Citrus Sinensis ID: 045477

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------9
Protein Sequence
MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHcccccccHHHHHHHccccccccHHHHHHHHHHHHHHHccEEEEEcccc
Secondary Structure Prediction (SSPRO)
ccccHHccHHHHHHHHHcccHHHHHHHHHHHccHHHHHHcccccccEcHHHHHccccccccccHHHHHHHHHHHHHHcccEEEEEEccc
Coil and Loop (DISEMBL)
MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAkagpgaklsASEIAaqlpatknkdapTMLDRILGLLASYGIVECSVDDVD
Flexible Loop (DISEMBL)
maneardenFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQlpatknkdapTMLDRILGLLASYGIVECSVDDVD
Low Complexity Region (SEG)
MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD
Disordered region (IsUnstruct)
********NFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGA********************TMLDRILGLLASYGIVECSV****
Disordered Region (DISOPRED)
********NFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD***
Disordered Region (DISEMBL)
MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD
Disordered Region (DISPRO)
******DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD
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	89	2.2.26 [Sep-21-2011]
Q00763	365	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.221	0.585	5e-18
Q43046	365	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.221	0.585	5e-18
Q9FQY8	359	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.225	0.524	8e-18
Q43047	364	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.222	0.585	1e-17
O81646	359	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.225	0.512	1e-17
Q41086	364	Caffeic acid 3-O-methyltr	N/A	no	0.910	0.222	0.560	1e-16
Q8LL87	350	Caffeic acid 3-O-methyltr	N/A	no	0.932	0.237	0.511	2e-16
Q8W013	363	Caffeic acid 3-O-methyltr	N/A	no	0.842	0.206	0.552	3e-16
Q43239	354	Caffeic acid 3-O-methyltr	N/A	no	0.988	0.248	0.443	4e-16
P46484	366	Caffeic acid 3-O-methyltr	N/A	no	0.853	0.207	0.545	5e-16

>sp|Q00763|COMT1_POPTM Caffeic acid 3-O-methyltransferase 1 OS=Populus tremuloides GN=OMT1 PE=1 SV=1

 Score = 89.4 bits (220), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 48/82 (58%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          +E   +A ++   SVL M +K  I L L EI+AKAGPGA LS SEIA+ LP TKN DAP 
Sbjct: 17 EEAHLFAMQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLP-TKNPDAPV 75

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 76 MLDRILRLLASYSILTCSLKDL 97

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.
Populus tremuloides (taxid: 3693)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 6EC: 8

>sp|Q43046|COMT1_POPKI Caffeic acid 3-O-methyltransferase 1 OS=Populus kitakamiensis GN=HOMT1 PE=3 SV=1

 Score = 89.4 bits (220), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 48/82 (58%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          +E   +A ++   SVL M +K  I L L EI+AKAGPGA LS SEIA+ LP TKN DAP 
Sbjct: 17 EEAHLFAMQLASASVLPMILKTAIELDLLEIMAKAGPGAFLSTSEIASHLP-TKNPDAPV 75

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 76 MLDRILRLLASYSILTCSLKDL 97

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Populus kitakamiensis (taxid: 34292)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q9FQY8|COMT1_CAPAN Caffeic acid 3-O-methyltransferase OS=Capsicum annuum GN=COMT PE=2 SV=2

 Score = 89.0 bits (219), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 60/82 (73%), Gaps = 1/82 (1%)

Query: 4  EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKD 63
          +  DE F +A ++   SVL M +K+ + L L EI+AKAGPGA +S SE+AAQLP TKN +
Sbjct: 10 QTEDEAFLFAMQLASASVLPMVLKSALELDLLEIMAKAGPGAAISPSELAAQLP-TKNPE 68

Query: 64 APTMLDRILGLLASYGIVECSV 85
          AP MLDR+L LLA+Y ++ C++
Sbjct: 69 APVMLDRMLRLLATYSVLNCTL 90

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Capsicum annuum (taxid: 4072)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q43047|COMT3_POPKI Caffeic acid 3-O-methyltransferase 3 OS=Populus kitakamiensis GN=HOMT3 PE=3 SV=1

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 48/82 (58%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          DE   +A ++   SVL M +K  I L L EI+AKAGPGA LS S+IA+ LP TKN DAP 
Sbjct: 16 DEEANFAMQLISSSVLPMVLKTAIELDLLEIMAKAGPGALLSPSDIASHLP-TKNPDAPV 74

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 75 MLDRILRLLASYSILICSLRDL 96

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Populus kitakamiensis (taxid: 34292)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|O81646|COMT1_CAPCH Caffeic acid 3-O-methyltransferase OS=Capsicum chinense GN=COMT PE=2 SV=1

 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/82 (51%), Positives = 59/82 (71%), Gaps = 1/82 (1%)

Query: 4  EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKD 63
          +  DE F +A ++   SVL M +KA + L L EI+AK+GPGA +S SE+AAQLP TKN +
Sbjct: 10 QTEDEAFVFAMQLASASVLPMVLKATVELDLLEIMAKSGPGAFISPSELAAQLP-TKNPE 68

Query: 64 APTMLDRILGLLASYGIVECSV 85
          AP MLDR+  LLA+Y ++ C++
Sbjct: 69 APVMLDRMFRLLATYSVLNCTL 90

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Capsicum chinense (taxid: 80379)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q41086|COMT2_POPTM Caffeic acid 3-O-methyltransferase 2 OS=Populus tremuloides GN=OMT2 PE=3 SV=1

 Score = 85.5 bits (210), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 46/82 (56%), Positives = 57/82 (69%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          DE   +A ++   SVL M +K  I L L EI+AKAGPGA L  S+IA+ LP TKN +AP 
Sbjct: 16 DEEANFALQLISSSVLPMVLKTAIELDLLEIMAKAGPGALLPPSDIASHLP-TKNPNAPV 74

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 75 MLDRILRLLASYSILICSLRDL 96

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Populus tremuloides (taxid: 3693)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q8LL87|COMT1_COFCA Caffeic acid 3-O-methyltransferase OS=Coffea canephora PE=2 SV=1

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 43/84 (51%), Positives = 60/84 (71%), Gaps = 1/84 (1%)

Query: 5  ARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDA 64
          A +E   +A  +   SVL M +K+ I L L E+IAKAGPGA +S SE+AAQLP T N +A
Sbjct: 2  AEEEACLFAMSLASASVLPMVLKSAIELDLLELIAKAGPGAYVSPSELAAQLP-THNPEA 60

Query: 65 PTMLDRILGLLASYGIVECSVDDV 88
          P MLDRIL LLA+Y +++C ++++
Sbjct: 61 PIMLDRILRLLATYSVLDCKLNNL 84

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Coffea canephora (taxid: 49390)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q8W013|COMT1_CATRO Caffeic acid 3-O-methyltransferase OS=Catharanthus roseus GN=COMT1 PE=2 SV=1

 Score = 83.6 bits (205), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 42/76 (55%), Positives = 55/76 (72%), Gaps = 1/76 (1%)

Query: 13 AFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRIL 72
          A  +   SVL M +K+ I L L E+I K+GPGA +S SE+AAQLP T+N DAP MLDRIL
Sbjct: 23 AMRLASASVLPMVLKSAIELDLLELIKKSGPGAYVSPSELAAQLP-TQNPDAPVMLDRIL 81

Query: 73 GLLASYGIVECSVDDV 88
           LLASY ++ C++ D+
Sbjct: 82 RLLASYSVLNCTLKDL 97

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|Q43239|COMT1_ZINEL Caffeic acid 3-O-methyltransferase OS=Zinnia elegans PE=2 SV=1

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/88 (44%), Positives = 55/88 (62%)

Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
          M +   D+ F +A ++   SVL M +K  I L L E IAKAGP   +S+SE+ AQLP   
Sbjct: 1  MGSNQDDQAFLFAMQLASASVLPMVLKTAIELDLLETIAKAGPHGSVSSSELVAQLPKVN 60

Query: 61 NKDAPTMLDRILGLLASYGIVECSVDDV 88
          N +AP M+DRI  LLASY ++ C++ + 
Sbjct: 61 NPEAPVMIDRICSLLASYSVLTCTLKET 88

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Zinnia elegans (taxid: 34245)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

>sp|P46484|COMT1_EUCGU Caffeic acid 3-O-methyltransferase OS=Eucalyptus gunnii GN=OMT PE=2 SV=1

 Score = 83.2 bits (204), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 42/77 (54%), Positives = 56/77 (72%), Gaps = 1/77 (1%)

Query: 12 YAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRI 71
          +A ++   SVL M +KA I L L EI+AKAGPGA LS  E+AAQLP T+N +AP MLDRI
Sbjct: 23 FAMQLASASVLPMVLKAAIELDLLEIMAKAGPGAFLSPGEVAAQLP-TQNPEAPVMLDRI 81

Query: 72 LGLLASYGIVECSVDDV 88
            LLASY ++ C++ ++
Sbjct: 82 FRLLASYSVLTCTLRNL 98

Catalyzes the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins.

Eucalyptus gunnii (taxid: 3933)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 6

EC: 8

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	89
224128073	358	catechol o-methyltransferase related [Po	0.932	0.231	0.678	1e-23
145695037	353	O-methyltransferase [Citrus sinensis x C	0.898	0.226	0.654	9e-22
224068173	359	catechol o-methyltransferase [Populus tr	0.932	0.231	0.607	3e-20
255548061	359	o-methyltransferase, putative [Ricinus c	0.977	0.242	0.528	5e-19
255548067	351	o-methyltransferase, putative [Ricinus c	0.977	0.247	0.528	5e-19
71482940	362	S-methyltransferase [Catharanthus roseus	0.955	0.234	0.523	1e-17
224061505	371	caffeic acid 3-O-methyltransferase [Popu	0.955	0.229	0.551	2e-17
403324062	138	caffeate O-methyltransferase, partial [P	0.910	0.586	0.597	3e-17
268528131	356	caffeic acid O-methyltransferase 3 [Goss	0.898	0.224	0.604	5e-17
403324026	138	caffeate O-methyltransferase, partial [P	0.910	0.586	0.585	6e-17

>gi|224128073|ref|XP_002320237.1| catechol o-methyltransferase related [Populus trichocarpa] gi|118481911|gb|ABK92890.1| unknown [Populus trichocarpa] gi|222861010|gb|EEE98552.1| catechol o-methyltransferase related [Populus trichocarpa]

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/84 (67%), Positives = 69/84 (82%), Gaps = 1/84 (1%)

Query: 3  NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK 62
          +EA+DENF YA ++ + SVL MTM + I LG+FEIIAKAGP AKLSAS++AAQLP TKN 
Sbjct: 13 DEAKDENFGYAMQLALSSVLPMTMYSAIQLGIFEIIAKAGPDAKLSASDVAAQLP-TKNP 71

Query: 63 DAPTMLDRILGLLASYGIVECSVD 86
          DAP MLDRIL LLAS+ ++ CSVD
Sbjct: 72 DAPMMLDRILRLLASHDVLGCSVD 95

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145695037|gb|ABP94018.1| O-methyltransferase [Citrus sinensis x Citrus reticulata]

 Score =  107 bits (267), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 53/81 (65%), Positives = 66/81 (81%), Gaps = 1/81 (1%)

Query: 6  RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAP 65
          RD++FAYA ++ MG++L M ++ V  LG+FEI+ K GPGAKL AS+IAAQL  TKNKDAP
Sbjct: 9  RDQSFAYANQLAMGTMLPMAIQTVYELGIFEILDKVGPGAKLCASDIAAQL-LTKNKDAP 67

Query: 66 TMLDRILGLLASYGIVECSVD 86
           MLDRIL LLASY +VECS+D
Sbjct: 68 MMLDRILRLLASYSVVECSLD 88

Source: Citrus sinensis x Citrus reticulata

Species: Citrus sinensis x Citrus reticulata

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068173|ref|XP_002302676.1| catechol o-methyltransferase [Populus trichocarpa] gi|222844402|gb|EEE81949.1| catechol o-methyltransferase [Populus trichocarpa]

 Score =  102 bits (254), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 51/84 (60%), Positives = 64/84 (76%), Gaps = 1/84 (1%)

Query: 3  NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK 62
          +EA+DENF YA ++ + SVL MT+   I LG+FEIIAKAGP  KLSA++IAA+LP T N 
Sbjct: 13 DEAKDENFGYAMQLALSSVLPMTLHTAIQLGIFEIIAKAGPDVKLSAADIAAKLP-TDNP 71

Query: 63 DAPTMLDRILGLLASYGIVECSVD 86
          D P MLDRIL LLAS+ ++ C VD
Sbjct: 72 DTPKMLDRILRLLASHQVLCCFVD 95

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548061|ref|XP_002515087.1| o-methyltransferase, putative [Ricinus communis] gi|223545567|gb|EEF47071.1| o-methyltransferase, putative [Ricinus communis]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 65/87 (74%)

Query: 3  NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK 62
          +E  DENF YA ++ +GS L M++ A I LG+FEIIAKAGP +KLSASEI A++P  +N 
Sbjct: 13 DEEHDENFGYAMQLALGSALPMSLHAAIELGVFEIIAKAGPESKLSASEITAEIPDVQNP 72

Query: 63 DAPTMLDRILGLLASYGIVECSVDDVD 89
          DA   LDR+L LLAS+ ++ CS++ ++
Sbjct: 73 DAAITLDRVLRLLASHNVLGCSLNGLE 99

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548067|ref|XP_002515090.1| o-methyltransferase, putative [Ricinus communis] gi|223545570|gb|EEF47074.1| o-methyltransferase, putative [Ricinus communis]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/87 (52%), Positives = 64/87 (73%)

Query: 3  NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK 62
          +E  DENF YA ++ +GS L M++   I LG+FEIIAKAGP +KLSASEI A++P  +N 
Sbjct: 13 DEEHDENFGYALQLALGSALPMSLHTAIELGVFEIIAKAGPESKLSASEITAEIPDVQNP 72

Query: 63 DAPTMLDRILGLLASYGIVECSVDDVD 89
          DA  MLDRIL LLA + ++ CS++ ++
Sbjct: 73 DAALMLDRILRLLARHNVLGCSLNGLE 99

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|71482940|gb|AAZ32409.1| S-methyltransferase [Catharanthus roseus]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 45/86 (52%), Positives = 63/86 (73%), Gaps = 1/86 (1%)

Query: 2  ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKN 61
          +N+  D++ +YA ++     L M + AVI L +FEIIAKAGPGAKLS S+I +Q+P TKN
Sbjct: 10 SNKEDDDHSSYALQLVFSGALPMVLNAVIKLNVFEIIAKAGPGAKLSPSQIVSQMP-TKN 68

Query: 62 KDAPTMLDRILGLLASYGIVECSVDD 87
           +AP +LDR+L +LASY ++ CSV D
Sbjct: 69 PEAPVVLDRMLRMLASYSVLTCSVVD 94

Source: Catharanthus roseus

Species: Catharanthus roseus

Genus: Catharanthus

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061505|ref|XP_002300513.1| caffeic acid 3-O-methyltransferase [Populus trichocarpa] gi|222847771|gb|EEE85318.1| caffeic acid 3-O-methyltransferase [Populus trichocarpa]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 48/87 (55%), Positives = 61/87 (70%), Gaps = 2/87 (2%)

Query: 1  MANEARDENF--AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPA 58
          MA  + +E++   YA ++   S L M  KAVI LG+ EII KAGPGA LSAS+I +QLP 
Sbjct: 1  MATSSNEEDYHLQYAMQLASASTLPMVFKAVIELGVLEIIEKAGPGALLSASQITSQLPT 60

Query: 59 TKNKDAPTMLDRILGLLASYGIVECSV 85
            N DAPT+LDRIL LLAS+ I+ CS+
Sbjct: 61 QTNPDAPTVLDRILCLLASHSILTCSL 87

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|403324062|gb|AFR39620.1| caffeate O-methyltransferase, partial [Populus nigra] gi|403324066|gb|AFR39622.1| caffeate O-methyltransferase, partial [Populus nigra] gi|403324072|gb|AFR39625.1| caffeate O-methyltransferase, partial [Populus nigra] gi|403324080|gb|AFR39629.1| caffeate O-methyltransferase, partial [Populus nigra] gi|403324084|gb|AFR39631.1| caffeate O-methyltransferase, partial [Populus nigra]

 Score = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 49/82 (59%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          DE   +A ++   SVL M +K  I L L EIIAKAGPGA LS S+IA+ LP TKN DAP 
Sbjct: 16 DEEANFAMQLISSSVLPMVLKTAIELDLLEIIAKAGPGALLSPSDIASHLP-TKNPDAPV 74

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 75 MLDRILRLLASYSILICSLRDL 96

Source: Populus nigra

Species: Populus nigra

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|268528131|gb|ACZ06242.1| caffeic acid O-methyltransferase 3 [Gossypium hirsutum]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 49/81 (60%), Positives = 61/81 (75%), Gaps = 1/81 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          +E+F+YA ++   SVL M+M A + L +F I+AK GP AKLSA EIAAQL AT N +A +
Sbjct: 10 EESFSYALQIVTSSVLPMSMHAAVQLDIFGIMAKCGPDAKLSAKEIAAQL-ATNNSEAAS 68

Query: 67 MLDRILGLLASYGIVECSVDD 87
          MLDRIL LLAS+GIV CSV D
Sbjct: 69 MLDRILLLLASHGIVGCSVVD 89

Source: Gossypium hirsutum

Species: Gossypium hirsutum

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|403324026|gb|AFR39602.1| caffeate O-methyltransferase, partial [Populus alba]

 Score = 91.3 bits (225), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 48/82 (58%), Positives = 58/82 (70%), Gaps = 1/82 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          DE   +A ++   SVL M +K  I L L EI+AKAGPGA LS S+IA+ LP TKN DAP 
Sbjct: 16 DEEANFAMQLISSSVLPMVLKTAIELDLLEIMAKAGPGALLSPSDIASHLP-TKNPDAPV 74

Query: 67 MLDRILGLLASYGIVECSVDDV 88
          MLDRIL LLASY I+ CS+ D+
Sbjct: 75 MLDRILRLLASYSILVCSLRDL 96

Source: Populus alba

Species: Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	89
UNIPROTKB|Q84N28	360	OMT1 "Flavone O-methyltransfer	0.966	0.238	0.448	1e-13
TAIR|locus:2153423	363	OMT1 "AT5G54160" [Arabidopsis	0.842	0.206	0.487	2.2e-12
UNIPROTKB|Q6ZD89	368	ROMT-9 "Flavone 3'-O-methyltra	0.977	0.236	0.419	2.9e-11
UNIPROTKB|P93324	372	P93324 "Isoliquiritigenin 2'-O	0.988	0.236	0.422	1.3e-10
TAIR|locus:2038026	352	AT1G33030 [Arabidopsis thalian	0.853	0.215	0.432	4.1e-09
TAIR|locus:2199582	373	IGMT4 "indole glucosinolate O-	0.797	0.190	0.432	7.6e-09
TAIR|locus:2199597	373	IGMT3 "indole glucosinolate O-	0.797	0.190	0.432	4.4e-08
TAIR|locus:2199587	373	IGMT2 "indole glucosinolate O-	0.797	0.190	0.432	4.4e-08
TAIR|locus:2204695	381	AT1G77530 [Arabidopsis thalian	0.674	0.157	0.475	4.6e-08
TAIR|locus:2199607	373	IGMT1 "indole glucosinolate O-	0.797	0.190	0.405	5.7e-08

UNIPROTKB|Q84N28 OMT1 "Flavone O-methyltransferase 1" [Triticum aestivum (taxid:4565)]

 Score = 183 (69.5 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 39/87 (44%), Positives = 57/87 (65%)

Query:     1 MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
             MA  A +E   YA ++   S+L MT+K  I LGL E +  AG G  L+ +E+AA+LP+T 
Sbjct:     8 MAASADEEACMYALQLVSSSILPMTLKNAIELGLLETLVAAG-GKLLTPAEVAAKLPSTA 66

Query:    61 NKDAPTMLDRILGLLASYGIVECSVDD 87
             N  A  M+DR+L LLASY +V C++++
Sbjct:    67 NPAAADMVDRMLRLLASYNVVSCTMEE 93

GO:0009611 "response to wounding" evidence=IDA

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

GO:0009751 "response to salicylic acid stimulus" evidence=IDA

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

TAIR|locus:2153423 OMT1 "AT5G54160" [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 2.2e-12, P = 2.2e-12
 Identities = 38/78 (48%), Positives = 53/78 (67%)

Query:     7 DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
             DE   +A ++   SVL M +K+ + L L EI+AK G  + +S +EIA++LP TKN +AP 
Sbjct:    17 DEAALFAMQLASASVLPMALKSALELDLLEIMAKNG--SPMSPTEIASKLP-TKNPEAPV 73

Query:    67 MLDRILGLLASYGIVECS 84
             MLDRIL LL SY ++ CS
Sbjct:    74 MLDRILRLLTSYSVLTCS 91

GO:0030744 "luteolin O-methyltransferase activity" evidence=IDA

GO:0030755 "quercetin 3-O-methyltransferase activity" evidence=IDA

GO:0033799 "myricetin 3'-O-methyltransferase activity" evidence=IDA

GO:0047763 "caffeate O-methyltransferase activity" evidence=ISS;IMP

GO:0051555 "flavonol biosynthetic process" evidence=IDA

GO:0009809 "lignin biosynthetic process" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006598 "polyamine catabolic process" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009698 "phenylpropanoid metabolic process" evidence=RCA

GO:0009805 "coumarin biosynthetic process" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0016126 "sterol biosynthetic process" evidence=RCA

GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA

GO:0005829 "cytosol" evidence=TAS

UNIPROTKB|Q6ZD89 ROMT-9 "Flavone 3'-O-methyltransferase 1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 161 (61.7 bits), Expect = 2.9e-11, P = 2.9e-11
 Identities = 39/93 (41%), Positives = 56/93 (60%)

Query:     1 MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEII---AKAGPGAK---LSASEIAA 54
             MA  A +E   YA ++   S+L MT+K  I LGL E +   A AG G K   L+ +E+A 
Sbjct:     8 MAAAADEEACMYALQLASSSILPMTLKNAIELGLLETLQSAAVAGGGGKAALLTPAEVAD 67

Query:    55 QLPATKNKDAPTMLDRILGLLASYGIVECSVDD 87
             +LP+  N  A  M+DR+L LLASY +V C +++
Sbjct:    68 KLPSKANPAAADMVDRMLRLLASYNVVRCEMEE 100

GO:0030744 "luteolin O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

UNIPROTKB|P93324 P93324 "Isoliquiritigenin 2'-O-methyltransferase" [Medicago sativa (taxid:3879)]

 Score = 155 (59.6 bits), Expect = 1.3e-10, P = 1.3e-10
 Identities = 38/90 (42%), Positives = 54/90 (60%)

Query:     2 ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGP-GAKLSASEIAAQLPA-T 59
             + +  D     A  +T   V    + A I+L LFEIIAKA P GA +S SEIA++LPA T
Sbjct:    17 SEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPAST 76

Query:    60 KNKDAPTMLDRILGLLASYGIVECSVDDVD 89
             ++ D P  LDR+L LLASY ++  +   ++
Sbjct:    77 QHSDLPNRLDRMLRLLASYSVLTSTTRTIE 106

GO:0030751 "licodione 2'-O-methyltransferase activity" evidence=IDA

GO:0033802 "isoliquiritigenin 2'-O-methyltransferase activity" evidence=IDA

TAIR|locus:2038026 AT1G33030 [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 4.1e-09, P = 4.1e-09
 Identities = 35/81 (43%), Positives = 53/81 (65%)

Query:     7 DENFA-YAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLP-ATKNKDA 64
             ++N + YA  ++  SVL M +K  I+LGLF+I+A++GP    SAS+I + L   TK    
Sbjct:     3 EQNLSSYAMILSSSSVLPMVLKTAIDLGLFDILAESGPS---SASQIFSLLSNETKKHHD 59

Query:    65 PTMLDRILGLLASYGIVECSV 85
              ++++RIL  LASY I+ CSV
Sbjct:    60 SSLVNRILRFLASYSILTCSV 80

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=IDA;TAS

GO:0009809 "lignin biosynthetic process" evidence=ISS

TAIR|locus:2199582 IGMT4 "indole glucosinolate O-methyltransferase 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 32/74 (43%), Positives = 48/74 (64%)

Query:    13 AFEVTMGSVLHMTMKAVINLGLFEII-AKAGPGAK-LSASEIAAQLPAT-KNKDAPTMLD 69
             A  +   +   M +KA + LG+F+ + A+A      LS SEIA++LP T +N +AP +LD
Sbjct:    29 AVRLANAAAFPMVLKAALELGVFDTLYAEASRSDSFLSPSEIASKLPTTPRNPEAPVLLD 88

Query:    70 RILGLLASYGIVEC 83
             R+L LLASY +V+C
Sbjct:    89 RMLRLLASYSVVKC 102

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199597 IGMT3 "indole glucosinolate O-methyltransferase 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 4.4e-08, P = 4.4e-08
 Identities = 32/74 (43%), Positives = 48/74 (64%)

Query:    13 AFEVTMGSVLHMTMKAVINLGLFEII-AKAG-PGAKLSASEIAAQLPAT-KNKDAPTMLD 69
             A  +   +   M +KA + LG+F+ + A+A    + LS SEIA++LP T +N  AP +LD
Sbjct:    29 AVRLANAAAFPMVLKASLELGVFDTLYAEASRTDSFLSPSEIASKLPTTPRNPGAPVLLD 88

Query:    70 RILGLLASYGIVEC 83
             R+L LLASY +V+C
Sbjct:    89 RMLRLLASYSMVKC 102

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199587 IGMT2 "indole glucosinolate O-methyltransferase 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 4.4e-08, P = 4.4e-08
 Identities = 32/74 (43%), Positives = 48/74 (64%)

Query:    13 AFEVTMGSVLHMTMKAVINLGLFEII-AKAG-PGAKLSASEIAAQLPAT-KNKDAPTMLD 69
             A  +   +   M +KA + LG+F+ + A+A    + LS SEIA++LP T +N  AP +LD
Sbjct:    29 AVRLANAAAFPMVLKASLELGVFDTLYAEASRTDSFLSPSEIASKLPTTPRNPGAPVLLD 88

Query:    70 RILGLLASYGIVEC 83
             R+L LLASY +V+C
Sbjct:    89 RMLRLLASYSMVKC 102

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA;IDA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0042343 "indole glucosinolate metabolic process" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2204695 AT1G77530 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 4.6e-08, P = 4.6e-08
 Identities = 29/61 (47%), Positives = 39/61 (63%)

Query:    24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLP-ATKNKDAPTMLDRILGLLASYGIVE 82
             M +KA + LG+ + IA A  G  LS SEIA  LP    N +AP +LDR+L LL S+ I++
Sbjct:    44 MVLKAALELGVIDTIAAASNGTWLSPSEIAVSLPNKPTNPEAPVLLDRMLRLLVSHSILK 103

Query:    83 C 83
             C
Sbjct:   104 C 104

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA;ISS

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0009809 "lignin biosynthetic process" evidence=ISS

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2199607 IGMT1 "indole glucosinolate O-methyltransferase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 131 (51.2 bits), Expect = 5.7e-08, P = 5.7e-08
 Identities = 30/74 (40%), Positives = 47/74 (63%)

Query:    13 AFEVTMGSVLHMTMKAVINLGLFEII--AKAGPGAKLSASEIAAQLPAT-KNKDAPTMLD 69
             A  +   +   M +KA + LG+F+ +  A +   + LS  EIA++LP T +N +AP +LD
Sbjct:    29 AVRLANAAAFPMVLKAALELGVFDTLYAAASRTDSFLSPYEIASKLPTTPRNPEAPVLLD 88

Query:    70 RILGLLASYGIVEC 83
             R+L LLASY +V+C
Sbjct:    89 RMLRLLASYSMVKC 102

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA;IDA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0042343 "indole glucosinolate metabolic process" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: COMT4 SubName- Full=Putative uncharacterized protein; (358 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	89
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	1e-14

>gnl|CDD|219719 pfam08100, Dimerisation, Dimerisation domain

 Score = 61.4 bits (150), Expect = 1e-14
 Identities = 29/53 (54%), Positives = 37/53 (69%), Gaps = 3/53 (5%)

Query: 24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA 76
          M +K  I LG+ +IIAK   G  LS SE+A++LP T N +AP MLDR+L LLA
Sbjct: 1  MVLKCAIELGIPDIIAKH--GKPLSPSELASKLP-TVNPEAPVMLDRLLRLLA 50

This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins. Length = 50

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	89
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.71
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.36
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	99.23
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	98.2
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.65
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	97.36
PRK11569	274	transcriptional repressor IclR; Provisional	97.33
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	97.27
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.22
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.18
COG1414	246	IclR Transcriptional regulator [Transcription]	97.17
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	97.11
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	97.09
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	97.08
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.06
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	97.05
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	97.03
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	97.01
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	96.99
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.94
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.84
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.74
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	96.66
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	96.64
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	96.56
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	96.53
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.5
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	96.44
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.37
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	96.28
COG1959	150	Predicted transcriptional regulator [Transcription	96.25
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.22
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.18
PRK06474	178	hypothetical protein; Provisional	96.17
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.15
PRK03573	144	transcriptional regulator SlyA; Provisional	96.14
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	95.98
COG3355	126	Predicted transcriptional regulator [Transcription	95.89
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.88
COG4190	144	Predicted transcriptional regulator [Transcription	95.83
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.81
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.74
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	95.64
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.58
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	95.56
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.54
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	95.47
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	95.45
PRK11639	169	zinc uptake transcriptional repressor; Provisional	95.45
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	95.35
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	95.28
PRK09462	148	fur ferric uptake regulator; Provisional	95.2
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	95.18
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	95.18
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.18
PRK06266	178	transcription initiation factor E subunit alpha; V	95.16
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	95.15
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	95.13
PRK11014	141	transcriptional repressor NsrR; Provisional	95.1
PRK10870	176	transcriptional repressor MprA; Provisional	94.88
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	94.84
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	94.77
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	94.74
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	94.62
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	94.59
COG1510	177	Predicted transcriptional regulators [Transcriptio	94.51
COG2512	258	Predicted membrane-associated trancriptional regul	94.49
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	94.32
PHA00738	108	putative HTH transcription regulator	94.16
PRK11169	164	leucine-responsive transcriptional regulator; Prov	94.12
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	94.04
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.95
COG1522	154	Lrp Transcriptional regulators [Transcription]	93.91
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.88
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	93.85
PRK13777	185	transcriptional regulator Hpr; Provisional	93.78
COG1846	126	MarR Transcriptional regulators [Transcription]	93.61
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.11
PRK03902	142	manganese transport transcriptional regulator; Pro	93.09
PRK15431	78	ferrous iron transport protein FeoC; Provisional	93.05
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	93.02
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.0
PRK11050	152	manganese transport regulator MntR; Provisional	92.96
PRK13509	251	transcriptional repressor UlaR; Provisional	92.96
COG2345	218	Predicted transcriptional regulator [Transcription	92.81
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	92.8
COG1378	247	Predicted transcriptional regulators [Transcriptio	92.73
COG4565	224	CitB Response regulator of citrate/malate metaboli	92.71
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	92.42
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	92.1
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	91.96
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	91.88
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	91.6
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	91.39
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	91.35
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	91.3
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	91.25
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	91.21
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	91.07
PRK09334	86	30S ribosomal protein S25e; Provisional	90.83
PRK10046	225	dpiA two-component response regulator DpiA; Provis	90.8
PRK00215	205	LexA repressor; Validated	90.72
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.66
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	90.54
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	90.51
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	90.49
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	90.32
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	90.25
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	90.08
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	89.9
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	89.75
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	89.67
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	89.52
PRK14096	528	pgi glucose-6-phosphate isomerase; Provisional	89.46
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	89.43
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	89.42
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	89.08
PRK00135	188	scpB segregation and condensation protein B; Revie	88.83
PHA02943	165	hypothetical protein; Provisional	88.67
PRK14165	217	winged helix-turn-helix domain-containing protein/	88.62
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	88.3
PRK09391	230	fixK transcriptional regulator FixK; Provisional	88.07
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	88.03
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	88.0
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	87.84
PF13730	55	HTH_36: Helix-turn-helix domain	87.65
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	87.31
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	87.11
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	86.89
PRK09954	362	putative kinase; Provisional	86.51
COG4189	308	Predicted transcriptional regulator [Transcription	86.11
PRK01381	99	Trp operon repressor; Provisional	86.0
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	85.93
COG1802	230	GntR Transcriptional regulators [Transcription]	85.84
smart00531	147	TFIIE Transcription initiation factor IIE.	85.77
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	85.72
TIGR03338	212	phnR_burk phosphonate utilization associated trans	85.65
PF10668	60	Phage_terminase: Phage terminase small subunit; In	84.42
PRK09775	442	putative DNA-binding transcriptional regulator; Pr	84.35
COG3413	215	Predicted DNA binding protein [General function pr	84.32
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	84.25
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	83.68
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	83.43
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	83.32
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	83.32
PRK13239	206	alkylmercury lyase; Provisional	83.25
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	83.24
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	82.9
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	82.88
PF13518	52	HTH_28: Helix-turn-helix domain	82.23
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	82.16
PRK12423	202	LexA repressor; Provisional	82.13
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	82.03
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	81.82
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	81.61
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	81.45
PRK11642	813	exoribonuclease R; Provisional	81.12
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	80.78
PHA02591	83	hypothetical protein; Provisional	80.76
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	80.75
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	80.24

>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases

Probab=99.71  E-value=1.4e-17  Score=94.56  Aligned_cols=51  Identities=57%  Similarity=0.862  Sum_probs=45.8

Q ss_pred             HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477           24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA   76 (89)
Q Consensus        24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~   76 (89)
                      ++||+|+||||||+|+++| ++|+|++||+++++ ..||.++..|+|+||+|+
T Consensus         1 MaLk~aveLgI~dii~~~g-~~~ls~~eia~~l~-~~~p~~~~~L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAG-GGPLSLSEIAARLP-TSNPSAPPMLDRIMRLLV   51 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHT-TS-BEHHHHHHTST-CT-TTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcC-CCCCCHHHHHHHcC-CCCcchHHHHHHHHHHhC
Confidence            6899999999999999987 58999999999999 788889999999999996

It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....

>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]

Probab=99.36  E-value=2.6e-12  Score=96.50  Aligned_cols=77  Identities=45%  Similarity=0.730  Sum_probs=67.3

Q ss_pred             HhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477            5 ARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus         5 ~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++.+....++++++++..++++++|+||||||+|++++  +   .+|||..+...++|.+|.++.|+||.|++++++++.
T Consensus         2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~--~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~   76 (342)
T KOG3178|consen    2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAG--S---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCR   76 (342)
T ss_pred             chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCC--C---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceee
Confidence            56677889999999999999999999999999999975  2   888888877225788999999999999999999976


Q ss_pred             cc
Q 045477           85 VD   86 (89)
Q Consensus        85 ~~   86 (89)
                      ..
T Consensus        77 ~~   78 (342)
T KOG3178|consen   77 LV   78 (342)
T ss_pred             ee
Confidence            43

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=99.23  E-value=1.7e-11  Score=89.43  Aligned_cols=55  Identities=25%  Similarity=0.338  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ...+|++|++|||||+|++    +|.|++|||++++ +    ++..++|+||+|++.|+|++..
T Consensus         3 ~~~~l~aa~~Lglfd~L~~----gp~t~~eLA~~~~-~----~~~~~~~lL~~L~~lgll~~~~   57 (306)
T TIGR02716         3 EFSCMKAAIELDLFSHMAE----GPKDLATLAADTG-S----VPPRLEMLLETLRQMRVINLED   57 (306)
T ss_pred             hHHHHHHHHHcCcHHHHhc----CCCCHHHHHHHcC-C----ChHHHHHHHHHHHhCCCeEecC
Confidence            4679999999999999986    6999999999999 9    9999999999999999998753

Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.

>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=98.20  E-value=9.2e-07  Score=49.47  Aligned_cols=46  Identities=35%  Similarity=0.481  Sum_probs=40.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.|.+.+++++  +++|+.|||+.++ .    +...++|+|+.|+..|++.++
T Consensus         6 l~iL~~l~~~~--~~~t~~eia~~~g-l----~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    6 LRILEALAESG--GPLTLSEIARALG-L----PKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHHCHHCTB--SCEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHcCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCcCeecC
Confidence            46788898876  7899999999999 9    899999999999999999875

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.65  E-value=0.00012  Score=44.17  Aligned_cols=47  Identities=26%  Similarity=0.369  Sum_probs=41.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.|.+.|.+.+  +++|+.|||+.++ .    +...++|+++.|...|++....
T Consensus         8 ~~Il~~l~~~~--~~~t~~~ia~~l~-i----~~~tv~r~l~~L~~~g~l~~~~   54 (91)
T smart00346        8 LAVLRALAEEP--GGLTLAELAERLG-L----SKSTAHRLLNTLQELGYVEQDG   54 (91)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeeecC
Confidence            56788888754  6899999999999 9    8999999999999999998753

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

Probab=97.36  E-value=0.00039  Score=39.22  Aligned_cols=53  Identities=26%  Similarity=0.367  Sum_probs=41.5

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +..|.-.|...++ .++|..|||+.++ .    ++..+.|+++.|...|++....+.+|
T Consensus         7 q~~vL~~l~~~~~-~~~t~~~la~~l~-~----~~~~vs~~v~~L~~~Glv~r~~~~~D   59 (62)
T PF12802_consen    7 QFRVLMALARHPG-EELTQSELAERLG-I----SKSTVSRIVKRLEKKGLVERERDPGD   59 (62)
T ss_dssp             HHHHHHHHHHSTT-SGEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred             HHHHHHHHHHCCC-CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence            3455666776641 3399999999999 9    99999999999999999998866554

...

