++..+..+++|.-||+. +|.|+.+++.+.+.-..   .+   .....++-.+|+-+...
T Consensus        22 I~~~v~~eL~~~~IsQ~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gr~~y~RM~~wL~~p~~~   86 (101)
T d1wh6a_          22 LTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQLGQ   86 (101)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHccChHHHHHHHhCCCCHHHHhHhhhHHHHHHHHHhcCHhhH
Confidence            3789999999999999999995 58999999999985322   21   34566666666655443

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=93.54  E-value=0.047  Score=30.35  Aligned_cols=34  Identities=12%  Similarity=0.005  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-|+|+.+||+.++++++++++..+
T Consensus        32 ~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~   65 (144)
T d1lj9a_          32 YLYLVRVCENPGIIQEKIAELIKVDRTTAARAIK   65 (144)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHH
Confidence            5667777777899999999999999999998753

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=93.49  E-value=0.018  Score=28.61  Aligned_cols=26  Identities=12%  Similarity=0.144  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+++|+++..++
T Consensus        21 ~~~ti~~Ia~~agvs~~~ly~~F~~K   46 (72)
T d2g3ba1          21 RGLRVNDVAEVAGVSPGLLYYHFKDR   46 (72)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHHCSH
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHCcCH
Confidence            47899999999999999999998654

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=93.29  E-value=0.044  Score=28.57  Aligned_cols=42  Identities=10%  Similarity=0.128  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC-----CCCCCHHHHHHHHHHhC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG-----KAVPNQTVLAKMEKAIG   73 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g-----~~~p~~~~~~~la~~lg   73 (82)
                      ..+|..++|..+|||+..|.++|..     +.......+..+...++
T Consensus        37 ~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l~~~~   83 (87)
T d1ttya_          37 KPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSLMD   83 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHHTT
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhhc
Confidence            4589999999999999999999964     22223344555544443

>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=93.29  E-value=0.11  Score=25.33  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ....+..++|+.+|+++++++...+
T Consensus        21 ~~~v~~~~iA~~L~vs~~SVt~mvk   45 (63)
T d2isya1          21 GVTPLRARIAERLDQSGPTVSQTVS   45 (63)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCcHHHHHHHhCCCchhHHHHHH
Confidence            4458999999999999999998753

>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=93.17  E-value=0.009  Score=29.74  Aligned_cols=25  Identities=16%  Similarity=0.292  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..++|+++|+|+++++.+..+
T Consensus        22 ~~~t~~~Ia~~agvs~~slY~yF~~   46 (72)
T d1zk8a1          22 QEVTLASLAQTLGVRSPSLYNHVKG   46 (72)
T ss_dssp             GGCCHHHHHHHHTSCHHHHTTTCSS
T ss_pred             CcccHHHHHHHhCCCHHHHHHHCcC
Confidence            5789999999999999999997654

>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=93.07  E-value=0.0048  Score=30.62  Aligned_cols=26  Identities=19%  Similarity=0.368  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|+|+.+++.+..++
T Consensus        23 ~~~si~~ia~~~gvs~~~~y~hF~~K   48 (68)
T d2g7la1          23 EKVTMRRLAQELDTGPASLYVYVANT   48 (68)
T ss_dssp             SSCCHHHHHHHTTSCHHHHTTTCCSH
T ss_pred             ccCCHHHHHHHHCcCHhHhhHHCcCH
Confidence            57899999999999999999876543

>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=92.87  E-value=0.037  Score=30.46  Aligned_cols=33  Identities=3%  Similarity=-0.037  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...-|+|+.+||+.++++++++++..
T Consensus        36 ~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i   68 (137)
T d1z91a1          36 YLALLLLWEHETLTVKKMGEQLYLDSGTLTPML   68 (137)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            345677778889999999999999999999874

>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=92.73  E-value=0.093  Score=28.80  Aligned_cols=33  Identities=6%  Similarity=0.046  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+...-++|+.+||+.+++++++++++.
T Consensus        37 ~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v   69 (138)
T d1jgsa_          37 FKVLCSIRCAACITPVELKKVLSVDLGALTRML   69 (138)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHH
Confidence            455666777789999999999999999999763

>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=92.55  E-value=0.066  Score=27.87  Aligned_cols=32  Identities=6%  Similarity=-0.006  Sum_probs=25.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ..|..+...-.+|..|||+.+|++++++++..
T Consensus        20 ~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l   51 (100)
T d1ub9a_          20 GIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHI   51 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHhccCCCeeHHHHHHHHhhccccccHHH
Confidence            34455556678999999999999999999874

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.36  E-value=0.13  Score=28.28  Aligned_cols=34  Identities=9%  Similarity=-0.006  Sum_probs=25.8

Q ss_pred             HHHHHHHHHhC-CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGK-KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~-g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+-... ++|+.+||+.+|++++++++..+
T Consensus        37 ~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~   71 (145)
T d2hr3a1          37 LVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLR   71 (145)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34445554443 48999999999999999998754

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.12  E-value=0.098  Score=28.54  Aligned_cols=34  Identities=24%  Similarity=0.071  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++++.+||+.++++++++++..+
T Consensus        33 ~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~   66 (136)
T d2fbia1          33 WRVIRILRQQGEMESYQLANQACILRPSMTGVLA   66 (136)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4556667777899999999999999999998753