>PRK11569 transcriptional repressor IclR; Provisional

Probab=97.33  E-value=0.00039  Score=50.41  Aligned_cols=48  Identities=25%  Similarity=0.333  Sum_probs=42.0

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +.|.+.+++..  +|+|++|||+.+| .    +...++|+|+.|+..|++..+.+
T Consensus        31 l~IL~~l~~~~--~~~~lseia~~lg-l----pksTv~RlL~tL~~~G~l~~~~~   78 (274)
T PRK11569         31 LKLLEWIAESN--GSVALTELAQQAG-L----PNSTTHRLLTTMQQQGFVRQVGE   78 (274)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcCC
Confidence            56788888754  7899999999999 9    89999999999999999986543

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=97.27  E-value=0.0005  Score=49.82  Aligned_cols=48  Identities=21%  Similarity=0.299  Sum_probs=42.0

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +.|.+.+++.+  .++|++|||+.++ .    ....++|+|..|+..|++..+.+
T Consensus        28 l~IL~~~~~~~--~~~tl~eIa~~lg-l----pkStv~RlL~tL~~~G~l~~~~~   75 (271)
T PRK10163         28 IAILQYLEKSG--GSSSVSDISLNLD-L----PLSTTFRLLKVLQAADFVYQDSQ   75 (271)
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcCC
Confidence            56788888765  6899999999999 9    89999999999999999987543

>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=97.22  E-value=0.00081  Score=36.53  Aligned_cols=45  Identities=18%  Similarity=0.389  Sum_probs=38.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      .+..|+..|.+.   +++|..|||+.++ .    ....+.+.++-|...|+++
T Consensus         4 ~~~~Il~~l~~~---~~~t~~ela~~~~-i----s~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    4 TQRKILNYLREN---PRITQKELAEKLG-I----SRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHHC---TTS-HHHHHHHHT-S-----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCcCcC
Confidence            466788999985   4799999999999 9    8999999999999999874

...

>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=97.18  E-value=0.00047  Score=40.08  Aligned_cols=48  Identities=25%  Similarity=0.275  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|+..|.+.   +++|+.|||..++ .    +...+++.|+.|...|++....
T Consensus         9 ~E~~vy~~Ll~~---~~~t~~eIa~~l~-i----~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen    9 NEAKVYLALLKN---GPATAEEIAEELG-I----SRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHHHH---CHEEHHHHHHHHT-S----SHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEc
Confidence            355667677654   6999999999999 9    9999999999999999998765

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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=97.17  E-value=0.00076  Score=48.50  Aligned_cols=50  Identities=28%  Similarity=0.465  Sum_probs=43.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      -+.|.+.|++.+  .+++++|||+++| .    ++..++|+|..|+..|+++++.+.
T Consensus         6 al~iL~~l~~~~--~~l~l~ela~~~g-l----pksT~~RlL~tL~~~G~v~~d~~~   55 (246)
T COG1414           6 ALAILDLLAEGP--GGLSLAELAERLG-L----PKSTVHRLLQTLVELGYVEQDPED   55 (246)
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEEcCCC
Confidence            357889998854  5688999999999 9    899999999999999999988754

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=97.11  E-value=0.0011  Score=47.78  Aligned_cols=48  Identities=19%  Similarity=0.193  Sum_probs=41.8

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +.|.+.|.+++  +++|++||++.++ .    +...++|+|+.|+..|++....+
T Consensus        14 l~iL~~l~~~~--~~ls~~eia~~lg-l----~kstv~RlL~tL~~~g~v~~~~~   61 (263)
T PRK09834         14 LMVLRALNRLD--GGATVGLLAELTG-L----HRTTVRRLLETLQEEGYVRRSAS   61 (263)
T ss_pred             HHHHHHHHhcC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEecC
Confidence            46778887764  6799999999999 9    99999999999999999987654

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

Probab=97.09  E-value=0.00076  Score=37.83  Aligned_cols=51  Identities=24%  Similarity=0.401  Sum_probs=41.3

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +..+...|.+.   +++|..|||..++ .    ++..+.|+++-|...|++....+.+|
T Consensus         5 q~~iL~~l~~~---~~~~~~~la~~~~-~----~~~~~t~~i~~L~~~g~I~r~~~~~D   55 (59)
T PF01047_consen    5 QFRILRILYEN---GGITQSELAEKLG-I----SRSTVTRIIKRLEKKGLIERERDPDD   55 (59)
T ss_dssp             HHHHHHHHHHH---SSEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEeccCCCC
Confidence            34455566666   4799999999999 9    99999999999999999997765543

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 ....

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

Probab=97.08  E-value=0.00081  Score=47.85  Aligned_cols=46  Identities=20%  Similarity=0.284  Sum_probs=40.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.|.+.++++.  .|+|++|||+.+| .    ....++|+|..|+..|++..+
T Consensus        12 l~IL~~l~~~~--~~~~l~eia~~lg-l----pksT~~RlL~tL~~~G~l~~~   57 (248)
T TIGR02431        12 LAVIEAFGAER--PRLTLTDVAEATG-L----TRAAARRFLLTLVELGYVTSD   57 (248)
T ss_pred             HHHHHHHhcCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeC
Confidence            56788887654  7999999999999 9    889999999999999999864

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.

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

Probab=97.06  E-value=0.0021  Score=37.84  Aligned_cols=51  Identities=20%  Similarity=0.236  Sum_probs=43.6

Q ss_pred             HHHhChHHHHHhcCCCC-CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           29 VINLGLFEIIAKAGPGA-KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~-~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ..+-.|...|.+.|  + ++|+.|||..+| .    +...++|+|-.|...|++....+
T Consensus         6 ~~~~~IL~~L~~~g--~~~~ta~eLa~~lg-l----~~~~v~r~L~~L~~~G~V~~~~~   57 (68)
T smart00550        6 SLEEKILEFLENSG--DETSTALQLAKNLG-L----PKKEVNRVLYSLEKKGKVCKQGG   57 (68)
T ss_pred             HHHHHHHHHHHHCC--CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCC
Confidence            35567888998875  4 499999999999 9    99999999999999999986543

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

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=97.05  E-value=0.0017  Score=39.24  Aligned_cols=42  Identities=36%  Similarity=0.557  Sum_probs=34.4

Q ss_pred             HHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           38 IAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        38 l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+.++.++++|..|||+.++ +    ++..++++|+.|...|+++..
T Consensus        17 la~~~~~~~~s~~eiA~~~~-i----~~~~l~kil~~L~~~Gli~s~   58 (83)
T PF02082_consen   17 LARHPDGKPVSSKEIAERLG-I----SPSYLRKILQKLKKAGLIESS   58 (83)
T ss_dssp             HHCTTTSC-BEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHhCCCCCCCCHHHHHHHHC-c----CHHHHHHHHHHHhhCCeeEec
Confidence            45444346799999999999 9    999999999999999998755

(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.

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

Probab=97.03  E-value=0.0014  Score=37.37  Aligned_cols=53  Identities=19%  Similarity=0.349  Sum_probs=43.2

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |---..+.|.+.|...   +|+|+.|||+.++ .    .+..+++=|+.|...|+++...+
T Consensus         7 L~~p~R~~Il~~L~~~---~~~t~~ela~~l~-~----~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen    7 LSDPTRLRILRLLASN---GPMTVSELAEELG-I----SQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HTSHHHHHHHHHHHHC---STBEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             hCCHHHHHHHHHHhcC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEecc
Confidence            3334567888888543   7999999999999 9    89999999999999999986643

...

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=97.01  E-value=0.002  Score=40.61  Aligned_cols=53  Identities=26%  Similarity=0.335  Sum_probs=42.4

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCC-CCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKN-KDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~-~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|++.|.+.+  +++|++||.+.+. ... .-+...++|.|+.|+..|++.+...
T Consensus         3 R~~Il~~l~~~~--~~~sa~ei~~~l~-~~~~~i~~~TVYR~L~~L~~~Gli~~~~~   56 (116)
T cd07153           3 RLAILEVLLESD--GHLTAEEIYERLR-KKGPSISLATVYRTLELLEEAGLVREIEL   56 (116)
T ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHH-hcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence            356888898764  8999999999985 321 1277889999999999999998754

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=96.99  E-value=0.0012  Score=47.21  Aligned_cols=46  Identities=13%  Similarity=0.338  Sum_probs=39.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.|.+.+++.   +++|++|||+.++ .    +...++|+|+.|+..|++.+..
T Consensus        17 l~IL~~l~~~---~~l~l~eia~~lg-l----~kstv~Rll~tL~~~G~l~~~~   62 (257)
T PRK15090         17 FGILQALGEE---REIGITELSQRVM-M----SKSTVYRFLQTMKTLGYVAQEG   62 (257)
T ss_pred             HHHHHHhhcC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcC
Confidence            4567777653   5899999999999 9    8999999999999999998764

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=96.94  E-value=0.0017  Score=37.08  Aligned_cols=39  Identities=26%  Similarity=0.388  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      ++++..+|+..++ .    +...+.|+++.|...|++....+..
T Consensus        17 ~~~t~~~l~~~~~-~----~~~~vs~~i~~L~~~glv~~~~~~~   55 (68)
T PF13463_consen   17 GPMTQSDLAERLG-I----SKSTVSRIIKKLEEKGLVEKERDPH   55 (68)
T ss_dssp             S-BEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred             CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEecCCCC
Confidence            7999999999999 9    9999999999999999998776554

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.84  E-value=0.004  Score=37.35  Aligned_cols=49  Identities=24%  Similarity=0.401  Sum_probs=41.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|+..|...   +++|..+|++.++ .    ++..+.|.++.|...|++.....
T Consensus        11 ~~~~il~~l~~~---~~~~~~~la~~~~-~----s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347       11 TQFLVLRILYEE---GPLSVSELAKRLG-V----SPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHC-C----CchhHHHHHHHHHHCCCeEecCC
Confidence            356778888764   5799999999999 9    88899999999999999986543

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

Probab=96.74  E-value=0.0019  Score=35.20  Aligned_cols=43  Identities=26%  Similarity=0.448  Sum_probs=37.4

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      ++.|...|.+    +|.++.||++.++ .    ++..+.+-|+.|...|+++
T Consensus         4 R~~Il~~L~~----~~~~~~el~~~l~-~----s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    4 RLRILKLLSE----GPLTVSELAEELG-L----SQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             HHHHHHHHTT----SSEEHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHh----CCCchhhHHHhcc-c----cchHHHHHHHHHHHCcCee
Confidence            4567777776    7999999999999 9    9999999999999999986

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 ....

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=96.66  E-value=0.0049  Score=39.69  Aligned_cols=35  Identities=31%  Similarity=0.429  Sum_probs=32.9

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|+|.+|||+.++ +    .+..++++|+.|+..|++...
T Consensus        24 ~~~s~~eia~~~~-i----~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        24 GPVSVKEIAERQG-I----SRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEec
Confidence            5999999999999 9    899999999999999999764

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=96.64  E-value=0.0048  Score=39.95  Aligned_cols=44  Identities=30%  Similarity=0.352  Sum_probs=36.5

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ...|+.++ ++++|+.|||++++ +    .+..+.++|+.|...|++...
T Consensus        15 l~~la~~~-~~~~s~~eia~~l~-i----s~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        15 LTTLAQND-SQPYSAAEIAEQTG-L----NAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             HHHHHhCC-CCCccHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEec
Confidence            33444443 37899999999999 9    899999999999999999754

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=96.56  E-value=0.0046  Score=36.23  Aligned_cols=45  Identities=16%  Similarity=0.297  Sum_probs=37.4

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|-+.|.+.   +.+|..|||..++ +    ++..+.-+|..|...|.+++..
T Consensus         4 ~i~~~l~~~---~~~S~~eLa~~~~-~----s~~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen    4 EIRDYLRER---GRVSLAELAREFG-I----SPEAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             HHHHHHHHS----SEEHHHHHHHTT-------HHHHHHHHHHHHCCTSCEEEE
T ss_pred             HHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEec
Confidence            466778874   6899999999999 9    9999999999999999998764

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=96.53  E-value=0.0069  Score=39.69  Aligned_cols=35  Identities=14%  Similarity=0.330  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|++|||+.++ +    .+..+.++|+.|+..|++...
T Consensus        24 ~~~s~~~ia~~~~-i----p~~~l~kil~~L~~~glv~s~   58 (135)
T TIGR02010        24 GPVTLADISERQG-I----SLSYLEQLFAKLRKAGLVKSV   58 (135)
T ss_pred             CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEE
Confidence            6899999999999 9    899999999999999999754

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

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

Probab=96.50  E-value=0.0048  Score=36.12  Aligned_cols=45  Identities=29%  Similarity=0.240  Sum_probs=37.9

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.|....  +|+|..|||+.++ .    +....+++|..|...|.+..+
T Consensus         4 ~Il~~i~~~~--~p~~T~eiA~~~g-l----s~~~aR~yL~~Le~eG~V~~~   48 (62)
T PF04703_consen    4 KILEYIKEQN--GPLKTREIADALG-L----SIYQARYYLEKLEKEGKVERS   48 (62)
T ss_dssp             CHHHHHHHHT--S-EEHHHHHHHHT-S-----HHHHHHHHHHHHHCTSEEEE
T ss_pred             HHHHHHHHcC--CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence            5677787744  7999999999999 9    999999999999999998865

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=96.44  E-value=0.0068  Score=41.43  Aligned_cols=35  Identities=14%  Similarity=0.316  Sum_probs=33.1

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|+|++|||+.++ +    .+..|.+||+.|...|++...
T Consensus        24 ~~vs~~eIA~~~~-i----p~~~l~kIl~~L~~aGLv~s~   58 (164)
T PRK10857         24 GPVPLADISERQG-I----SLSYLEQLFSRLRKNGLVSSV   58 (164)
T ss_pred             CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeC
Confidence            6999999999999 9    899999999999999999864

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.37  E-value=0.011  Score=37.45  Aligned_cols=50  Identities=20%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      +..|...|...   +++|..|||..++ .    ++..+.|+++-|...|++.......
T Consensus        30 q~~iL~~l~~~---~~~t~~ela~~~~-~----~~~tvs~~l~~Le~~GlI~r~~~~~   79 (118)
T TIGR02337        30 QWRILRILAEQ---GSMEFTQLANQAC-I----LRPSLTGILARLERDGLVTRLKASN   79 (118)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHhC-C----CchhHHHHHHHHHHCCCEEeccCCC
Confidence            33466667654   5899999999999 9    8889999999999999999765443

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.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=96.28  E-value=0.012  Score=37.16  Aligned_cols=53  Identities=19%  Similarity=0.258  Sum_probs=41.8

Q ss_pred             HhChHHHHH--hcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           31 NLGLFEIIA--KAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        31 ~LgIfd~l~--~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +..|...|.  ... ++++|..|||..++ .    ++..+.|+++.|...|++....+..|
T Consensus        27 q~~vL~~l~~~~~~-~~~~t~~eL~~~l~-~----~~stvs~~i~~Le~kg~I~r~~~~~D   81 (109)
T TIGR01889        27 ELLILYYLGKLENN-EGKLTLKEIIKEIL-I----KQSALVKIIKKLSKKGYLSKERSEDD   81 (109)
T ss_pred             HHHHHHHHHhhhcc-CCcCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeccCCccc
Confidence            344555555  221 27899999999999 9    99999999999999999997766554

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=96.25  E-value=0.0094  Score=40.10  Aligned_cols=43  Identities=30%  Similarity=0.454  Sum_probs=36.6

Q ss_pred             HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|+.++.+++.|+++||+..+ +    ++..|.|+|..|...|+++-.
T Consensus        16 ~LA~~~~~~~~s~~~IA~~~~-i----s~~~L~kil~~L~kaGlV~S~   58 (150)
T COG1959          16 YLALLPGGGPVSSAEIAERQG-I----SPSYLEKILSKLRKAGLVKSV   58 (150)
T ss_pred             HHHhCCCCCcccHHHHHHHhC-c----CHHHHHHHHHHHHHcCCEEee
Confidence            456554335899999999999 9    999999999999999999854

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.22  E-value=0.016  Score=30.91  Aligned_cols=44  Identities=25%  Similarity=0.371  Sum_probs=37.5

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |.+.+.+.   +++|..+|++.++ .    .+..++|.|..|...|++....
T Consensus         5 il~~l~~~---~~~s~~~l~~~l~-~----s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        5 ILELLAQQ---GKVSVEELAELLG-V----SEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEee
Confidence            56666653   5799999999999 9    8999999999999999988653

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.18  E-value=0.012  Score=36.57  Aligned_cols=45  Identities=22%  Similarity=0.420  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      .|..|...|...   +++|..|||+.++ .    ++..+.|.++.|...|++.
T Consensus         4 ~D~~il~~L~~~---~~~~~~~la~~l~-~----s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        4 IDRKILEELQKD---ARISLAELAKKVG-L----SPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHHh---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCee
Confidence            577889999874   5899999999999 9    9999999999999999987

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

>PRK06474 hypothetical protein; Provisional

Probab=96.17  E-value=0.011  Score=40.71  Aligned_cols=56  Identities=14%  Similarity=0.259  Sum_probs=45.2

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|---..+.|++.|...+  +++|+.||++.++.+    ....++|-|+.|+..|++.....
T Consensus         7 ~La~p~R~~Il~~L~~~~--~~~ta~el~~~l~~i----s~aTvYrhL~~L~e~GLI~~~~~   62 (178)
T PRK06474          7 ILMHPVRMKICQVLMRNK--EGLTPLELVKILKDV----PQATLYRHLQTMVDSGILHVVKE   62 (178)
T ss_pred             hhCCHHHHHHHHHHHhCC--CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCEEEeec
Confidence            344456788999998764  569999999999426    67789999999999999997653

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.15  E-value=0.0096  Score=31.53  Aligned_cols=36  Identities=25%  Similarity=0.258  Sum_probs=32.3

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -|+|..|||+.++ .    .+..+.|.|+.|...|++....
T Consensus         7 ~~~s~~~la~~l~-~----s~~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419        7 LPLTRQEIAELLG-L----TRETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             eccCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence            3689999999999 9    8899999999999999997543

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.14  E-value=0.092  Score=34.19  Aligned_cols=48  Identities=19%  Similarity=0.194  Sum_probs=39.2

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ...|...+  ++.|.+|||..++ .    ++..+.|++.-|...|++....+..|
T Consensus        37 L~~l~~~~--~~~t~~eLa~~l~-~----~~~tvt~~v~~Le~~GlV~r~~~~~D   84 (144)
T PRK03573         37 LHNIHQLP--PEQSQIQLAKAIG-I----EQPSLVRTLDQLEEKGLISRQTCASD   84 (144)
T ss_pred             HHHHHHcC--CCCCHHHHHHHhC-C----ChhhHHHHHHHHHHCCCEeeecCCCC
Confidence            34454443  5689999999999 9    99999999999999999998766544

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=95.98  E-value=0.022  Score=37.31  Aligned_cols=48  Identities=27%  Similarity=0.239  Sum_probs=39.7

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      |.-.|...   +++|..|||..++ .    ++..+.|++.-|...|++....+.+|
T Consensus        45 vL~~l~~~---~~~t~~eLa~~l~-i----~~~tvsr~l~~Le~~GlI~R~~~~~D   92 (144)
T PRK11512         45 VLCSIRCA---ACITPVELKKVLS-V----DLGALTRMLDRLVCKGWVERLPNPND   92 (144)
T ss_pred             HHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeccCccc
Confidence            34445543   6899999999999 9    99999999999999999997765544

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.89  E-value=0.02  Score=37.92  Aligned_cols=49  Identities=20%  Similarity=0.333  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|..++-+|-+.  ++|+|++|||+.++ .    +...++|-++-|...|++...+
T Consensus        28 ~Dv~v~~~LL~~--~~~~tvdelae~ln-r----~rStv~rsl~~L~~~GlV~Rek   76 (126)
T COG3355          28 LDVEVYKALLEE--NGPLTVDELAEILN-R----SRSTVYRSLQNLLEAGLVEREK   76 (126)
T ss_pred             HHHHHHHHHHhh--cCCcCHHHHHHHHC-c----cHHHHHHHHHHHHHcCCeeeee
Confidence            355666666642  27999999999999 9    9999999999999999998654

>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=95.88  E-value=0.016  Score=32.77  Aligned_cols=36  Identities=25%  Similarity=0.246  Sum_probs=33.4

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .++|..|||+.++ .    ++..+.|+|+.|...|++....
T Consensus        24 ~~~s~~ela~~~g-~----s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          24 LPLTRQEIADYLG-L----TRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecC
Confidence            6899999999999 9    8999999999999999998654

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=95.83  E-value=0.017  Score=38.86  Aligned_cols=57  Identities=25%  Similarity=0.241  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |-..+.+-.=-.+.+...|++.   +|.|..|+|+.+| -    |+..+.|=||.|..+|++.-.
T Consensus        55 ye~la~vLsp~nleLl~~Ia~~---~P~Si~ElAe~vg-R----dv~nvhr~Ls~l~~~GlI~fe  111 (144)
T COG4190          55 YEDLARVLSPRNLELLELIAQE---EPASINELAELVG-R----DVKNVHRTLSTLADLGLIFFE  111 (144)
T ss_pred             HHHHHHHhChhHHHHHHHHHhc---CcccHHHHHHHhC-c----chHHHHHHHHHHHhcCeEEEe
Confidence            4444445555567888999875   6999999999999 8    999999999999999998744

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.81  E-value=0.027  Score=30.73  Aligned_cols=42  Identities=24%  Similarity=0.390  Sum_probs=35.7

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+..|. .   ++.|..+|++.++ .    .+..+.+.++.|...|++...
T Consensus         2 il~~l~-~---~~~~~~~i~~~l~-i----s~~~v~~~l~~L~~~g~i~~~   43 (66)
T smart00418        2 ILKLLA-E---GELCVCELAEILG-L----SQSTVSHHLKKLREAGLVESR   43 (66)
T ss_pred             HHHHhh-c---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeee
Confidence            455565 2   6899999999999 9    888999999999999999854

>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=95.74  E-value=0.025  Score=32.04  Aligned_cols=44  Identities=20%  Similarity=0.400  Sum_probs=38.7

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.|.+.   +.+|++|||+.++ +    .+..++|=+..|...|++..+
T Consensus         4 ~Il~~l~~~---~~~s~~ela~~~~-V----S~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    4 QILELLKEK---GKVSVKELAEEFG-V----SEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHc---CCEEHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            467778764   6999999999999 9    999999999999999998765

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

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

Probab=95.64  E-value=0.039  Score=30.82  Aligned_cols=46  Identities=26%  Similarity=0.413  Sum_probs=37.7

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ...|...+..    ++.+..||++.++ +    +...+.|.++.|...|++....
T Consensus         9 ~~~il~~l~~----~~~~~~ei~~~~~-i----~~~~i~~~l~~L~~~g~i~~~~   54 (78)
T cd00090           9 RLRILRLLLE----GPLTVSELAERLG-L----SQSTVSRHLKKLEEAGLVESRR   54 (78)
T ss_pred             HHHHHHHHHH----CCcCHHHHHHHHC-c----CHhHHHHHHHHHHHCCCeEEEE
Confidence            3445666665    3499999999999 9    8889999999999999998653

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.

>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=95.58  E-value=0.028  Score=30.98  Aligned_cols=40  Identities=18%  Similarity=0.382  Sum_probs=34.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      .|...|.+++  +++|++|||+.++ +    ....++|-+..|...|
T Consensus         4 ~il~~L~~~~--~~it~~eLa~~l~-v----S~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESK--EPITAKELAEELG-V----SRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTT--TSBEHHHHHHHCT-S-----HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcC--CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCC
Confidence            4667786654  6899999999999 9    9999999999999988

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 ....

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=95.56  E-value=0.029  Score=32.50  Aligned_cols=44  Identities=18%  Similarity=0.341  Sum_probs=38.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ++.|...+.+    ++.|..|||+.++ +    ....+.|-++.|...|+.-+
T Consensus         2 ~~~il~~L~~----~~~~~~eLa~~l~-v----S~~tv~~~l~~L~~~g~~i~   45 (69)
T TIGR00122         2 PLRLLALLAD----NPFSGEKLGEALG-M----SRTAVNKHIQTLREWGVDVL   45 (69)
T ss_pred             hHHHHHHHHc----CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEE
Confidence            5678888875    5789999999999 9    88999999999999998543

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.

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

Probab=95.54  E-value=0.014  Score=29.93  Aligned_cols=31  Identities=26%  Similarity=0.398  Sum_probs=25.8

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      |+|-+|||..+| .    -+..+.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG-~----t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLG-L----TRETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHT-S-----HHHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhC-C----cHHHHHHHHHHHHHcCCC
Confidence            688999999999 9    899999999999988874

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 ....

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=95.47  E-value=0.041  Score=35.81  Aligned_cols=55  Identities=18%  Similarity=0.344  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ...+|.--..+.|+..|.+.   +++++.||++.++ .    .+..+.+=|+.|...|+++..
T Consensus         9 ~fkaLadptRl~IL~~L~~~---~~~~v~ela~~l~-l----sqstvS~HL~~L~~AGLV~~~   63 (117)
T PRK10141          9 LFKILSDETRLGIVLLLRES---GELCVCDLCTALD-Q----SQPKISRHLALLRESGLLLDR   63 (117)
T ss_pred             HHHHhCCHHHHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEE
Confidence            34455556788899999763   5899999999999 9    888999999999999999754

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=95.45  E-value=0.02  Score=36.42  Aligned_cols=57  Identities=23%  Similarity=0.292  Sum_probs=44.1

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeeccc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..+.-|++.|.+.+  +++|+.||-..+. .. +.-+...++|.|..|+..|++......
T Consensus         7 T~~R~~Il~~l~~~~--~~~ta~ei~~~l~-~~~~~is~~TVYR~L~~L~e~Gli~~~~~~   64 (120)
T PF01475_consen    7 TPQRLAILELLKESP--EHLTAEEIYDKLR-KKGPRISLATVYRTLDLLEEAGLIRKIEFG   64 (120)
T ss_dssp             HHHHHHHHHHHHHHS--SSEEHHHHHHHHH-HTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHcCC--CCCCHHHHHHHhh-hccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence            345667899999876  7999999999886 32 222667799999999999999987543

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=95.45  E-value=0.036  Score=37.86  Aligned_cols=55  Identities=18%  Similarity=0.248  Sum_probs=44.4

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeec
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +-...-|++.|.+.+  +++|++||.+.+. .. +.-+...++|.|+.|+..|++.+..
T Consensus        25 T~qR~~IL~~l~~~~--~hlSa~eI~~~L~-~~~~~is~aTVYRtL~~L~e~Glv~~~~   80 (169)
T PRK11639         25 TPQRLEVLRLMSLQP--GAISAYDLLDLLR-EAEPQAKPPTVYRALDFLLEQGFVHKVE   80 (169)
T ss_pred             CHHHHHHHHHHHhcC--CCCCHHHHHHHHH-hhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence            456677899998764  7999999999987 43 2226778999999999999999764

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=95.35  E-value=0.037  Score=36.97  Aligned_cols=56  Identities=25%  Similarity=0.271  Sum_probs=45.0

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeecccC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      -.+.|.++|.+++  ++.|+.||=..+. .. ++-.+..++|.|..|+..|++.+....+
T Consensus        22 qR~~vl~~L~~~~--~~~sAeei~~~l~-~~~p~islaTVYr~L~~l~e~Glv~~~~~~~   78 (145)
T COG0735          22 QRLAVLELLLEAD--GHLSAEELYEELR-EEGPGISLATVYRTLKLLEEAGLVHRLEFEG   78 (145)
T ss_pred             HHHHHHHHHHhcC--CCCCHHHHHHHHH-HhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence            4667899999876  7899999998877 42 3336778999999999999999876543

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=95.28  E-value=0.057  Score=35.84  Aligned_cols=52  Identities=12%  Similarity=0.215  Sum_probs=44.5

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..+...|.+.+.++   |.+|..|+...+| +    .-..+.+.+|-|++.|-+-..+.
T Consensus        10 r~eLk~rIvElVRe~---GRiTi~ql~~~TG-a----sR~Tvk~~lreLVa~G~l~~~G~   61 (127)
T PF06163_consen   10 REELKARIVELVREH---GRITIKQLVAKTG-A----SRNTVKRYLRELVARGDLYRHGR   61 (127)
T ss_pred             HHHHHHHHHHHHHHc---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHcCCeEeCCC
Confidence            456778889999886   6999999999999 9    89999999999999887765543

>PRK09462 fur ferric uptake regulator; Provisional

Probab=95.20  E-value=0.048  Score=36.15  Aligned_cols=56  Identities=18%  Similarity=0.268  Sum_probs=43.3

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCC-CCcchHHHHHHHHhccCceeeec
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK-DAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~-~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +-...-|++.|.+.. ++++|+.||-+.+. -..| -+...++|.|..|+..|++.+..
T Consensus        16 T~qR~~Il~~l~~~~-~~h~sa~eI~~~l~-~~~~~i~~aTVYR~L~~L~e~Gli~~~~   72 (148)
T PRK09462         16 TLPRLKILEVLQEPD-NHHVSAEDLYKRLI-DMGEEIGLATVYRVLNQFDDAGIVTRHN   72 (148)
T ss_pred             CHHHHHHHHHHHhCC-CCCCCHHHHHHHHH-hhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            345667888898642 26999999999886 4322 26788999999999999998764

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=95.18  E-value=0.048  Score=29.75  Aligned_cols=36  Identities=36%  Similarity=0.402  Sum_probs=32.2

Q ss_pred             CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..+ |..|||+.++ +    ....+.|.++.|...|++....
T Consensus        18 ~~l~s~~~la~~~~-v----s~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       18 DKLPSERELAAQLG-V----SRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CcCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence            456 9999999999 9    8999999999999999987553

>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=95.18  E-value=0.047  Score=31.97  Aligned_cols=43  Identities=26%  Similarity=0.295  Sum_probs=32.9

Q ss_pred             HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+.+.|  -|-|+.|||+.+| .+   .+..+.+.|+.|...|+++...
T Consensus        18 ~~~~~G--~~Pt~rEIa~~~g-~~---S~~tv~~~L~~Le~kG~I~r~~   60 (65)
T PF01726_consen   18 YIEENG--YPPTVREIAEALG-LK---STSTVQRHLKALERKGYIRRDP   60 (65)
T ss_dssp             HHHHHS--S---HHHHHHHHT-SS---SHHHHHHHHHHHHHTTSEEEGC
T ss_pred             HHHHcC--CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCcCccCCC
Confidence            344555  6789999999999 82   3789999999999999998664

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.

>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=95.18  E-value=0.05  Score=31.28  Aligned_cols=37  Identities=27%  Similarity=0.405  Sum_probs=33.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++..+||+.++ +    .+..+..+++-|...|++.....
T Consensus        21 ~~v~~~~iA~~L~-v----s~~tvt~ml~~L~~~GlV~~~~y   57 (60)
T PF01325_consen   21 GPVRTKDIAERLG-V----SPPTVTEMLKRLAEKGLVEYEPY   57 (60)
T ss_dssp             SSBBHHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCccHHHHHHHHC-C----ChHHHHHHHHHHHHCCCEEecCC
Confidence            8999999999999 9    89999999999999999986643

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 ....

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=95.16  E-value=0.098  Score=36.24  Aligned_cols=46  Identities=17%  Similarity=0.218  Sum_probs=40.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..|+++|-.+   |++|.+|||..+| .    ....++|+|..|...|++....
T Consensus        25 ~~Vl~~L~~~---g~~tdeeLA~~Lg-i----~~~~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         25 FEVLKALIKK---GEVTDEEIAEQTG-I----KLNTVRKILYKLYDARLADYKR   70 (178)
T ss_pred             hHHHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEee
Confidence            4588888875   5899999999999 9    9999999999999999998543

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=95.15  E-value=0.046  Score=38.00  Aligned_cols=45  Identities=22%  Similarity=0.373  Sum_probs=39.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|...|...   +++|..|||+.++ +    ++..++|.|+.|...|++...
T Consensus         4 ~~IL~~L~~~---~~~t~~eLA~~lg-i----s~~tV~~~L~~Le~~GlV~r~   48 (203)
T TIGR02702         4 EDILSYLLKQ---GQATAAALAEALA-I----SPQAVRRHLKDLETEGLIEYE   48 (203)
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEe
Confidence            4577777764   5799999999999 9    999999999999999999865

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.

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=95.13  E-value=0.046  Score=32.06  Aligned_cols=47  Identities=17%  Similarity=0.319  Sum_probs=37.5

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCC--cchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDA--PTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d--~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |.++|.+++  +|++..+|++.+. .. +.+  +..++|.||.|-..|+....
T Consensus         3 IL~~L~~~~--~P~g~~~l~~~L~-~~-g~~~se~avRrrLr~me~~Glt~~~   51 (66)
T PF08461_consen    3 ILRILAESD--KPLGRKQLAEELK-LR-GEELSEEAVRRRLRAMERDGLTRKV   51 (66)
T ss_pred             HHHHHHHcC--CCCCHHHHHHHHH-hc-ChhhhHHHHHHHHHHHHHCCCcccc
Confidence            678888876  8999999999987 42 224  47899999999999966543

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=95.10  E-value=0.046  Score=35.96  Aligned_cols=37  Identities=22%  Similarity=0.255  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.+.|..|||+..+ +    ++..++++|+.|...|++.-..
T Consensus        23 g~~~s~~~ia~~~~-i----s~~~vrk~l~~L~~~Glv~s~~   59 (141)
T PRK11014         23 GRMTSISEVTEVYG-V----SRNHMVKIINQLSRAGYVTAVR   59 (141)
T ss_pred             CCccCHHHHHHHHC-c----CHHHHHHHHHHHHhCCEEEEec
Confidence            36889999999999 9    9999999999999999998654

>PRK10870 transcriptional repressor MprA; Provisional

Probab=94.88  E-value=0.072  Score=36.45  Aligned_cols=40  Identities=28%  Similarity=0.317  Sum_probs=36.1

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +++|..|||..++ .    ++..+.|++.-|...|++....+.+|
T Consensus        70 ~~it~~eLa~~l~-l----~~~tvsr~v~rLe~kGlV~R~~~~~D  109 (176)
T PRK10870         70 HSIQPSELSCALG-S----SRTNATRIADELEKRGWIERRESDND  109 (176)
T ss_pred             CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCCCCC
Confidence            6899999999999 9    99999999999999999998766544

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=94.84  E-value=0.057  Score=36.66  Aligned_cols=46  Identities=13%  Similarity=0.104  Sum_probs=39.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..|+++|-.+   +.+|-+|||..+| .    ...-++|++..|...|++....
T Consensus        17 v~Vl~aL~~~---~~~tdEeLa~~Lg-i----~~~~VRk~L~~L~e~~Lv~~~r   62 (158)
T TIGR00373        17 GLVLFSLGIK---GEFTDEEISLELG-I----KLNEVRKALYALYDAGLADYKR   62 (158)
T ss_pred             HHHHHHHhcc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCceeee
Confidence            4578888764   5899999999999 9    9999999999999999996443

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

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

Probab=94.77  E-value=0.058  Score=32.61  Aligned_cols=49  Identities=20%  Similarity=0.302  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++|...|...   +.++..+|.+.++ +    +...|.+-|+.|...|+++..++
T Consensus         1 vRl~Il~~L~~~---~~~~f~~L~~~l~-l----t~g~Ls~hL~~Le~~GyV~~~k~   49 (80)
T PF13601_consen    1 VRLAILALLYAN---EEATFSELKEELG-L----TDGNLSKHLKKLEEAGYVEVEKE   49 (80)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHHTT-------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CHHHHHHHHhhc---CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEEEEe
Confidence            467888888875   5899999999999 9    99999999999999999986644

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=94.74  E-value=0.061  Score=36.18  Aligned_cols=35  Identities=29%  Similarity=0.261  Sum_probs=32.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|+.|||+..+ +    ++..|.++|+.|+..|++.-.
T Consensus        23 ~~~s~~eIA~~~~-i----s~~~L~kIl~~L~~aGlv~S~   57 (153)
T PRK11920         23 KLSRIPEIARAYG-V----SELFLFKILQPLVEAGLVETV   57 (153)
T ss_pred             CcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEee
Confidence            6899999999999 9    999999999999999998854

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=94.62  E-value=0.06  Score=33.70  Aligned_cols=46  Identities=20%  Similarity=0.345  Sum_probs=34.9

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .|+++|..+   +.++-++||..++ .    ++.-++++|..|-..|++.....
T Consensus        17 ~Il~~L~~~---~~l~de~la~~~~-l----~~~~vRkiL~~L~~~~lv~~~~~   62 (105)
T PF02002_consen   17 RILDALLRK---GELTDEDLAKKLG-L----KPKEVRKILYKLYEDGLVSYRRR   62 (105)
T ss_dssp             HHHHHHHHH-----B-HHHHHHTT--S-----HHHHHHHHHHHHHHSS-EEEEE
T ss_pred             HHHHHHHHc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeEEEEE
Confidence            468888865   5799999999999 9    99999999999999999975543

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

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

Probab=94.59  E-value=0.11  Score=32.23  Aligned_cols=36  Identities=19%  Similarity=0.111  Sum_probs=33.4

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .++|.+|||+.++ +    ++..+.|++..|...|++....
T Consensus        46 ~~is~~eLa~~~g-~----sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        46 DRVTATVIAELTG-L----SRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             CccCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeeeec
Confidence            6899999999999 9    8999999999999999998654

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

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=94.51  E-value=0.045  Score=38.14  Aligned_cols=40  Identities=23%  Similarity=0.245  Sum_probs=35.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +|+|++||++.+| .    ....+.--||.|...|++..+...||
T Consensus        40 ~Pmtl~Ei~E~lg-~----Sks~vS~~lkkL~~~~lV~~~~~~G~   79 (177)
T COG1510          40 KPLTLDEIAEALG-M----SKSNVSMGLKKLQDWNLVKKVFEKGD   79 (177)
T ss_pred             CCccHHHHHHHHC-C----CcchHHHHHHHHHhcchHHhhhccCc
Confidence            8999999999999 9    78889999999999999988766543

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=94.49  E-value=0.068  Score=39.16  Aligned_cols=49  Identities=22%  Similarity=0.424  Sum_probs=43.8

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |..|.++|.++|  |-++-+||.+++| .    ....+.|++|-|..+|+++.-+.
T Consensus       197 e~~il~~i~~~G--Gri~Q~eL~r~lg-l----sktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         197 EKEILDLIRERG--GRITQAELRRALG-L----SKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             HHHHHHHHHHhC--CEEeHHHHHHhhC-C----ChHHHHHHHHHHHhCCceEEEEe
Confidence            567888999887  8899999999999 9    88899999999999999987643

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

Probab=94.32  E-value=0.046  Score=31.01  Aligned_cols=41  Identities=22%  Similarity=0.396  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      +-.+|++|.++|-||.=      ...|++|||+.+| +    .+..+..-||
T Consensus         5 Q~e~L~~A~~~GYfd~P------R~~tl~elA~~lg-i----s~st~~~~LR   45 (53)
T PF04967_consen    5 QREILKAAYELGYFDVP------RRITLEELAEELG-I----SKSTVSEHLR   45 (53)
T ss_pred             HHHHHHHHHHcCCCCCC------CcCCHHHHHHHhC-C----CHHHHHHHHH
Confidence            45689999999999742      5689999999999 9    6666555555

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

>PHA00738 putative HTH transcription regulator

Probab=94.16  E-value=0.15  Score=33.03  Aligned_cols=48  Identities=31%  Similarity=0.295  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..+.|++.|.+.   +++++.||++.++ .    ....+.+=|+.|...|++....
T Consensus        13 tRr~IL~lL~~~---e~~~V~eLae~l~-l----SQptVS~HLKvLreAGLV~srK   60 (108)
T PHA00738         13 LRRKILELIAEN---YILSASLISHTLL-L----SYTTVLRHLKILNEQGYIELYK   60 (108)
T ss_pred             HHHHHHHHHHHc---CCccHHHHHHhhC-C----CHHHHHHHHHHHHHCCceEEEE
Confidence            467888889863   4799999999999 9    7889999999999999998653

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=94.12  E-value=0.088  Score=35.50  Aligned_cols=47  Identities=17%  Similarity=0.269  Sum_probs=41.5

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .+|..|..+|.+.   +.+|..|||+++| .    .+..+.|=++-|...|+++.
T Consensus        14 ~~D~~IL~~Lq~d---~R~s~~eiA~~lg-l----S~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         14 RIDRNILNELQKD---GRISNVELSKRVG-L----SPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHHHHHhccC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEE
Confidence            3788999999874   6899999999999 9    88899999999999999873

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=94.04  E-value=0.11  Score=32.18  Aligned_cols=51  Identities=18%  Similarity=0.272  Sum_probs=40.3

Q ss_pred             HHHhChHHHHHh-cCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           29 VINLGLFEIIAK-AGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        29 av~LgIfd~l~~-~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -+.-.|++.|.. .....++++.+|+++++ .    +..-++..++.|+..|.+=.+
T Consensus        47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~-~----~~~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLG-M----SENEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             HHHHHHHHHHHC----TTTEEHHHHHHHST-S-----HHHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHHHHHhcCCCCCcccHHHHHHHhC-c----CHHHHHHHHHHHHhCCeEecc
Confidence            345678888887 22347899999999998 9    899999999999999987644

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.95  E-value=0.14  Score=34.14  Aligned_cols=46  Identities=20%  Similarity=0.373  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .|..|.+.|.+.   +..|.+|||+++| .    .+..+.|=++-|...|+++.
T Consensus        10 ~D~~Il~~Lq~d---~R~s~~eiA~~lg-l----S~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179         10 LDRGILEALMEN---ARTPYAELAKQFG-V----SPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeee
Confidence            688899999874   6899999999999 9    88899999999999999873

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=93.91  E-value=0.14  Score=33.36  Aligned_cols=48  Identities=19%  Similarity=0.366  Sum_probs=41.7

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+|..|..+|.+.   ++.|..|||+.+| .    .+..+.+-++-|...|++...
T Consensus         8 ~~D~~IL~~L~~d---~r~~~~eia~~lg-l----S~~~v~~Ri~~L~~~GiI~~~   55 (154)
T COG1522           8 DIDRRILRLLQED---ARISNAELAERVG-L----SPSTVLRRIKRLEEEGVIKGY   55 (154)
T ss_pred             HHHHHHHHHHHHh---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCceeeE
Confidence            3677889999875   5799999999999 9    888999999999999988754

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.88  E-value=0.14  Score=35.50  Aligned_cols=47  Identities=26%  Similarity=0.340  Sum_probs=40.5

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +..|...|.++   +++|..|||+.++ .    ++..+.|.++.|...|++....
T Consensus       145 ~~~IL~~l~~~---g~~s~~eia~~l~-i----s~stv~r~L~~Le~~GlI~r~~  191 (203)
T TIGR01884       145 ELKVLEVLKAE---GEKSVKNIAKKLG-K----SLSTISRHLRELEKKGLVEQKG  191 (203)
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEc
Confidence            45667777764   5799999999999 9    8889999999999999998765

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.