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=92.08  E-value=0.083  Score=29.06  Aligned_cols=34  Identities=9%  Similarity=0.209  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.++++++++++..+
T Consensus        38 ~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l~   71 (143)
T d1s3ja_          38 LFVLASLKKHGSLKVSEIAERMEVKPSAVTLMAD   71 (143)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4556667777799999999999999999998754

>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=92.06  E-value=0.21  Score=25.56  Aligned_cols=35  Identities=14%  Similarity=0.257  Sum_probs=26.8

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      |....|+.+|+|+++|++           .+..|...||+++-++.
T Consensus        17 s~~~AA~~L~isq~avs~-----------~i~~LE~~lg~~Lf~R~   51 (89)
T d1ixca1          17 NMAAAAKRLHVSQPPITR-----------QMQALEADLGVVLLERS   51 (89)
T ss_dssp             SHHHHHHHHTCCHHHHHH-----------HHHHHHHHHTSCCBC--
T ss_pred             CHHHHHHHhCCChHHHHH-----------HHHHHHhcCCceeeEec
Confidence            667799999999999998           45677777777776654

>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=91.90  E-value=0.24  Score=22.85  Aligned_cols=29  Identities=10%  Similarity=0.157  Sum_probs=26.6

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           28 ARLGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .+...++|.-++|+.+.-|+..|.+|.+.
T Consensus        16 Vm~~L~~slhemaR~i~rSR~~ir~Yl~~   44 (51)
T d1tc3c_          16 VMKLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHhCCcHHHHHHHHHHhHHHHHHHhcC
Confidence            56789999999999999999999999875

>d2np3a1 a.4.1.9 (A:35-99) Putative transcriptional regulator SCO0857 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO0857
species: Streptomyces coelicolor [TaxId: 1902]

Probab=91.56  E-value=0.014  Score=28.54  Aligned_cols=28  Identities=14%  Similarity=0.132  Sum_probs=3.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGKAV   59 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~~~   59 (82)
                      .++|..++|+.+|||+++++.+..++..
T Consensus        15 ~~~s~~~IA~~agvs~~~ly~~F~sK~~   42 (65)
T d2np3a1          15 DATSLRRIAETAGVDQSLVHHFYGTKEN   42 (65)
T ss_dssp             ----------------------CCC-CH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCCCHHH
Confidence            4688999999999999999999877653

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.55  E-value=0.032  Score=26.12  Aligned_cols=25  Identities=8%  Similarity=0.040  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+|..+||+.+|+|+.++.+....
T Consensus        18 ~~itl~~lA~~~~~S~~~l~r~Fk~   42 (54)
T d1d5ya1          18 QPLSLDNVAAKAGYSKWHLQRMFKD   42 (54)
T ss_dssp             SSCCCHHHHTTTSSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4689999999999999999998764

>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=91.41  E-value=0.11  Score=27.73  Aligned_cols=28  Identities=14%  Similarity=0.017  Sum_probs=22.9

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .+.....++..++|+.+|++++++|+-.
T Consensus        39 ~L~~~~~~~v~ela~~l~~s~s~vS~HL   66 (108)
T d1u2wa1          39 ALCQDEELCVCDIANILGVTIANASHHL   66 (108)
T ss_dssp             HHHHSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHhCCCccHHHHHHHHccChhHHHHHH
Confidence            3334566899999999999999999864

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.29  E-value=0.18  Score=27.30  Aligned_cols=34  Identities=9%  Similarity=0.048  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhC-CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGK-KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~-g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.... ++|+.+||+.+++++++++++.+
T Consensus        31 ~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~   65 (137)
T d2fbha1          31 WLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLD   65 (137)
T ss_dssp             HHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            44566665444 69999999999999999998753

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=91.18  E-value=0.045  Score=27.01  Aligned_cols=25  Identities=0%  Similarity=-0.001  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      .++|..++|+.+|||+.+++.+-.+
T Consensus        21 ~~~si~~Ia~~agvs~~~iy~~F~~   45 (73)
T d1sgma1          21 HATGLNQIVKESGAPKGSLYHFFPN   45 (73)
T ss_dssp             TTCCHHHHHHHHCCCSCHHHHSTTT
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            5789999999999999999998643

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=91.04  E-value=0.12  Score=29.50  Aligned_cols=34  Identities=9%  Similarity=-0.082  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+...-++|+.+||+.+++++++++++.+
T Consensus        44 ~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~   77 (162)
T d2fxaa1          44 HHILWIAYQLNGASISEIAKFGVMHVSTAFNFSK   77 (162)
T ss_dssp             HHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHH
Confidence            4556667777899999999999999999998753

>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=90.96  E-value=0.14  Score=28.10  Aligned_cols=33  Identities=15%  Similarity=0.058  Sum_probs=25.0

Q ss_pred             HHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARL-GKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      +..+-.+-. ..++|+.|+|+.+|+|++++++..
T Consensus        29 ~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l   62 (151)
T d1ku9a_          29 GAVYAILYLSDKPLTISDIMEELKISKGNVSMSL   62 (151)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHH
Confidence            444444433 345899999999999999999874