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=93.85  E-value=0.13  Score=30.51  Aligned_cols=50  Identities=22%  Similarity=0.248  Sum_probs=43.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++..+.+.|+.++. .+++..||+..++ .    |+..+...++.|...|++....
T Consensus         3 ~~~~~Le~I~rsR~-~Gi~q~~L~~~~~-~----D~r~i~~~~k~L~~~gLI~k~~   52 (75)
T PF04182_consen    3 IQYCLLERIARSRY-NGITQSDLSKLLG-I----DPRSIFYRLKKLEKKGLIVKQS   52 (75)
T ss_pred             hHHHHHHHHHhcCC-CCEehhHHHHHhC-C----CchHHHHHHHHHHHCCCEEEEE
Confidence            45567888988764 7899999999999 9    9999999999999999987543

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=93.78  E-value=0.31  Score=33.98  Aligned_cols=48  Identities=21%  Similarity=0.039  Sum_probs=39.1

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      |.-.|...   +++|.+|||..+. .    ++..+.|++.-|...|++....+.+|
T Consensus        50 iL~~L~~~---~~itq~eLa~~l~-l----~~sTvtr~l~rLE~kGlI~R~~~~~D   97 (185)
T PRK13777         50 ILWIAYHL---KGASISEIAKFGV-M----HVSTAFNFSKKLEERGYLTFSKKEDD   97 (185)
T ss_pred             HHHHHHhC---CCcCHHHHHHHHC-C----CHhhHHHHHHHHHHCCCEEecCCCCC
Confidence            34445543   5899999999999 9    88899999999999999997765554

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=93.61  E-value=0.19  Score=30.69  Aligned_cols=52  Identities=23%  Similarity=0.332  Sum_probs=40.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .+..+...|...+   +.+..+||+.++ .    ++..+.|+++-|...|++....+.+|
T Consensus        23 ~q~~~L~~l~~~~---~~~~~~la~~l~-i----~~~~vt~~l~~Le~~glv~r~~~~~D   74 (126)
T COG1846          23 PQYQVLLALYEAG---GITVKELAERLG-L----DRSTVTRLLKRLEDKGLIERLRDPED   74 (126)
T ss_pred             HHHHHHHHHHHhC---CCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeecCCccc
Confidence            3444555666643   444499999999 9    99999999999999999997766544

>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=93.11  E-value=0.12  Score=27.76  Aligned_cols=23  Identities=30%  Similarity=0.369  Sum_probs=17.8

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      ++|..+||..++ +    ....++|+++
T Consensus        21 G~si~~IA~~~g-v----sr~TvyR~l~   43 (45)
T PF02796_consen   21 GMSIAEIAKQFG-V----SRSTVYRYLN   43 (45)
T ss_dssp             T--HHHHHHHTT-S-----HHHHHHHHC
T ss_pred             CCCHHHHHHHHC-c----CHHHHHHHHh
Confidence            399999999999 9    8888998875

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 ....

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=93.09  E-value=0.27  Score=32.23  Aligned_cols=35  Identities=17%  Similarity=0.226  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++.++++||..++ +    ++..+.+.++.|...|++...
T Consensus        21 ~~~~~~ela~~l~-v----s~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         21 GYARVSDIAEALS-V----HPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             CCcCHHHHHHHhC-C----ChhHHHHHHHHHHHCCCEEEe
Confidence            7889999999999 9    888999999999999999743

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=93.05  E-value=0.33  Score=29.69  Aligned_cols=45  Identities=22%  Similarity=0.324  Sum_probs=39.6

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|=|.|+.+   |-+++.+||.+.+ .    ++..++=+|-.|+.+|-+++..
T Consensus         6 qlRd~l~~~---gr~s~~~Ls~~~~-~----p~~~VeaMLe~l~~kGkverv~   50 (78)
T PRK15431          6 QVRDLLALR---GRMEAAQISQTLN-T----PQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_pred             HHHHHHHHc---CcccHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEeec
Confidence            355788876   5899999999999 9    8999999999999999998775

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

Probab=93.02  E-value=0.14  Score=29.15  Aligned_cols=38  Identities=26%  Similarity=0.371  Sum_probs=32.1

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |..+ |..+||+..+ +    ....+++.|+.|+..|++.....
T Consensus        21 g~~lps~~~la~~~~-v----sr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen   21 GDRLPSERELAERYG-V----SRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             TSBE--HHHHHHHHT-S-----HHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCEeCCHHHHHHHhc-c----CCcHHHHHHHHHHHCCcEEEECC
Confidence            4678 9999999999 9    99999999999999999986543

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>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=93.00  E-value=0.15  Score=29.51  Aligned_cols=35  Identities=34%  Similarity=0.428  Sum_probs=32.1

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -++|-++||..+| +    ....+.|+|+.|...|++.-.
T Consensus        27 ~~lt~~~iA~~~g-~----sr~tv~r~l~~l~~~g~I~~~   61 (76)
T PF13545_consen   27 LPLTQEEIADMLG-V----SRETVSRILKRLKDEGIIEVK   61 (76)
T ss_dssp             EESSHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             ecCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEc
Confidence            4689999999999 9    899999999999999999844

...

>PRK11050 manganese transport regulator MntR; Provisional

Probab=92.96  E-value=0.3  Score=32.66  Aligned_cols=44  Identities=27%  Similarity=0.357  Sum_probs=37.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -|..++.. +  ++.+..|||+.++ +    ++..+.|.++.|...|++...
T Consensus        41 ~I~~~l~~-~--~~~t~~eLA~~l~-i----s~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         41 LIADLIAE-V--GEARQVDIAARLG-V----SQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             HHHHHHHh-c--CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence            35556654 2  6899999999999 9    999999999999999999754

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=92.96  E-value=0.22  Score=35.86  Aligned_cols=45  Identities=18%  Similarity=0.256  Sum_probs=39.1

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|.+.|.+.   +.+++.|||+.++ +    .+..++|-|+.|...|++..+
T Consensus         8 ~~Il~~l~~~---~~~~~~ela~~l~-v----S~~TirRdL~~Le~~g~i~r~   52 (251)
T PRK13509          8 QILLELLAQL---GFVTVEKVIERLG-I----SPATARRDINKLDESGKLKKV   52 (251)
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEe
Confidence            3477888874   6899999999999 9    899999999999999998753

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=92.81  E-value=0.2  Score=36.04  Aligned_cols=43  Identities=33%  Similarity=0.524  Sum_probs=36.4

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |.-.|.+.   +|+|+.|||+++| +    .+..++|-|-.|...|++.-.
T Consensus        16 il~lL~~~---g~~sa~elA~~Lg-i----s~~avR~HL~~Le~~Glv~~~   58 (218)
T COG2345          16 ILELLKKS---GPVSADELAEELG-I----SPMAVRRHLDDLEAEGLVEVE   58 (218)
T ss_pred             HHHHHhcc---CCccHHHHHHHhC-C----CHHHHHHHHHHHHhCcceeee
Confidence            44455554   6999999999999 9    999999999999999988743

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

Probab=92.80  E-value=0.27  Score=27.19  Aligned_cols=33  Identities=30%  Similarity=0.329  Sum_probs=29.9

Q ss_pred             CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|..+||..++ +    +...+.+.+..|...|++...
T Consensus        26 ~~~~~la~~~~-i----s~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377          26 PSERELAEELG-V----SRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             CCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            45999999999 9    899999999999999998754

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

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=92.73  E-value=0.31  Score=35.34  Aligned_cols=44  Identities=18%  Similarity=0.203  Sum_probs=36.9

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++.-.|-..   |++|+.||++.+| +    ....++.+||.|...|++...
T Consensus        20 ~vY~aLl~~---g~~tA~eis~~sg-v----P~~kvY~vl~sLe~kG~v~~~   63 (247)
T COG1378          20 KVYLALLCL---GEATAKEISEASG-V----PRPKVYDVLRSLEKKGLVEVI   63 (247)
T ss_pred             HHHHHHHHh---CCccHHHHHHHcC-C----CchhHHHHHHHHHHCCCEEee
Confidence            344455554   6999999999999 9    778999999999999999865

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=92.71  E-value=0.2  Score=36.15  Aligned_cols=46  Identities=28%  Similarity=0.356  Sum_probs=38.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -.|.+.+...  +.+.|++|+|+.+| +    .....+|-|-+|++.|++...
T Consensus       161 ~~i~~~~~~~--~~~~Taeela~~~g-i----SRvTaRRYLeyl~~~~~l~a~  206 (224)
T COG4565         161 QKVREALKEP--DQELTAEELAQALG-I----SRVTARRYLEYLVSNGILEAE  206 (224)
T ss_pred             HHHHHHHhCc--CCccCHHHHHHHhC-c----cHHHHHHHHHHHHhcCeeeEE
Confidence            3455667632  38999999999999 9    899999999999999998754

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=92.42  E-value=0.37  Score=29.46  Aligned_cols=34  Identities=24%  Similarity=0.411  Sum_probs=32.3

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .|+...+||+.++ .    ++..++-.|..|..+|++..
T Consensus        22 ~PVgSk~ia~~l~-~----s~aTIRN~M~~Le~lGlve~   55 (78)
T PF03444_consen   22 EPVGSKTIAEELG-R----SPATIRNEMADLEELGLVES   55 (78)
T ss_pred             CCcCHHHHHHHHC-C----ChHHHHHHHHHHHHCCCccC
Confidence            8999999999999 9    89999999999999999973

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=92.10  E-value=1.1  Score=32.98  Aligned_cols=71  Identities=21%  Similarity=0.290  Sum_probs=50.6

Q ss_pred             hhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477            6 RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus         6 ~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++.....+.+++.+.....=+.++ + .|++.|...  ++-++..+||+++| +    .+..+++-+|.|.+.|++.-..
T Consensus       162 ee~Rkka~Vq~Ai~tLSySEleAv-~-~IL~~L~~~--egrlse~eLAerlG-V----SRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       162 EEARKKAAVQMAINTLSYSELEAV-E-HIFEELDGN--EGLLVASKIADRVG-I----TRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHHHHHHHHHHhccHhHHHHH-H-HHHHHhccc--cccccHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecc
Confidence            334444455665544433333333 2 578888652  26899999999999 9    8999999999999999998544

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=91.96  E-value=0.44  Score=32.72  Aligned_cols=51  Identities=22%  Similarity=0.223  Sum_probs=38.9

Q ss_pred             HHhChHHHHHhcC--CCCCCCHHHHHhhCCCCCCCCC-cchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAG--PGAKLSASEIAAQLPATKNKDA-PTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g--~~~~~t~~eLA~~~~~~~~~~d-~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|++.|.+..  .+-|.|..|||+.++ .    + +..+.+.|+.|...|++....
T Consensus         7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~-~----~s~~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498         7 RQQEVLDLIRAHIESTGYPPSIREIARAVG-L----RSPSAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhC-C----CChHHHHHHHHHHHHCCCEecCC
Confidence            3445556555320  126789999999999 9    7 889999999999999998653

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=91.88  E-value=0.3  Score=35.25  Aligned_cols=45  Identities=18%  Similarity=0.276  Sum_probs=39.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -.|.+.|.+.   +.+++.|||+.++ +    .+.-++|-|..|...|++..+
T Consensus         8 ~~Il~~l~~~---~~~~~~ela~~l~-v----S~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          8 DAIIELVKQQ---GYVSTEELVEHFS-V----SPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHc---CCEeHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence            4577888764   6899999999999 9    999999999999999998764

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

Probab=91.60  E-value=0.53  Score=28.00  Aligned_cols=43  Identities=19%  Similarity=0.245  Sum_probs=31.7

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +|+|..-. .++.+.++|+..++ .    +...+.+.+..|...|+++.
T Consensus         9 ~~IL~~l~-~~~~~~t~i~~~~~-L----~~~~~~~yL~~L~~~gLI~~   51 (77)
T PF14947_consen    9 FDILKILS-KGGAKKTEIMYKAN-L----NYSTLKKYLKELEEKGLIKK   51 (77)
T ss_dssp             HHHHHHH--TT-B-HHHHHTTST-------HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHH-cCCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCcCeeC
Confidence            45554321 27899999999999 9    99999999999999999965

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=91.39  E-value=0.48  Score=33.04  Aligned_cols=46  Identities=20%  Similarity=0.260  Sum_probs=39.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .-|++++-+.   |.+|-+|||..++ .    ...-++|+|+.|-..|++....
T Consensus        21 ~~v~~~l~~k---ge~tDeela~~l~-i----~~~~vrriL~~L~e~~li~~~k   66 (176)
T COG1675          21 VLVVDALLEK---GELTDEELAELLG-I----KKNEVRRILYALYEDGLISYRK   66 (176)
T ss_pred             hHHHHHHHhc---CCcChHHHHHHhC-c----cHHHHHHHHHHHHhCCceEEEe
Confidence            3567888764   4799999999999 9    9999999999999999998543

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=91.35  E-value=0.38  Score=35.04  Aligned_cols=46  Identities=11%  Similarity=0.210  Sum_probs=40.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ...|.+.|.+.   +.+|+.|||+.++ +    .+.-++|=|+.|...|++..+
T Consensus        19 ~~~Il~~L~~~---~~vtv~eLa~~l~-V----S~~TIRRDL~~Le~~G~l~r~   64 (269)
T PRK09802         19 REQIIQRLRQQ---GSVQVNDLSALYG-V----STVTIRNDLAFLEKQGIAVRA   64 (269)
T ss_pred             HHHHHHHHHHc---CCEeHHHHHHHHC-C----CHHHHHHHHHHHHhCCCeEEE
Confidence            34678888875   5799999999999 9    899999999999999998754

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=91.30  E-value=0.56  Score=30.70  Aligned_cols=51  Identities=14%  Similarity=0.254  Sum_probs=38.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++.|..+|.+.   +|.|+.||.+.++ -..+-+...+.++|+-|...|++...
T Consensus         5 ~E~~VM~vlW~~---~~~t~~eI~~~l~-~~~~~~~tTv~T~L~rL~~KG~v~~~   55 (130)
T TIGR02698         5 AEWEVMRVVWTL---GETTSRDIIRILA-EKKDWSDSTIKTLLGRLVDKGCLTTE   55 (130)
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHh-hccCCcHHHHHHHHHHHHHCCceeee
Confidence            466788888764   5899999877764 22222678899999999999999754

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=91.25  E-value=0.28  Score=32.66  Aligned_cols=34  Identities=24%  Similarity=0.377  Sum_probs=31.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+|-+|||..+| +    .+..+.|+|+.|...|++.-.
T Consensus       143 ~~t~~~iA~~lG-~----tretvsR~l~~l~~~g~I~~~  176 (193)
T TIGR03697       143 RLSHQAIAEAIG-S----TRVTITRLLGDLRKKKLISIH  176 (193)
T ss_pred             CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEec
Confidence            689999999999 9    899999999999999999754

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.

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=91.21  E-value=0.39  Score=36.24  Aligned_cols=49  Identities=20%  Similarity=0.274  Sum_probs=39.7

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      -|.++|.++|. .++...+|..+++ .    ....|.|+|+.|.+.+++.++++.
T Consensus        88 lvy~~I~~ag~-~GIw~~~i~~~t~-l----~~~~~~k~lk~Le~k~lIK~vksv  136 (327)
T PF05158_consen   88 LVYQLIEEAGN-KGIWTKDIKKKTN-L----HQTQLTKILKSLESKKLIKSVKSV  136 (327)
T ss_dssp             HHHHHHHHHTT-T-EEHHHHHHHCT-------HHHHHHHHHHHHHTTSEEEE--S
T ss_pred             HHHHHHHHhCC-CCCcHHHHHHHcC-C----CHHHHHHHHHHHHhCCCEEEecCc
Confidence            46788888874 8999999999999 9    899999999999999999998765

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=91.07  E-value=0.46  Score=30.10  Aligned_cols=52  Identities=23%  Similarity=0.376  Sum_probs=41.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|+.|.++|.+.|   ++|+.||.+.++ -..+-.+..+.-+|+-|+..|+++...
T Consensus         4 ~E~~IM~~lW~~~---~~t~~eI~~~l~-~~~~~~~sTv~t~L~rL~~Kg~l~~~~   55 (115)
T PF03965_consen    4 LELEIMEILWESG---EATVREIHEALP-EERSWAYSTVQTLLNRLVEKGFLTREK   55 (115)
T ss_dssp             HHHHHHHHHHHHS---SEEHHHHHHHHC-TTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHhCC---CCCHHHHHHHHH-hccccchhHHHHHHHHHHhCCceeEee
Confidence            4677889998874   699999999998 632335778999999999999998654

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=90.83  E-value=0.34  Score=30.11  Aligned_cols=49  Identities=14%  Similarity=0.194  Sum_probs=39.2

Q ss_pred             HhChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           31 NLGLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        31 ~LgIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |-..+|.|.+. ..-.-+|...|+++++ +    ...+-+++||.|...|++..+
T Consensus        25 dk~t~dkl~kEV~~~K~ITps~lserlk-I----~~SlAr~~Lr~L~~kG~Ik~V   74 (86)
T PRK09334         25 DEELLKRVAKEVKKEKIVTPYTLASKYG-I----KISVAKKVLRELEKRGVLVLY   74 (86)
T ss_pred             CHHHHHHHHHHhccCcEEcHHHHHHHhc-c----hHHHHHHHHHHHHHCCCEEEE
Confidence            44466666542 2235689999999999 9    999999999999999999765

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=90.80  E-value=0.56  Score=32.34  Aligned_cols=45  Identities=20%  Similarity=0.266  Sum_probs=37.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.+++..  ++.|.+|||++++ .    .+..+++-+.+|+..|++...
T Consensus       166 ~Vl~~~~~g~--~g~s~~eIa~~l~-i----S~~Tv~~~~~~~~~~~~~~~~  210 (225)
T PRK10046        166 AVRKLFKEPG--VQHTAETVAQALT-I----SRTTARRYLEYCASRHLIIAE  210 (225)
T ss_pred             HHHHHHHcCC--CCcCHHHHHHHhC-c----cHHHHHHHHHHHHhCCeEEEE
Confidence            4566676521  4789999999999 9    999999999999999998765

>PRK00215 LexA repressor; Validated

Probab=90.72  E-value=0.78  Score=31.60  Aligned_cols=37  Identities=24%  Similarity=0.276  Sum_probs=31.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+.|..|||+.++ .+   +...+.|+++.|...|+++...
T Consensus        22 ~~~s~~ela~~~~-~~---~~~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215         22 YPPSRREIADALG-LR---SPSAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCCCEEeCC
Confidence            7899999999999 62   3568999999999999997654

>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=90.66  E-value=0.6  Score=24.93  Aligned_cols=33  Identities=15%  Similarity=0.351  Sum_probs=24.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR   70 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R   70 (89)
                      +|..|...|.+.   +..|..+||+.+| .    .+..+.+
T Consensus         4 ~D~~Il~~Lq~d---~r~s~~~la~~lg-l----S~~~v~~   36 (42)
T PF13404_consen    4 LDRKILRLLQED---GRRSYAELAEELG-L----SESTVRR   36 (42)
T ss_dssp             HHHHHHHHHHH----TTS-HHHHHHHHT-S-----HHHHHH
T ss_pred             HHHHHHHHHHHc---CCccHHHHHHHHC-c----CHHHHHH
Confidence            577889999874   6899999999999 8    5555443

...

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=90.54  E-value=0.47  Score=34.22  Aligned_cols=45  Identities=27%  Similarity=0.310  Sum_probs=39.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|.+.|.+.   +.+++.|||+.++ +    .+..++|=|+.|...|++..+
T Consensus         8 ~~Il~~L~~~---~~v~v~eLa~~l~-V----S~~TIRRDL~~Le~~g~l~r~   52 (256)
T PRK10434          8 AAILEYLQKQ---GKTSVEELAQYFD-T----TGTTIRKDLVILEHAGTVIRT   52 (256)
T ss_pred             HHHHHHHHHc---CCEEHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEE
Confidence            4577888875   6899999999999 9    899999999999999988764

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=90.51  E-value=0.78  Score=31.03  Aligned_cols=37  Identities=24%  Similarity=0.349  Sum_probs=33.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +++...+||+.++ +    .|..+..+++-|...|++.....
T Consensus        23 ~~~~~~diA~~L~-V----sp~sVt~ml~rL~~~GlV~~~~y   59 (154)
T COG1321          23 GFARTKDIAERLK-V----SPPSVTEMLKRLERLGLVEYEPY   59 (154)
T ss_pred             CcccHHHHHHHhC-C----CcHHHHHHHHHHHHCCCeEEecC
Confidence            7999999999999 9    88899999999999999987644

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=90.49  E-value=1.1  Score=27.96  Aligned_cols=48  Identities=21%  Similarity=0.236  Sum_probs=39.8

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHH----------HHHhccCce
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRIL----------GLLASYGIV   81 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlL----------R~L~s~gi~   81 (89)
                      .=+..+|+..|.+.-+ .++++.|||..++ +    |+.-+.-.|          +.|+.+|++
T Consensus         8 S~~R~~vl~~L~~~yp-~~~~~~eIar~v~-~----~~snV~GaL~G~g~rY~~e~SLv~lGLV   65 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYP-EPAYPSEIARSVG-S----DYSNVLGALRGDGKRYNKEDSLVGLGLV   65 (90)
T ss_pred             HHHHHHHHHHHHHcCC-CcCCHHHHHHHHC-C----CHHHHHHHHhcCCCCcCcchhHHHcCCe
Confidence            5567889999988732 8999999999999 9    888777666          468899999

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=90.32  E-value=0.42  Score=32.34  Aligned_cols=35  Identities=23%  Similarity=0.427  Sum_probs=32.1

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++|-.|||+.+| +    .+..+.|+|+.|...|+++-..
T Consensus       168 ~~t~~~lA~~lG-~----tr~tvsR~l~~l~~~gii~~~~  202 (211)
T PRK11753        168 KITRQEIGRIVG-C----SREMVGRVLKMLEDQGLISAHG  202 (211)
T ss_pred             CCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEecC
Confidence            789999999999 9    9999999999999999997543

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=90.25  E-value=0.48  Score=36.43  Aligned_cols=37  Identities=27%  Similarity=0.319  Sum_probs=33.8

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++|.|.+||+++++ +    ++..+++++..|...|++.+..
T Consensus       308 g~~~t~~~La~~l~-~----~~~~v~~iL~~L~~agLI~~~~  344 (412)
T PRK04214        308 GKALDVDEIRRLEP-M----GYDELGELLCELARIGLLRRGE  344 (412)
T ss_pred             CCCCCHHHHHHHhC-C----CHHHHHHHHHHHHhCCCeEecC
Confidence            37999999999999 9    9999999999999999998643

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=90.08  E-value=0.5  Score=34.10  Aligned_cols=44  Identities=20%  Similarity=0.312  Sum_probs=39.8

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.|.+.   |.++++|||+.++ +    .+.-++|=|+.|...|++..+
T Consensus         9 ~Il~~l~~~---g~v~v~eLa~~~~-V----S~~TIRRDL~~Le~~g~l~R~   52 (253)
T COG1349           9 KILELLKEK---GKVSVEELAELFG-V----SEMTIRRDLNELEEQGLLLRV   52 (253)
T ss_pred             HHHHHHHHc---CcEEHHHHHHHhC-C----CHHHHHHhHHHHHHCCcEEEE
Confidence            577888875   6899999999999 9    999999999999999999875

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

Probab=89.90  E-value=0.99  Score=28.30  Aligned_cols=49  Identities=22%  Similarity=0.266  Sum_probs=42.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|..+|...   +|=++.-||..++ .    +..-+.++++-|..+|++++...
T Consensus         8 l~~~IL~hl~~~---~~Dy~k~ia~~l~-~----~~~~v~~~l~~Le~~GLler~~g   56 (92)
T PF10007_consen    8 LDLKILQHLKKA---GPDYAKSIARRLK-I----PLEEVREALEKLEEMGLLERVEG   56 (92)
T ss_pred             hHHHHHHHHHHH---CCCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEEecC
Confidence            356778888876   5788999999999 9    99999999999999999998754

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=89.75  E-value=0.62  Score=26.80  Aligned_cols=45  Identities=18%  Similarity=0.252  Sum_probs=36.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|++.|-+.   |..|+.+|.+.++ .    ++..+..-|-.|..+|++....
T Consensus        17 ~V~~~Ll~~---G~ltl~~i~~~t~-l----~~~~Vk~~L~~LiQh~~v~y~~   61 (62)
T PF08221_consen   17 KVGEVLLSR---GRLTLREIVRRTG-L----SPKQVKKALVVLIQHNLVQYFE   61 (62)
T ss_dssp             HHHHHHHHC----SEEHHHHHHHHT-------HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHcCCeeeec
Confidence            467777765   6899999999999 9    8999999999999999987543

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=89.67  E-value=0.47  Score=30.47  Aligned_cols=47  Identities=15%  Similarity=0.215  Sum_probs=38.2

Q ss_pred             ChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+|.|... ..-.-+|...||++++ +    .-.+-+++||.|...|++..+
T Consensus        45 ~~~~kl~kEV~~~K~ITp~~lserlk-I----~~SlAr~~Lr~L~~kG~Ik~V   92 (105)
T PF03297_consen   45 ETYDKLLKEVPKMKLITPSVLSERLK-I----NGSLARKALRELESKGLIKPV   92 (105)
T ss_dssp             HHHHHHHHHCTTSSCECHHHHHHHHC-C----SCHHHHHHHHHHHHCCSSEEE
T ss_pred             HHHHHHHHHhccCcEeeHHHHHHhHh-h----HHHHHHHHHHHHHHCCCEEEE
Confidence            456666543 2225689999999999 9    999999999999999999876

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.

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

Probab=89.52  E-value=0.57  Score=28.20  Aligned_cols=32  Identities=34%  Similarity=0.499  Sum_probs=29.2

Q ss_pred             HHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           49 ASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        49 ~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..|||+.++ +    ++..+.|+++.|...|++....
T Consensus         2 ~~ela~~l~-i----s~stvs~~l~~L~~~glI~r~~   33 (96)
T smart00529        2 TSEIAERLN-V----SPPTVTQMLKKLEKDGLVEYEP   33 (96)
T ss_pred             HHHHHHHhC-C----ChHHHHHHHHHHHHCCCEEEcC
Confidence            579999999 9    9999999999999999998754

iron dependent repressor

>PRK14096 pgi glucose-6-phosphate isomerase; Provisional

Probab=89.46  E-value=0.56  Score=37.69  Aligned_cols=42  Identities=31%  Similarity=0.373  Sum_probs=33.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      -.|-..+.+.+  ++.|++||+++++ .  |++...++.|||+|+++
T Consensus       466 ~~~~~~~~~~~--~~~~~~~~~~~~~-~--~~~~~~~~~i~~~~~~n  507 (528)
T PRK14096        466 KKVEELLKEDG--GELSIEEIAAALG-A--PEQVETIYKILRHLAAN  507 (528)
T ss_pred             HHHHHHHhccC--CCCCHHHHHHHcC-C--CccHHHHHHHHHHHhcC
Confidence            34555665544  8999999999999 5  44778999999999985

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=89.43  E-value=0.5  Score=31.79  Aligned_cols=34  Identities=18%  Similarity=0.337  Sum_probs=31.3

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      -|+|-++||..+| +    .+..+.|+|+.|...|++..
T Consensus       148 ~~~t~~~iA~~lG-~----tretvsR~l~~l~~~g~I~~  181 (202)
T PRK13918        148 IYATHDELAAAVG-S----VRETVTKVIGELSREGYIRS  181 (202)
T ss_pred             ecCCHHHHHHHhC-c----cHHHHHHHHHHHHHCCCEEc
Confidence            3689999999999 9    89999999999999999974

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=89.42  E-value=0.52  Score=32.60  Aligned_cols=35  Identities=17%  Similarity=0.339  Sum_probs=32.0

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+|-++||+.+| +    .+..+.|+|+.|...|++.-..
T Consensus       184 ~lt~~~iA~~lG-~----sr~tvsR~l~~l~~~g~I~~~~  218 (235)
T PRK11161        184 TMTRGDIGNYLG-L----TVETISRLLGRFQKSGMLAVKG  218 (235)
T ss_pred             cccHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEecC
Confidence            689999999999 9    9999999999999999998543

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=89.08  E-value=0.32  Score=33.60  Aligned_cols=45  Identities=16%  Similarity=0.062  Sum_probs=38.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -.|.+.|.+.   +.+++.||++.++ +    .+..++|=++.|+..|++..+
T Consensus        10 ~~Il~~l~~~---~~~~~~~La~~~~-v----S~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424         10 KALQELIEEN---PFITDEELAEKFG-V----SIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHC---CCEEHHHHHHHHC-c----CHHHHHHHHHHHhcchHHHHH
Confidence            3467778775   6899999999999 9    899999999999999988754

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=88.83  E-value=1  Score=31.51  Aligned_cols=44  Identities=23%  Similarity=0.231  Sum_probs=36.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |.+..+|+-.   +|+|-.||++..| +    ++   ..+++.|...|++.+.+.
T Consensus        93 LEtLaiIay~---qPiTr~eI~~irG-v----~~---~~ii~~L~~~gLI~e~gr  136 (188)
T PRK00135         93 LEVLAIIAYK---QPITRIEIDEIRG-V----NS---DGALQTLLAKGLIKEVGR  136 (188)
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHC-C----CH---HHHHHHHHHCCCeEEcCc
Confidence            4567778764   7999999999999 8    54   889999999999988643

>PHA02943 hypothetical protein; Provisional

Probab=88.67  E-value=1  Score=30.99  Aligned_cols=44  Identities=23%  Similarity=0.193  Sum_probs=37.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|.+.| +.   |..|.+|||+.+| .    .....+=+|..|...|.+.++.
T Consensus        15 eILE~L-k~---G~~TtseIAkaLG-l----S~~qa~~~LyvLErEG~VkrV~   58 (165)
T PHA02943         15 KTLRLL-AD---GCKTTSRIANKLG-V----SHSMARNALYQLAKEGMVLKVE   58 (165)
T ss_pred             HHHHHH-hc---CCccHHHHHHHHC-C----CHHHHHHHHHHHHHcCceEEEe
Confidence            455666 32   7899999999999 9    8888999999999999998764

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

Probab=88.62  E-value=1.2  Score=31.81  Aligned_cols=36  Identities=31%  Similarity=0.387  Sum_probs=33.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..+|.+|||+.++ .    ++..+.|.++.|...|++....
T Consensus        20 ~~IS~~eLA~~L~-i----S~~Tvsr~Lk~LEe~GlI~R~~   55 (217)
T PRK14165         20 VKISSSEFANHTG-T----SSKTAARILKQLEDEGYITRTI   55 (217)
T ss_pred             CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEE
Confidence            5699999999999 9    9999999999999999998653

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=88.30  E-value=1.1  Score=35.37  Aligned_cols=47  Identities=17%  Similarity=0.266  Sum_probs=38.9

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +..|...|...   +++|..+||+.++ .    ++..+.|++.-|.+.|++....
T Consensus         8 e~~vL~~L~~~---~~~s~~eLA~~l~-l----~~~tVt~~i~~Le~kGlV~~~~   54 (489)
T PRK04172          8 EKKVLKALKEL---KEATLEELAEKLG-L----PPEAVMRAAEWLEEKGLVKVEE   54 (489)
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHhC-c----CHHHHHHHHHHHHhCCCEEEEe
Confidence            34455566553   5899999999999 9    9999999999999999998653

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=88.07  E-value=0.65  Score=32.44  Aligned_cols=34  Identities=26%  Similarity=0.325  Sum_probs=31.3

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       179 ~lt~~~IA~~lG-i----sretlsR~L~~L~~~GlI~~~  212 (230)
T PRK09391        179 PMSRRDIADYLG-L----TIETVSRALSQLQDRGLIGLS  212 (230)
T ss_pred             cCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEec
Confidence            578999999999 9    999999999999999999743

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=88.03  E-value=1  Score=31.23  Aligned_cols=39  Identities=21%  Similarity=0.215  Sum_probs=34.6

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|..++..+||+..| +    ....++--|+.|.+.|++.....
T Consensus        27 pG~~L~e~eLae~lg-V----SRtpVREAL~~L~~eGlv~~~~~   65 (224)
T PRK11534         27 PDEKLRMSLLTSRYA-L----GVGPLREALSQLVAERLVTVVNQ   65 (224)
T ss_pred             CCCcCCHHHHHHHHC-C----ChHHHHHHHHHHHHCCCEEEeCC
Confidence            457899999999999 9    88899999999999999986544

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

Probab=88.00  E-value=0.79  Score=29.60  Aligned_cols=38  Identities=13%  Similarity=0.139  Sum_probs=33.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .++|++|||+.+. |    .+....++|+-|...|.+.=.+..
T Consensus        18 ~~vtl~elA~~l~-c----S~Rn~r~lLkkm~~~gWi~W~pg~   55 (115)
T PF12793_consen   18 VEVTLDELAELLF-C----SRRNARTLLKKMQEEGWITWQPGR   55 (115)
T ss_pred             cceeHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeeeeCCC
Confidence            5689999999999 9    999999999999999998755443

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=87.84  E-value=1.2  Score=31.79  Aligned_cols=44  Identities=18%  Similarity=0.289  Sum_probs=37.8

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ..|.+.|.+.   +.++.+|||+.++ +    .+..++|-|..|...|.+..
T Consensus         7 ~~Il~~l~~~---~~~~~~eLa~~l~-V----S~~TiRRdL~~L~~~~~l~r   50 (240)
T PRK10411          7 QAIVDLLLNH---TSLTTEALAEQLN-V----SKETIRRDLNELQTQGKILR   50 (240)
T ss_pred             HHHHHHHHHc---CCCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEE
Confidence            3477788764   6899999999999 9    89999999999999887754

>PF13730 HTH_36: Helix-turn-helix domain

Probab=87.65  E-value=0.74  Score=25.08  Aligned_cols=30  Identities=20%  Similarity=0.306  Sum_probs=27.5

Q ss_pred             CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477           47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      -|.+.||+.+| +    ....+.|.++.|...|++
T Consensus        26 pS~~~la~~~g-~----s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   26 PSQETLAKDLG-V----SRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             cCHHHHHHHHC-c----CHHHHHHHHHHHHHCcCC
Confidence            38999999999 9    899999999999999874

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=87.31  E-value=1.2  Score=32.11  Aligned_cols=36  Identities=17%  Similarity=0.342  Sum_probs=32.2

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHH-HHhccCceeee
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILG-LLASYGIVECS   84 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR-~L~s~gi~~e~   84 (89)
                      +++.+++++|+.+| .    ++..+.++++ .|...|++..+
T Consensus       253 ~~~~~~~~ia~~lg-~----~~~~~~~~~e~~Li~~~li~~~  289 (305)
T TIGR00635       253 GGPVGLKTLAAALG-E----DADTIEDVYEPYLLQIGFLQRT  289 (305)
T ss_pred             CCcccHHHHHHHhC-C----CcchHHHhhhHHHHHcCCcccC
Confidence            37899999999999 9    9999999999 79999999643

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

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

Probab=87.11  E-value=0.98  Score=24.11  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=17.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      .++|..+||..+| .    ++..+.|.++
T Consensus        19 ~G~s~~~IA~~lg-~----s~sTV~relk   42 (44)
T PF13936_consen   19 QGMSIREIAKRLG-R----SRSTVSRELK   42 (44)
T ss_dssp             S---HHHHHHHTT-------HHHHHHHHH
T ss_pred             cCCCHHHHHHHHC-c----CcHHHHHHHh
Confidence            4699999999999 9    8999999876

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

Probab=86.89  E-value=1.3  Score=28.52  Aligned_cols=50  Identities=16%  Similarity=0.202  Sum_probs=41.0

Q ss_pred             HHhChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++-.++|.+.+. +...-+|...||.+.| +    +-..-+++||.|...|++...
T Consensus        42 vdee~~~ki~KEV~~~r~VTpy~la~r~g-I----~~SvAr~vLR~LeeeGvv~lv   92 (107)
T COG4901          42 VDEELLDKIRKEVPRERVVTPYVLASRYG-I----NGSVARIVLRHLEEEGVVQLV   92 (107)
T ss_pred             ccHHHHHHHHHhcccceeecHHHHHHHhc-c----chHHHHHHHHHHHhCCceeee
Confidence            556778877653 2235689999999999 9    899999999999999998755

>PRK09954 putative kinase; Provisional

Probab=86.51  E-value=1.4  Score=32.80  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=38.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      +..|...|.++   +++|.+|||+.++ +    ....+.+.++.|...|++.
T Consensus         5 ~~~il~~l~~~---~~~s~~~la~~l~-~----s~~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          5 EKEILAILRRN---PLIQQNEIADILQ-I----SRSRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCcC
Confidence            45678888874   5899999999999 9    8999999999999999875

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=86.11  E-value=2.7  Score=31.16  Aligned_cols=55  Identities=13%  Similarity=0.321  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           21 VLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        21 ~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      -+..+|...+++.|.+.|+..   +|+.+.|||+.+| .    ....+.-=+..|...|+++-
T Consensus        15 dv~kalaS~vRv~Il~lL~~k---~plNvneiAe~lg-L----pqst~s~~ik~Le~aGlirT   69 (308)
T COG4189          15 DVLKALASKVRVAILQLLHRK---GPLNVNEIAEALG-L----PQSTMSANIKVLEKAGLIRT   69 (308)
T ss_pred             hHHHHHHHHHHHHHHHHHHHh---CCCCHHHHHHHhC-C----chhhhhhhHHHHHhcCceee
Confidence            355678888999999999985   6999999999999 8    66667777888888898874

>PRK01381 Trp operon repressor; Provisional

Probab=86.00  E-value=1.4  Score=28.13  Aligned_cols=41  Identities=20%  Similarity=0.196  Sum_probs=34.9

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      +..++|+..|-+    |++|-.|||+.+| +    ....+.|.=|.|-..
T Consensus        42 ~~R~~I~~~L~~----g~~sQREIa~~lG-v----SiaTITRgsn~Lk~~   82 (99)
T PRK01381         42 GTRVRIVEELLR----GELSQREIKQELG-V----GIATITRGSNSLKTA   82 (99)
T ss_pred             HHHHHHHHHHHc----CCcCHHHHHHHhC-C----ceeeehhhHHHhccC
Confidence            567899998876    7899999999999 9    888899988887643

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=85.93  E-value=1.6  Score=32.89  Aligned_cols=35  Identities=11%  Similarity=0.220  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhh--CCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQ--LPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~--~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|+++.+|++.  ++ +    .+..++|-|..|...|++...
T Consensus        20 ~pv~s~~l~~~~~~~-v----S~aTiR~d~~~Le~~G~l~~~   56 (337)
T TIGR00331        20 QPVGSKTLLEKYNLG-L----SSATIRNDMADLEDLGFIEKP   56 (337)
T ss_pred             CCcCHHHHHhhcCCC-C----ChHHHHHHHHHHHHCCCccCC
Confidence            89999999999  88 8    888999999999999999765

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

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=85.84  E-value=1.6  Score=30.39  Aligned_cols=40  Identities=33%  Similarity=0.471  Sum_probs=35.7

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +|.+++-.+||+..| +    ....++.-|+.|++-|++.-....
T Consensus        36 pG~~l~e~~La~~~g-v----SrtPVReAL~rL~~eGlv~~~p~r   75 (230)
T COG1802          36 PGERLSEEELAEELG-V----SRTPVREALRRLEAEGLVEIEPNR   75 (230)
T ss_pred             CCCCccHHHHHHHhC-C----CCccHHHHHHHHHHCCCeEecCCC
Confidence            458999999999999 9    899999999999999999876544

>smart00531 TFIIE Transcription initiation factor IIE

Probab=85.77  E-value=1.6  Score=29.00  Aligned_cols=39  Identities=18%  Similarity=0.228  Sum_probs=33.8

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      -|+|+|-.+   +.+|-++||..+| .    +..-++++|..|-..+
T Consensus         5 ~v~d~L~~~---~~~~dedLa~~l~-i----~~n~vRkiL~~L~ed~   43 (147)
T smart00531        5 LVLDALMRN---GCVTEEDLAELLG-I----KQKQLRKILYLLYDEK   43 (147)
T ss_pred             eehHHHHhc---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHhhh
Confidence            478888765   5899999999999 9    9999999999999833

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

Probab=85.72  E-value=1  Score=23.43  Aligned_cols=28  Identities=25%  Similarity=0.374  Sum_probs=22.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      .++|+++||..+| .    ++..+.|+.+....
T Consensus         7 ~~~~l~~iA~~~g-~----S~~~f~r~Fk~~~g   34 (42)
T PF00165_consen    7 QKLTLEDIAEQAG-F----SPSYFSRLFKKETG   34 (42)
T ss_dssp             SS--HHHHHHHHT-S-----HHHHHHHHHHHTS
T ss_pred             CCCCHHHHHHHHC-C----CHHHHHHHHHHHHC
Confidence            5799999999999 9    99999999987654

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=85.65  E-value=1.5  Score=29.96  Aligned_cols=39  Identities=33%  Similarity=0.463  Sum_probs=34.4

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|..++-.+||+..| +    ....++.-|+.|.+.|++.....
T Consensus        31 pG~~L~e~~La~~lg-V----SRtpVReAL~~L~~eGlv~~~~~   69 (212)
T TIGR03338        31 PGAKLNESDIAARLG-V----SRGPVREAFRALEEAGLVRNEKN   69 (212)
T ss_pred             CCCEecHHHHHHHhC-C----ChHHHHHHHHHHHHCCCEEEecC
Confidence            347889999999999 9    89999999999999999986543

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>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=84.42  E-value=1.6  Score=25.37  Aligned_cols=29  Identities=24%  Similarity=0.477  Sum_probs=22.2

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHH
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR   70 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~R   70 (89)
                      |++.-+++  |.++..|||+.++ +    .+..+++
T Consensus        13 ~e~y~~~~--g~i~lkdIA~~Lg-v----s~~tIr~   41 (60)
T PF10668_consen   13 FEIYKESN--GKIKLKDIAEKLG-V----SESTIRK   41 (60)
T ss_pred             HHHHHHhC--CCccHHHHHHHHC-C----CHHHHHH
Confidence            55555554  8999999999999 9    7666553

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 [].

>PRK09775 putative DNA-binding transcriptional regulator; Provisional

Probab=84.35  E-value=1.7  Score=34.03  Aligned_cols=40  Identities=33%  Similarity=0.361  Sum_probs=31.5

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |-..|.+    ||.|+.||++.++ +    ....+.|.|+.|  .|++...
T Consensus         5 ~~~~L~~----g~~~~~eL~~~l~-~----sq~~~s~~L~~L--~~~V~~~   44 (442)
T PRK09775          5 LTTLLLQ----GPLSAAELAARLG-V----SQATLSRLLAAL--GDQVVRF   44 (442)
T ss_pred             HHHHHhc----CCCCHHHHHHHhC-C----CHHHHHHHHHHh--hcceeEe
Confidence            3445554    7999999999999 9    788899999999  6666543

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=84.32  E-value=0.71  Score=32.26  Aligned_cols=50  Identities=16%  Similarity=0.222  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHh
Q 045477           20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLA   76 (89)
Q Consensus        20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~   76 (89)
                      ..+-.+|+.|.++|-||.=      ...++.|||+.+| ++++.=...|+|-.|-|.
T Consensus       158 drQ~~vL~~A~~~GYFd~P------R~~~l~dLA~~lG-ISkst~~ehLRrAe~Kl~  207 (215)
T COG3413         158 DRQLEVLRLAYKMGYFDYP------RRVSLKDLAKELG-ISKSTLSEHLRRAERKLI  207 (215)
T ss_pred             HHHHHHHHHHHHcCCCCCC------ccCCHHHHHHHhC-CCHHHHHHHHHHHHHHHH
Confidence            4567899999999999752      5689999999999 943333334555555443

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=84.25  E-value=1.7  Score=32.01  Aligned_cols=43  Identities=16%  Similarity=0.276  Sum_probs=37.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      +..|.+.|.+.   .+.+.+|||+.++ +    ....+.|.++.|...|+.
T Consensus         6 ~~~il~~L~~~---~~~s~~~LA~~lg-v----sr~tV~~~l~~L~~~G~~   48 (319)
T PRK11886          6 MLQLLSLLADG---DFHSGEQLGEELG-I----SRAAIWKHIQTLEEWGLD   48 (319)
T ss_pred             HHHHHHHHHcC---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCc
Confidence            45677778752   6899999999999 9    899999999999999983

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=83.68  E-value=2.3  Score=32.08  Aligned_cols=35  Identities=11%  Similarity=0.254  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhh--CCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQ--LPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~--~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|++..+|++.  .+ +    .+..++|-|..|...|++...
T Consensus        24 ~pv~s~~l~~~~~l~-~----S~aTIR~dm~~Le~~G~l~~~   60 (339)
T PRK00082         24 EPVGSKTLSKRYGLG-V----SSATIRNDMADLEELGLLEKP   60 (339)
T ss_pred             CCcCHHHHHHHhCCC-C----ChHHHHHHHHHHHhCCCcCCC
Confidence            89999999977  88 8    889999999999999999865

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=83.43  E-value=1.5  Score=30.38  Aligned_cols=36  Identities=17%  Similarity=0.061  Sum_probs=32.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -+.|-.|||+.+| +    .+..|.|+|+-|...|++....
T Consensus       168 ~~~t~~~lA~~lG-~----sretvsR~L~~L~~~G~I~~~~  203 (226)
T PRK10402        168 YHEKHTQAAEYLG-V----SYRHLLYVLAQFIQDGYLKKSK  203 (226)
T ss_pred             ccchHHHHHHHHC-C----cHHHHHHHHHHHHHCCCEEeeC
Confidence            3578899999999 9    8999999999999999987543

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=83.32  E-value=2.4  Score=29.32  Aligned_cols=38  Identities=29%  Similarity=0.317  Sum_probs=33.8

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +|..++..+||+..| +    ....++--|+.|...|++.-..
T Consensus        31 pG~~L~e~~La~~lg-V----SRtpVREAL~~L~~eGLV~~~~   68 (221)
T PRK11414         31 PGARLITKNLAEQLG-M----SITPVREALLRLVSVNALSVAP   68 (221)
T ss_pred             CCCccCHHHHHHHHC-C----CchhHHHHHHHHHHCCCEEecC
Confidence            457899999999999 9    8889999999999999997543

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

Probab=83.32  E-value=2.3  Score=25.74  Aligned_cols=37  Identities=32%  Similarity=0.492  Sum_probs=32.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ||..-.||.+.++++    .+..|.+-|+.|...|++....
T Consensus        17 g~~rf~el~~~l~~i----s~~~L~~~L~~L~~~GLv~r~~   53 (90)
T PF01638_consen   17 GPMRFSELQRRLPGI----SPKVLSQRLKELEEAGLVERRV   53 (90)
T ss_dssp             SSEEHHHHHHHSTTS-----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCcHHHHHHhcchh----HHHHHHHHHHHHHHcchhhccc
Confidence            799999999999438    8889999999999999998653

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>PRK13239 alkylmercury lyase; Provisional

Probab=83.25  E-value=1.7  Score=30.94  Aligned_cols=39  Identities=23%  Similarity=0.352  Sum_probs=31.2

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      -.-|+..|++ |  +|.|.++||+.++ .    +...+.++|+.|..
T Consensus        24 ~~~llr~la~-G--~pvt~~~lA~~~~-~----~~~~v~~~L~~l~~   62 (206)
T PRK13239         24 LVPLLRLLAK-G--RPVSVTTLAAALG-W----PVEEVEAVLEAMPD   62 (206)
T ss_pred             HHHHHHHHHc-C--CCCCHHHHHHHhC-C----CHHHHHHHHHhCCC
Confidence            3446777884 4  8999999999999 9    88888888887753

>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4

Probab=83.24  E-value=1.3  Score=26.99  Aligned_cols=34  Identities=24%  Similarity=0.370  Sum_probs=21.7

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHH
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLL   75 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L   75 (89)
                      |+..|++ |  +|+|.++||..+| .    ...-+..+|..+
T Consensus        29 LLr~LA~-G--~PVt~~~LA~a~g-~----~~e~v~~~L~~~   62 (77)
T PF12324_consen   29 LLRLLAK-G--QPVTVEQLAAALG-W----PVEEVRAALAAM   62 (77)
T ss_dssp             HHHHHTT-T--S-B-HHHHHHHHT-------HHHHHHHHHH-
T ss_pred             HHHHHHc-C--CCcCHHHHHHHHC-C----CHHHHHHHHHhC
Confidence            6777876 4  8999999999999 8    555555555444

99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=82.90  E-value=1.8  Score=24.43  Aligned_cols=28  Identities=21%  Similarity=0.336  Sum_probs=23.0

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      ++|+++||+.++ +    ++..+.|+++.....
T Consensus         1 ~~~~~~la~~~~-~----s~~~l~~~f~~~~~~   28 (84)
T smart00342        1 PLTLEDLAEALG-M----SPRHLQRLFKKETGT   28 (84)
T ss_pred             CCCHHHHHHHhC-C----CHHHHHHHHHHHhCc
Confidence            478999999999 9    888898888866543

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=82.88  E-value=2.5  Score=26.64  Aligned_cols=41  Identities=17%  Similarity=0.165  Sum_probs=34.2

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      .+...||+..|-+    +++|=.|||+.+| +    ....+.|.=|.|..
T Consensus        41 l~~R~~i~~~Ll~----~~~tQrEIa~~lG-i----S~atIsR~sn~lk~   81 (94)
T TIGR01321        41 LGDRIRIVNELLN----GNMSQREIASKLG-V----SIATITRGSNNLKT   81 (94)
T ss_pred             HHHHHHHHHHHHh----CCCCHHHHHHHhC-C----ChhhhhHHHhhccc
Confidence            3567788887766    6899999999999 9    88899998888764

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.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=82.23  E-value=3.4  Score=21.80  Aligned_cols=28  Identities=25%  Similarity=0.260  Sum_probs=25.6

Q ss_pred             CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477           48 SASEIAAQLPATKNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus        48 t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      |..++|...+ +    ++..++|.++..-..|+
T Consensus        14 s~~~~a~~~g-i----s~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen   14 SVREIAREFG-I----SRSTVYRWIKRYREGGI   41 (52)
T ss_pred             CHHHHHHHHC-C----CHhHHHHHHHHHHhcCH
Confidence            9999999999 9    88999999998888774

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=82.16  E-value=2.9  Score=30.83  Aligned_cols=37  Identities=16%  Similarity=0.319  Sum_probs=33.3

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHH-HHhccCceeeec
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILG-LLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR-~L~s~gi~~e~~   85 (89)
                      ++|.+++.+|+.+| .    ++..+.++++ +|...|++..+.
T Consensus       274 ~~~~~~~~~a~~lg-~----~~~~~~~~~e~~Li~~~li~~~~  311 (328)
T PRK00080        274 GGPVGLDTLAAALG-E----ERDTIEDVYEPYLIQQGFIQRTP  311 (328)
T ss_pred             CCceeHHHHHHHHC-C----CcchHHHHhhHHHHHcCCcccCC
Confidence            37999999999999 9    8999999999 999999997553

>PRK12423 LexA repressor; Provisional

Probab=82.13  E-value=4.2  Score=28.18  Aligned_cols=37  Identities=22%  Similarity=0.236  Sum_probs=30.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -+-|..|||+.+| ..   .+..+++-|+.|+..|+++...
T Consensus        24 ~~Ps~~eia~~~g-~~---s~~~v~~~l~~L~~~G~l~~~~   60 (202)
T PRK12423         24 QPPSLAEIAQAFG-FA---SRSVARKHVQALAEAGLIEVVP   60 (202)
T ss_pred             CCCCHHHHHHHhC-CC---ChHHHHHHHHHHHHCCCEEecC
Confidence            4679999999999 73   3457899999999999998653

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

Probab=82.03  E-value=1.5  Score=24.39  Aligned_cols=31  Identities=26%  Similarity=0.428  Sum_probs=20.8

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      |-..+.+    ..+|..+||+.+| .    ++..+.|++.
T Consensus         2 L~~~m~~----~~it~~~La~~~g-i----s~~tl~~~~~   32 (63)
T PF13443_consen    2 LKELMAE----RGITQKDLARKTG-I----SRSTLSRILN   32 (63)
T ss_dssp             HHHHHHH----TT--HHHHHHHHT-------HHHHHHHHT
T ss_pred             HHHHHHH----cCCCHHHHHHHHC-c----CHHHHHHHHh
Confidence            4566776    4679999999999 9    7877877764

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=81.82  E-value=3.1  Score=26.69  Aligned_cols=41  Identities=12%  Similarity=0.125  Sum_probs=31.0

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      .+.+.|.++- ..+.|+++||+.++ +    .+..+.|+++.-....
T Consensus        13 ~~~~~I~~~~-~~~~sl~~lA~~~g-~----S~~~l~r~Fk~~~G~s   53 (127)
T PRK11511         13 SILDWIEDNL-ESPLSLEKVSERSG-Y----SKWHLQRMFKKETGHS   53 (127)
T ss_pred             HHHHHHHHhc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence            3455666553 26899999999999 9    9999999987665443

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

Probab=81.61  E-value=1.2  Score=24.24  Aligned_cols=20  Identities=20%  Similarity=0.396  Sum_probs=11.6

Q ss_pred             CHHHHHhhCCCCCCCCCcchHHHHH
Q 045477           48 SASEIAAQLPATKNKDAPTMLDRIL   72 (89)
Q Consensus        48 t~~eLA~~~~~~~~~~d~~~l~RlL   72 (89)
                      |+.|||+.+| +    .+..+.|+|
T Consensus         1 Ti~dIA~~ag-v----S~~TVSr~l   20 (46)
T PF00356_consen    1 TIKDIAREAG-V----SKSTVSRVL   20 (46)
T ss_dssp             CHHHHHHHHT-S----SHHHHHHHH
T ss_pred             CHHHHHHHHC-c----CHHHHHHHH
Confidence            4566666666 6    555555544

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 ....

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

Probab=81.45  E-value=2.3  Score=25.08  Aligned_cols=43  Identities=21%  Similarity=0.162  Sum_probs=26.7

Q ss_pred             HhChHHHHHhcC-CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           31 NLGLFEIIAKAG-PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        31 ~LgIfd~l~~~g-~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      +-.|++.|-++. .-..+|+.|||+.++ +    .+..+.|+.+.|=-.
T Consensus        18 e~~Ia~yil~~~~~~~~~si~elA~~~~-v----S~sti~Rf~kkLG~~   61 (77)
T PF01418_consen   18 EKKIADYILENPDEIAFMSISELAEKAG-V----SPSTIVRFCKKLGFS   61 (77)
T ss_dssp             HHHHHHHHHH-HHHHCT--HHHHHHHCT-S-----HHHHHHHHHHCTTT
T ss_pred             HHHHHHHHHhCHHHHHHccHHHHHHHcC-C----CHHHHHHHHHHhCCC
Confidence            334555554321 014689999999999 9    888999988876433

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.

>PRK11642 exoribonuclease R; Provisional

Probab=81.12  E-value=2.9  Score=35.24  Aligned_cols=50  Identities=20%  Similarity=0.215  Sum_probs=39.3

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|.+.|.+.+  +|++..+|++.++ .+...+...|.+.|+.|...|.+....
T Consensus        23 ~Il~~l~~~~--~~~~~~~L~~~l~-l~~~~~~~~l~~~L~~L~~~g~l~~~~   72 (813)
T PRK11642         23 FILEHLTKRE--KPASREELAVELN-IEGEEQLEALRRRLRAMERDGQLVFTR   72 (813)
T ss_pred             HHHHHHHhcC--CCCCHHHHHHHhC-CCChHHHHHHHHHHHHHHHCCCEEEcC
Confidence            4677776644  8999999999999 843334567999999999999987543

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=80.78  E-value=5.7  Score=23.88  Aligned_cols=44  Identities=23%  Similarity=0.231  Sum_probs=36.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|...++.    +..|++||-+.|| +    +...|-..|--|+..|++...
T Consensus         8 ~~IL~~ls~----~c~TLeeL~ekTg-i----~k~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen    8 QKILIILSK----RCCTLEELEEKTG-I----SKNTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             HHHHHHHHh----ccCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeee
Confidence            345556665    5899999999999 9    999999999999999998764

>PHA02591 hypothetical protein; Provisional

Probab=80.76  E-value=3.2  Score=25.56  Aligned_cols=33  Identities=18%  Similarity=0.221  Sum_probs=26.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL   74 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~   74 (89)
                      .+...|.+    .++|.++||+.+| +    +...+++.++-
T Consensus        50 ~vA~eL~e----qGlSqeqIA~~LG-V----sqetVrKYL~~   82 (83)
T PHA02591         50 SVTHELAR----KGFTVEKIASLLG-V----SVRKVRRYLES   82 (83)
T ss_pred             HHHHHHHH----cCCCHHHHHHHhC-C----CHHHHHHHHhc
Confidence            35556776    5799999999999 9    88888888763

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=80.75  E-value=2.6  Score=29.18  Aligned_cols=35  Identities=20%  Similarity=0.168  Sum_probs=32.1

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++|.+|||++++ .    .+..++.-++.|+..|++.+.
T Consensus       177 ~g~s~~eIA~~l~-i----S~~Tv~~~~~~~~~~~~~~~~  211 (239)
T PRK10430        177 YEFSTDELANAVN-I----SRVSCRKYLIWLVNCHILFTS  211 (239)
T ss_pred             CCcCHHHHHHHhC-c----hHHHHHHHHHHHHhCCEEEEE
Confidence            6789999999999 9    999999999999999999544

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

Probab=80.24  E-value=1.3  Score=23.57  Aligned_cols=30  Identities=23%  Similarity=0.243  Sum_probs=18.9

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      +.|..+||+.+| +    ++..++|.++-....|+
T Consensus        17 G~s~~~ia~~lg-v----s~~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen   17 GWSIREIAKRLG-V----SRSTVYRWIKRYREEGL   46 (50)
T ss_dssp             T--HHHHHHHHT-S-----HHHHHHHHT-------
T ss_pred             CCCHHHHHHHHC-c----CHHHHHHHHHHcccccc
Confidence            579999999999 9    99999999987766663

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	89
1kyw_A	365	Crystal Structure Analysis Of Caffeic Acid5-Hydroxy		8e-17
3p9c_A	364	Crystal Structure Of Perennial Ryegrass Lpomt1 Boun		2e-15
3reo_A	368	Monolignol O-Methyltransferase (Momt) Length = 368		9e-12
1fp1_D	372	Crystal Structure Analysis Of Chalcone O-Methyltran		6e-11
1fpq_A	372	Crystal Structure Analysis Of Selenomethionine Subs		3e-06

>pdb|1KYW|A Chain A, Crystal Structure Analysis Of Caffeic Acid5-Hydroxyferulic Acid 35-O-Methyltransferase In Complex With 5- Hydroxyconiferaldehyde Length = 365

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 54/74 (72%), Gaps = 1/74 (1%)
Query: 12 YAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRI 71
          +A ++   SVL M +K+ + L L EIIAKAGPGA++S  EIA+QLP T N DAP MLDR+
Sbjct: 22 FAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTT-NPDAPVMLDRM 80
Query: 72 LGLLASYGIVECSV 85
          L LLA Y I+ CSV
Sbjct: 81 LRLLACYIILTCSV 94

>pdb|3P9C|A Chain A, Crystal Structure Of Perennial Ryegrass Lpomt1 Bound To Sah Length = 364

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 41/87 (47%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
          MA  A ++   +A ++   SVL MT+K  I LGL EI+  AG G  L+ +E+AA+LP+  
Sbjct: 12 MAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAG-GKSLTPTEVAAKLPSAA 70
Query: 61 NKDAPTMLDRILGLLASYGIVECSVDD 87
          N +AP M+DRIL LLASY +V C V++
Sbjct: 71 NPEAPDMVDRILRLLASYNVVTCLVEE 97

>pdb|3REO|A Chain A, Monolignol O-Methyltransferase (Momt) Length = 368

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 57/87 (65%), Gaps = 2/87 (2%)
Query: 3   NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKA-GPGAKLSASEIAAQLPATKN 61
           + + +E   +A ++   +VL M +KA I L + EI+AK+  P   +S +EIAAQLP T N
Sbjct: 15  HSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTT-N 73
Query: 62  KDAPTMLDRILGLLASYGIVECSVDDV 88
            +AP MLDR+L LLASY +V  ++ ++
Sbjct: 74  PEAPVMLDRVLRLLASYSVVTYTLREL 100

>pdb|1FP1|D Chain D, Crystal Structure Analysis Of Chalcone O-Methyltransferase Length = 372

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 38/90 (42%), Positives = 54/90 (60%), Gaps = 2/90 (2%)
Query: 2   ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGP-GAKLSASEIAAQLPA-T 59
           + +  D     A  +T   V    + A I+L LFEIIAKA P GA +S SEIA++LPA T
Sbjct: 17  SEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPAST 76
Query: 60  KNKDAPTMLDRILGLLASYGIVECSVDDVD 89
           ++ D P  LDR+L LLASY ++  +   ++
Sbjct: 77  QHSDLPNRLDRMLRLLASYSVLTSTTRTIE 106

>pdb|1FPQ|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Chalcone O- Methyltransferase Length = 372

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/90 (42%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 2   ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGP-GAKLSASEIAAQLPA-T 59
           + +  D     A  +T   V    + A I+L LFEIIAKA P GA  S SEIA++LPA T
Sbjct: 17  SEQTEDSACLSAXVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFXSPSEIASKLPAST 76
Query: 60  KNKDAPTMLDRILGLLASYGIVECSVDDVD 89
           ++ D P  LDR L LLASY ++  +   ++
Sbjct: 77  QHSDLPNRLDRXLRLLASYSVLTSTTRTIE 106
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	89
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	3e-19
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	4e-19
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	5e-19
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	6e-15
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	2e-13
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	6e-13
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	1e-12
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	2e-12
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	3e-12
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	4e-12
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	1e-10
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	2e-10
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	3e-10
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	4e-09
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	9e-09

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 1kyz_A* 1kyw_A* Length = 368

 Score = 78.7 bits (194), Expect = 3e-19
 Identities = 37/90 (41%), Positives = 57/90 (63%), Gaps = 2/90 (2%)

Query: 1   MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAG-PGAKLSASEIAAQLPAT 59
             + + +E   +A ++   +VL M +KA I L + EI+AK+  P   +S +EIAAQLP T
Sbjct: 13  PTHSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLP-T 71

Query: 60  KNKDAPTMLDRILGLLASYGIVECSVDDVD 89
            N +AP MLDR+L LLASY +V  ++ ++ 
Sbjct: 72  TNPEAPVMLDRVLRLLASYSVVTYTLRELP 101

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A* Length = 372

 Score = 78.3 bits (193), Expect = 4e-19
 Identities = 38/90 (42%), Positives = 54/90 (60%), Gaps = 2/90 (2%)

Query: 2   ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAG-PGAKLSASEIAAQLPA-T 59
           + +  D     A  +T   V    + A I+L LFEIIAKA  PGA +S SEIA++LPA T
Sbjct: 17  SEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPAST 76

Query: 60  KNKDAPTMLDRILGLLASYGIVECSVDDVD 89
           ++ D P  LDR+L LLASY ++  +   ++
Sbjct: 77  QHSDLPNRLDRMLRLLASYSVLTSTTRTIE 106

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A* Length = 364

 Score = 78.3 bits (193), Expect = 5e-19
 Identities = 40/89 (44%), Positives = 58/89 (65%), Gaps = 1/89 (1%)

Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
          MA  A ++   +A ++   SVL MT+K  I LGL EI+  AG  + L+ +E+AA+LP+  
Sbjct: 12 MAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKS-LTPTEVAAKLPSAA 70

Query: 61 NKDAPTMLDRILGLLASYGIVECSVDDVD 89
          N +AP M+DRIL LLASY +V C V++  
Sbjct: 71 NPEAPDMVDRILRLLASYNVVTCLVEEGK 99

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A* Length = 358

 Score = 66.8 bits (163), Expect = 6e-15
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 11 AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70
           + ++     V  M +K+ + LG+ + I   G     + SE+A+ L    +     +L R
Sbjct: 12 IHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPM--TLSELASSLKL--HPSKVNILHR 67

Query: 71 ILGLLASYGIVECSVDDVD 89
           L LL   G    ++    
Sbjct: 68 FLRLLTHNGFFAKTIVKGK 86

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A* Length = 374

 Score = 62.8 bits (153), Expect = 2e-13
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 9/87 (10%)

Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
             E  D++     +     V  M ++    L L + +  AG     + + +A +     
Sbjct: 8  EPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLADRTDT-- 61

Query: 61 NKDAPTMLDRILGLLASYGIVECSVDD 87
              P  L R++  L   G++E     
Sbjct: 62 ---HPQALSRLVRHLTVVGVLEGGEKQ 85

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score = 61.1 bits (149), Expect = 6e-13
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 3  NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK 62
          N +         +V  G      +     LGL ++I   G     S   +AA + +    
Sbjct: 2  NNSNLAAARNLIQVVTGEWKSRCVYVATRLGLADLIES-GI---DSDETLAAAVGS---- 53

Query: 63 DAPTMLDRILGLLASYGIVECSVDDV 88
               + R++ LL ++ I +    D 
Sbjct: 54 -DAERIHRLMRLLVAFEIFQGDTRDG 78

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A* Length = 352

 Score = 60.6 bits (147), Expect = 1e-12
 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 4/77 (5%)

Query: 11 AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70
          A  ++     +  M++K  + + +  II   G     S S + + L           + R
Sbjct: 18 ALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPI--SLSNLVSILQV--PSSKIGNVRR 73

Query: 71 ILGLLASYGIVECSVDD 87
          ++  LA  G  E    +
Sbjct: 74 LMRYLAHNGFFEIITKE 90

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A* Length = 332

 Score = 59.6 bits (145), Expect = 2e-12
 Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 9/83 (10%)

Query: 6  RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAP 65
                            M ++    L + + IA AG     +A+EIA+   A       
Sbjct: 2  GKRAAHIGLRALADLATPMAVRVAATLRVADHIA-AGH---RTAAEIASAAGA-----HA 52

Query: 66 TMLDRILGLLASYGIVECSVDDV 88
            LDR+L  L + G+       V
Sbjct: 53 DSLDRLLRHLVAVGLFTRDGQGV 75

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A* Length = 369

 Score = 59.3 bits (144), Expect = 3e-12
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 11  AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70
               ++  G+     +   + LG+ E++ + GP    +A+ +A    A         L R
Sbjct: 40  ETVNDILQGAWKARAIHVAVELGVPELLQE-GP---RTATALAEATGA-----HEQTLRR 90

Query: 71  ILGLLASYGIVECSVDD 87
           +L LLA+ G+ +    D
Sbjct: 91  LLRLLATVGVFDDLGHD 107

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora} Length = 348

 Score = 58.8 bits (143), Expect = 4e-12
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 9/81 (11%)

Query: 4  EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKD 63
            R ++    +E  MG      ++A   +G+ + +         + +E+AA         
Sbjct: 17 MDRLQSALALYEEAMGYTYAAALRAAAAVGVADHLV----DGPRTPAELAAATGT----- 67

Query: 64 APTMLDRILGLLASYGIVECS 84
              L R+L LLA   +V  S
Sbjct: 68 DADALRRVLRLLAVRDVVRES 88

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A* Length = 360

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
          +A   +  +              M ++    L L + I  AG     +   +AA+     
Sbjct: 11 VAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHIL-AGA---RTVKALAARTDT-- 64

Query: 61 NKDAPTMLDRILGLLASYGIVECSVDDV 88
              P  L R++  L + G++E      
Sbjct: 65 ---RPEALLRLIRHLVAIGLLEEDAPGE 89

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 11/83 (13%)

Query: 2  ANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKN 61
          A EA+      A E+  G V+    + ++  G+F++++    G   +  EI+ +      
Sbjct: 12 AAEAQRL----AQEIAFGPVVFQVSRLMLKFGIFQLLSGKREG--YTLQEISGRTGL--- 62

Query: 62 KDAPTMLDRILGLLASYGIVECS 84
                   +L    + G +   
Sbjct: 63 --TRYAAQVLLEASLTIGTILLE 83

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A* Length = 359

 Score = 53.6 bits (129), Expect = 3e-10
 Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 16 VTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLL 75
          V  G +    MKA I L LF  +A+ GP      + +AA   +      P  L+ +L  L
Sbjct: 38 VFKGLIEFSCMKAAIELDLFSHMAE-GP---KDLATLAADTGS-----VPPRLEMLLETL 88

Query: 76 ASYGIVECS 84
              ++   
Sbjct: 89 RQMRVINLE 97

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score = 50.5 bits (121), Expect = 4e-09
 Identities = 10/83 (12%), Positives = 27/83 (32%), Gaps = 10/83 (12%)

Query: 1  MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATK 60
            ++A   +     +++        +   +   LF++          + +E+AA      
Sbjct: 16 TEDKAALTSVVDLVKLSDQYRQSAILHYAVADKLFDLTQTG-----RTPAEVAASFGM-- 68

Query: 61 NKDAPTMLDRILGLLASYGIVEC 83
                    +L  LA+ G++  
Sbjct: 69 ---VEGKAAILLHALAALGLLTK 88

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme} Length = 335

 Score = 49.7 bits (119), Expect = 9e-09
 Identities = 10/70 (14%), Positives = 22/70 (31%), Gaps = 9/70 (12%)

Query: 14 FEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG 73
          F           +KA + L +F  I++       S+  +A +        +   +  +  
Sbjct: 11 FNTVNAYQRSAAIKAAVELNVFTAISQGI----ESSQSLAQKCQT-----SERGMRMLCD 61