>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=90.93  E-value=0.22  Score=24.58  Aligned_cols=33  Identities=12%  Similarity=0.159  Sum_probs=24.7

Q ss_pred             HHHHHHHHhCC--CCHHHHHHHhCC-CHHHHHHHHc
Q 038591           23 RQIQRARLGKK--MSQPDLANQINQ-RPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~g--~s~~elA~~~gi-s~~~i~~~e~   55 (82)
                      ..|+......|  -|.+|+|+.+|+ |+++|..+..
T Consensus        12 ~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1          12 DLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            34555555555  688999999998 7999888753

>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=90.80  E-value=0.3  Score=24.90  Aligned_cols=45  Identities=9%  Similarity=0.104  Sum_probs=31.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591           23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI   80 (82)
Q Consensus        23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~   80 (82)
                      ..+..+-+..  |....|+.+|+|+++|++.           +..+.+.||+++-.+.
T Consensus        12 ~~f~~v~~~g--s~t~AA~~l~isq~avs~~-----------l~~lE~~~g~~Lf~R~   56 (89)
T d2esna1          12 LVFDALYRHR--NVGTAASELAISASAFSHA-----------LGRLRQGLDDELFLRQ   56 (89)
T ss_dssp             HHHHHHHHHS--SHHHHHHHHTCCHHHHHHH-----------HHHHHHHHTSCCEEEE
T ss_pred             HHHHHHHHhC--CHHHHHHHHCCCCcHhhHH-----------HHHHHhcCCceeEEEC
Confidence            3344445544  5566999999999999984           5667777887776553

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.79  E-value=0.04  Score=30.26  Aligned_cols=33  Identities=6%  Similarity=-0.080  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ...|..+....|+|+.+||+.++++++++++..
T Consensus        37 ~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l   69 (136)
T d2bv6a1          37 FLVLTILWDESPVNVKKVVTELALDTGTVSPLL   69 (136)
T ss_dssp             HHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHH
Confidence            455677777889999999999999999988874

>d2fd5a1 a.4.1.9 (A:1-76) Probable transcriptional regulator PA3133 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA3133
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.71  E-value=0.013  Score=29.32  Aligned_cols=26  Identities=8%  Similarity=-0.147  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           32 KKMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        32 ~g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      .++|..++|+.+|||+++++++..++
T Consensus        26 ~~~si~~Ia~~agvs~~t~Y~~F~~K   51 (76)
T d2fd5a1          26 VEPSVGEVMGAAGLTVGGFYAHFQSK   51 (76)
T ss_dssp             TSCCHHHHHHHTTCCGGGGGGTCSCH
T ss_pred             ccccHHHHHHHhCCCccchhhcCCCH
Confidence            57899999999999999999986654

>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=90.61  E-value=0.024  Score=28.02  Aligned_cols=25  Identities=20%  Similarity=0.306  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ++|..++|+.+|+|+++++++-.++
T Consensus        26 ~~sv~~Ia~~agvs~~t~Y~~F~~k   50 (71)
T d2iu5a1          26 QISVSDIMQTAKIRRQTFYNYFQNQ   50 (71)
T ss_dssp             GCCHHHHHHHHTSCGGGGGGTCSSH
T ss_pred             cCCHHHHHHHhCccccHHHHHcCCH
Confidence            5789999999999999999986653

>d1t33a1 a.4.1.9 (A:1-88) Putative transcriptional repressor YbiH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional repressor YbiH
species: Salmonella typhimurium [TaxId: 90371]

Probab=90.28  E-value=0.086  Score=26.89  Aligned_cols=25  Identities=20%  Similarity=0.236  Sum_probs=21.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           34 MSQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      .|..++|..+|||+.+++++..++.
T Consensus        32 ~t~~~Ia~~agvs~~~~Y~~F~sK~   56 (88)
T d1t33a1          32 ATTRDIAALAGQNIAAITYYFGSKE   56 (88)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHSSHH
T ss_pred             cCHHHHHHHhCCChhhhhccCCCHH
Confidence            3888999999999999999987653

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.96  E-value=0.15  Score=25.47  Aligned_cols=22  Identities=14%  Similarity=0.196  Sum_probs=19.1

Q ss_pred             CC-CHHHHHHHhCCCHHHHHHHH
Q 038591           33 KM-SQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~-s~~elA~~~gis~~~i~~~e   54 (82)
                      .+ |+.+||+.+|||+.||.+-.
T Consensus        26 ~LPs~~eLa~~~~vSr~tvr~Al   48 (74)
T d1hw1a1          26 ILPAERELSELIGVTRTTLREVL   48 (74)
T ss_dssp             BCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCccHHHHHHHHCCCHHHHHHHH
Confidence            45 89999999999999998754

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=89.89  E-value=0.18  Score=25.54  Aligned_cols=41  Identities=12%  Similarity=0.063  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHH---HhCCC--------CHHHHHHHhCCCHHHHHHHHcCCC
Q 038591           18 EPDTPRQIQRAR---LGKKM--------SQPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        18 ~~~~~~~lk~~r---~~~g~--------s~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..|....+..|.   +..++        ...+||..+|+++..|.-|..+.+
T Consensus        22 t~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R   73 (80)
T d1wh7a_          22 TKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNK   73 (80)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTS
T ss_pred             ccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCc
Confidence            345566666553   43322        367899999999999999998754

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.87  E-value=0.048  Score=25.28  Aligned_cols=22  Identities=18%  Similarity=0.196  Sum_probs=19.1

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCC
Q 038591           36 QPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..+||..+|++...|..|..++
T Consensus        28 ~~~LA~~l~l~~~~V~~WFqNr   49 (50)
T d1s7ea1          28 QITISQQLGLELSTVSNFFMNA   49 (50)
T ss_dssp             HHHHHTTSCSSSHHHHHHHHHC
T ss_pred             HHHHHHHHCcCHHHhhhcCCcC
Confidence            4789999999999999998654

>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=89.79  E-value=0.33  Score=25.16  Aligned_cols=25  Identities=20%  Similarity=0.090  Sum_probs=22.0

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ....++..|+|+.+|+|++++|+-.
T Consensus        28 ~~~~~~v~el~~~l~~s~~~vS~HL   52 (94)
T d1r1ua_          28 SVSEASVGHISHQLNLSQSNVSHQL   52 (94)
T ss_dssp             HHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCccHHHHHHHHCCCHHHHHHHH
Confidence            4567999999999999999999864

>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=89.66  E-value=0.3  Score=25.50  Aligned_cols=25  Identities=24%  Similarity=0.195  Sum_probs=21.9

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ....++..++|+.+|++++++|+-.
T Consensus        33 ~~~~~~v~ela~~l~is~stvS~HL   57 (98)
T d1r1ta_          33 ARSELCVGDLAQAIGVSESAVSHQL   57 (98)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3467999999999999999999864

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.24  E-value=0.18  Score=27.42  Aligned_cols=34  Identities=15%  Similarity=0.034  Sum_probs=26.9

Q ss_pred             HHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           22 PRQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        22 ~~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...|..+.. ..++|+.+||+.++++++++++..+
T Consensus        34 ~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~   68 (140)
T d3deua1          34 WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLD   68 (140)
T ss_dssp             HHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHH
Confidence            455666655 3469999999999999999998753

>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=88.85  E-value=0.15  Score=27.31  Aligned_cols=33  Identities=15%  Similarity=0.136  Sum_probs=24.7

Q ss_pred             HHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHHc
Q 038591           23 RQIQRARLGK--KMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        23 ~~lk~~r~~~--g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..|..+....  ++|+.+||+.++++++++++..+
T Consensus        37 ~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~   71 (115)
T d2frha1          37 AVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVK   71 (115)
T ss_dssp             HHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHH
Confidence            3344454443  38999999999999999998753

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.59  E-value=0.16  Score=24.15  Aligned_cols=21  Identities=5%  Similarity=0.172  Sum_probs=18.8

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|.-|..+
T Consensus        30 r~~LA~~l~l~~~~V~~WFqN   50 (58)
T d1ig7a_          30 RAEFSSSLSLTETQVKIWFQN   50 (58)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCChhheeecCcc
Confidence            478999999999999999865

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.54  E-value=0.22  Score=23.19  Aligned_cols=21  Identities=14%  Similarity=0.177  Sum_probs=18.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|+++..|..|..+
T Consensus        27 ~~~LA~~lgl~~~qV~~WFqN   47 (53)
T d1le8a_          27 KEEVAKKCGITPLQVRVWFIN   47 (53)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHh
Confidence            378999999999999999864

>d1bl0a2 a.4.1.8 (A:63-124) 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=88.53  E-value=0.45  Score=22.63  Aligned_cols=33  Identities=12%  Similarity=0.014  Sum_probs=25.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHcC
Q 038591           24 QIQRARLGKKMSQPDLANQINQ-RPQVVSEYENG   56 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gi-s~~~i~~~e~g   56 (82)
                      ....+....+++..++|..+|. +.++++++...
T Consensus         5 ~a~~lL~~t~~~i~~IA~~~Gf~~~~~F~r~Fk~   38 (62)
T d1bl0a2           5 EIAQKLKESNEPILYLAERYGFESQQTLTRTFKN   38 (62)
T ss_dssp             HHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHH
T ss_pred             HHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHH
Confidence            3455667789999999999998 57777776553

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.81  E-value=0.27  Score=23.47  Aligned_cols=21  Identities=10%  Similarity=0.097  Sum_probs=18.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|.+.
T Consensus        32 ~~~LA~~lgls~~qV~~WFqN   52 (59)
T d2cqxa1          32 LKGLSKQLDWSVRKIQCWFRH   52 (59)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHh
Confidence            367999999999999999865

>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=87.79  E-value=0.27  Score=24.47  Aligned_cols=22  Identities=14%  Similarity=0.146  Sum_probs=19.1