Query: 74 LLASYGIVEC 83
           L   G +  
Sbjct: 62 YLVIIGFMTK 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	89
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.67
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.66
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.66
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.55
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.54
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.53
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.51
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.51
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.51
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.48
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.45
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.44
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.39
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.37
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.36
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.29
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.5
3r0a_A	123	Putative transcriptional regulator; structural gen	97.32
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.26
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	97.21
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	97.18
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.17
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.16
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	97.12
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	97.1
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.05
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	97.04
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.03
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.03
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.0
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.99
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	96.98
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.93
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.92
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.92
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.91
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.91
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.9
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.89
2nnn_A	140	Probable transcriptional regulator; structural gen	96.89
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	96.85
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.83
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.82
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.81
1ku9_A	152	Hypothetical protein MJ223; putative transcription	96.8
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.8
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	96.8
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.79
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	96.78
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.77
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.77
3f3x_A	144	Transcriptional regulator, MARR family, putative;	96.77
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	96.76
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.76
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.76
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.74
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.72
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.72
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.72
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.71
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.7
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.69
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.69
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.67
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.67
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.65
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.65
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.64
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	96.63
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.62
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.62
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.61
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.6
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.59
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.58
3jth_A	98	Transcription activator HLYU; transcription factor	96.57
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.56
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.55
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.55
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.54
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	96.54
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.52
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	96.51
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.5
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.49
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.48
3nqo_A	189	MARR-family transcriptional regulator; structural	96.47
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.47
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.41
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	96.4
2g7u_A	257	Transcriptional regulator; ICLR family, structural	96.38
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	96.38
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	96.36
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.36
1z91_A	147	Organic hydroperoxide resistance transcriptional;	96.35
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	96.35
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.33
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.3
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.29
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.26
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	96.24
2w25_A	150	Probable transcriptional regulatory protein; trans	96.21
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	96.18
2kko_A	108	Possible transcriptional regulatory protein (possi	96.15
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.13
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	96.12
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	96.1
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.05
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.04
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.03
2pg4_A	95	Uncharacterized protein; structural genomics, join	96.01
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.0
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.99
3k69_A	162	Putative transcription regulator; putative transcr	95.94
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.94
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	95.89
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.87
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	95.85
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	95.85
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	95.84
2fxa_A	207	Protease production regulatory protein HPR; protea	95.77
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.77
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.73
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	95.72
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	95.7
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	95.62
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	95.61
4fx0_A	148	Probable transcriptional repressor protein; helix-	95.57
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	95.56
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	95.53
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	95.51
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.46
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.45
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	95.45
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.45
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	95.39
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	95.38
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	95.29
1p6r_A	82	Penicillinase repressor; transcription regulation,	95.27
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	95.26
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.25
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.22
1xd7_A	145	YWNA; structural genomics, protein structure initi	95.22
1bja_A	95	Transcription regulatory protein MOTA; activation	95.13
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	95.11
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.06
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	94.96
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	94.87
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	94.85
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	94.84
2obp_A	96	Putative DNA-binding protein; structural genomics,	94.69
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	94.69
2w57_A	150	Ferric uptake regulation protein; gene regulation,	94.64
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.58
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	94.55
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	94.49
1z05_A	429	Transcriptional regulator, ROK family; structural	94.49
1hsj_A	487	Fusion protein consisting of staphylococcus access	94.38
4ets_A	162	Ferric uptake regulation protein; metal binding pr	94.34
2vn2_A	128	DNAD, chromosome replication initiation protein; D	94.33
1okr_A	123	MECI, methicillin resistance regulatory protein ME	94.25
2qm3_A	373	Predicted methyltransferase; putative methyltransf	94.24
2h09_A	155	Transcriptional regulator MNTR; transcription regu	94.1
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	93.91
4g6q_A	182	Putative uncharacterized protein; structural genom	93.78
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	93.62
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	93.41
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	92.95
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	92.82
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	92.52
3cta_A	230	Riboflavin kinase; structural genomics, transferas	92.1
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	92.04
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	91.29
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	91.27
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	91.08
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	91.02
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	90.98
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	90.83
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	90.74
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	90.73
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	90.73
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	90.43
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	90.28
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	90.27
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	90.26
3b02_A	195	Transcriptional regulator, CRP family; structural	90.05
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	90.0
1ft9_A	222	Carbon monoxide oxidation system transcription reg	89.95
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	89.94
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	89.88
4esf_A	117	PADR-like transcriptional regulator; PADR family,	89.81
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	89.77
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	89.76
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	89.54
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	89.42
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	89.41
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	89.24
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	89.17
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	89.11
3by6_A	126	Predicted transcriptional regulator; structural ge	88.74
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	88.64
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	88.36
3frw_A	107	Putative Trp repressor protein; structural genomic	88.34
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	88.28
3c7j_A	237	Transcriptional regulator, GNTR family; structural	88.23
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	88.22
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.94
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	87.78
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	87.69
2z99_A	219	Putative uncharacterized protein; winged helix dom	87.63
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	87.42
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	87.35
3lsg_A	103	Two-component response regulator YESN; structural	87.17
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	87.01
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	86.73
1xma_A	145	Predicted transcriptional regulator; southea colla	86.49
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	86.37
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	86.35
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	86.34
3mn2_A	108	Probable ARAC family transcriptional regulator; st	86.3
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	86.07
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	86.01
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	85.96
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	85.7
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	85.42
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	85.34
1t6s_A	162	Conserved hypothetical protein; A winged helix-tur	85.16
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	84.66
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	84.24
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	83.92
2o0m_A	345	Transcriptional regulator, SORC family; structural	83.51
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	83.46
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	83.27
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	83.07
2fq3_A	104	Transcription regulatory protein SWI3; four-helix	82.95
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	82.88
1lva_A	258	Selenocysteine-specific elongation factor; winged-	82.39
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	82.28
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	81.91
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	81.88
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	80.89
1bl0_A	129	Protein (multiple antibiotic resistance protein),	80.82
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	80.81

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=99.67  E-value=1.3e-16  Score=117.07  Aligned_cols=78  Identities=18%  Similarity=0.336  Sum_probs=70.6

Q ss_pred             CchhHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477            1 MANEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus         1 ~~~~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      |++. +++.+..+++++.||+.+++|++|++|||||+|++.+  +|+|++|||++++ +    ++..++|+||+|++.|+
T Consensus         1 M~~~-e~~~~~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~--~p~t~~eLA~~~g-~----~~~~l~rlLr~L~~~gl   72 (353)
T 4a6d_A            1 MGSS-EDQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAP--GPLDVAAVAAGVR-A----SAHGTELLLDICVSLKL   72 (353)
T ss_dssp             CCTT-SCHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSS--SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTS
T ss_pred             CCCh-hHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCC--CCCCHHHHHHhhC-c----CHHHHHHHHHHHHHCCC
Confidence            5554 4588888999999999999999999999999999865  8999999999999 9    99999999999999999


Q ss_pred             eeeecc
Q 045477           81 VECSVD   86 (89)
Q Consensus        81 ~~e~~~   86 (89)
                      |++..+
T Consensus        73 l~~~~~   78 (353)
T 4a6d_A           73 LKVETR   78 (353)
T ss_dssp             EEEEEE
T ss_pred             EEEecc
Confidence            986543

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A*

Probab=99.66  E-value=2.7e-16  Score=115.74  Aligned_cols=81  Identities=48%  Similarity=0.813  Sum_probs=71.9

Q ss_pred             hhHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCC-CCCCCcchHHHHHHHHhccCce
Q 045477            3 NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPAT-KNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus         3 ~~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~-~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      .+++++++..+++++++|+.+++|++|++|||||+|+++| ++|+|++|||++++ + .+|.++..|+|+||+|++.|+|
T Consensus        14 ~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lgifd~L~~~g-~~~~t~~eLA~~~g-~~~~~~~~~~l~rlLr~L~~~g~l   91 (364)
T 3p9c_A           14 ASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAG-GKSLTPTEVAAKLP-SAANPEAPDMVDRILRLLASYNVV   91 (364)
T ss_dssp             HHHHHHHHHHHHHHTTTTHHHHHHHHHHHHTHHHHHHHTT-TCCBCHHHHHHTTT-CTTCTTHHHHHHHHHHHHHHTTSE
T ss_pred             chHHHHHHHHHHHHHHhHHHHHHHHHHHHCChHHHHhhcC-CCCCCHHHHHHhcC-CCCCccchhhHHHHHHHHHhCCCE
Confidence            4678899999999999999999999999999999999864 37999999999999 6 3444566999999999999999


Q ss_pred             eeec
Q 045477           82 ECSV   85 (89)
Q Consensus        82 ~e~~   85 (89)
                      +++.
T Consensus        92 ~~~~   95 (364)
T 3p9c_A           92 TCLV   95 (364)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            9873

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 3tky_A* 1kyz_A* 1kyw_A*

Probab=99.66  E-value=2.4e-16  Score=116.01  Aligned_cols=80  Identities=46%  Similarity=0.724  Sum_probs=71.1

Q ss_pred             hHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477            4 EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus         4 ~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      +++++.+..+++++++|+.+++|++|++|||||+|++. |+++|+|++|||++++ ..+|.++..|+|+||+|++.|+|+
T Consensus        16 ~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~-~~~~~~~~~l~rlLr~L~~~gll~   94 (368)
T 3reo_A           16 SSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLP-TTNPEAPVMLDRVLRLLASYSVVT   94 (368)
T ss_dssp             -CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSS-CCCTTHHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcC-cCCCcchhhHHHHHHHHHhCCCeE
Confidence            36788899999999999999999999999999999986 5447899999999997 545556679999999999999999


Q ss_pred             ee
Q 045477           83 CS   84 (89)
Q Consensus        83 e~   84 (89)
                      ++
T Consensus        95 ~~   96 (368)
T 3reo_A           95 YT   96 (368)
T ss_dssp             EE
T ss_pred             Ee
Confidence            86

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A*

Probab=99.55  E-value=1e-14  Score=106.26  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=69.4

Q ss_pred             hHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477            4 EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus         4 ~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ++..+++..+++++++++.+++|+++++|||||+|++.+  +|+|++|||++++ + +|.++..|+|+||+|++.|+|.+
T Consensus         5 ~~~~~~~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~eLA~~~g-~-~~~~~~~l~rlLr~L~~~gll~~   80 (358)
T 1zg3_A            5 SELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHG--KPMTLSELASSLK-L-HPSKVNILHRFLRLLTHNGFFAK   80 (358)
T ss_dssp             SCCTTHHHHHHHHHTTHHHHHHHHHHHHHTHHHHHHHHT--SCEEHHHHHHHTT-C-CTTTHHHHHHHHHHHHHTTSEEE
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHCChHhHHhhcC--CCcCHHHHHHhcC-C-CCcchHHHHHHHHHHhhCCcEEE
Confidence            345677888999999999999999999999999999864  6999999999999 8 55568899999999999999998


Q ss_pred             e
Q 045477           84 S   84 (89)
Q Consensus        84 ~   84 (89)
                      .
T Consensus        81 ~   81 (358)
T 1zg3_A           81 T   81 (358)
T ss_dssp             E
T ss_pred             e
Confidence            7

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=99.54  E-value=9.8e-15  Score=106.96  Aligned_cols=73  Identities=15%  Similarity=0.263  Sum_probs=67.8

Q ss_pred             HhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477            5 ARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus         5 ~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +..+++..+++++++|+.+++|+++++|||||+|++++  +|+|++|||++++ +    ++..++|+||+|++.|+|++.
T Consensus        11 ~~~~a~~~l~~l~~g~~~~~~l~~a~~lgifd~L~~~~--~~~t~~eLA~~~g-~----~~~~l~rlLr~l~~~g~l~~~   83 (363)
T 3dp7_A           11 TAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKR--EGYTLQEISGRTG-L----TRYAAQVLLEASLTIGTILLE   83 (363)
T ss_dssp             CSTTHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHTCT--TCBCHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHHhCHHHHHHhcC--CCCCHHHHHHHhC-c----CHHHHHHHHHHHhhCCCeEec
Confidence            35678888999999999999999999999999999754  7999999999999 9    999999999999999999875

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A*

Probab=99.53  E-value=2.1e-14  Score=104.43  Aligned_cols=77  Identities=18%  Similarity=0.226  Sum_probs=69.5

Q ss_pred             hHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477            4 EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus         4 ~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ++..++...+++++++++.+++|+++++|||||+|++.+  +|+|++|||++++ + +|.++..++|+||+|++.|+|++
T Consensus        11 ~~~~~a~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~--~~~t~~ela~~~~-~-~~~~~~~l~rlLr~L~~~gll~~   86 (352)
T 1fp2_A           11 SEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQ-V-PSSKIGNVRRLMRYLAHNGFFEI   86 (352)
T ss_dssp             THHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHT-C-CGGGHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHhhHHHHHHHHHHHHHHHHHHHHHHHCChhhhhhhcC--CCccHHHHHHHhC-c-CCCChHHHHHHHHHHHhCCeEEE
Confidence            456688889999999999999999999999999999864  6999999999999 8 45558899999999999999998


Q ss_pred             e
Q 045477           84 S   84 (89)
Q Consensus        84 ~   84 (89)
                      .
T Consensus        87 ~   87 (352)
T 1fp2_A           87 I   87 (352)
T ss_dssp             E
T ss_pred             e
Confidence            7

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=99.51  E-value=4.9e-14  Score=101.24  Aligned_cols=69  Identities=19%  Similarity=0.266  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477            8 ENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus         8 ~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++...+++++++++.+.+|+++++|||||+|++    +|+|++|||++++ +    ++..++|+||+|++.|+|.+..
T Consensus         7 ~~~~~l~~~~~~~~~~~~l~~~~~lgi~~~l~~----~~~t~~ela~~~~-~----~~~~l~r~Lr~L~~~g~l~~~~   75 (334)
T 2ip2_A            7 AAARNLIQVVTGEWKSRCVYVATRLGLADLIES----GIDSDETLAAAVG-S----DAERIHRLMRLLVAFEIFQGDT   75 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCcHHHHhC----CCCCHHHHHHHhC-c----CHHHHHHHHHHHHhCCceEecC
Confidence            566789999999999999999999999999975    6999999999999 9    9999999999999999999864

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A*

Probab=99.51  E-value=3.3e-14  Score=104.15  Aligned_cols=81  Identities=44%  Similarity=0.634  Sum_probs=67.8

Q ss_pred             hhHhhHHHHHHH--HHHHhHHHHHHHHHHHHhChHHHHHhcC-CCCCCCHHHHHhhCCCCC--CCCCcchHHHHHHHHhc
Q 045477            3 NEARDENFAYAF--EVTMGSVLHMTMKAVINLGLFEIIAKAG-PGAKLSASEIAAQLPATK--NKDAPTMLDRILGLLAS   77 (89)
Q Consensus         3 ~~~~~~~~~~~~--~l~~~~~~~~aL~~av~LgIfd~l~~~g-~~~~~t~~eLA~~~~~~~--~~~d~~~l~RlLR~L~s   77 (89)
                      .++..+++..+|  +++++++.+++|++|++|||||+|++.| +++++|++|||++++ ++  +|.++..|+|+||+|++
T Consensus        16 ~~~~~~~~~~l~~~~l~~~~~~~~~l~~a~~lgif~~L~~~g~pg~~~t~~eLA~~~~-~~~~~~~~~~~l~rlLr~L~~   94 (372)
T 1fp1_D           16 TSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLP-ASTQHSDLPNRLDRMLRLLAS   94 (372)
T ss_dssp             ---CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSC-GGGCCTTHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHHhcCCCCCCcCHHHHHHhcC-CCCCCCcChHHHHHHHHHHhh
Confidence            345667777888  9999999999999999999999999743 112399999999999 72  56678999999999999


Q ss_pred             cCceeee
Q 045477           78 YGIVECS   84 (89)
Q Consensus        78 ~gi~~e~   84 (89)
                      .|+|++.
T Consensus        95 ~gll~~~  101 (372)
T 1fp1_D           95 YSVLTST  101 (372)
T ss_dssp             TTSEEEE
T ss_pred             CCceEec
Confidence            9999987

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=99.51  E-value=3.6e-14  Score=103.26  Aligned_cols=76  Identities=25%  Similarity=0.331  Sum_probs=68.2

Q ss_pred             CchhHhhHHHHHHHHHHH-hHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477            1 MANEARDENFAYAFEVTM-GSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus         1 ~~~~~~~~~~~~~~~l~~-~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      |..++..+.+..++++++ +++.+++|+++++|||||+|++    +|.|++|||++++ +    ++..++|+||+|++.|
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~----~~~t~~eLA~~~g-~----~~~~l~rlLr~L~~~g   92 (359)
T 1x19_A           22 MSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE----GPKDLATLAADTG-S----VPPRLEMLLETLRQMR   92 (359)
T ss_dssp             ECCCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTT
T ss_pred             CCccccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC----CCCCHHHHHHHhC-c----ChHHHHHHHHHHHhCC
Confidence            334556778888999987 8999999999999999999975    6899999999999 9    9999999999999999


Q ss_pred             ceeeec
Q 045477           80 IVECSV   85 (89)
Q Consensus        80 i~~e~~   85 (89)
                      +|++..
T Consensus        93 ll~~~~   98 (359)
T 1x19_A           93 VINLED   98 (359)
T ss_dssp             SEEEET
T ss_pred             CeEeeC
Confidence            999863

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora}

Probab=99.48  E-value=4.8e-14  Score=102.52  Aligned_cols=69  Identities=25%  Similarity=0.326  Sum_probs=65.0

Q ss_pred             hhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477            6 RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus         6 ~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ..+....+++++++|+.+++|++|++|||||+|++    +|+|++|||++++ +    ++..|+|+||+|++.|+|++
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~g-~----~~~~l~rlLr~l~~~g~l~~   87 (348)
T 3lst_A           19 RLQSALALYEEAMGYTYAAALRAAAAVGVADHLVD----GPRTPAELAAATG-T----DADALRRVLRLLAVRDVVRE   87 (348)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHTGGGGGTT----SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEE
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhC----CCCCHHHHHHHhC-c----CHHHHHHHHHHHHhCCCEEe
Confidence            45677889999999999999999999999999974    6999999999999 9    99999999999999999998

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A*

Probab=99.45  E-value=9.2e-14  Score=101.97  Aligned_cols=71  Identities=20%  Similarity=0.278  Sum_probs=65.5

Q ss_pred             hhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477            6 RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus         6 ~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.+....+++++++|+.+++|+++++|||||+|++    +|+|++|||++++ +    ++..++|+||+|++.|+|.++.
T Consensus        35 ~~~~~~~l~~l~~~~~~~~~l~~a~~lglf~~l~~----g~~t~~eLA~~~g-~----~~~~l~rlLr~L~~~g~l~~~~  105 (369)
T 3gwz_A           35 RAAAEETVNDILQGAWKARAIHVAVELGVPELLQE----GPRTATALAEATG-A----HEQTLRRLLRLLATVGVFDDLG  105 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGTT----SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSSEECS
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHCChhhhhcC----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHhCCCEEEeC
Confidence            44666779999999999999999999999999984    6999999999999 9    9999999999999999999853

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=99.44  E-value=1.3e-13  Score=99.17  Aligned_cols=65  Identities=22%  Similarity=0.261  Sum_probs=60.8

Q ss_pred             HHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           12 YAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        12 ~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+++++.+|+.+++|++|++|||||+|++    +|+|++|||++++ +    ++..++|+||+|++.|+|.++.
T Consensus         8 ~l~~~~~g~~~~~~l~~a~~lglf~~l~~----g~~t~~elA~~~~-~----~~~~l~rlLr~l~~~gl~~~~~   72 (332)
T 3i53_A            8 IGLRALADLATPMAVRVAATLRVADHIAA----GHRTAAEIASAAG-A----HADSLDRLLRHLVAVGLFTRDG   72 (332)
T ss_dssp             SCHHHHTCCHHHHHHHHHHHHTHHHHHHT----TCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHhhHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHhCCcEEecC
Confidence            36789999999999999999999999975    6999999999999 9    9999999999999999999863

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=99.39  E-value=5.7e-13  Score=95.22  Aligned_cols=65  Identities=18%  Similarity=0.234  Sum_probs=60.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           11 AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        11 ~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+++++++++.+++|+++++|||||+|++    +|+|++|||++++ +    ++..++|+||+|++.|+|++.
T Consensus         8 ~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~-~----~~~~l~r~L~~L~~~g~l~~~   72 (335)
T 2r3s_A            8 ALFFNTVNAYQRSAAIKAAVELNVFTAISQ----GIESSQSLAQKCQ-T----SERGMRMLCDYLVIIGFMTKQ   72 (335)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHTTHHHHHTT----SEECHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcChHHHHhc----CCCCHHHHHHHhC-C----CchHHHHHHHHHHhcCCeEec
Confidence            458899999999999999999999999985    6999999999999 9    999999999999999999864

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=99.37  E-value=7.4e-13  Score=96.19  Aligned_cols=70  Identities=19%  Similarity=0.283  Sum_probs=64.1

Q ss_pred             hhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477            6 RDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus         6 ~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++....+++++++++.+.+|++++++||||+|++    +|+|++|||++++ +    ++..++|+||+|++.|+|.+.
T Consensus        13 ~~~~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~eLA~~~g-~----~~~~l~r~Lr~L~~~Gll~~~   82 (374)
T 1qzz_A           13 TDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTD-T----HPQALSRLVRHLTVVGVLEGG   82 (374)
T ss_dssp             CHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEECC
T ss_pred             CchHHHHHHHHHHhhHHHHHHHHHHHcChHHHHhC----CCCCHHHHHHHhC-c----CHHHHHHHHHHHhhCCCEEEe
Confidence            34556679999999999999999999999999964    6999999999999 9    999999999999999999974

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=99.36  E-value=5.6e-13  Score=96.30  Aligned_cols=65  Identities=14%  Similarity=0.136  Sum_probs=60.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           11 AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        11 ~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..+++++++|+.+++|+++++|||||+|+     +|+|++|||++++ +    ++..++|+||+|++.|+|++..
T Consensus        26 ~~l~~~~~~~~~~~~l~~a~~lgif~~l~-----~~~t~~elA~~~~-~----~~~~l~rlLr~L~~~gll~~~~   90 (352)
T 3mcz_A           26 VDLVKLSDQYRQSAILHYAVADKLFDLTQ-----TGRTPAEVAASFG-M----VEGKAAILLHALAALGLLTKEG   90 (352)
T ss_dssp             HHHHHHHHTHHHHHHHHHHHHTTHHHHTT-----SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCChHHHhC-----CCCCHHHHHHHhC-c----ChHHHHHHHHHHHHCCCeEecC
Confidence            34899999999999999999999999994     3899999999999 9    9999999999999999999864

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=99.29  E-value=7e-12  Score=90.74  Aligned_cols=68  Identities=19%  Similarity=0.197  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477            8 ENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus         8 ~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .....+++++++|+.+.+|++++++|||++|.+    +|+|++|||++++ +    ++..+.|+||+|++.|+|.+.
T Consensus        18 ~~~~~~~~~~~~~~~~~~l~~~~~l~i~~~l~~----~~~t~~ela~~~~-~----~~~~l~r~L~~L~~~g~~~~~   85 (360)
T 1tw3_A           18 IDALRTLIRLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTD-T----RPEALLRLIRHLVAIGLLEED   85 (360)
T ss_dssp             HHHHHHHHHHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cchHHHHHHHHhHHHHHHHHHHHHhCHHHHHhC----CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEec
Confidence            345567899999999999999999999999964    6999999999999 9    999999999999999999985

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=97.50  E-value=0.00012  Score=41.99  Aligned_cols=47  Identities=11%  Similarity=0.248  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .+..|.++|.+.+  .|+|..|||+.++ +    +...+.|++..|...|++..
T Consensus        11 ~~~~IL~~L~~~~--~~~s~~eLA~~lg-l----sr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           11 LEQKILQVLSDDG--GPVAIFQLVKKCQ-V----PKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHHHHC--SCEEHHHHHHHHC-S----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHcC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEec
Confidence            3567899998765  6899999999999 9    89999999999999999865

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=97.32  E-value=0.00022  Score=45.01  Aligned_cols=49  Identities=12%  Similarity=0.204  Sum_probs=42.3

Q ss_pred             HHhChHHHHHhcCCCCC-CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAK-LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~-~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|...|.+.+  +| +|+.|||+.++ .    +...++|.++.|...|++....
T Consensus        27 ~e~~il~~L~~~~--~~~~t~~eLa~~l~-~----s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           27 ADLNVMKSFLNEP--DRWIDTDALSKSLK-L----DVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHHHHST--TCCEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHCC--CCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeeC
Confidence            3566788888765  67 99999999999 9    9999999999999999998653

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.26  E-value=0.004  Score=38.81  Aligned_cols=50  Identities=24%  Similarity=0.302  Sum_probs=41.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|+..|....  +++|..+||+.++ .    ++..+.|+++.|...|++....+
T Consensus        36 ~~~~iL~~l~~~~--~~~~~~~la~~l~-i----~~~~vs~~l~~Le~~glv~r~~~   85 (147)
T 2hr3_A           36 SQLVVLGAIDRLG--GDVTPSELAAAER-M----RSSNLAALLRELERGGLIVRHAD   85 (147)
T ss_dssp             HHHHHHHHHHHTT--SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHhC-C----ChhhHHHHHHHHHHCCCEeeCCC
Confidence            4566777777622  6899999999999 9    99999999999999999987644

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=97.21  E-value=0.00024  Score=41.43  Aligned_cols=50  Identities=20%  Similarity=0.305  Sum_probs=41.5

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhC-----CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQL-----PATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~-----~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ...|.+.|.+.+ ++++|++||++.+     + +    +...++|.|+.|+..|++.....
T Consensus        19 r~~IL~~l~~~~-~~~~s~~el~~~l~~~~~~-i----s~~TVyR~L~~L~~~Glv~~~~~   73 (83)
T 2fu4_A           19 RLKILEVLQEPD-NHHVSAEDLYKRLIDMGEE-I----GLATVYRVLNQFDDAGIVTRHNF   73 (83)
T ss_dssp             HHHHHHHHTSGG-GSSBCHHHHHHHHHHTTCC-C----CHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHhCC-CCCCCHHHHHHHHHHhCCC-C----CHhhHHHHHHHHHHCCCeEEEee
Confidence            456888887642 1589999999999     6 7    88899999999999999987643

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=97.18  E-value=0.00029  Score=50.02  Aligned_cols=47  Identities=15%  Similarity=0.322  Sum_probs=40.4

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.|.+.+++.+  +++|++|||+.++ .    +...++|+|+.|+..|++..+.
T Consensus        33 l~IL~~l~~~~--~~ltl~eia~~lg-l----~ksTv~RlL~tL~~~G~v~~~~   79 (275)
T 3mq0_A           33 VRILDLVAGSP--RDLTAAELTRFLD-L----PKSSAHGLLAVMTELDLLARSA   79 (275)
T ss_dssp             HHHHHHHHHCS--SCEEHHHHHHHHT-C----C--CHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHhhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEECC
Confidence            46888998865  7899999999999 9    8889999999999999998764

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=97.17  E-value=0.00049  Score=40.57  Aligned_cols=52  Identities=19%  Similarity=0.319  Sum_probs=45.0

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -.+..|.+.|.+.++++++|+.|||+.++ +    +...+.|.|..|...|++...+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lg-v----s~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLG-T----PKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHC-C----CHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEecC
Confidence            34678889998876556899999999999 9    8899999999999999997654

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=97.16  E-value=0.00096  Score=39.86  Aligned_cols=54  Identities=19%  Similarity=0.293  Sum_probs=46.1

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..-++..|.+.|.+.++|.++|+.|||++++ +    ....+.|.|..|...|++...+
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lg-v----sr~tV~~~L~~Le~~G~I~~~g   61 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLG-T----PKKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEES
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEecC
Confidence            3345777899998876567899999999999 9    8899999999999999997654

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

Probab=97.12  E-value=0.0013  Score=41.39  Aligned_cols=46  Identities=20%  Similarity=0.216  Sum_probs=37.8

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |...|+.+.+++++|+.|||+.++ +    .+..++|+|+.|...|++...
T Consensus        14 iL~~la~~~~~~~~s~~ela~~~~-i----~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           14 IMIELAKKHGEGPTSLKSIAQTNN-L----SEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             HHHHHHHTTTSCCBCHHHHHHHTT-S----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHhCCCCCcCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEec
Confidence            444555542237899999999999 9    999999999999999998765

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=97.10  E-value=0.0009  Score=39.74  Aligned_cols=44  Identities=23%  Similarity=0.342  Sum_probs=39.6

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.|.+.   +.+|++|||+.++ +    .+..++|.|..|...|++..+
T Consensus         6 ~Il~~L~~~---g~vsv~eLa~~l~-V----S~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALR---GRMEAAQISQTLN-T----PQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHS---CSBCHHHHHHHTT-C----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHc---CCCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEe
Confidence            467778775   6999999999999 9    999999999999999999876

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=97.05  E-value=0.00077  Score=39.31  Aligned_cols=45  Identities=24%  Similarity=0.245  Sum_probs=39.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|.+.|.+.   +++|..|||+.++ +    .+..++|.|+.|...|++...
T Consensus         3 ~~Il~~L~~~---~~~s~~eLa~~lg-v----s~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            3 NEILEFLNRH---NGGKTAEIAEALA-V----TDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHHS---CCCCHHHHHHHHT-S----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEe
Confidence            4577788764   5899999999999 9    899999999999999999854

>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=97.04  E-value=0.00062  Score=47.26  Aligned_cols=48  Identities=19%  Similarity=0.183  Sum_probs=41.4

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +.|.+.|.+.+  +++|+.|||+.++ .    +...++|+|+.|...|++....+
T Consensus         9 l~iL~~l~~~~--~~~s~~ela~~~g-l----~~stv~r~l~~L~~~G~v~~~~~   56 (241)
T 2xrn_A            9 ASIMRALGSHP--HGLSLAAIAQLVG-L----PRSTVQRIINALEEEFLVEALGP   56 (241)
T ss_dssp             HHHHHHHHTCT--TCEEHHHHHHHTT-S----CHHHHHHHHHHHHTTTSEEECGG
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeCC
Confidence            45677887654  6899999999999 9    99999999999999999987643

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

Probab=97.03  E-value=0.0037  Score=37.23  Aligned_cols=50  Identities=18%  Similarity=0.183  Sum_probs=42.4

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++.--..+.|+..| +    +++|..|||+.++ +    .+..++|.++.|...|++...
T Consensus        27 ~l~~~~r~~Il~~L-~----~~~~~~eLa~~l~-i----s~~tv~~~L~~L~~~Glv~~~   76 (96)
T 1y0u_A           27 AVTNPVRRKILRML-D----KGRSEEEIMQTLS-L----SKKQLDYHLKVLEAGFCIERV   76 (96)
T ss_dssp             HHSCHHHHHHHHHH-H----TTCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCCHHHHHHHHHH-c----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            34444567788888 4    6899999999999 9    899999999999999999864

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

Probab=97.03  E-value=0.0037  Score=39.01  Aligned_cols=51  Identities=12%  Similarity=0.227  Sum_probs=38.3

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ..+..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        37 ~~~~~vL~~l~~~---~~~t~~eLa~~l~-~----~~~tvs~~l~~L~~~Glv~r~~~~   87 (142)
T 3ech_A           37 PPDVHVLKLIDEQ---RGLNLQDLGRQMC-R----DKALITRKIRELEGRNLVRRERNP   87 (142)
T ss_dssp             HHHHHHHHHHHHT---TTCCHHHHHHHHC--------CHHHHHHHHHHHTTSEEC----
T ss_pred             HHHHHHHHHHHhC---CCcCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEeeccCC
Confidence            4556677778764   5899999999999 9    999999999999999999876543

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=97.00  E-value=0.0011  Score=39.15  Aligned_cols=53  Identities=23%  Similarity=0.319  Sum_probs=44.5

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++.--.++.|+..|...   +++|..|||+.++ .    ++..+.|.++.|...|++....
T Consensus        12 ~l~~~~~~~iL~~L~~~---~~~~~~ela~~l~-i----s~~tvs~~l~~L~~~gli~~~~   64 (100)
T 1ub9_A           12 ILGNPVRLGIMIFLLPR---RKAPFSQIQKVLD-L----TPGNLDSHIRVLERNGLVKTYK   64 (100)
T ss_dssp             HHHSHHHHHHHHHHHHH---SEEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             ccCChHHHHHHHHHHhc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEe
Confidence            44455677888888754   5899999999999 9    9999999999999999998543

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=96.99  E-value=0.00096  Score=40.55  Aligned_cols=45  Identities=20%  Similarity=0.361  Sum_probs=40.2

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|.+.|.+.   +.+|++|||+.++ +    .+..++|.|..|...|++..+.
T Consensus         6 ~Il~~L~~~---g~vsv~eLA~~l~-V----S~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQ---GRMEAKQLSARLQ-T----PQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHS---CSEEHHHHHHHTT-C----CHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHc---CCCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEe
Confidence            467778775   6999999999999 9    9999999999999999998773

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=96.98  E-value=0.0013  Score=41.81  Aligned_cols=57  Identities=21%  Similarity=0.209  Sum_probs=44.3

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeeccc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +-.+.-|.+.|.+.+  +++|++||.+.+. .. +.-+...++|.|+.|+..|++.+....
T Consensus        10 T~qR~~Il~~l~~~~--~~~sa~ei~~~l~-~~~~~is~~TVYR~L~~L~e~Glv~~~~~~   67 (131)
T 2o03_A           10 TRQRAAISTLLETLD--DFRSAQELHDELR-RRGENIGLTTVYRTLQSMASSGLVDTLHTD   67 (131)
T ss_dssp             HHHHHHHHHHHHHCC--SCEEHHHHHHHHH-HTTCCCCHHHHHHHHHHHHTTTSEEEEECT
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHH-HhCCCCCHhhHHHHHHHHHHCCCEEEEEeC
Confidence            445667889998754  7999999999983 11 111788999999999999999987543

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=96.93  E-value=0.0011  Score=46.04  Aligned_cols=46  Identities=22%  Similarity=0.295  Sum_probs=40.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.|.+.|.+.+  +++|+.|||+.++ .    +...+.|+|+.|...|++...
T Consensus        11 l~iL~~l~~~~--~~~~~~ela~~~g-l----~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           11 FEILDFIVKNP--GDVSVSEIAEKFN-M----SVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHHHCS--SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEC
Confidence            46778888754  6899999999999 9    899999999999999999876

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=96.92  E-value=0.0013  Score=38.93  Aligned_cols=49  Identities=18%  Similarity=0.333  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+..|...|...   +++|..|||+.++ .    ++..+.|.++.|...|++.....
T Consensus        21 ~~~~il~~l~~~---~~~s~~ela~~l~-i----s~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           21 SDVRIYSLLLER---GGMRVSEIARELD-L----SARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEEee
Confidence            355667777664   5899999999999 9    99999999999999999987543

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=96.92  E-value=0.0061  Score=38.27  Aligned_cols=49  Identities=18%  Similarity=0.286  Sum_probs=41.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|+..|...   +++|..+||+.++ .    ++..+.|+++.|...|++......
T Consensus        39 ~~~iL~~l~~~---~~~t~~ela~~l~-~----s~~tvs~~l~~Le~~glv~r~~~~   87 (155)
T 1s3j_A           39 QLFVLASLKKH---GSLKVSEIAERME-V----KPSAVTLMADRLEQKNLIARTHNT   87 (155)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeecCCC
Confidence            34466677764   5899999999999 9    999999999999999999876543

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.91  E-value=0.001  Score=39.44  Aligned_cols=45  Identities=20%  Similarity=0.263  Sum_probs=39.0

Q ss_pred             ChHHHHHhc-----CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           33 GLFEIIAKA-----GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        33 gIfd~l~~~-----g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+.|.+.     |  +|.|+.|||+.++ +    .+..++|-|..|...|++..+
T Consensus         8 ~IL~~I~~~i~~~~g--~~psv~EIa~~lg-v----S~~TVrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            8 KIISIVQERQNMDDG--APVKTRDIADAAG-L----SIYQVRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             HHHHHHHHHHHHHTT--SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhhccC--CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEec
Confidence            366666665     5  7999999999999 9    788999999999999999876

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=96.91  E-value=0.0089  Score=37.06  Aligned_cols=48  Identities=10%  Similarity=0.131  Sum_probs=39.9

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ++.|...|. .   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        39 ~~~iL~~l~-~---~~~~~~ela~~l~-~----s~~tvs~~l~~Le~~glv~r~~~~   86 (146)
T 2gxg_A           39 DFLVLRATS-D---GPKTMAYLANRYF-V----TQSAITASVDKLEEMGLVVRVRDR   86 (146)
T ss_dssp             HHHHHHHHT-T---SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHh-c---CCcCHHHHHHHhC-C----CchhHHHHHHHHHHCCCEEeecCC
Confidence            444555665 2   7899999999999 9    999999999999999999876543

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=96.90  E-value=0.0012  Score=41.05  Aligned_cols=53  Identities=15%  Similarity=0.100  Sum_probs=43.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      .+..|...|...+ ++++|..|||+.++ .    ++..+.|+++.|...|++....+..
T Consensus        32 ~~~~vL~~l~~~~-~~~~t~~ela~~l~-~----~~~tvs~~l~~Le~~Gli~r~~~~~   84 (139)
T 3eco_A           32 EQGHTLGYLYAHQ-QDGLTQNDIAKALQ-R----TGPTVSNLLRNLERKKLIYRYVDAQ   84 (139)
T ss_dssp             HHHHHHHHHHHST-TTCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECCC
T ss_pred             HHHHHHHHHHhcC-CCCcCHHHHHHHhC-C----CcccHHHHHHHHHHCCCEeecCCCC
Confidence            3455666777653 25999999999999 9    9999999999999999999765443

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=96.89  E-value=0.0017  Score=40.21  Aligned_cols=51  Identities=4%  Similarity=0.178  Sum_probs=41.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...+ ++++|..|||+.++ .    ++..+.|+++.|...|++......
T Consensus        36 ~~~iL~~l~~~~-~~~~~~~ela~~l~-~----~~~tvs~~l~~Le~~Gli~r~~~~   86 (141)
T 3bro_A           36 QMTIIDYLSRNK-NKEVLQRDLESEFS-I----KSSTATVLLQRMEIKKLLYRKVSG   86 (141)
T ss_dssp             HHHHHHHHHHTT-TSCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHCC-CCCcCHHHHHHHHC-C----CcchHHHHHHHHHHCCCEEeeCCC
Confidence            444566677654 23899999999999 9    999999999999999999876543

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

Probab=96.89  E-value=0.0016  Score=40.25  Aligned_cols=49  Identities=8%  Similarity=0.188  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        39 ~~~~iL~~l~~~---~~~t~~ela~~l~-~----~~~tvs~~l~~L~~~glv~r~~~   87 (140)
T 2nnn_A           39 TQWAALVRLGET---GPCPQNQLGRLTA-M----DAATIKGVVERLDKRGLIQRSAD   87 (140)
T ss_dssp             HHHHHHHHHHHH---SSBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeeCC
Confidence            356677778765   5899999999999 9    99999999999999999987543

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=96.85  E-value=0.0019  Score=41.72  Aligned_cols=56  Identities=16%  Similarity=0.121  Sum_probs=43.8

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCC-CCCcchHHHHHHHHhccCceeeeccc
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKN-KDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~-~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      -.+.-|.+.|.+.+  +++|+.||.+.+. ... .-+...++|.|+.|+..|++.+....
T Consensus        22 ~qR~~Il~~L~~~~--~~~sa~ei~~~l~-~~~~~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           22 PQRHAILEYLVNSM--AHPTADDIYKALE-GKFPNMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             HHHHHHHHHHHHCS--SCCCHHHHHHHHG-GGCTTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             HHHHHHHHHHHhCC--CCCCHHHHHHHHH-HhCCCCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            34566889998754  7999999999984 221 11788999999999999999987543