Q ss_pred             CC-CHHHHHHHhCCCHHHHHHHH
Q 038591           33 KM-SQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~-s~~elA~~~gis~~~i~~~e   54 (82)
                      .+ |..+||+.+|+|+.||.+..
T Consensus        21 ~LPse~~La~~~~vSr~tvr~Al   43 (78)
T d3bwga1          21 KLPVLETLMAQFEVSKSTITKSL   43 (78)
T ss_dssp             BCCCHHHHHHHTTCCHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHH
Confidence            45 89999999999999998754

>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=87.62  E-value=0.41  Score=27.40  Aligned_cols=25  Identities=20%  Similarity=0.313  Sum_probs=21.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      ....+|..++|+.+|+|+++++.-.
T Consensus        29 ~~~~~s~~ela~~lg~s~~~v~~hl   53 (190)
T d1ulya_          29 RNKEMTISQLSEILGKTPQTIYHHI   53 (190)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHCcCHHHHHHHH
Confidence            4568999999999999999998754

>d2dt5a1 a.4.5.38 (A:4-77) Transcriptional repressor Rex, N-terminal domain {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional repressor Rex, N-terminal domain
domain: Transcriptional repressor Rex, N-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=87.57  E-value=0.47  Score=23.78  Aligned_cols=42  Identities=12%  Similarity=0.157  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc-----CCC---CCCHHHHHHHHHHhCC
Q 038591           33 KMSQPDLANQINQRPQVVSEYEN-----GKA---VPNQTVLAKMEKAIGV   74 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e~-----g~~---~p~~~~~~~la~~lgv   74 (82)
                      .+|-.+||+.+|+++.+|.+=.+     |+.   ..-.+.+..|.++||+
T Consensus        25 ~vSS~~La~~~gi~~~qVRKDls~fG~~G~~g~GY~V~~L~~~i~~iLGl   74 (74)
T d2dt5a1          25 RTSSEQLGGLAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGL   74 (74)
T ss_dssp             EECHHHHHHHHTSCHHHHHHHHHHTTCCCCTTTCEEHHHHHHHHHHHHTT
T ss_pred             eEcHHHHHHHHCcCHHHHHHHHHHhcCCCCCCCCccHHHHHHHHHHHhCc
Confidence            47899999999999999987543     332   3345667778888774

>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=87.54  E-value=0.15  Score=27.73  Aligned_cols=26  Identities=15%  Similarity=0.043  Sum_probs=22.0

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...++++.++|+.+|++++++++..+
T Consensus        46 ~~~~~~~~~ia~~l~~~~~~vs~~v~   71 (125)
T d1p4xa2          46 NKNIVLLKDLIETIHHKYPQTVRALN   71 (125)
T ss_dssp             TTCCEEHHHHHHHSSSCHHHHHHHHH
T ss_pred             cCCCccHHHHHHHHCCCcchHHHHHH
Confidence            34578999999999999999988743

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.35  E-value=0.23  Score=25.00  Aligned_cols=23  Identities=22%  Similarity=0.260  Sum_probs=20.0

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCCC
Q 038591           36 QPDLANQINQRPQVVSEYENGKA   58 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g~~   58 (82)
                      ..+||..+|++...|.-|.++.+
T Consensus        39 r~~LA~~l~l~~~qV~~WFqNrR   61 (77)
T d1vnda_          39 REHLASLIRLTPTQVKIWFQNHR   61 (77)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHSS
T ss_pred             HHHHHHHhCCChhhhhhcchhHH
Confidence            47899999999999999987643

>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=87.08  E-value=0.74  Score=23.90  Aligned_cols=27  Identities=7%  Similarity=-0.122  Sum_probs=23.5

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591           30 LGKKMSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        30 ~~~g~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      +-.|.+..+||.+.|+|..+|.++.+.
T Consensus        63 ef~G~n~~eLA~kY~lS~~~I~~Ii~~   89 (94)
T d1rr7a_          63 DFNGRNVSELTTRYGVTFNTVYKAIRR   89 (94)
T ss_dssp             HCCSSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            346999999999999999999998753

>d1rp3a1 a.4.13.1 (A:87-163) 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: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=87.07  E-value=0.61  Score=22.95  Aligned_cols=30  Identities=3%  Similarity=0.152  Sum_probs=23.7

Q ss_pred             HHHHHh--CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           26 QRARLG--KKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        26 k~~r~~--~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..+...  +.-|..|+|..+|++...|.+|..
T Consensus        17 ~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1          17 EKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444  347899999999999999999874

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=86.71  E-value=0.36  Score=22.36  Aligned_cols=21  Identities=5%  Similarity=0.183  Sum_probs=18.6

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|.-|.++
T Consensus        29 r~~LA~~lgL~~~qV~vWFqN   49 (53)
T d1p7ia_          29 RQQLSSELGLNEAQIKIWFQN   49 (53)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCChHHhhhcccc
Confidence            478999999999999999764

>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=86.71  E-value=0.29  Score=23.82  Aligned_cols=22  Identities=23%  Similarity=0.430  Sum_probs=18.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .++..+||+.+|+|+.+|.+..
T Consensus        25 ~l~~~~La~~~~vSr~tvr~Al   46 (69)
T d2hs5a1          25 RLSEPDICAALDVSRNTVREAF   46 (69)
T ss_dssp             EECHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCHHHHHHHHCCCHHHHHHHH
Confidence            3678999999999999988754