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=96.83  E-value=0.0012  Score=41.74  Aligned_cols=51  Identities=14%  Similarity=0.263  Sum_probs=39.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...+  +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        40 ~q~~vL~~l~~~~--~~~t~~eLa~~l~-i----~~~tvs~~l~~Le~~Glv~r~~~~   90 (150)
T 3fm5_A           40 RSYSVLVLACEQA--EGVNQRGVAATMG-L----DPSQIVGLVDELEERGLVVRTLDP   90 (150)
T ss_dssp             HHHHHHHHHHHST--TCCCSHHHHHHHT-C----CHHHHHHHHHHHHTTTSEEC----
T ss_pred             HHHHHHHHHHhCC--CCcCHHHHHHHHC-C----CHhHHHHHHHHHHHCCCEEeeCCc
Confidence            3455556676654  6899999999999 9    999999999999999999876543

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

Probab=96.82  E-value=0.0021  Score=39.58  Aligned_cols=49  Identities=18%  Similarity=0.422  Sum_probs=41.0

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        34 ~~~~iL~~l~~~---~~~~~~ela~~l~-~----~~~tvs~~l~~L~~~gli~r~~~   82 (139)
T 3bja_A           34 VQFGVIQVLAKS---GKVSMSKLIENMG-C----VPSNMTTMIQRMKRDGYVMTEKN   82 (139)
T ss_dssp             HHHHHHHHHHHS---CSEEHHHHHHHCS-S----CCTTHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCeeeccC
Confidence            345566677664   5899999999999 9    88999999999999999987544

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

Probab=96.81  E-value=0.0021  Score=39.72  Aligned_cols=50  Identities=18%  Similarity=0.248  Sum_probs=42.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .++.|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        32 ~~~~iL~~l~~~---~~~~~~ela~~l~-i----s~~~vs~~l~~L~~~gli~~~~~~   81 (142)
T 3bdd_A           32 TRYSILQTLLKD---APLHQLALQERLQ-I----DRAAVTRHLKLLEESGYIIRKRNP   81 (142)
T ss_dssp             HHHHHHHHHHHH---CSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCCC
Confidence            345577777765   5899999999999 9    999999999999999999876543

>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=96.80  E-value=0.0015  Score=40.53  Aligned_cols=46  Identities=20%  Similarity=0.244  Sum_probs=38.3

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+...|.-..  +|+|..|||+.++ .    ++..+.|+++.|...|++....
T Consensus        30 ~il~~L~~~~--~~~t~~ela~~l~-~----~~stvs~~l~~L~~~G~v~r~~   75 (152)
T 1ku9_A           30 AVYAILYLSD--KPLTISDIMEELK-I----SKGNVSMSLKKLEELGFVRKVW   75 (152)
T ss_dssp             HHHHHHHHCS--SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHcC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEe
Confidence            3455664222  6899999999999 9    9999999999999999998764

>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=96.80  E-value=0.0014  Score=38.91  Aligned_cols=37  Identities=19%  Similarity=0.266  Sum_probs=34.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +++|..|||+.++ +    ++..+.|.++.|...|++.....
T Consensus        35 ~~~t~~ela~~l~-i----s~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           35 KPITSEELADIFK-L----SKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEeecc
Confidence            6899999999999 9    99999999999999999987643

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

Probab=96.80  E-value=0.011  Score=37.40  Aligned_cols=49  Identities=14%  Similarity=0.224  Sum_probs=39.7

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++.|...|...+  +++|..|||+.++ .    ++..+.|+++.|...|++.....
T Consensus        49 ~~~iL~~L~~~~--~~~~~~ela~~l~-i----~~~tvs~~l~~Le~~Gli~r~~~   97 (160)
T 3boq_A           49 KFDAMAQLARNP--DGLSMGKLSGALK-V----TNGNVSGLVNRLIKDGMVVKAMS   97 (160)
T ss_dssp             HHHHHHHHHHCT--TCEEHHHHHHHCS-S----CCSCHHHHHHHHHHHTSEEEC--
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCEEeecC
Confidence            445666774333  6899999999999 9    89999999999999999987644

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

Probab=96.79  E-value=0.0028  Score=40.56  Aligned_cols=50  Identities=22%  Similarity=0.312  Sum_probs=41.9

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.+
T Consensus        48 q~~iL~~l~~~---~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~~   97 (162)
T 3k0l_A           48 QFTALSVLAAK---PNLSNAKLAERSF-I----KPQSANKILQDLLANGWIEKAPDPT   97 (162)
T ss_dssp             HHHHHHHHHHC---TTCCHHHHHHHHT-S----CGGGHHHHHHHHHHTTSEEEEECCS
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCcCeEecCCCC
Confidence            34466677764   5899999999999 9    9999999999999999999775543

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

Probab=96.78  E-value=0.0022  Score=40.13  Aligned_cols=51  Identities=12%  Similarity=0.175  Sum_probs=42.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      .+..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+..
T Consensus        32 ~q~~iL~~l~~~---~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~~   82 (145)
T 3g3z_A           32 NLFAVLYTLATE---GSRTQKHIGEKWS-L----PKQTVSGVCKTLAGQGLIEWQEGEQ   82 (145)
T ss_dssp             HHHHHHHHHHHH---CSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECCCSS
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeeccCCC
Confidence            455667777765   4799999999999 9    9999999999999999999765443

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=96.77  E-value=0.016  Score=36.34  Aligned_cols=42  Identities=12%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .|...| ..   +++|..|||+.++ .    ++..+.|+++.|...|++..
T Consensus        42 ~iL~~l-~~---~~~t~~eLa~~l~-~----~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           42 HVLNML-SI---EALTVGQITEKQG-V----NKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HHHHHH-HH---SCBCHHHHHHHHC-S----CSSHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHH-Hc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEe
Confidence            366777 43   6899999999999 9    89999999999999999986

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

Probab=96.77  E-value=0.0072  Score=38.55  Aligned_cols=49  Identities=18%  Similarity=0.276  Sum_probs=40.3

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        55 q~~vL~~l~~~---~~~t~~eLa~~l~-~----~~~~vs~~l~~Le~~Glv~r~~~~  103 (161)
T 3e6m_A           55 KLRLLSSLSAY---GELTVGQLATLGV-M----EQSTTSRTVDQLVDEGLAARSISD  103 (161)
T ss_dssp             HHHHHHHHHHH---SEEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEECC--
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeeCCc
Confidence            34466677765   5899999999999 9    999999999999999999876543

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

Probab=96.77  E-value=0.0099  Score=36.98  Aligned_cols=48  Identities=13%  Similarity=0.229  Sum_probs=40.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...   ++ |..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        39 ~~~iL~~l~~~---~~-~~~~la~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~   86 (144)
T 3f3x_A           39 DFSILKATSEE---PR-SMVYLANRYF-V----TQSAITAAVDKLEAKGLVRRIRDS   86 (144)
T ss_dssp             HHHHHHHHHHS---CE-EHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHC---CC-CHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEeccCC
Confidence            44566677765   35 9999999999 9    999999999999999999876543

>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=96.76  E-value=0.00027  Score=49.70  Aligned_cols=48  Identities=17%  Similarity=0.209  Sum_probs=40.5

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +.|.+.|++.+  +++|++|||+.+| .    +...++|+|+.|+..|++.....
T Consensus         9 l~IL~~l~~~~--~~lsl~eia~~lg-l----~ksT~~RlL~tL~~~G~v~~~~~   56 (260)
T 3r4k_A            9 LTLLTYFNHGR--LEIGLSDLTRLSG-M----NKATVYRLMSELQEAGFVEQVEG   56 (260)
T ss_dssp             HHHHTTCBTTB--SEEEHHHHHHHHC-S----CHHHHHHHHHHHHHTTSEEECSS
T ss_pred             HHHHHHHhhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEcCC
Confidence            34666666543  7899999999999 9    89999999999999999987654

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

Probab=96.76  E-value=0.0022  Score=38.84  Aligned_cols=46  Identities=26%  Similarity=0.429  Sum_probs=39.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+.|...|.+    +|+|..|||+.++ .    ++..+.|.++.|...|++...
T Consensus        22 ~r~~IL~~L~~----~~~~~~ela~~l~-i----s~~tv~~~l~~L~~~gli~~~   67 (114)
T 2oqg_A           22 TRWEILTELGR----ADQSASSLATRLP-V----SRQAIAKHLNALQACGLVESV   67 (114)
T ss_dssp             HHHHHHHHHHH----SCBCHHHHHHHSS-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeeEE
Confidence            45677787833    5899999999999 9    999999999999999999754

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

Probab=96.76  E-value=0.0017  Score=40.66  Aligned_cols=50  Identities=14%  Similarity=0.198  Sum_probs=39.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        41 ~~~~iL~~l~~~---~~~t~~ela~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~   90 (148)
T 3nrv_A           41 TEWRIISVLSSA---SDCSVQKISDILG-L----DKAAVSRTVKKLEEKKYIEVNGHS   90 (148)
T ss_dssp             HHHHHHHHHHHS---SSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEC----
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeecCC
Confidence            345566677764   5999999999999 9    999999999999999999876443

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=96.74  E-value=0.0024  Score=38.81  Aligned_cols=48  Identities=21%  Similarity=0.302  Sum_probs=41.2

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      --.++.|+..|.+    +++|+.|||+.++ .    .+..+.|.++.|...|++...
T Consensus        25 ~~~r~~IL~~L~~----~~~~~~ela~~l~-i----s~stvs~~L~~L~~~Glv~~~   72 (106)
T 1r1u_A           25 DYNRIRIMELLSV----SEASVGHISHQLN-L----SQSNVSHQLKLLKSVHLVKAK   72 (106)
T ss_dssp             SHHHHHHHHHHHH----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            3456678888874    6899999999999 9    899999999999999999754

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.72  E-value=0.0018  Score=40.19  Aligned_cols=51  Identities=12%  Similarity=0.194  Sum_probs=43.7

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|.--..+.|...|.+    +|+|+.|||+.++ +    .+..+.+.|+.|...|++...
T Consensus        14 al~~~~R~~Il~~L~~----~~~~~~eLa~~l~-i----s~~tvs~hL~~L~~~GlV~~~   64 (118)
T 3f6o_A           14 ALADPTRRAVLGRLSR----GPATVSELAKPFD-M----ALPSFMKHIHFLEDSGWIRTH   64 (118)
T ss_dssp             HHTSHHHHHHHHHHHT----CCEEHHHHHTTCC-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCCHHHHHHHHHHHh----CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            4444567788888874    6899999999999 9    899999999999999999754

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=96.72  E-value=0.0019  Score=40.66  Aligned_cols=50  Identities=12%  Similarity=0.149  Sum_probs=34.1

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ..|...|...+ ++++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        44 ~~vL~~l~~~~-~~~~t~~eLa~~l~-~----~~~~vs~~l~~L~~~Glv~r~~~~   93 (148)
T 3jw4_A           44 GRMIGYIYENQ-ESGIIQKDLAQFFG-R----RGASITSMLQGLEKKGYIERRIPE   93 (148)
T ss_dssp             HHHHHHHHHHT-TTCCCHHHHHHC-----------CHHHHHHHHHHTTSBCCC---
T ss_pred             HHHHHHHHhCC-CCCCCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEeeCCC
Confidence            44556666653 26899999999999 9    899999999999999999876543

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

Probab=96.72  E-value=0.0026  Score=39.45  Aligned_cols=50  Identities=20%  Similarity=0.181  Sum_probs=40.3

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...+  +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        39 ~~~iL~~l~~~~--~~~t~~~la~~l~-~----s~~~vs~~l~~L~~~glv~r~~~~   88 (146)
T 2fbh_A           39 RWLVLLHLARHR--DSPTQRELAQSVG-V----EGPTLARLLDGLESQGLVRRLAVA   88 (146)
T ss_dssp             HHHHHHHHHHCS--SCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             HHHHHHHHHHcC--CCCCHHHHHHHhC-C----ChhhHHHHHHHHHHCCCeeecCCC
Confidence            344566662222  7899999999999 9    999999999999999999876543

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

Probab=96.71  E-value=0.0019  Score=39.80  Aligned_cols=48  Identities=19%  Similarity=0.258  Sum_probs=40.7

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++.|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        31 ~~~iL~~l~~~---~~~~~~ela~~l~-~----s~~tvs~~l~~L~~~glv~~~~~   78 (138)
T 3bpv_A           31 QVACLLRIHRE---PGIKQDELATFFH-V----DKGTIARTLRRLEESGFIEREQD   78 (138)
T ss_dssp             HHHHHHHHHHS---TTCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeecC
Confidence            44566677764   6899999999999 9    99999999999999999987543

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

Probab=96.70  E-value=0.0014  Score=38.65  Aligned_cols=50  Identities=12%  Similarity=0.151  Sum_probs=42.2

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      --..+.|...|.+ +  +++|..|||+.++ .    ++..+.|.++.|...|++....
T Consensus        23 ~~~~~~il~~l~~-~--~~~s~~ela~~l~-i----s~~tvs~~l~~L~~~glv~~~~   72 (99)
T 3cuo_A           23 HPKRLLILCMLSG-S--PGTSAGELTRITG-L----SASATSQHLARMRDEGLIDSQR   72 (99)
T ss_dssp             SHHHHHHHHHHTT-C--CSEEHHHHHHHHC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             ChHHHHHHHHHHh-C--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEe
Confidence            3456678888865 2  6899999999999 9    8999999999999999998653

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=96.69  E-value=0.0033  Score=39.82  Aligned_cols=50  Identities=24%  Similarity=0.244  Sum_probs=42.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .++.|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++......
T Consensus        45 ~~~~iL~~l~~~---~~~t~~ela~~l~-i----s~~tvs~~l~~Le~~Gli~r~~~~   94 (154)
T 2eth_A           45 TELYAFLYVALF---GPKKMKEIAEFLS-T----TKSNVTNVVDSLEKRGLVVREMDP   94 (154)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHTT-S----CHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeeCCC
Confidence            456677778765   5899999999999 9    999999999999999999876543

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

Probab=96.69  E-value=0.0016  Score=40.69  Aligned_cols=50  Identities=18%  Similarity=0.225  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        38 ~~~~iL~~l~~~---~~~t~~eLa~~l~-~----~~~~vs~~l~~L~~~Glv~r~~~~   87 (143)
T 3oop_A           38 EQWSVLEGIEAN---EPISQKEIALWTK-K----DTPTVNRIVDVLLRKELIVREIST   87 (143)
T ss_dssp             HHHHHHHHHHHH---SSEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHC-C----CHhhHHHHHHHHHHCCCeeccCCC
Confidence            445566677765   5899999999999 9    999999999999999999876543

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

Probab=96.67  E-value=0.0033  Score=37.75  Aligned_cols=50  Identities=26%  Similarity=0.399  Sum_probs=41.5

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |.--..+.|...|.+    +|+|+.|||+.++ .    .+..+.+-|+.|...|++...
T Consensus        20 l~~~~r~~Il~~L~~----~~~~~~ela~~l~-i----s~~tvs~~L~~L~~~Glv~~~   69 (102)
T 3pqk_A           20 LSHPVRLMLVCTLVE----GEFSVGELEQQIG-I----GQPTLSQQLGVLRESGIVETR   69 (102)
T ss_dssp             HCSHHHHHHHHHHHT----CCBCHHHHHHHHT-C----CTTHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            333455677778864    6899999999999 9    888999999999999999754

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

Probab=96.67  E-value=0.0025  Score=38.82  Aligned_cols=48  Identities=25%  Similarity=0.370  Sum_probs=40.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+.|...+...|  .++|..|||+.+| +    +...+++.|+.|...|++...
T Consensus        19 ~~l~Il~~l~~~g--~~~s~~eLa~~lg-v----s~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           19 DVIDVLRILLDKG--TEMTDEEIANQLN-I----KVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             TTHHHHHHHHHHC--SCBCHHHHHHTTT-S----CHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            3456777775544  5899999999999 9    899999999999999999765

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

Probab=96.65  E-value=0.0032  Score=38.86  Aligned_cols=49  Identities=24%  Similarity=0.228  Sum_probs=41.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ++.|...|...   +++|..+||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        36 ~~~iL~~l~~~---~~~~~~~la~~l~-~----~~~tvs~~l~~L~~~gli~r~~~~   84 (138)
T 1jgs_A           36 QFKVLCSIRCA---ACITPVELKKVLS-V----DLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             HHHHHHHHHHH---SSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             HHHHHHHHHhc---CCCCHHHHHHHHC-C----ChHHHHHHHHHHHHCCCEEecCCc
Confidence            44566667664   5899999999999 9    999999999999999999876543

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=96.65  E-value=0.0034  Score=38.11  Aligned_cols=51  Identities=18%  Similarity=0.226  Sum_probs=43.3

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ++.|...|.++|+ .+++..||+.+++ .    +...+.|+|+.|...|++....+.
T Consensus        22 q~~Vl~~I~~~g~-~gi~qkeLa~~~~-l----~~~tvt~iLk~LE~kglIkr~~~~   72 (91)
T 2dk5_A           22 EKLVYQIIEDAGN-KGIWSRDVRYKSN-L----PLTEINKILKNLESKKLIKAVKSV   72 (91)
T ss_dssp             HHHHHHHHHHHCT-TCEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHHcCC-CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEecCC
Confidence            4567788887652 5899999999999 9    999999999999999999966554

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=96.64  E-value=0.0026  Score=39.78  Aligned_cols=52  Identities=15%  Similarity=0.137  Sum_probs=43.9

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|.--.++.|+..|...   +++|..|||+.++ .    .+..+.|.|+.|...|++...
T Consensus        38 al~~~~rl~IL~~L~~~---~~~s~~eLa~~l~-i----s~stvs~~L~~L~~~Glv~~~   89 (122)
T 1u2w_A           38 AIADENRAKITYALCQD---EELCVCDIANILG-V----TIANASHHLRTLYKQGVVNFR   89 (122)
T ss_dssp             HHHSHHHHHHHHHHHHS---SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HhCCHHHHHHHHHHHHC---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            34444577889999853   6899999999999 9    899999999999999999754

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=96.63  E-value=0.0041  Score=40.46  Aligned_cols=57  Identities=18%  Similarity=0.282  Sum_probs=44.5

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeeccc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +-...-|.+.|.+.+  +++|+.||.+.+. .. +.-+...++|.|..|+..|++.+....
T Consensus        26 T~qR~~IL~~l~~~~--~~~sa~ei~~~l~-~~~~~is~aTVYR~L~~L~e~Glv~~~~~~   83 (150)
T 2xig_A           26 SKQREEVVSVLYRSG--THLSPEEITHSIR-QKDKNTSISSVYRILNFLEKENFISVLETS   83 (150)
T ss_dssp             HHHHHHHHHHHHHCS--SCBCHHHHHHHHH-HHSTTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHH-HhCCCCCHhhHHHHHHHHHHCCcEEEEEeC
Confidence            456667899998765  7999999999983 11 111788999999999999999977543

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=96.62  E-value=0.0026  Score=39.55  Aligned_cols=49  Identities=14%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|...|...   +++|..+||+.++ .    ++..+.|+++.|...|++....+
T Consensus        34 ~~~~iL~~l~~~---~~~~~~~la~~l~-~----s~~tvs~~l~~L~~~glv~r~~~   82 (145)
T 2a61_A           34 AQFDILQKIYFE---GPKRPGELSVLLG-V----AKSTVTGLVKRLEADGYLTRTPD   82 (145)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-C----CchhHHHHHHHHHHCCCeeecCC
Confidence            355566677764   5899999999999 9    99999999999999999987643

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

Probab=96.62  E-value=0.0022  Score=41.26  Aligned_cols=52  Identities=13%  Similarity=0.215  Sum_probs=39.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...| ++++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        47 ~q~~vL~~l~~~~-~~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           47 QQYNTLRLLRSVH-PEGMATLQIADRLI-S----RAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             HHHHHHHHHHHHT-TSCEEHHHHHHHC--------CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHHHHhcC-CCCcCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCEeecCCC
Confidence            3455566677653 26999999999999 9    899999999999999999976544

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

Probab=96.61  E-value=0.0033  Score=39.31  Aligned_cols=48  Identities=13%  Similarity=0.221  Sum_probs=40.7

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++.....
T Consensus        44 ~~~iL~~l~~~---~~~t~~ela~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~   91 (150)
T 2rdp_A           44 QFVALQWLLEE---GDLTVGELSNKMY-L----ACSTTTDLVDRMERNGLVARVRD   91 (150)
T ss_dssp             HHHHHHHHHHH---CSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHc---CCCCHHHHHHHHC-C----CchhHHHHHHHHHHCCCeeecCC
Confidence            44566677764   5899999999999 9    99999999999999999987644

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=96.60  E-value=0.0023  Score=41.37  Aligned_cols=35  Identities=20%  Similarity=0.333  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|++|||+.++ +    ++..|.++|+.|...|++...
T Consensus        27 ~~~s~~~IA~~~~-i----~~~~l~kil~~L~~aGlv~s~   61 (143)
T 3t8r_A           27 GCISLKSIAEENN-L----SDLYLEQLVGPLRNAGLIRSV   61 (143)
T ss_dssp             CCEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCEEEec
Confidence            6899999999999 9    999999999999999998754

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

Probab=96.59  E-value=0.004  Score=38.30  Aligned_cols=45  Identities=16%  Similarity=0.180  Sum_probs=37.8

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      |...|.+    ++++..||++.+ + +    ++..+.|.++.|...|++......
T Consensus        27 IL~~L~~----~~~~~~eLa~~l~~-i----s~~tvs~~L~~Le~~GlI~r~~~~   72 (112)
T 1z7u_A           27 LMDELFQ----GTKRNGELMRALDG-I----TQRVLTDRLREMEKDGLVHRESFN   72 (112)
T ss_dssp             HHHHHHH----SCBCHHHHHHHSTT-C----CHHHHHHHHHHHHHHTSEEEEEEC
T ss_pred             HHHHHHh----CCCCHHHHHHHhcc-C----CHHHHHHHHHHHHHCCCEEEeecC
Confidence            4445554    589999999999 9 9    999999999999999999876543

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=96.58  E-value=0.0032  Score=39.12  Aligned_cols=50  Identities=6%  Similarity=0.185  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        38 ~~~~iL~~l~~~---~~~~~~ela~~l~-~----~~~tvs~~l~~L~~~gli~r~~~~   87 (142)
T 2bv6_A           38 PQFLVLTILWDE---SPVNVKKVVTELA-L----DTGTVSPLLKRMEQVDLIKRERSE   87 (142)
T ss_dssp             HHHHHHHHHHHS---SEEEHHHHHHHTT-C----CTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCEEeecCC
Confidence            345566677664   5899999999999 9    888999999999999999876543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.57  E-value=0.0014  Score=39.13  Aligned_cols=50  Identities=24%  Similarity=0.351  Sum_probs=41.9

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.--..+.|...|.+    +++|+.|||+.++ .    .+..+.|-|+.|...|++...
T Consensus        20 l~~~~r~~Il~~L~~----~~~~~~ela~~l~-i----s~~tvs~~L~~L~~~Glv~~~   69 (98)
T 3jth_A           20 MANERRLQILCMLHN----QELSVGELCAKLQ-L----SQSALSQHLAWLRRDGLVTTR   69 (98)
T ss_dssp             HCSHHHHHHHHHTTT----SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHHHhc----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            333456677777865    5899999999999 9    899999999999999999755

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

Probab=96.56  E-value=0.0023  Score=40.44  Aligned_cols=48  Identities=13%  Similarity=0.228  Sum_probs=39.1

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++.....
T Consensus        45 ~~~iL~~l~~~---~~~t~~ela~~l~-i----~~~tvs~~l~~Le~~Glv~r~~~   92 (155)
T 3cdh_A           45 EWRVLACLVDN---DAMMITRLAKLSL-M----EQSRMTRIVDQMDARGLVTRVAD   92 (155)
T ss_dssp             HHHHHHHHSSC---SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEECC-
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeccC
Confidence            34455556543   6899999999999 9    99999999999999999986543

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

Probab=96.55  E-value=0.0026  Score=39.28  Aligned_cols=49  Identities=16%  Similarity=0.191  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+..|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        37 ~~~~iL~~l~~~---~~~t~~ela~~l~-~----s~~~vs~~l~~Le~~glv~r~~~   85 (142)
T 2fbi_A           37 QQWRVIRILRQQ---GEMESYQLANQAC-I----LRPSMTGVLARLERDGIVRRWKA   85 (142)
T ss_dssp             HHHHHHHHHHHH---CSEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-C----CHhHHHHHHHHHHHCCCEEeecC
Confidence            355566777765   5899999999999 9    99999999999999999987643

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=96.55  E-value=0.0021  Score=41.66  Aligned_cols=51  Identities=16%  Similarity=0.126  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...+  +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        54 ~q~~vL~~L~~~~--~~~t~~eLa~~l~-i----~~~tvs~~l~~Le~~GlV~r~~~~  104 (166)
T 3deu_A           54 THWVTLHNIHQLP--PDQSQIQLAKAIG-I----EQPSLVRTLDQLEDKGLISRQTCA  104 (166)
T ss_dssp             HHHHHHHHHHHSC--SSEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEC---
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHC-C----CHhhHHHHHHHHHHCCCEEeeCCC
Confidence            3455666676644  6899999999999 9    999999999999999999976543

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=96.54  E-value=0.003  Score=39.30  Aligned_cols=49  Identities=14%  Similarity=0.142  Sum_probs=41.1

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        31 ~~~iL~~l~~~---~~~t~~~la~~l~-~----s~~~vs~~l~~Le~~gli~r~~~~   79 (144)
T 1lj9_A           31 QYLYLVRVCEN---PGIIQEKIAELIK-V----DRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHC---cCcCHHHHHHHHC-C----CHhHHHHHHHHHHHCCCEEeecCC
Confidence            34466667764   5899999999999 9    999999999999999999876543

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.54  E-value=0.0028  Score=39.10  Aligned_cols=53  Identities=17%  Similarity=0.199  Sum_probs=47.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      -+.-|..+|.++|+ .+++..||..+++ .    +...+.|+|+.|.+.|++..+.+..
T Consensus        38 ~E~lVy~~I~~aGn-~GIw~kdL~~~tn-L----~~~~vtkiLK~LE~k~lIK~Vksv~   90 (95)
T 2yu3_A           38 QEKLVYQIIEDAGN-KGIWSRDVRYKSN-L----PLTEINKILKNLESKKLIKAVKSVS   90 (95)
T ss_dssp             HHHHHHHHHHHHTT-SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEECCSC
T ss_pred             HHHHHHHHHHHhCC-CCCCHHHHHHHhC-C----CHHHHHHHHHHHHhCCCEEEecCcc
Confidence            46678899998874 8899999999999 9    9999999999999999999987764

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=96.52  E-value=0.003  Score=39.59  Aligned_cols=49  Identities=18%  Similarity=0.295  Sum_probs=41.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        42 ~~~iL~~l~~~---~~~t~~ela~~l~-~----~~~~vs~~l~~Le~~Glv~r~~~~   90 (152)
T 3bj6_A           42 QRAILEGLSLT---PGATAPQLGAALQ-M----KRQYISRILQEVQRAGLIERRTNP   90 (152)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeecCCc
Confidence            44566667664   5899999999999 9    999999999999999999876543

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=96.51  E-value=0.0038  Score=41.32  Aligned_cols=51  Identities=22%  Similarity=0.305  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           23 HMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        23 ~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      --||++.+.|.      ...+++|+|++|||+.++ +    ++..|+++|+.|...|++...
T Consensus        27 ~yAlr~L~~LA------~~~~~~~~s~~eIA~~~~-i----~~~~l~kil~~L~~aGlv~s~   77 (159)
T 3lwf_A           27 RYGLTITLELA------KRIGDGPISLRSIAQDKN-L----SEHYLEQLIGPLRNAGIVKSI   77 (159)
T ss_dssp             HHHHHHHHHHH------HTTTSCCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH------hcCCCCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCeEEEe
Confidence            34555555543      222237899999999999 9    999999999999999999855

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

Probab=96.50  E-value=0.0034  Score=39.85  Aligned_cols=48  Identities=19%  Similarity=0.234  Sum_probs=39.1

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++.|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        51 ~~~iL~~l~~~---~~~t~~ela~~l~-i----s~~tvs~~l~~Le~~glv~r~~~   98 (162)
T 2fa5_A           51 EWRVITILALY---PGSSASEVSDRTA-M----DKVAVSRAVARLLERGFIRRETH   98 (162)
T ss_dssp             HHHHHHHHHHS---TTCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEC---
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeeecC
Confidence            44566677663   6899999999999 9    99999999999999999986543

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

Probab=96.49  E-value=0.0041  Score=39.12  Aligned_cols=47  Identities=19%  Similarity=0.184  Sum_probs=41.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhC--CCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQL--PATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~--~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|+.+||+.+  + .    .+..+.+-++.|...|+++..
T Consensus        14 ~d~~IL~~L~~~---g~~s~~eLA~~l~~g-i----S~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           14 WDDRILEIIHEE---GNGSPKELEDRDEIR-I----SKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             HHHHHHHHHHHH---SCBCHHHHHTSTTCC-S----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHhcC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            456788899875   599999999999  9 9    888999999999999999865

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

Probab=96.48  E-value=0.0031  Score=40.74  Aligned_cols=50  Identities=12%  Similarity=0.224  Sum_probs=42.0

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .+..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        46 ~~~~iL~~L~~~---~~~t~~eLa~~l~-i----s~~tvs~~l~~Le~~GlV~r~~~~   95 (168)
T 2nyx_A           46 PQFRTLVILSNH---GPINLATLATLLG-V----QPSATGRMVDRLVGAELIDRLPHP   95 (168)
T ss_dssp             HHHHHHHHHHHH---CSEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEeccCC
Confidence            345566777764   5899999999999 9    999999999999999999876543

>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=96.47  E-value=0.018  Score=37.98  Aligned_cols=54  Identities=15%  Similarity=0.130  Sum_probs=43.9

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      ..+..|...|...+ ++++|..+||+.++ .    ++..+.|+++.|...|++....+.+
T Consensus        41 ~~q~~vL~~L~~~~-~~~~t~~eLa~~l~-i----s~~tvs~~l~~Le~~GlV~r~~~~~   94 (189)
T 3nqo_A           41 SRQYMTILSILHLP-EEETTLNNIARKMG-T----SKQNINRLVANLEKNGYVDVIPSPH   94 (189)
T ss_dssp             HHHHHHHHHHHHSC-GGGCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             HHHHHHHHHHHhcc-CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEeccCCC
Confidence            34556667777532 27999999999999 9    9999999999999999999765544

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=96.47  E-value=0.0045  Score=37.76  Aligned_cols=37  Identities=24%  Similarity=0.276  Sum_probs=34.1

Q ss_pred             CCCCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++..||++.+ + +    ++..+.+.|+.|...|+++....
T Consensus        26 ~~~~~~eLa~~l~~-i----s~~tls~~L~~Le~~GlI~r~~~   63 (107)
T 2hzt_A           26 GKKRTSELKRLMPN-I----TQKMLTQQLRELEADGVINRIVY   63 (107)
T ss_dssp             CCBCHHHHHHHCTT-S----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCHHHHHHHhcC-C----CHHHHHHHHHHHHHCCCEEEeec
Confidence            689999999999 8 9    99999999999999999987654

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

Probab=96.41  E-value=0.0034  Score=39.52  Aligned_cols=45  Identities=18%  Similarity=0.254  Sum_probs=39.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++..
T Consensus        43 ~~~iL~~l~~~---~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           43 QLAMINVIYST---PGISVADLTKRLI-I----TGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             HHHHHHHHHHS---TTEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEe
Confidence            44566667664   5899999999999 9    99999999999999999987

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=96.40  E-value=0.001  Score=46.63  Aligned_cols=46  Identities=15%  Similarity=0.235  Sum_probs=38.6

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|.+.|.+.+  +++|++|||+.++ .    +...++|+|+.|...|++....
T Consensus        27 ~iL~~l~~~~--~~~~~~eia~~~g-l----~kstv~r~l~tL~~~G~v~~~~   72 (260)
T 2o0y_A           27 DLLELFDAAH--PTRSLKELVEGTK-L----PKTTVVRLVATMCARSVLTSRA   72 (260)
T ss_dssp             HHHTTCBTTB--SSBCHHHHHHHHC-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHhhCC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEECC
Confidence            4555565433  6899999999999 9    9999999999999999998754

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=96.38  E-value=0.0013  Score=45.87  Aligned_cols=46  Identities=20%  Similarity=0.223  Sum_probs=39.0

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.|.+.|.+.+  +++|+.|||+.++ .    +...++|+|+.|+..|++...
T Consensus        17 l~iL~~l~~~~--~~~~~~eia~~~g-l----~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           17 FAVLLAFDAQR--PNPTLAELATEAG-L----SRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             HHHHHTCSSSC--SSCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeC
Confidence            34566665543  7899999999999 9    899999999999999999865

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

Probab=96.38  E-value=0.0037  Score=39.76  Aligned_cols=49  Identities=20%  Similarity=0.269  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|+..|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        53 ~~~~iL~~l~~~---~~~t~~ela~~l~-i----s~~tvs~~l~~Le~~Gli~r~~~  101 (162)
T 3cjn_A           53 AKMRALAILSAK---DGLPIGTLGIFAV-V----EQSTLSRALDGLQADGLVRREVD  101 (162)
T ss_dssp             HHHHHHHHHHHS---CSEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEecCC
Confidence            345566777764   5899999999999 9    99999999999999999987643

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

Probab=96.36  E-value=0.0068  Score=38.90  Aligned_cols=49  Identities=18%  Similarity=0.184  Sum_probs=40.3

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +.-.|...+  ++.+..|||+.++ +    ++..+.|++.-|...|++....+..|
T Consensus        36 vL~~L~~~~--~~~~~~eLa~~l~-~----~~~tvs~~v~~Le~~GlV~R~~~~~D   84 (151)
T 4aik_A           36 TLYNINRLP--PEQSQIQLAKAIG-I----EQPSLVRTLDQLEEKGLITRHTSAND   84 (151)
T ss_dssp             HHHHHHHSC--TTSCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             HHHHHHHcC--CCCcHHHHHHHHC-c----CHHHHHHHHHHHHhCCCeEeecCCCC
Confidence            444566554  5788899999999 9    99999999999999999997765544

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

Probab=96.36  E-value=0.0036  Score=39.46  Aligned_cols=48  Identities=21%  Similarity=0.227  Sum_probs=40.5

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        49 ~~~iL~~l~~~---~~~t~~ela~~l~-~----s~~tvs~~l~~Le~~glv~r~~~   96 (153)
T 2pex_A           49 QYLVMLVLWET---DERSVSEIGERLY-L----DSATLTPLLKRLQAAGLVTRTRA   96 (153)
T ss_dssp             HHHHHHHHHHS---CSEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             HHHHHHHHHhC---CCcCHHHHHHHhC-C----CcccHHHHHHHHHHCCCEeecCC
Confidence            45566677764   5899999999999 9    99999999999999999987644

>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=96.35  E-value=0.0033  Score=39.21  Aligned_cols=49  Identities=12%  Similarity=0.146  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|+..|...   +++|..+||+.++ .    ++..+.|+++.|...|++.....
T Consensus        41 ~~~~iL~~l~~~---~~~~~~~la~~l~-~----~~~tvs~~l~~L~~~glv~r~~~   89 (147)
T 1z91_A           41 PQYLALLLLWEH---ETLTVKKMGEQLY-L----DSGTLTPMLKRMEQQGLITRKRS   89 (147)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHTTT-C----CHHHHHHHHHHHHHHTSEECCBC
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHC-C----CcCcHHHHHHHHHHCCCEEeccC
Confidence            355566677764   5899999999999 9    99999999999999999987644

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

Probab=96.35  E-value=0.0032  Score=39.25  Aligned_cols=52  Identities=8%  Similarity=0.144  Sum_probs=41.4

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      +..|...|...+ ++++|..|||+.++ .    ++..+.|+++.|...|++....+..
T Consensus        39 q~~vL~~l~~~~-~~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~~   90 (127)
T 2frh_A           39 EFAVLTYISENK-EKEYYLKDIINHLN-Y----KQPQVVKAVKILSQEDYFDKKRNEH   90 (127)
T ss_dssp             HHHHHHHHHHTC-CSEEEHHHHHHHSS-S----HHHHHHHHHHHHHHTTSSCCBCCSS
T ss_pred             HHHHHHHHHhcc-CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecCCCC
Confidence            344555666642 26899999999999 9    9999999999999999998754443

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

Probab=96.33  E-value=0.0035  Score=39.94  Aligned_cols=48  Identities=13%  Similarity=0.145  Sum_probs=39.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      ..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        53 ~~vL~~l~~~---~~~t~~eLa~~l~-~----~~~tvs~~l~~Le~~Glv~r~~~~  100 (159)
T 3s2w_A           53 FPFLMRLYRE---DGINQESLSDYLK-I----DKGTTARAIQKLVDEGYVFRQRDE  100 (159)
T ss_dssp             HHHHHHHHHS---CSEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEecCC
Confidence            3345556654   6899999999999 9    999999999999999999876544

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

Probab=96.30  E-value=0.0038  Score=38.85  Aligned_cols=48  Identities=21%  Similarity=0.367  Sum_probs=38.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+..|...|...   + +|..|||+.++ .    ++..+.|+++.|...|++....+
T Consensus        39 ~~~~iL~~l~~~---~-~t~~eLa~~l~-~----s~~tvs~~l~~L~~~Glv~r~~~   86 (146)
T 3tgn_A           39 TQEHILMLLSEE---S-LTNSELARRLN-V----SQAAVTKAIKSLVKEGMLETSKD   86 (146)
T ss_dssp             HHHHHHHHHTTC---C-CCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEC---
T ss_pred             HHHHHHHHHHhC---C-CCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeEeccC
Confidence            445566666542   4 99999999999 9    99999999999999999987654

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

Probab=96.29  E-value=0.0029  Score=39.93  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=38.9

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        43 q~~iL~~l~~~---~~~~~~eLa~~l~-~----~~~~vs~~l~~L~~~Glv~r~~~~   91 (149)
T 4hbl_A           43 QYLVMLTLWEE---NPQTLNSIGRHLD-L----SSNTLTPMLKRLEQSGWVKRERQQ   91 (149)
T ss_dssp             HHHHHHHHHHS---SSEEHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEC----
T ss_pred             HHHHHHHHHHC---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeeCCCC
Confidence            44555666654   6899999999999 9    999999999999999999876543

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

Probab=96.26  E-value=0.0031  Score=41.23  Aligned_cols=51  Identities=18%  Similarity=0.228  Sum_probs=40.7