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.67  E-value=0.12  Score=27.75  Aligned_cols=25  Identities=12%  Similarity=0.231  Sum_probs=21.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ..++|+.+||+.++++++++++..+
T Consensus        46 ~~~~t~~ela~~l~~~~~~vs~~i~   70 (115)
T d1hsja1          46 SNEISSKEIAKCSEFKPYYLTKALQ   70 (115)
T ss_dssp             CSEEEHHHHHHSSCCCHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCChhhHHHHHH
Confidence            4479999999999999999998754

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.51  E-value=0.25  Score=23.34  Aligned_cols=21  Identities=19%  Similarity=0.260  Sum_probs=18.7

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|.-|..+
T Consensus        29 r~~LA~~lgl~~~qV~vWFqN   49 (57)
T d1jgga_          29 RCELAAQLNLPESTIKVWFQN   49 (57)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHhCCChhHhhhcchh
Confidence            378999999999999999865

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.03  E-value=0.27  Score=24.06  Aligned_cols=22  Identities=14%  Similarity=0.197  Sum_probs=19.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCC
Q 038591           36 QPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..+||..+|++...|.-|..+.
T Consensus        31 r~~LA~~l~l~~~~V~iWFqNr   52 (67)
T d1zq3p1          31 LADLSAKLALGTAQVKIWFKNR   52 (67)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCccceeeccccH
Confidence            4889999999999999998753

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=85.68  E-value=1.3  Score=22.53  Aligned_cols=36  Identities=3%  Similarity=0.047  Sum_probs=27.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ....|++|+|..+|++..+|.+..           ..|.+.|++++.
T Consensus        60 ~~~~t~~eIa~~~~is~~ti~k~y-----------k~i~~~L~l~~~   95 (98)
T d1aisb1          60 KVPRTLDEIADIARVDKKEIGRSY-----------RFIARNLNLTPK   95 (98)
T ss_dssp             TCCCCHHHHHHHTTSCHHHHHHHH-----------HHHHHHTTCCTT
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH-----------HHHHHHcCCCcc
Confidence            456899999999999999998863           455566666554

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=85.61  E-value=0.44  Score=22.04  Aligned_cols=20  Identities=10%  Similarity=0.204  Sum_probs=18.1

Q ss_pred             HHHHHHhCCCHHHHHHHHcC
Q 038591           37 PDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g   56 (82)
                      .+||..+|++...|..|...
T Consensus        25 ~~LA~~~~ls~~qV~~WFqN   44 (52)
T d1x2ma1          25 EGLSKQLDWDVRSIQRWFRQ   44 (52)
T ss_dssp             HHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHh
Confidence            67999999999999999865

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.30  E-value=0.45  Score=22.40  Aligned_cols=21  Identities=19%  Similarity=0.256  Sum_probs=18.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|...
T Consensus        28 ~~~LA~~lgL~~~qV~~WFqN   48 (57)
T d1e3oc1          28 ITLIAEQLNMEKEVIRVWFSN   48 (57)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHH
Confidence            478999999999999999864

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.67  E-value=0.5  Score=22.38  Aligned_cols=21  Identities=0%  Similarity=0.093  Sum_probs=18.8

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|+++..|.-|.++
T Consensus        31 r~~LA~~l~l~~~qV~vWFqN   51 (58)
T d2craa1          31 RRKISAATSLSERQITIWFQN   51 (58)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHeeecccc
Confidence            478999999999999999865

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.65  E-value=0.51  Score=22.25  Aligned_cols=21  Identities=19%  Similarity=0.211  Sum_probs=18.6

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|+++..|..|..+
T Consensus        29 ~~~La~~l~l~~~~V~~WFqN   49 (58)
T d1au7a1          29 IMRMAEELNLEKEVVRVWFCN   49 (58)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHH
Confidence            478999999999999999864

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=84.65  E-value=0.34  Score=23.57  Aligned_cols=21  Identities=14%  Similarity=0.298  Sum_probs=18.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|..+
T Consensus        33 ~~~LA~~l~l~~~~V~~WFqN   53 (66)
T d1bw5a_          33 KEQLVEMTGLSPRVIRVWFQN   53 (66)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHcCcCHHHhhhhhHh
Confidence            368999999999999999865

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.37  E-value=0.5  Score=22.19  Aligned_cols=21  Identities=14%  Similarity=0.203  Sum_probs=18.6

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|.-|..+
T Consensus        30 r~~LA~~l~L~~~qV~~WFqN   50 (57)
T d2e1oa1          30 RKRLAKMLQLSERQVKTWFQN   50 (57)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHhhHhhhh
Confidence            478999999999999999764

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.05  E-value=1.3  Score=22.55  Aligned_cols=38  Identities=13%  Similarity=0.122  Sum_probs=25.5

Q ss_pred             CCCHHHHHHHHHhCCCC-------HHHHHHHhCCCHHHHHHHHcC
Q 038591           19 PDTPRQIQRARLGKKMS-------QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        19 ~~~~~~lk~~r~~~g~s-------~~elA~~~gis~~~i~~~e~g   56 (82)
                      .|....|..|......+       ..+||..+|++...|.-|.++
T Consensus        33 ~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqN   77 (88)
T d1b72a_          33 NFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQN   77 (88)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHh
Confidence            34566666555544433       577888888888888888764