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++.|...|...++.+++|..|||+.++ .    ++..+.|+++.|...|++.....
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~-i----s~~tvs~~l~~Le~~GlV~r~~~  121 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAA-I----SGPSTSNRIVRLLEKGLIERRED  121 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCS-C----CSGGGSSHHHHHHHHTSEECCC-
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCcCEEecCC
Confidence            455677777765112399999999999 9    89999999999999999987643

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=96.24  E-value=0.0051  Score=39.50  Aligned_cols=56  Identities=21%  Similarity=0.122  Sum_probs=43.8

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCC-CCcchHHHHHHHHhccCceeeecc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNK-DAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~-~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..+.-|++.|.+.+  +++|++||.+.+. ...| -+...++|.|..|+..|++.+...
T Consensus        13 T~qR~~Il~~L~~~~--~h~sa~eI~~~l~-~~~~~is~aTVYR~L~~L~e~Glv~~~~~   69 (139)
T 3mwm_A           13 TRQRAAVSAALQEVE--EFRSAQELHDMLK-HKGDAVGLTTVYRTLQSLADAGEVDVLRT   69 (139)
T ss_dssp             HHHHHHHHHHHTTCS--SCEEHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHTTSSEEEEC
T ss_pred             CHHHHHHHHHHHhCC--CCCCHHHHHHHHH-HhCCCCCHHHHHHHHHHHHHCCCEEEEEc
Confidence            345667889998764  7999999999884 2211 277889999999999999998754

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=96.21  E-value=0.0065  Score=38.81  Aligned_cols=47  Identities=21%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|..|||+.++ .    .+..+.|.++.|...|++...
T Consensus         8 ~~~~iL~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            8 IDRILVRELAAD---GRATLSELATRAG-L----SVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            456788888764   6899999999999 9    899999999999999999654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=96.18  E-value=0.0012  Score=46.41  Aligned_cols=46  Identities=17%  Similarity=0.222  Sum_probs=38.8

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.|.+.|.+.+  +++|++|||+.++ .    ....++|+|+.|+..|++...
T Consensus        24 l~iL~~l~~~~--~~~~~~eia~~~g-l----~~stv~r~l~tL~~~G~v~~~   69 (265)
T 2ia2_A           24 LAVIRCFDHRN--QRRTLSDVARATD-L----TRATARRFLLTLVELGYVATD   69 (265)
T ss_dssp             HHHHHTCCSSC--SSEEHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEES
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEec
Confidence            34566665443  7899999999999 9    899999999999999999864

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.15  E-value=0.002  Score=39.49  Aligned_cols=46  Identities=24%  Similarity=0.274  Sum_probs=39.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++.|...|.+    +++|..|||+.++ .    .+..+.|.++.|...|++...
T Consensus        26 ~r~~IL~~L~~----~~~s~~eLa~~lg-i----s~stvs~~L~~L~~~GlV~~~   71 (108)
T 2kko_A           26 RRLQILDLLAQ----GERAVEAIATATG-M----NLTTASANLQALKSGGLVEAR   71 (108)
T ss_dssp             TTHHHHHHHTT----CCEEHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            45567777753    6899999999999 9    999999999999999999754

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

Probab=96.12  E-value=0.0033  Score=40.12  Aligned_cols=40  Identities=25%  Similarity=0.331  Sum_probs=35.4

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +++|.+|||+.++ .    ++..+.|+++-|...|++....+.+|
T Consensus        50 ~~~t~~eLa~~l~-~----~~~tvs~~v~~Le~~Glv~r~~~~~D   89 (147)
T 4b8x_A           50 GELPMSKIGERLM-V----HPTSVTNTVDRLVRSGLVAKRPNPND   89 (147)
T ss_dssp             GEEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECC--
T ss_pred             CCcCHHHHHHHHC-C----CHHHHHHHHHHHHhCCCEEEeecCCc
Confidence            6899999999999 9    99999999999999999997765543

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=96.10  E-value=0.0022  Score=40.09  Aligned_cols=38  Identities=16%  Similarity=0.184  Sum_probs=34.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        49 ~~~t~~eLa~~l~-~----~~~tvs~~l~~L~~~Glv~r~~~~   86 (140)
T 3hsr_A           49 EKLNIKKLGERVF-L----DSGTLTPLLKKLEKKDYVVRTREE   86 (140)
T ss_dssp             CEEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCcCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCeEecCCC
Confidence            6999999999999 9    999999999999999999976544

>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=96.05  E-value=0.0067  Score=38.05  Aligned_cols=46  Identities=17%  Similarity=0.330  Sum_probs=40.4

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++.|+..|.+    ++++..|||+.++ .    .+..+.|.++.|...|++...
T Consensus        47 ~rl~IL~~L~~----~~~s~~ela~~lg-i----s~stvs~~L~~Le~~Glv~~~   92 (122)
T 1r1t_A           47 NRLRLLSLLAR----SELCVGDLAQAIG-V----SESAVSHQLRSLRNLRLVSYR   92 (122)
T ss_dssp             HHHHHHHHHTT----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            46778888864    6899999999999 9    899999999999999998754

>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=96.04  E-value=0.0073  Score=38.46  Aligned_cols=46  Identities=26%  Similarity=0.377  Sum_probs=40.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .+..|...|.+.   +++|..|||+.+| .    ++..+.|.++.|...|++..
T Consensus         4 ~~~~il~~L~~~---~~~~~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            4 IDLRILKILQYN---AKYSLDEIAREIR-I----PKATLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             HHHHHHHHHTTC---TTSCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEE
Confidence            466788888763   6899999999999 9    99999999999999999985

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=96.03  E-value=0.0093  Score=37.96  Aligned_cols=47  Identities=26%  Similarity=0.474  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|.+.|.+.   +++|..|||+.+| .    .+..+.|.++.|...|++...
T Consensus         6 ~d~~il~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            6 IDLNIIEELKKD---SRLSMRELGRKIK-L----SPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHHC---SCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            456788888764   6899999999999 9    899999999999999999753

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=96.01  E-value=0.0053  Score=36.42  Aligned_cols=42  Identities=19%  Similarity=0.155  Sum_probs=36.0

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcch-HHHHHHHHhccCcee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTM-LDRILGLLASYGIVE   82 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~-l~RlLR~L~s~gi~~   82 (89)
                      +.-.+...+  .++|..|||+.++ .    ++.. +.|+++.|...|++.
T Consensus        20 ~L~~l~~~~--~~~t~~eLa~~l~-i----s~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           20 TLLEFEKKG--YEPSLAEIVKASG-V----SEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHTT--CCCCHHHHHHHHC-C----CHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHhcC--CCCCHHHHHHHHC-C----CchHHHHHHHHHHHHCCCee
Confidence            444556543  4899999999999 9    9999 999999999999998

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

Probab=96.00  E-value=0.0054  Score=40.05  Aligned_cols=53  Identities=15%  Similarity=0.283  Sum_probs=45.3

Q ss_pred             HHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           23 HMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        23 ~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+|.--..+.|...|.+    +|+|+.|||+.++ .    .+..+.+-|+.|...|++...
T Consensus        52 l~aL~~p~R~~IL~~L~~----~~~t~~eLa~~lg-l----s~stvs~hL~~L~~aGlV~~~  104 (151)
T 3f6v_A           52 LEVAAEPTRRRLVQLLTS----GEQTVNNLAAHFP-A----SRSAISQHLRVLTEAGLVTPR  104 (151)
T ss_dssp             HHHHTSHHHHHHHHHGGG----CCEEHHHHHTTSS-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            445555677888888874    6899999999999 9    899999999999999999864

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=95.99  E-value=0.0067  Score=39.21  Aligned_cols=49  Identities=16%  Similarity=0.290  Sum_probs=39.6

Q ss_pred             HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .++++.+.|.      .++ ++++|++|||+.++ +    ++..+.++|+.|...|++...
T Consensus        15 yAl~~L~~La------~~~-~~~~~~~~iA~~~~-i----~~~~l~kil~~L~~~Glv~s~   63 (149)
T 1ylf_A           15 IAVHILSILK------NNP-SSLCTSDYMAESVN-T----NPVVIRKIMSYLKQAGFVYVN   63 (149)
T ss_dssp             HHHHHHHHHH------HSC-GGGCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHH------hCC-CCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEc
Confidence            4666666553      222 26899999999999 9    999999999999999998754

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=95.94  E-value=0.014  Score=38.58  Aligned_cols=35  Identities=29%  Similarity=0.489  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|.++||+.++ +    ++..|.++|+.|...|++...
T Consensus        27 ~~~s~~~IA~~~~-i----s~~~l~kil~~L~~aGlv~s~   61 (162)
T 3k69_A           27 SKVASRELAQSLH-L----NPVMIRNILSVLHKHGYLTGT   61 (162)
T ss_dssp             SCBCHHHHHHHHT-S----CGGGTHHHHHHHHHTTSSEEE
T ss_pred             CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEee
Confidence            7899999999999 9    999999999999999998654

>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=95.94  E-value=0.0093  Score=35.36  Aligned_cols=47  Identities=11%  Similarity=0.181  Sum_probs=39.0

Q ss_pred             HhChHHHHHhcCCCCCCCHHHH----HhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEI----AAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eL----A~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +..|+..|.+.   +++|..||    |+.++ .    ++..+.|+++.|...|++....
T Consensus        10 q~~iL~~l~~~---~~~~~~el~~~la~~l~-i----s~~tvs~~l~~Le~~gli~r~~   60 (99)
T 1tbx_A           10 EAIVLAYLYDN---EGIATYDLYKKVNAEFP-M----STATFYDAKKFLIQEGFVKERQ   60 (99)
T ss_dssp             HHHHHHHHTTC---TTCBHHHHHHHHHTTSC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc---CCcCHHHHHHHHHHHcC-C----CHHHHHHHHHHHHHCCCEEEEe
Confidence            34566666653   68999999    99999 9    9999999999999999998653

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=95.89  E-value=0.011  Score=38.22  Aligned_cols=47  Identities=19%  Similarity=0.369  Sum_probs=41.0

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|..|||+.+| .    .+..+.|.++.|...|++...
T Consensus        11 ~~~~il~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           11 TDIKILQVLQEN---GRLTNVELSERVA-L----SPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEeee
Confidence            456788888874   5899999999999 9    899999999999999999853

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=95.87  E-value=0.011  Score=36.13  Aligned_cols=47  Identities=15%  Similarity=0.266  Sum_probs=40.7

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -.++.|+..|.+    ++.|..|||+.++ .    ++..+.|.++.|...|++...
T Consensus        32 ~~~~~il~~L~~----~~~s~~ela~~l~-i----s~stvsr~l~~Le~~Glv~~~   78 (119)
T 2lkp_A           32 PSRLMILTQLRN----GPLPVTDLAEAIG-M----EQSAVSHQLRVLRNLGLVVGD   78 (119)
T ss_dssp             HHHHHHHHHHHH----CCCCHHHHHHHHS-S----CHHHHHHHHHHHHHHCSEEEE
T ss_pred             HHHHHHHHHHHH----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            356778888876    4799999999999 9    999999999999999998754

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=95.85  E-value=0.013  Score=37.34  Aligned_cols=55  Identities=15%  Similarity=0.182  Sum_probs=41.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+.-|.+.|.+.+ ++++|+.||.+.+. .. +.-+...++|.|+.|+..|++.+...
T Consensus        19 qR~~Il~~L~~~~-~~~~sa~ei~~~l~-~~~~~is~aTVYR~L~~L~e~Glv~~~~~   74 (136)
T 1mzb_A           19 PRVKILQMLDSAE-QRHMSAEDVYKALM-EAGEDVGLATVYRVLTQFEAAGLVVRHNF   74 (136)
T ss_dssp             HHHHHHHHHHCC--CCSBCHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHHTSEEEECS
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHH-hhCCCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            4556888887642 16999999999983 21 11178889999999999999997754

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=95.85  E-value=0.013  Score=37.35  Aligned_cols=47  Identities=23%  Similarity=0.399  Sum_probs=41.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|.+|||+.+| .    .+..+.|.++.|...|++...
T Consensus        10 ~d~~il~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           10 VDMQLVKILSEN---SRLTYRELADILN-T----TRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHTT-S----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            466788888874   6899999999999 9    899999999999999999743

>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=95.84  E-value=0.0097  Score=36.16  Aligned_cols=37  Identities=16%  Similarity=0.187  Sum_probs=33.8

Q ss_pred             CCCCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++..||++.+ + .    ++..+.+.|+.|...|++.....
T Consensus        37 ~~~~~~eL~~~l~g-i----s~~~ls~~L~~Le~~GlV~r~~~   74 (107)
T 2fsw_A           37 RIIRYGELKRAIPG-I----SEKMLIDELKFLCGKGLIKKKQY   74 (107)
T ss_dssp             SCEEHHHHHHHSTT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCcCHHHHHHHccc-C----CHHHHHHHHHHHHHCCCEEEeec
Confidence            689999999999 7 8    89999999999999999987654

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

Probab=95.77  E-value=0.0094  Score=40.24  Aligned_cols=49  Identities=18%  Similarity=-0.031  Sum_probs=40.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +..|...|...   +++|..|||+.++ .    ++..+.|+++.|...|++....+.
T Consensus        50 q~~iL~~L~~~---~~~t~~eLa~~l~-i----~~stvs~~l~~Le~~GlV~r~~~~   98 (207)
T 2fxa_A           50 EHHILWIAYQL---NGASISEIAKFGV-M----HVSTAFNFSKKLEERGYLRFSKRL   98 (207)
T ss_dssp             HHHHHHHHHHH---TSEEHHHHHHHTT-C----CHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             HHHHHHHHHHC---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEecCC
Confidence            34456667665   5899999999999 9    999999999999999999876544

>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=95.77  E-value=0.013  Score=36.68  Aligned_cols=47  Identities=28%  Similarity=0.333  Sum_probs=40.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|..|||+.++ .    .+..+.|.++.|...|++...
T Consensus         5 ~~~~il~~L~~~---~~~~~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            5 RDKIILEILEKD---ARTPFTEIAKKLG-I----SETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHT-S----CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEecc
Confidence            356677888763   5899999999999 9    899999999999999999643

>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=95.73  E-value=0.014  Score=37.34  Aligned_cols=46  Identities=17%  Similarity=0.258  Sum_probs=40.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .+..|...|.+.   +++|..|||+.+| .    .+..+.|.++.|...|++..
T Consensus         8 ~~~~il~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~   53 (151)
T 2cyy_A            8 IDKKIIKILQND---GKAPLREISKITG-L----AESTIHERIRKLRESGVIKK   53 (151)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHC-S----CHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEE
Confidence            456788888874   6899999999999 9    89999999999999999875

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

Probab=95.72  E-value=0.015  Score=36.28  Aligned_cols=35  Identities=23%  Similarity=0.257  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|..|||+.++ .    ++..+.|+++.|...|++...
T Consensus        30 ~~~s~~ela~~l~-i----s~~tv~~~l~~Le~~Gli~r~   64 (139)
T 2x4h_A           30 EGAKINRIAKDLK-I----APSSVFEEVSHLEEKGLVKKK   64 (139)
T ss_dssp             SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHhC-C----ChHHHHHHHHHHHHCCCEEec
Confidence            7899999999999 9    999999999999999999864

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=95.70  E-value=0.018  Score=37.09  Aligned_cols=37  Identities=19%  Similarity=0.134  Sum_probs=34.1

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++..||++.++ +    ++..+.+.|+.|...|+++....
T Consensus        36 g~~~~~eLa~~lg-i----s~~tls~~L~~Le~~GlI~r~~~   72 (146)
T 2f2e_A           36 GLTRFGEFQKSLG-L----AKNILAARLRNLVEHGVMVAVPA   72 (146)
T ss_dssp             TCCSHHHHHHHHC-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEEec
Confidence            6899999999999 9    99999999999999999987654

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=95.62  E-value=0.0074  Score=37.04  Aligned_cols=51  Identities=20%  Similarity=0.253  Sum_probs=40.2

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +..|...|.+.   +|+|+.||++.++ ...+-++..+.|+|+-|...|++....
T Consensus        37 e~~VL~~L~~~---~~~t~~eL~~~l~-~~~~~s~sTVt~~L~rLe~KGlV~R~~   87 (99)
T 2k4b_A           37 ELIVMRVIWSL---GEARVDEIYAQIP-QELEWSLATVKTLLGRLVKKEMLSTEK   87 (99)
T ss_dssp             CSHHHHHHHHH---SCEEHHHHHHTCC-GGGCCCHHHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHHHhC---CCCCHHHHHHHHh-cccCCCHhhHHHHHHHHHHCCCEEEEe
Confidence            45677788764   5899999999998 621224678999999999999998654

>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=95.61  E-value=0.019  Score=35.94  Aligned_cols=35  Identities=17%  Similarity=0.225  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|..+||+.++ +    ++..+.|+++.|...|++...
T Consensus        21 ~~~~~~ela~~l~-v----s~~tvs~~l~~Le~~Glv~r~   55 (142)
T 1on2_A           21 GYARVSDIAEALA-V----HPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_dssp             SSCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence            5899999999999 9    999999999999999999765

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=95.57  E-value=0.0083  Score=38.37  Aligned_cols=35  Identities=31%  Similarity=0.415  Sum_probs=29.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +++|..|||+.++ .    ++..+.|+++.|...|+++..
T Consensus        51 ~~~t~~eLa~~l~-~----~~~tvsr~v~~Le~~glVr~~   85 (148)
T 4fx0_A           51 IDLTMSELAARIG-V----ERTTLTRNLEVMRRDGLVRVM   85 (148)
T ss_dssp             ---CHHHHHHHHT-C----CHHHHHHHHHHHHHTTSBC--
T ss_pred             CCcCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCEEee
Confidence            6799999999999 9    999999999999999999543

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

Probab=95.56  E-value=0.012  Score=34.94  Aligned_cols=47  Identities=15%  Similarity=0.127  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcc-hHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT-MLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~-~l~RlLR~L~s~gi~~e~   84 (89)
                      .+-.|.+.|...   ||.|+.+||+.++ +    .+. .++|.|..|...|++...
T Consensus        12 ~~~~IL~~Lk~~---g~~ta~eiA~~Lg-i----t~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           12 IKEKICDYLFNV---SDSSALNLAKNIG-L----TKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHHHHT---CCEEHHHHHHHHC-G----GGHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHcC-C----CcHHHHHHHHHHHHHCCCEEec
Confidence            455678888875   6999999999999 9    898 999999999999999743

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=95.53  E-value=0.018  Score=37.99  Aligned_cols=47  Identities=21%  Similarity=0.388  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++..|...|.+.   +++|..|||+.++ .    .+..+.|.++.|...|++...
T Consensus        18 ~d~~IL~~L~~~---~~~s~~eLA~~lg-l----S~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           18 LDRNILRLLKKD---ARLTISELSEQLK-K----PESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEee
Confidence            466788888874   5899999999999 9    899999999999999999743

>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=95.51  E-value=0.017  Score=36.89  Aligned_cols=47  Identities=19%  Similarity=0.369  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..|...|.+.   +++|..|||+.+| .    .+..+.|.++.|...|++...
T Consensus         9 ~d~~il~~L~~~---~~~s~~ela~~lg-~----s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A            9 LDRGILEALMGN---ARTAYAELAKQFG-V----SPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHHC---TTSCHHHHHHHHT-S----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHcCCcceE
Confidence            456788888874   6899999999999 9    899999999999999999853

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

Probab=95.46  E-value=0.012  Score=37.34  Aligned_cols=37  Identities=16%  Similarity=0.138  Sum_probs=34.0

Q ss_pred             CCCCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ++++..||++.+ + +    ++..|.+.|+.|...|++.....
T Consensus        47 g~~~~~eLa~~l~g-i----s~~tls~~L~~Le~~GlV~r~~~   84 (131)
T 1yyv_A           47 GTHRFSDLRRXMGG-V----SEXMLAQSLQALEQDGFLNRVSY   84 (131)
T ss_dssp             CCEEHHHHHHHSTT-C----CHHHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCCCHHHHHHHhcc-C----CHHHHHHHHHHHHHCCcEEEEec
Confidence            689999999999 8 9    99999999999999999987644

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.45  E-value=0.013  Score=35.21  Aligned_cols=48  Identities=19%  Similarity=0.129  Sum_probs=40.1

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .....|.+.|.+.   + +|+.|||+.+| +    ....++|.|..|...|++....
T Consensus        17 ~~~~~IL~lL~~~---g-~sa~eLAk~Lg-i----Sk~aVr~~L~~Le~eG~I~~~~   64 (82)
T 1oyi_A           17 EIVCEAIKTIGIE---G-ATAAQLTRQLN-M----EKREVNKALYDLQRSAMVYSSD   64 (82)
T ss_dssp             HHHHHHHHHHSSS---T-EEHHHHHHHSS-S----CHHHHHHHHHHHHHHTSSEECS
T ss_pred             HHHHHHHHHHHHc---C-CCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeCC
Confidence            3455677788742   4 99999999999 9    8999999999999999998653

>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=95.45  E-value=0.011  Score=43.03  Aligned_cols=58  Identities=21%  Similarity=0.212  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           20 SVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        20 ~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|.+++...+..|++.|. +   +++|-.|||+.++ .    .+..+.++++.|...|++.|.+.
T Consensus        11 ~~~~~~~~~~~~~~il~~l~-~---~~~sr~~la~~~g-l----s~~tv~~~v~~L~~~gli~~~~~   68 (380)
T 2hoe_A           11 HHMPKSVRAENISRILKRIM-K---SPVSRVELAEELG-L----TKTTVGEIAKIFLEKGIVVEEKD   68 (380)
T ss_dssp             -----------CCCSHHHHH-H---SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             ccCchhHHHHHHHHHHHHHH-c---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeecC
Confidence            45678889999999999999 6   6999999999999 9    89999999999999999998753

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=95.45  E-value=0.022  Score=39.93  Aligned_cols=48  Identities=17%  Similarity=0.251  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .++.|...|.+.   +++|.+|||+.++ .    ++..+.|.++.|...|++....
T Consensus       153 ~~~~IL~~L~~~---~~~s~~eLA~~lg-l----sksTv~r~L~~Le~~GlV~r~~  200 (244)
T 2wte_A          153 EEMKLLNVLYET---KGTGITELAKMLD-K----SEKTLINKIAELKKFGILTQKG  200 (244)
T ss_dssp             HHHHHHHHHHHH---TCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeC
Confidence            355667777654   5899999999999 9    9999999999999999998763

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=95.39  E-value=0.021  Score=34.16  Aligned_cols=48  Identities=10%  Similarity=0.241  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+-.|.+.|.++|  +|++..|||+.+| +    |..-+.++|-.|-.-|.+...
T Consensus        20 ~eekVLe~LkeaG--~PlkageIae~~G-v----dKKeVdKaik~LKkEgkI~SP   67 (80)
T 2lnb_A           20 LEQRILQVLTEAG--SPVKLAQLVKECQ-A----PKRELNQVLYRMKKELKVSLT   67 (80)
T ss_dssp             HHHHHHHHHHHHT--SCEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHcCCccCC
Confidence            3557889999987  8999999999999 9    999999999999988876544

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=95.38  E-value=0.017  Score=40.61  Aligned_cols=53  Identities=13%  Similarity=0.122  Sum_probs=42.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +..|...|..++ ++++|..|||+.++ .    ++..+.|++.-|...|++....+.+|
T Consensus       160 q~~vL~~L~~~~-~~~~t~~eLa~~l~-i----~~~tvt~~v~rLe~~GlV~R~~~~~D  212 (250)
T 1p4x_A          160 EFTILAIITSQN-KNIVLLKDLIETIH-H----KYPQTVRALNNLKKQGYLIKERSTED  212 (250)
T ss_dssp             HHHHHHHHHTTT-TCCEEHHHHHHHSS-S----CHHHHHHHHHHHHHHTSSEEEECSSS
T ss_pred             HHHHHHHHHhCC-CCCcCHHHHHHHHC-C----ChhhHHHHHHHHHHCCCEEeeCCCCC
Confidence            344555666554 13699999999999 9    99999999999999999998766554

>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=95.29  E-value=0.027  Score=38.01  Aligned_cols=50  Identities=16%  Similarity=0.296  Sum_probs=42.9

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.-..+..|...|.+    +++|..|||+.++ .    .+..+.|.++.|...|++...
T Consensus        17 l~d~~~~~IL~~L~~----~~~s~~eLA~~lg-l----S~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           17 MLEDTRRKILKLLRN----KEMTISQLSEILG-K----TPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHSHHHHHHHHHHTT----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             hCCHHHHHHHHHHHc----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            344567778888863    5899999999999 9    899999999999999999876

>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=95.27  E-value=0.02  Score=33.01  Aligned_cols=52  Identities=17%  Similarity=0.296  Sum_probs=40.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|.+.|.+.   +|+|+.||++.++ ...+-++..+.|+++.|...|++....
T Consensus        10 ~e~~vL~~L~~~---~~~t~~ei~~~l~-~~~~~s~~Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           10 AELEVMKVIWKH---SSINTNEVIKELS-KTSTWSPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHHHTS---SSEEHHHHHHHHH-HHSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHh-hcCCccHHHHHHHHHHHHHCCCeEEEe
Confidence            355677788763   6999999999986 411115788999999999999998654

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=95.26  E-value=0.025  Score=38.55  Aligned_cols=53  Identities=17%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|.--..+.|...|.+    +|+|..||++.++ .    ++..+++.|+.|...|++.....
T Consensus        11 aL~~~~rl~IL~~L~~----~~~s~~eLa~~l~-i----s~stvs~hLk~Le~~GLV~~~~~   63 (202)
T 2p4w_A           11 VLGNETRRRILFLLTK----RPYFVSELSRELG-V----GQKAVLEHLRILEEAGLIESRVE   63 (202)
T ss_dssp             HHHSHHHHHHHHHHHH----SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HhCCHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEEee
Confidence            3334455667777754    6899999999999 9    99999999999999999987543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=95.22  E-value=0.017  Score=37.53  Aligned_cols=46  Identities=13%  Similarity=0.274  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .+..|.+.|.+.   +++|..|||+.+| .    .+..+.|-++.|...|++..
T Consensus         4 ~d~~il~~L~~~---~~~s~~~la~~lg-~----s~~tv~~rl~~L~~~g~i~~   49 (162)
T 3i4p_A            4 LDRKILRILQED---STLAVADLAKKVG-L----STTPCWRRIQKMEEDGVIRR   49 (162)
T ss_dssp             HHHHHHHHHTTC---SCSCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHHC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeee
Confidence            567888889764   6899999999999 9    89999999999999999874

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=95.22  E-value=0.022  Score=36.57  Aligned_cols=47  Identities=19%  Similarity=0.321  Sum_probs=37.2

Q ss_pred             HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+|++.+.|      +...  ++ |++|||+.++ +    .+..|.+||+.|...|++...
T Consensus        10 yAl~~L~~L------a~~~--~~-s~~~IA~~~~-i----~~~~l~kIl~~L~~aGlv~s~   56 (145)
T 1xd7_A           10 VAIHILSLI------SMDE--KT-SSEIIADSVN-T----NPVVVRRMISLLKKADILTSR   56 (145)
T ss_dssp             HHHHHHHHH------HTCS--CC-CHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHH------HhCC--CC-CHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEee
Confidence            355555543      4433  35 9999999999 9    999999999999999999754

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=95.13  E-value=0.034  Score=34.18  Aligned_cols=43  Identities=23%  Similarity=0.367  Sum_probs=36.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHh-hCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAA-QLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~-~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      ..|.-.|++.   ++.|+++||+ ..+ .    |...+.|=++.|...|+++
T Consensus        19 fsiL~~L~~~---~~~t~~~Lae~~l~-~----drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           19 ATILITIAKK---DFITAAEVREVHPD-L----GNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             HHHHHHHHHS---TTBCHHHHHHTCTT-S----CHHHHHHHHHHHHTTTSEE
T ss_pred             HHHHHHHHHC---CCCCHHHHHHHHhc-c----cHHHHHHHHHHHHHCCCee
Confidence            3444556664   5999999999 999 9    9999999999999999998

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

Probab=95.11  E-value=0.033  Score=35.73  Aligned_cols=37  Identities=27%  Similarity=0.179  Sum_probs=34.0

Q ss_pred             CCCCHHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |+++..||++.+ + +    ++..|.+.|+.|...|++.....
T Consensus        38 g~~rf~eL~~~l~g-I----s~~~Ls~~L~~Le~~GLV~R~~~   75 (131)
T 4a5n_A           38 GKKRFNEFRRICPS-I----TQRMLTLQLRELEADGIVHREVY   75 (131)
T ss_dssp             SCBCHHHHHHHCTT-S----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCcCHHHHHHHhcc-c----CHHHHHHHHHHHHHCCCEEEEec
Confidence            799999999999 8 9    89999999999999999987643

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

Probab=95.06  E-value=0.032  Score=34.29  Aligned_cols=35  Identities=23%  Similarity=0.311  Sum_probs=32.1

Q ss_pred             CCCC--HHHHHhhC-CCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLS--ASEIAAQL-PATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t--~~eLA~~~-~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+.+  ..||++.+ + +    .+..|.|.|+.|...|+++..
T Consensus        39 g~~~~~~~eL~~~l~g-i----s~~~ls~~L~~Le~~GlV~r~   76 (111)
T 3df8_A           39 GSTRQNFNDIRSSIPG-I----SSTILSRRIKDLIDSGLVERR   76 (111)
T ss_dssp             SSSCBCHHHHHHTSTT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCCHHHHHHHccC-C----CHHHHHHHHHHHHHCCCEEEe
Confidence            5777  99999999 8 9    899999999999999999865

>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=94.96  E-value=0.032  Score=37.28  Aligned_cols=42  Identities=31%  Similarity=0.257  Sum_probs=35.5

Q ss_pred             HHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           36 EIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        36 d~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +.+.+.|  .|.|..|||+.++ .    ....+.|.|+.|...|++...
T Consensus        16 ~~~~~~g--~~~s~~eia~~lg-l----~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A           16 EFIEKNG--YPPSVREIARRFR-I----TPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             HHHHHHS--SCCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHhC--CCCCHHHHHHHcC-C----CcHHHHHHHHHHHHCCCEEec
Confidence            3455555  7999999999999 9    666899999999999998764

>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=94.87  E-value=0.043  Score=40.09  Aligned_cols=54  Identities=13%  Similarity=0.171  Sum_probs=45.6

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      -+|..-+..|++.|.++   +++|-.|||+.++ .    .+..+.++++.|...|++.|.+.
T Consensus        12 ~~r~~n~~~il~~l~~~---~~~sr~~la~~~~-l----s~~tv~~~v~~L~~~g~i~~~~~   65 (406)
T 1z6r_A           12 QIKQTNAGAVYRLIDQL---GPVSRIDLSRLAQ-L----APASITKIVHEMLEAHLVQELEI   65 (406)
T ss_dssp             CHHHHHHHHHHHHHHSS---CSCCHHHHHHHTT-C----CHHHHHHHHHHHHHHTSEEEC--
T ss_pred             HHHHhHHHHHHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEeecc
Confidence            35566667789999875   6999999999999 9    89999999999999999998643

>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=94.85  E-value=0.018  Score=34.13  Aligned_cols=32  Identities=13%  Similarity=0.122  Sum_probs=30.4

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      .++|..|||+.++ .    ++..+.|++..|...|++
T Consensus        29 ~~~t~~eLa~~l~-i----~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A           29 NDVYIQYIASKVN-S----PHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             CCEEHHHHHHHSS-S----CHHHHHHHHHHHHHTTSE
T ss_pred             CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCcCc
Confidence            4599999999999 9    999999999999999999

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=94.84  E-value=0.028  Score=31.73  Aligned_cols=45  Identities=16%  Similarity=0.268  Sum_probs=40.4

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      |-.|.+.|..+|  |-+.++..++..+ +    +...+..+||-|...|+++
T Consensus        12 e~~lL~yIr~sG--GildI~~~a~kyg-V----~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           12 ERELLDYIVNNG--GFLDIEHFSKVYG-V----EKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHHTT--SEEEHHHHHHHHC-C----CHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcC--CEEeHHHHHHHhC-C----CHHHHHHHHHHHHHCCCee
Confidence            445778888876  8999999999999 9    9999999999999999986

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=94.69  E-value=0.041  Score=33.75  Aligned_cols=38  Identities=26%  Similarity=0.389  Sum_probs=34.7

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +++++..+||+.+. .    +...|.|++..|...|++.....
T Consensus        34 g~~~s~~eLa~~l~-l----~~stLsR~l~rLe~~GLV~r~~~   71 (96)
T 2obp_A           34 ATPWSLPKIAKRAQ-L----PMSVLRRVLTQLQAAGLADVSVE   71 (96)
T ss_dssp             CCCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCcCHHHHHHHhC-C----chhhHHHHHHHHHHCCCEEeecC
Confidence            47899999999999 9    99999999999999999996544

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

Probab=94.69  E-value=0.042  Score=34.63  Aligned_cols=53  Identities=13%  Similarity=0.105  Sum_probs=41.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|..+|.+..  +|+|..||++.++ ...+-++..+.|++.-|...|++....
T Consensus        10 ~e~~vL~~L~~~~--~~~t~~el~~~l~-~~~~~~~~Tvt~~l~rLe~kGlv~r~~   62 (138)
T 2g9w_A           10 LERAVMDHLWSRT--EPQTVRQVHEALS-ARRDLAYTTVMAVLQRLAKKNLVLQIR   62 (138)
T ss_dssp             HHHHHHHHHHTCS--SCEEHHHHHHHHT-TTCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHhcC--CCCCHHHHHHHHh-ccCCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            3556677787632  6899999999997 422227889999999999999998654

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=94.64  E-value=0.023  Score=36.85  Aligned_cols=55  Identities=20%  Similarity=0.228  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCC-CCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATK-NKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~-~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+.-|.+.|.+.+ ++++|+.||.+.+. .. +.-+...++|.|+.|+..|++.+...
T Consensus        18 qR~~Il~~L~~~~-~~h~sa~ei~~~l~-~~~~~is~aTVYR~L~~L~e~Glv~~~~~   73 (150)
T 2w57_A           18 PRLKILEVLQQPE-CQHISAEELYKKLI-DLGEEIGLATVYRVLNQFDDAGIVTRHHF   73 (150)
T ss_dssp             HHHHHHHHHTSGG-GSSEEHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHH-HhCCCCCHHHHHHHHHHHHHCCcEEEEEe
Confidence            4556788887542 15899999999983 21 11178889999999999999987643

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=94.58  E-value=0.034  Score=33.96  Aligned_cols=52  Identities=15%  Similarity=0.197  Sum_probs=40.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|...|.+.   +|+|..||++.++ ...+-++..+.++++-|...|++....
T Consensus        11 ~q~~vL~~L~~~---~~~t~~el~~~l~-~~~~~~~~Tvt~~l~rLe~kGlv~R~~   62 (126)
T 1sd4_A           11 AEWDVMNIIWDK---KSVSANEIVVEIQ-KYKEVSDKTIRTLITRLYKKEIIKRYK   62 (126)
T ss_dssp             HHHHHHHHHHHS---SSEEHHHHHHHHH-TTSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHhc---CCCCHHHHHHHHh-hcCCCChhhHHHHHHHHHHCCceEEEe
Confidence            345666777764   5899999999997 522226889999999999999998654

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=94.55  E-value=0.047  Score=35.11  Aligned_cols=54  Identities=15%  Similarity=0.147  Sum_probs=41.8

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCC-CCCcchHHHHHHHHhccCceeeecc
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKN-KDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~-~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ..+.-|++.|.+.   +++|+.||.+.+. ... .-+...++|.|..|+..|++.+...
T Consensus        19 ~qR~~Il~~l~~~---~h~ta~ei~~~l~-~~~~~is~~TVYR~L~~L~e~Glv~~i~~   73 (145)
T 3eyy_A           19 PQRQLVLEAVDTL---EHATPDDILGEVR-KTASGINISTVYRTLELLEELGLVSHAHL   73 (145)
T ss_dssp             HHHHHHHHHHHHH---SSBCHHHHHHHHH-TTCTTCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHHHHhc---CCCCHHHHHHHHH-hhCCCCCHhHHHHHHHHHHHCCcEEEEEe
Confidence            3456688888775   3899999999875 322 2277889999999999999987654

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=94.49  E-value=0.036  Score=33.18  Aligned_cols=47  Identities=13%  Similarity=0.189  Sum_probs=38.3

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -.++.|+..+...   +++|+.|||+.++ .    .+..+.|-++.|... ++...
T Consensus        27 ~~Rl~IL~~l~~~---~~~~~~ela~~l~-i----s~stvs~hL~~L~~~-lv~~~   73 (99)
T 2zkz_A           27 PMRLKIVNELYKH---KALNVTQIIQILK-L----PQSTVSQHLCKMRGK-VLKRN   73 (99)
T ss_dssp             HHHHHHHHHHHHH---SCEEHHHHHHHHT-C----CHHHHHHHHHHHBTT-TBEEE
T ss_pred             HHHHHHHHHHHHC---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHH-hhhhe
Confidence            4566777555443   5899999999999 9    899999999999999 87643

>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=94.49  E-value=0.064  Score=39.62  Aligned_cols=52  Identities=13%  Similarity=0.263  Sum_probs=46.7

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +|..-+..|++.|.+.   +++|-.|||+.++ .    .+..+.++++.|...|++.|..
T Consensus        36 ~r~~n~~~il~~l~~~---~~~sr~ela~~~g-l----s~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           36 IKQINAGRVYKLIDQK---GPISRIDLSKESE-L----APASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHHHHHHH---CSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecc
Confidence            6666777899999876   6999999999999 9    8999999999999999999875

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

Probab=94.38  E-value=0.033  Score=41.21  Aligned_cols=52  Identities=19%  Similarity=0.211  Sum_probs=41.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ..|...|.++. ++++|..|||+.++ .    ++..+.|+++-|...|++....+..|
T Consensus       407 ~~vl~~l~~~~-~~~~~~~~l~~~~~-~----~~~~~t~~~~~le~~g~v~r~~~~~D  458 (487)
T 1hsj_A          407 IYILNHILRSE-SNEISSKEIAKCSE-F----KPYYLTKALQKLKDLKLLSKKRSLQD  458 (487)
T ss_dssp             HHHHHHHHTCS-CSEEEHHHHHHSSC-C----CHHHHHHHHHHHHTTTTSCCEECCSS
T ss_pred             HHHHHHHHhCC-CCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEeecCCCCC
Confidence            34555666542 26899999999999 9    99999999999999999987755443