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=83.91  E-value=0.26  Score=24.58  Aligned_cols=28  Identities=7%  Similarity=0.095  Sum_probs=21.6

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           27 RARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        27 ~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .+....+.|..+||..+|++...|.+..
T Consensus        18 ~L~~~~~~tA~~LAk~Lg~~Kk~VNr~L   45 (70)
T d1sfua_          18 SLNTNDYTTAISLSNRLKINKKKINQQL   45 (70)
T ss_dssp             TSCTTCEECHHHHHHHTTCCHHHHHHHH
T ss_pred             hcCCCCCchHHHHHHHhCCCHHHHHHHH
Confidence            3444556889999999999988877653

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.81  E-value=0.5  Score=23.16  Aligned_cols=20  Identities=10%  Similarity=0.240  Sum_probs=18.1

Q ss_pred             HHHHHHhCCCHHHHHHHHcC
Q 038591           37 PDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g   56 (82)
                      .+||..+|++...|..|..+
T Consensus        39 ~~La~~lgl~~~qV~~WFqN   58 (71)
T d1wi3a_          39 HTLSAQLDLPKHTIIKFFQN   58 (71)
T ss_dssp             HHHHHHSCCCHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHhHh
Confidence            67999999999999999865

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=83.78  E-value=0.4  Score=23.19  Aligned_cols=23  Identities=13%  Similarity=0.261  Sum_probs=19.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCC
Q 038591           35 SQPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        35 s~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ...+||..+|++...|..|..+.
T Consensus        31 ~r~~LA~~lgl~~~~V~~WFqNr   53 (65)
T d1fjla_          31 TREELAQRTNLTEARIQVWFQNR   53 (65)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhhhhH
Confidence            34789999999999999998653

>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.57  E-value=1.2  Score=22.63  Aligned_cols=36  Identities=8%  Similarity=0.116  Sum_probs=27.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR   77 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~   77 (82)
                      ....|+.|+|+..|++..+|.+.           ...|.+.|++++|
T Consensus        60 ~~p~t~~eIa~~~~i~~~~i~k~-----------~k~i~~~L~~~v~   95 (95)
T d1vola1          60 GVPRTFKEICAVSRISKKEIGRC-----------FKLILKALETSVD   95 (95)
T ss_dssp             TCCCCHHHHHTTTCSCHHHHHHH-----------HHHHHHHTTCCCC
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHH-----------HHHHHHHHCCcCC
Confidence            34579999999999999999885           3466777776654

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.47  E-value=0.53  Score=22.52  Aligned_cols=21  Identities=19%  Similarity=0.135  Sum_probs=18.5

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|..+
T Consensus        35 ~~~La~~~~l~~~qI~~WF~N   55 (62)
T d1x2na1          35 KKQIAAQTNLTLLQVNNWFIN   55 (62)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHhHHHHHH
Confidence            378999999999999999864

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.26  E-value=0.41  Score=23.38  Aligned_cols=37  Identities=16%  Similarity=0.108  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHhCCC-------CHHHHHHHhCCCHHHHHHHHcC
Q 038591           20 DTPRQIQRARLGKKM-------SQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        20 ~~~~~lk~~r~~~g~-------s~~elA~~~gis~~~i~~~e~g   56 (82)
                      |....|..|-.....       ...+||..+|++...|..|..+
T Consensus         8 ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqN   51 (68)
T d2cuea1           8 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSN   51 (68)
T ss_dssp             SCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcc
Confidence            445555555444332       3488999999999999999875

>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=83.22  E-value=0.65  Score=26.73  Aligned_cols=30  Identities=10%  Similarity=0.040  Sum_probs=23.8

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591           24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e   54 (82)
                      .|..++ ...+|..+||+.+|+|+++|++-.
T Consensus        20 Il~~L~-~~~~~~~ela~~l~~s~~~v~~HL   49 (194)
T d2p4wa1          20 ILFLLT-KRPYFVSELSRELGVGQKAVLEHL   49 (194)
T ss_dssp             HHHHHH-HSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHH-hCCCCHHHHHHHHCcCHHHHHHHH
Confidence            344443 467999999999999999998764

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.09  E-value=0.53  Score=23.18  Aligned_cols=20  Identities=20%  Similarity=0.210  Sum_probs=18.2

Q ss_pred             HHHHHHhCCCHHHHHHHHcC
Q 038591           37 PDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g   56 (82)
                      .+||..+|++...|..|...
T Consensus        35 ~~La~~~gl~~~qv~~WF~N   54 (73)
T d1pufb_          35 EELAKKCGITVSQVSNWFGN   54 (73)
T ss_dssp             HHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHhHHHHHH
Confidence            67999999999999999865

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.88  E-value=0.67  Score=21.93  Aligned_cols=20  Identities=5%  Similarity=0.140  Sum_probs=17.9

Q ss_pred             HHHHHHhCCCHHHHHHHHcC
Q 038591           37 PDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g   56 (82)
                      .+||..+|+++..|..|..+
T Consensus        32 ~~La~~~gL~~~qV~~WF~N   51 (60)
T d1k61a_          32 ENLMKNTSLSRIQIKNWVSN   51 (60)
T ss_dssp             HHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHhHHhHh
Confidence            67999999999999999865

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=82.56  E-value=0.65  Score=22.63  Aligned_cols=21  Identities=24%  Similarity=0.308  Sum_probs=18.9

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|..+
T Consensus        32 r~~LA~~l~L~~~~V~~WFqN   52 (68)
T d1ftta_          32 REHLASMIHLTPTQVKIWFQN   52 (68)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHhCCCccceeeeccc
Confidence            478999999999999999865

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=82.37  E-value=0.73  Score=21.64  Aligned_cols=21  Identities=5%  Similarity=0.196  Sum_probs=18.7

Q ss_pred             HHHHHHhCCCHHHHHHHHcCC
Q 038591           37 PDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        37 ~elA~~~gis~~~i~~~e~g~   57 (82)
                      .+||..+|+++..|.-|.++.
T Consensus        28 ~~LA~~l~l~~~~V~iWFQNr   48 (56)
T d9anta_          28 IEIAHALSLTERQIKIWFQNR   48 (56)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHhCCChhHeeeccccc
Confidence            789999999999999998653

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.32  E-value=0.53  Score=22.30  Aligned_cols=23  Identities=13%  Similarity=0.082  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 038591           34 MSQPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        34 ~s~~elA~~~gis~~~i~~~e~g   56 (82)
                      ....+||..+|++...|..|..+
T Consensus        29 ~~r~~LA~~l~l~~~~V~~WFqN   51 (60)
T d1yz8p1          29 STREEIAVWTNLTEARVRVWFKN   51 (60)
T ss_dssp             TTTTHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCChHHHHHHhHH
Confidence            35588999999999999999864

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.78  E-value=0.75  Score=22.34  Aligned_cols=21  Identities=24%  Similarity=0.257  Sum_probs=18.7

Q ss_pred             HHHHHHHhCCCHHHHHHHHcC
Q 038591           36 QPDLANQINQRPQVVSEYENG   56 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g   56 (82)
                      ..+||..+|++...|..|..+
T Consensus        38 r~~La~~~~l~~~~V~~WFqN   58 (67)
T d1ocpa_          38 ITHIANQLGLEKDVVRVWFCN   58 (67)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHhHH
Confidence            368999999999999999865

>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=81.22  E-value=1.4  Score=23.49  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=21.9

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591           31 GKKMSQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        31 ~~g~s~~elA~~~gis~~~i~~~e~   55 (82)
                      ...+|-+++|+.+|+++..|.++..
T Consensus        16 ~~~~ss~~IA~~~~~~~~~v~kIl~   40 (127)
T d1xd7a_          16 DEKTSSEIIADSVNTNPVVVRRMIS   40 (127)
T ss_dssp             CSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHhCcCHHHHHHHHH
Confidence            4569999999999999999998853

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=80.67  E-value=0.12  Score=29.52  Aligned_cols=22  Identities=9%  Similarity=0.001  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 038591           33 KMSQPDLANQINQRPQVVSEYE   54 (82)
Q Consensus        33 g~s~~elA~~~gis~~~i~~~e   54 (82)
                      |+|+.+||+.++++++++++..
T Consensus        79 ~lt~~eLa~~l~i~~~tvsr~l  100 (172)
T d2fbka1          79 GLRPTELSALAAISGPSTSNRI  100 (172)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHH
T ss_pred             CcCHHHHHHHHCcCHhHHHHHH
Confidence            6899999999999988877664

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.54  E-value=0.82  Score=22.64  Aligned_cols=22  Identities=14%  Similarity=0.105  Sum_probs=19.2

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCC
Q 038591           36 QPDLANQINQRPQVVSEYENGK   57 (82)
Q Consensus        36 ~~elA~~~gis~~~i~~~e~g~   57 (82)
                      ..+||..+|++...|..|..+.
T Consensus        34 r~~LA~~l~l~~~~V~~WFqNr   55 (76)
T d2ecba1          34 LNRLRAQTKLTRREIDAWFTEK   55 (76)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHhHHHH
Confidence            4789999999999999998653

>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=80.02  E-value=0.4  Score=25.05  Aligned_cols=23  Identities=22%  Similarity=0.219  Sum_probs=19.8

Q ss_pred             CC-CHHHHHHHhCCCHHHHHHHHc
Q 038591           33 KM-SQPDLANQINQRPQVVSEYEN   55 (82)
Q Consensus        33 g~-s~~elA~~~gis~~~i~~~e~   55 (82)
                      .+ |..+||+.+|+|+.||.+-.+
T Consensus        32 ~LPs~r~La~~~~vSr~tvr~Al~   55 (100)
T d1v4ra1          32 TLPSVADIRAQFGVAAKTVSRALA   55 (100)
T ss_dssp             BCCCHHHHHHHSSSCTTHHHHHTT
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHH
Confidence            35 899999999999999988643