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=94.34  E-value=0.057  Score=35.48  Aligned_cols=53  Identities=11%  Similarity=0.107  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCC---CCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATK---NKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~---~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+.-|++.|.+.+  +++|++||.+.+. ..   +.-+...++|-|..|+..|++.+..
T Consensus        34 qR~~IL~~L~~~~--~h~sA~eI~~~l~-~~~~~~~is~aTVYRtL~~L~e~Glv~~i~   89 (162)
T 4ets_A           34 QREVLLKTLYHSD--THYTPESLYMEIK-QAEPDLNVGIATVYRTLNLLEEAEMVTSIS   89 (162)
T ss_dssp             HHHHHHHHHHSCC--SCBCHHHHHHHHH-HHCGGGCCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             HHHHHHHHHHhCC--CCCCHHHHHHHHH-hhcCCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            5567889998765  8999999988764 21   1116778999999999999999874

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=94.33  E-value=0.048  Score=34.36  Aligned_cols=37  Identities=11%  Similarity=0.155  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+.|.++||+.++ .    ++.-+.|+++.|...|++....+
T Consensus        50 ~~ps~~~LA~~l~-~----s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           50 LFPTPAELAERMT-V----SAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             SSCCHHHHHHTSS-S----CHHHHHHHHHHHHHTTSSEECC-
T ss_pred             CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEeE
Confidence            3479999999999 9    99999999999999999987544

>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=94.25  E-value=0.015  Score=35.47  Aligned_cols=51  Identities=16%  Similarity=0.235  Sum_probs=38.8

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +..|...|...   +|+|..|||+.++ ...+-.+..+.|+++.|...|++....
T Consensus        12 ~~~vL~~l~~~---~~~t~~ela~~l~-~~~~~s~~tv~~~l~~L~~~Glv~r~~   62 (123)
T 1okr_A           12 EWEVMNIIWMK---KYASANNIIEEIQ-MQKDWSPKTIRTLITRLYKKGFIDRKK   62 (123)
T ss_dssp             HHHHHHHHHHH---SSEEHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHhC---CCcCHHHHHHHHh-ccCCCcHhhHHHHHHHHHHCCCeEEEe
Confidence            34556666653   6899999999988 611113789999999999999998654

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=94.24  E-value=0.032  Score=40.57  Aligned_cols=41  Identities=17%  Similarity=0.132  Sum_probs=37.3

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +||..| .    +|.|+.|||..++ .    ++..++++|+.|++.|+++.
T Consensus        47 ~ll~~L-~----~~~t~~eLa~~~g-~----~~~~v~~~L~~l~~~gll~~   87 (373)
T 2qm3_A           47 NVLSAV-L----ASDDIWRIVDLSE-E----PLPLVVAILESLNELGYVTF   87 (373)
T ss_dssp             HHHHHH-H----HCSCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHh-c----CCCCHHHHHHHhC-C----ChHHHHHHHHHHhhCCcEEE
Confidence            778888 4    5899999999999 9    99999999999999999864

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

Probab=94.10  E-value=0.14  Score=32.34  Aligned_cols=43  Identities=21%  Similarity=0.405  Sum_probs=36.3

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |...|...   ++.|..+||+.++ +    ++..+.|.++.|...|++...
T Consensus        45 i~~~l~~~---~~~~~~~la~~l~-v----s~~tvs~~l~~Le~~Glv~r~   87 (155)
T 2h09_A           45 ISDLIREV---GEARQVDMAARLG-V----SQPTVAKMLKRLATMGLIEMI   87 (155)
T ss_dssp             HHHHHHHH---SCCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHhC---CCcCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCEEEe
Confidence            34456553   5789999999999 9    999999999999999998754

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=93.91  E-value=0.061  Score=37.68  Aligned_cols=51  Identities=14%  Similarity=0.119  Sum_probs=40.9

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|...|.+.+ .+++|..|||+.+. .    ++..+.|++.-|...|++....+..|
T Consensus        38 ~vL~~L~~~~-~~~~~~~el~~~l~-~----~~~t~t~~l~rLe~~G~i~R~~~~~D   88 (250)
T 1p4x_A           38 ILLTYLFHQQ-ENTLPFKKIVSDLC-Y----KQSDLVQHIKVLVKHSYISKVRSKID   88 (250)
T ss_dssp             HHHHHHHSCS-CSEEEHHHHHHHSS-S----CGGGTHHHHHHHHHTTSCEEEECSSS
T ss_pred             HHHHHHHhcC-CCCcCHHHHHHHHC-C----CHhhHHHHHHHHHHCCCEEecCCCCC
Confidence            3445566542 25899999999999 9    99999999999999999987755544

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=93.78  E-value=0.036  Score=36.98  Aligned_cols=48  Identities=25%  Similarity=0.445  Sum_probs=39.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.+.|...|.+    +|+|+.||++.++..    ....+++-|+.|...|+++...
T Consensus        24 ~Rl~il~~L~~----~~~~~~~l~~~l~~~----~~~~~s~Hl~~L~~aglv~~~~   71 (182)
T 4g6q_A           24 LRWRITQLLIG----RSLTTRELAELLPDV----ATTTLYRQVGILVKAGVLMVTA   71 (182)
T ss_dssp             HHHHHHHHTTT----SCEEHHHHHHHCTTB----CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHhcCC----CHHHHHHHHHHHHHCCCeEEEE
Confidence            56778888864    799999999998515    5568999999999999998543

>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=93.62  E-value=0.11  Score=32.23  Aligned_cols=41  Identities=15%  Similarity=0.193  Sum_probs=34.7

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      .+...||+..|.+    |++|-.|||+.+| +    ....+.|+=|.|-.
T Consensus        44 l~~R~~l~~~L~~----ge~TQREIA~~lG-i----S~stISRi~r~L~~   84 (101)
T 1jhg_A           44 LGTRVRIIEELLR----GEMSQRELKNELG-A----GIATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHH----CCSCHHHHHHHHC-C----CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc----CCcCHHHHHHHHC-C----ChhhhhHHHHHHHH
Confidence            3456888988876    6899999999999 9    89999999888753

>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=93.41  E-value=0.11  Score=34.43  Aligned_cols=47  Identities=15%  Similarity=0.265  Sum_probs=40.1

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc-ee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI-VE   82 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi-~~   82 (89)
                      --...|.+.|.+.+  +++|.+|||+.++ +    ....++|=++.|...|+ +.
T Consensus        21 ~R~~~Il~~L~~~~--~~~s~~eLa~~l~-v----S~~Ti~rdi~~L~~~G~~I~   68 (187)
T 1j5y_A           21 ERLKSIVRILERSK--EPVSGAQLAEELS-V----SRQVIVQDIAYLRSLGYNIV   68 (187)
T ss_dssp             HHHHHHHHHHHHCS--SCBCHHHHHHHHT-S----CHHHHHHHHHHHHHHTCCCE
T ss_pred             HHHHHHHHHHHHcC--CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEE
Confidence            44567888888654  6899999999999 9    89999999999999998 54

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=92.95  E-value=0.03  Score=39.16  Aligned_cols=50  Identities=10%  Similarity=0.216  Sum_probs=42.5

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +|.--..+.|...|.+    +|+|..|||+.++ .    .+..+.+.|+.|...|++..
T Consensus         8 aL~~~~R~~IL~~L~~----g~~s~~ELa~~lg-l----S~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A            8 ILGNKVRRDLLSHLTC----MECYFSLLSSKVS-V----SSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             HHTSHHHHHHHHHHTT----TTTCSSSSCTTCC-C----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HhCCHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEE
Confidence            3444456778888864    6899999999999 9    89999999999999999987

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=92.82  E-value=0.32  Score=32.08  Aligned_cols=50  Identities=24%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+.|+..|..++ .+..|+.||++.++.+    ....|+|-|+.|+..|++.+.
T Consensus        30 tR~~IL~~Ll~~p-~~~~ta~eL~~~l~~l----S~aTVyrhL~~L~eaGLV~~~   79 (151)
T 3u1d_A           30 TRLDVLHQILAQP-DGVLSVEELLYRNPDE----TEANLRYHVDELVDRGIVEKI   79 (151)
T ss_dssp             HHHHHHHHHHHST-TSCBCHHHHHHHCTTS----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCC-CCCCCHHHHHHhcCCC----CHHHHHHHHHHHHHCCCeEEe
Confidence            4566777776653 3679999999988755    778999999999999999865

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=92.52  E-value=0.25  Score=29.68  Aligned_cols=44  Identities=11%  Similarity=0.157  Sum_probs=36.3

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+++|..-.. + ++..+||..++ .    ++..+.+.++.|...|++...
T Consensus        10 i~~IL~~i~~-~-~~~t~La~~~~-l----s~~~~~~~l~~L~~~GLI~~~   53 (95)
T 1r7j_A           10 IQAILEACKS-G-SPKTRIMYGAN-L----SYALTGRYIKMLMDLEIIRQE   53 (95)
T ss_dssp             HHHHHHHHTT-C-BCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHc-C-CCHHHHHHHhC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            3455544332 4 99999999999 9    999999999999999999875

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=92.10  E-value=0.13  Score=34.90  Aligned_cols=49  Identities=22%  Similarity=0.213  Sum_probs=38.9

Q ss_pred             HhChHHHHHhcC---CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           31 NLGLFEIIAKAG---PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        31 ~LgIfd~l~~~g---~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+.+|..|+..+   ..+++|.+++|+.++ .    ++..+.|.++.|...|+|...
T Consensus         9 ~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~-i----sq~avSr~I~~LE~~~L~~R~   60 (230)
T 3cta_A            9 YYRAIKKIKEAAEASNRAYLTSSKLADMLG-I----SQQSASRIIIDLEKNGYITRT   60 (230)
T ss_dssp             HHHHHHHHHHHTTTSSEEECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhcccccCCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEE
Confidence            345555555433   125789999999999 9    899999999999999999876

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

Probab=92.04  E-value=0.16  Score=34.41  Aligned_cols=36  Identities=17%  Similarity=0.266  Sum_probs=33.7

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++++..+||+.++ +    ++..+.|+++.|...|++....
T Consensus        19 ~~~~~~~lA~~l~-v----s~~tvs~~l~~Le~~GlV~r~~   54 (214)
T 3hrs_A           19 NKITNKEIAQLMQ-V----SPPAVTEMMKKLLAEELLIKDK   54 (214)
T ss_dssp             SCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCHHHHHHHHC-C----ChhHHHHHHHHHHHCCCEEEec
Confidence            7999999999999 9    9999999999999999998654

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=91.29  E-value=0.35  Score=25.98  Aligned_cols=29  Identities=14%  Similarity=0.184  Sum_probs=24.6

Q ss_pred             CCCCHHHHHhhC-----CCCCCCCCcchHHHHHHHHhccCce
Q 045477           45 AKLSASEIAAQL-----PATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        45 ~~~t~~eLA~~~-----~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      +++|++||++.+     + +    +...++|-|.   ..|++
T Consensus        18 ~~~t~~el~~~l~~~~~~-v----s~~Tv~R~L~---~lg~v   51 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYK-V----TQATVSRDIK---ELHLV   51 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCC-C----CHHHHHHHHH---HHTCE
T ss_pred             CCCCHHHHHHHHHHhCCC-c----CHHHHHHHHH---HcCCE
Confidence            699999999999     7 8    8888998888   44766

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=91.27  E-value=0.15  Score=30.42  Aligned_cols=36  Identities=33%  Similarity=0.429  Sum_probs=32.3

Q ss_pred             CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..+ |..|||+.++ +    ....+++.++.|...|++....
T Consensus        33 ~~lps~~eLa~~~~-v----Sr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           33 DTLPSVADIRAQFG-V----AAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             SBCCCHHHHHHHSS-S----CTTHHHHHTTTTTTSSCCEEET
T ss_pred             CCCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeC
Confidence            566 9999999999 9    8889999999999999997543

>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=91.08  E-value=0.18  Score=32.41  Aligned_cols=34  Identities=26%  Similarity=0.424  Sum_probs=31.6

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       164 ~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  197 (207)
T 2oz6_A          164 KITRQEIGRIVG-C----SREMVGRVLKSLEEQGLVHVK  197 (207)
T ss_dssp             ECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            589999999999 9    999999999999999998754

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=91.02  E-value=0.24  Score=31.70  Aligned_cols=35  Identities=6%  Similarity=0.041  Sum_probs=32.5

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+.|.++||+.++ .    ++.-+.|+++.|...|++.-.
T Consensus        50 ~~ps~~~LA~~~~-~----s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           50 YFPTPNQLQEGMS-I----SVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             CSCCHHHHHTTSS-S----CHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEE
Confidence            5679999999999 9    999999999999999999864

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=90.98  E-value=0.26  Score=35.04  Aligned_cols=33  Identities=27%  Similarity=0.347  Sum_probs=31.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      +++|.+|||++++ +    ....++|.|..|...|+++
T Consensus        20 ~~~~~~ela~~l~-v----S~~tIrRdL~~l~~~G~v~   52 (315)
T 2w48_A           20 QDMTQAQIARELG-I----YRTTISRLLKRGREQGIVT   52 (315)
T ss_dssp             SCCCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEE
Confidence            6799999999999 9    9999999999999999997

>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=90.83  E-value=0.28  Score=32.18  Aligned_cols=35  Identities=20%  Similarity=0.110  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       179 ~~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  213 (232)
T 2gau_A          179 IYLSREELATLSN-M----TVSNAIRTLSTFVSERMLALD  213 (232)
T ss_dssp             CCCCHHHHHHHTT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cccCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEeeC
Confidence            4689999999999 9    999999999999999998754

>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=90.74  E-value=0.24  Score=32.54  Aligned_cols=34  Identities=26%  Similarity=0.396  Sum_probs=31.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+|+.|...|++...
T Consensus       175 ~~t~~~iA~~lg-~----sr~tvsR~l~~L~~~g~I~~~  208 (231)
T 3e97_A          175 PLGTQDIMARTS-S----SRETVSRVLKRLEAHNILEVS  208 (231)
T ss_dssp             CCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCcEEec
Confidence            689999999999 9    999999999999999999754

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=90.73  E-value=0.25  Score=32.06  Aligned_cols=34  Identities=26%  Similarity=0.429  Sum_probs=31.9

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|+++..
T Consensus       169 ~~t~~~lA~~lg-~----sr~tvsR~l~~L~~~g~I~~~  202 (220)
T 3dv8_A          169 KITHETIANHLG-S----HREVITRMLRYFQVEGLVKLS  202 (220)
T ss_dssp             CCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEeC
Confidence            889999999999 9    999999999999999999754

>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=90.73  E-value=0.21  Score=32.18  Aligned_cols=35  Identities=20%  Similarity=0.334  Sum_probs=32.2

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|+++...
T Consensus       167 ~~t~~~iA~~lg-~----sr~tvsR~l~~L~~~g~I~~~~  201 (210)
T 3ryp_A          167 KITRQEIGQIVG-C----SRETVGRILKMLEDQNLISAHG  201 (210)
T ss_dssp             ECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ccCHHHHHHHhC-C----cHHHHHHHHHHHHHCCcEEeCC
Confidence            689999999999 9    9999999999999999998543

>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=90.43  E-value=0.23  Score=32.47  Aligned_cols=35  Identities=23%  Similarity=0.337  Sum_probs=32.0

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+|-++||..+| +    .+..+.|+++.|...|+++...
T Consensus       187 ~lt~~~lA~~lg-~----sr~tvsR~l~~L~~~g~I~~~~  221 (230)
T 3iwz_A          187 RVSRQELARLVG-C----SREMAGRVLKKLQADGLLHARG  221 (230)
T ss_dssp             ECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEECC
Confidence            489999999999 9    9999999999999999998653

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

Probab=90.28  E-value=0.25  Score=30.24  Aligned_cols=37  Identities=16%  Similarity=0.265  Sum_probs=32.8

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    ....+++.++.|...|++....
T Consensus        30 G~~lPs~~~La~~~~-v----Sr~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           30 GEMIPSIRKISTEYQ-I----NPLTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             TCEECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEec
Confidence            3566 9999999999 9    8999999999999999987553

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=90.27  E-value=0.24  Score=31.96  Aligned_cols=34  Identities=24%  Similarity=0.413  Sum_probs=31.5

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       146 ~~t~~~lA~~lg-~----sr~tvsR~l~~L~~~g~I~~~  179 (202)
T 2zcw_A          146 KATHDELAAAVG-S----VRETVTKVIGELAREGYIRSG  179 (202)
T ss_dssp             ECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEeC
Confidence            589999999999 9    999999999999999999754

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

Probab=90.26  E-value=0.42  Score=30.06  Aligned_cols=37  Identities=27%  Similarity=0.262  Sum_probs=33.0

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    ....+++.++.|...|++....
T Consensus        25 G~~LPse~~La~~~g-v----Sr~tVr~Al~~L~~~Gli~~~~   62 (129)
T 2ek5_A           25 DQRVPSTNELAAFHR-I----NPATARNGLTLLVEAGILYKKR   62 (129)
T ss_dssp             TSCBCCHHHHHHHTT-C----CHHHHHHHHHHHHTTTSEEEET
T ss_pred             CCcCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEec
Confidence            4667 9999999999 9    9999999999999999997554

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=90.05  E-value=0.26  Score=31.73  Aligned_cols=34  Identities=21%  Similarity=0.320  Sum_probs=31.5

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+|+.|...|+++..
T Consensus       139 ~~t~~~lA~~lg-~----sr~tvsR~l~~L~~~g~I~~~  172 (195)
T 3b02_A          139 TVSHEEIADATA-S----IRESVSKVLADLRREGLIATA  172 (195)
T ss_dssp             ECCHHHHHHTTT-S----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             cCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            589999999999 9    999999999999999998754

>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=90.00  E-value=0.26  Score=32.20  Aligned_cols=34  Identities=29%  Similarity=0.337  Sum_probs=31.8

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       167 ~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  200 (220)
T 2fmy_A          167 GLNTEEIALMLG-T----TRQTVSVLLNDFKKMGILERV  200 (220)
T ss_dssp             SSCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEES
T ss_pred             cCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEEc
Confidence            789999999999 9    999999999999999998753

>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=89.95  E-value=0.28  Score=32.13  Aligned_cols=34  Identities=18%  Similarity=0.227  Sum_probs=31.4

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       163 ~~t~~~lA~~lG-~----sr~tvsR~l~~L~~~g~I~~~  196 (222)
T 1ft9_A          163 DFTVEEIANLIG-S----SRQTTSTALNSLIKEGYISRQ  196 (222)
T ss_dssp             CCCHHHHHHHHC-S----CHHHHHHHHHHHHHTTSSEEC
T ss_pred             cCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCcEEEc
Confidence            489999999999 9    999999999999999998754

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=89.94  E-value=0.26  Score=31.85  Aligned_cols=35  Identities=29%  Similarity=0.357  Sum_probs=32.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       162 ~~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  196 (216)
T 4ev0_A          162 FQIRHHELAALAG-T----SRETVSRVLHALAEEGVVRLG  196 (216)
T ss_dssp             EECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            3689999999999 9    999999999999999999754

>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=89.88  E-value=0.31  Score=31.87  Aligned_cols=34  Identities=21%  Similarity=0.299  Sum_probs=31.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       177 ~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  210 (227)
T 3d0s_A          177 DLTQEEIAQLVG-A----SRETVNKALADFAHRGWIRLE  210 (227)
T ss_dssp             CCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCEEec
Confidence            689999999999 9    999999999999999998754

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=89.81  E-value=1.1  Score=27.59  Aligned_cols=51  Identities=22%  Similarity=0.230  Sum_probs=40.8

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhC------CCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQL------PATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~------~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++-.+++-|.-+|.+    +|++--||++.+      + +    ++..|+++|+-|...|++....
T Consensus         8 ~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~-i----s~gtlY~~L~rLe~~GlI~~~~   64 (117)
T 4esf_A            8 LKGSLEGCVLEIISR----RETYGYEITRHLNDLGFTE-V----VEGTVYTILVRLEKKKLVNIEK   64 (117)
T ss_dssp             HHHHHHHHHHHHHHH----SCBCHHHHHHHHHHHTCTT-C----CHHHHHHHHHHHHHTTCEEEEE
T ss_pred             HHChHHHHHHHHHHc----CCCCHHHHHHHHHHcCCCC-C----CccHHHHHHHHHHHCCCEEEEe
Confidence            344455556667775    699999999987      5 6    8889999999999999998653

>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=89.77  E-value=0.43  Score=31.69  Aligned_cols=34  Identities=18%  Similarity=0.242  Sum_probs=31.5

Q ss_pred             CCCHHHHHhhCCCCCCCCCc-chHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAP-TMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~-~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+ ..+.|+|+.|...|++...
T Consensus       169 ~~t~~~lA~~lG-~----sr~etvsR~l~~l~~~glI~~~  203 (238)
T 2bgc_A          169 NLTMQELGYSSG-I----AHSSAVSRIISKLKQEKVIVYK  203 (238)
T ss_dssp             CCCHHHHHHHTT-C----CCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhC-C----ChHHHHHHHHHHHHHCCCEEec
Confidence            789999999999 9    89 6999999999999998754

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=89.76  E-value=0.26  Score=32.09  Aligned_cols=35  Identities=23%  Similarity=0.401  Sum_probs=32.0

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -++|-++||..+| +    .+..+.|+++.|...|++...
T Consensus       177 ~~~t~~~lA~~lg-~----sr~tvsR~l~~l~~~g~I~~~  211 (227)
T 3dkw_A          177 IPVAKQLVAGHLS-I----QPETFSRIMHRLGDEGIIHLD  211 (227)
T ss_dssp             CCSCTHHHHHHTT-S----CHHHHHHHHHHHHHHTSEEES
T ss_pred             ecCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCcEEec
Confidence            4689999999999 9    999999999999999999754

>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=89.54  E-value=0.34  Score=32.35  Aligned_cols=35  Identities=26%  Similarity=0.348  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -++|-++||..+| +    .+..+.|+|+.|...|++...
T Consensus       192 ~~lt~~~lA~~lG-~----sr~tvsR~l~~L~~~GlI~~~  226 (243)
T 3la7_A          192 LKLSHQAIAEAIG-S----TRVTVTRLLGDLREKKMISIH  226 (243)
T ss_dssp             SCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCCHHHHHHHHC-C----cHHHHHHHHHHHHHCCCEEEc
Confidence            3689999999999 9    999999999999999999854

>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=89.42  E-value=0.33  Score=32.44  Aligned_cols=35  Identities=20%  Similarity=0.198  Sum_probs=32.2

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|+++...
T Consensus       177 ~~t~~~iA~~lG-~----sr~tvsR~l~~L~~~g~I~~~~  211 (250)
T 3e6c_C          177 PLSQKSIGEITG-V----HHVTVSRVLASLKRENILDKKK  211 (250)
T ss_dssp             CCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCCHHHHHHHhC-C----cHHHHHHHHHHHHHCCCeEeCC
Confidence            789999999999 9    9999999999999999997543

>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=89.41  E-value=0.3  Score=29.67  Aligned_cols=36  Identities=28%  Similarity=0.347  Sum_probs=32.3

Q ss_pred             CCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.+ |..|||+.++ +    ....+++-++.|...|++....
T Consensus        41 ~~lps~~eLa~~lg-V----Sr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           41 EGLLVASKIADRVG-I----TRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             EEEECHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEEe
Confidence            556 9999999999 9    8999999999999999997554

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=89.24  E-value=0.47  Score=29.78  Aligned_cols=47  Identities=19%  Similarity=0.161  Sum_probs=37.8

Q ss_pred             hHHHHHhc-CCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           34 LFEIIAKA-GPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        34 Ifd~l~~~-g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+|.|.+. ..-.-+|...|++++. +    .-.+-+++||.|.+.|++..+.
T Consensus        46 t~dkl~KEVpk~KlITpsvlseRlk-I----~gSLAR~aLreL~~kGlIk~V~   93 (108)
T 3u5c_Z           46 KYDRILKEVPTYRYVSVSVLVDRLK-I----GGSLARIALRHLEKEGIIKPIS   93 (108)
T ss_dssp             HHHHHHHHCSSCSSBSHHHHHHTTC-C----CTTHHHHHHHHHSSSSSCEEEE
T ss_pred             HHHHHHHHccCCeEEeHHHhhhhhh-h----hHHHHHHHHHHHHHCCCEEEEe
Confidence            45555543 2225689999999999 9    8999999999999999998763

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=89.17  E-value=0.56  Score=34.18  Aligned_cols=40  Identities=10%  Similarity=0.090  Sum_probs=35.2

Q ss_pred             HHHhcCCCCCCCHHHHHhhC--CCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           37 IIAKAGPGAKLSASEIAAQL--PATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        37 ~l~~~g~~~~~t~~eLA~~~--~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+..+   +|+++.+|++..  + +    .+..++|-|..|...|++..+
T Consensus        30 yl~~~---~pV~s~~La~~~~l~-V----S~aTIRrDL~~LE~~GlL~r~   71 (338)
T 1stz_A           30 YIENK---KPVSSQRVLEVSNIE-F----SSATIRNDMKKLEYLGYIYQP   71 (338)
T ss_dssp             HHHHC---SCBCHHHHHHHSCCC-S----CHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHcC---CCccHHHHHHHhCCC-C----CHHHHHHHHHHHHHCCCEEEc
Confidence            45543   799999999998  8 8    899999999999999999865

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

Probab=89.11  E-value=0.65  Score=30.38  Aligned_cols=48  Identities=15%  Similarity=0.351  Sum_probs=38.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCC-------CCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPA-------TKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~-------~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +++-|.-.|.+    +|++.-||++.+..       +    .+..|++.|+-|...|++....
T Consensus         3 l~~~iL~lL~~----~~~~gyel~~~l~~~~~~~~~~----s~~~ly~~L~~Le~~GlI~~~~   57 (179)
T 1yg2_A            3 LPHVILTVLST----RDATGYDITKEFSASIGYFWKA----SHQQVYRELNKMGEQGLVTCVL   57 (179)
T ss_dssp             HHHHHHHHHHH----CCBCHHHHHHHHTTGGGGTCCC----CHHHHHHHHHHHHHTTSEEECC
T ss_pred             hHHHHHHHHhc----CCCCHHHHHHHHHHHhCCccCC----CcCcHHHHHHHHHHCCCeEEEe
Confidence            45556777775    69999999998831       5    7889999999999999998653

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

Probab=88.74  E-value=0.37  Score=30.13  Aligned_cols=37  Identities=19%  Similarity=0.201  Sum_probs=33.0

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    ....+++-++.|...|++....
T Consensus        32 G~~lPse~~La~~~~-v----Sr~tvr~Al~~L~~~Gli~~~~   69 (126)
T 3by6_A           32 NDQLPSVRETALQEK-I----NPNTVAKAYKELEAQKVIRTIP   69 (126)
T ss_dssp             TCEECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEec
Confidence            3667 9999999999 9    8999999999999999997553

>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=88.64  E-value=0.34  Score=32.04  Aligned_cols=34  Identities=21%  Similarity=0.331  Sum_probs=31.5

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|+++..
T Consensus       186 ~~t~~~lA~~lG-~----sr~tvsR~l~~l~~~glI~~~  219 (232)
T 1zyb_A          186 KVKMDDLARCLD-D----TRLNISKTLNELQDNGLIELH  219 (232)
T ss_dssp             ECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSCEEE
T ss_pred             cCCHHHHHHHhC-C----ChhHHHHHHHHHHHCCCEEec
Confidence            589999999999 9    999999999999999998754

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=88.36  E-value=0.34  Score=31.82  Aligned_cols=46  Identities=17%  Similarity=0.200  Sum_probs=37.2

Q ss_pred             hHHHHHhc-CCC-CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           34 LFEIIAKA-GPG-AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        34 Ifd~l~~~-g~~-~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+|.|.+. ..- .-+|...|++++. +    +-.+-+++||.|...|++..+
T Consensus        49 tydKL~KEVpk~gKlITpsvlseRlk-I----~gSLARkaLreL~~kGlIk~V   96 (143)
T 2xzm_8           49 NVESIINNPSKVGKVLTVSTVVEKLK-V----NGSLARQLMRTMADRKLVEKV   96 (143)
T ss_dssp             HHHHHHTCCTTSCSEECHHHHHHHHC-B----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhcccceeecHHHHHHHhc-c----hHHHHHHHHHHHHHCCCEEEE
Confidence            45556543 211 4689999999999 9    999999999999999999876

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=88.34  E-value=0.65  Score=29.05  Aligned_cols=40  Identities=10%  Similarity=0.149  Sum_probs=34.1

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      .+-.+.|+..|.+     +.|..||++.+| +    ....+.|+-|.|-.
T Consensus        45 laqR~~Ia~lL~~-----G~SyreIa~~tG-~----StaTIsRv~r~L~~   84 (107)
T 3frw_A           45 LSQRFEVAKMLTD-----KRTYLDISEKTG-A----STATISRVNRSLNY   84 (107)
T ss_dssp             HHHHHHHHHHHHT-----TCCHHHHHHHHC-C----CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-----CCCHHHHHHHHC-c----cHHHHHHHHHHHHc
Confidence            4567889999885     399999999999 9    88899999998864

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=88.28  E-value=0.65  Score=32.42  Aligned_cols=48  Identities=21%  Similarity=0.375  Sum_probs=39.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHH-HHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILG-LLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR-~L~s~gi~~e~~   85 (89)
                      ..++..+.+.+ +.+.+.+++|+.++ .    +...++|.++ +|...|++..+.
T Consensus       266 ~~~l~~l~~~~-~~~~~~~~~a~~lg-~----~~~tl~~~l~~~l~~~gli~~~~  314 (338)
T 3pfi_A          266 LRYLELLTAAK-QKPIGLASIAAALS-E----DENTIEDVIEPYLLANGYIERTA  314 (338)
T ss_dssp             HHHHHHHHHSC-SCCBCHHHHHHHTT-C----CHHHHHHTTHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHhc-CCCchHHHHHHHhC-C----CHHHHHHHHhHHHHHcCceecCC
Confidence            44566666653 47899999999999 9    9999999999 999999987653

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=88.23  E-value=0.49  Score=32.37  Aligned_cols=38  Identities=16%  Similarity=0.246  Sum_probs=34.3

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +|..++..+||+.+| +    ....+++-|+.|...|++....
T Consensus        46 pG~~L~e~~La~~lg-V----Sr~~VReAL~~L~~~Glv~~~~   83 (237)
T 3c7j_A           46 SGTALRQQELATLFG-V----SRMPVREALRQLEAQSLLRVET   83 (237)
T ss_dssp             TTCBCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CcCeeCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence            357899999999999 9    9999999999999999998653

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

Probab=88.22  E-value=0.58  Score=29.07  Aligned_cols=37  Identities=24%  Similarity=0.333  Sum_probs=32.8

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    ....+++.++.|+..|++....
T Consensus        34 g~~Lps~~~La~~~~-v----Sr~tvr~Al~~L~~~G~i~~~~   71 (125)
T 3neu_A           34 EDKLPSVREMGVKLA-V----NPNTVSRAYQELERAGYIYAKR   71 (125)
T ss_dssp             TCBCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCeEEEec
Confidence            3566 7999999999 9    9999999999999999997653

>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=87.94  E-value=0.48  Score=34.01  Aligned_cols=46  Identities=17%  Similarity=0.339  Sum_probs=38.6

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +..|.+.|.+ +  +++|.+|||+.++ +    .+..++|-++.|...|+..+.
T Consensus         7 ~~~Il~~L~~-~--~~~s~~eLa~~l~-v----S~~ti~r~l~~L~~~G~~i~~   52 (321)
T 1bia_A            7 PLKLIALLAN-G--EFHSGEQLGETLG-M----SRAAINKHIQTLRDWGVDVFT   52 (321)
T ss_dssp             HHHHHHHHTT-S--SCBCHHHHHHHHT-S----CHHHHHHHHHHHHHTTCCCEE
T ss_pred             HHHHHHHHHc-C--CCcCHHHHHHHHC-C----CHHHHHHHHHHHHhCCCcEEE
Confidence            3457777854 2  6899999999999 9    999999999999999987643

>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=87.78  E-value=1.3  Score=25.97  Aligned_cols=37  Identities=14%  Similarity=0.082  Sum_probs=32.3

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +..|+.+||.++| .    ...-+.|+|=-|...|.+....+
T Consensus        28 ~~~Ta~~IAkkLg-~----sK~~vNr~LY~L~kkG~V~~~~~   64 (75)
T 1sfu_A           28 DYTTAISLSNRLK-I----NKKKINQQLYKLQKEDTVKMVPS   64 (75)
T ss_dssp             CEECHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEECC
T ss_pred             cchHHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEecCCC
Confidence            5699999999999 9    88889999999999998876543

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

Probab=87.69  E-value=0.6  Score=28.22  Aligned_cols=49  Identities=18%  Similarity=0.235  Sum_probs=38.5

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhC----CCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQL----PATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~----~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -..++-|.-.|.+    +|++--||.+.+    + +    ++..|+++|+-|...|++....
T Consensus         8 g~l~~~IL~~L~~----~~~~gyel~~~l~~~~~-i----~~~tly~~L~~Le~~GlI~~~~   60 (108)
T 3l7w_A            8 LLIEYLILAIVSK----HDSYGYDISQTIKLIAS-I----KESTLYPILKKLEKAGYLSTYT   60 (108)
T ss_dssp             HHHHHHHHHHHHH----SCEEHHHHHHHHTTTCC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHHc----CCCcHHHHHHHHHHHhC-C----CcChHHHHHHHHHHCCCeEEEe
Confidence            3455566677776    588888887774    6 7    8889999999999999998654

>2z99_A Putative uncharacterized protein; winged helix domain, cell cycle, cell division, chromosome partition, cytoplasm; 2.30A {Mycobacterium tuberculosis}

Probab=87.63  E-value=0.57  Score=32.63  Aligned_cols=45  Identities=16%  Similarity=0.239  Sum_probs=38.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      |.+..+|+-+   +|+|-.||++..| +    ++   ..++|.|...|++.+.++.
T Consensus       103 LEtLaiIAy~---QPITR~eI~~irG-v----~~---~~~v~~Lle~gLI~e~Gr~  147 (219)
T 2z99_A          103 LETLAVVAYR---QPVTRARVSAVRG-V----NV---DAVMRTLLARGLITEVGTD  147 (219)
T ss_dssp             HHHHHHHHHH---CSEEHHHHHHHHT-S----CC---HHHHHHHHHTTSEEEEEEC
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHC-C----CH---HHHHHHHHHCCCEEEcccc
Confidence            4577888875   6999999999999 8    54   7899999999999998643

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=87.42  E-value=2.1  Score=26.13  Aligned_cols=52  Identities=19%  Similarity=0.213  Sum_probs=40.8

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhC--------CCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQL--------PATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~--------~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .++-..++-|.-+|.+    +|++--||.+.+        + +    ++..|+++|+-|...|++....
T Consensus         8 ~~~g~l~~~IL~~L~~----~~~~Gyei~~~l~~~~~~~~~-i----~~gtly~~L~rLe~~GlI~~~~   67 (116)
T 3f8b_A            8 MLRAQTNVILLNVLKQ----GDNYVYGIIKQVKEASNGEME-L----NEATLYTIFKRLEKDGIISSYW   67 (116)
T ss_dssp             HHHHHHHHHHHHHHHH----CCBCHHHHHHHHHHHTTTCCC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHhchHHHHHHHHHHh----CCCCHHHHHHHHHHHhCCCCC-C----CcchHHHHHHHHHHCCCEEEEe
Confidence            3444456666677776    689999998887        4 5    7889999999999999998653

>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=87.35  E-value=0.45  Score=32.20  Aligned_cols=34  Identities=21%  Similarity=0.376  Sum_probs=31.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+|+.|...|+++..
T Consensus       217 ~lt~~~lA~~lG-~----sr~tvsR~l~~L~~~GlI~~~  250 (260)
T 3kcc_A          217 KITRQEIGQIVG-C----SRETVGRILKMLEDQNLISAH  250 (260)
T ss_dssp             ECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEc
Confidence            689999999999 9    999999999999999999854

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=87.17  E-value=1.3  Score=25.98  Aligned_cols=40  Identities=13%  Similarity=0.154  Sum_probs=29.4

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      |-+.|.++-.++++|+++||+.++ .    .+..|.|+++.....
T Consensus         7 i~~~i~~~~~~~~~~~~~lA~~~~-~----S~~~l~r~fk~~~g~   46 (103)
T 3lsg_A            7 IQNIIEESYTDSQFTLSVLSEKLD-L----SSGYLSIMFKKNFGI   46 (103)
T ss_dssp             HHHHHHHHTTCTTCCHHHHHHHTT-C----CHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHccCCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCc
Confidence            344455442224899999999999 9    999999998766543

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=87.01  E-value=0.91  Score=28.86  Aligned_cols=41  Identities=12%  Similarity=0.152  Sum_probs=34.2

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      ..+-.+.|+..|.+    | .|-.|||+.+| +    .+..+.|+-|.|-.
T Consensus        61 aLs~R~eV~klL~~----G-~syreIA~~~g-~----S~aTIsRv~r~L~~  101 (119)
T 3kor_A           61 SLSQRLQVAKMIKQ----G-YTYATIEQESG-A----STATISRVKRSLQW  101 (119)
T ss_dssp             HHHHHHHHHHHHHH----T-CCHHHHHHHHC-C----CHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHc----C-CCHHHHHHHHC-C----CHHHHHHHHHHHhc
Confidence            44455888999986    3 99999999999 9    89999999998853

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=86.73  E-value=0.11  Score=33.58  Aligned_cols=46  Identities=17%  Similarity=0.289  Sum_probs=37.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      ++..|.+.|...   +.+|..|||+.+| +    ....+++-++.|...|++..
T Consensus        14 l~~~Il~~l~~~---~~ls~~eLa~~lg-v----Sr~~vr~al~~L~~~Gli~~   59 (163)
T 2gqq_A           14 IDRNILNELQKD---GRISNVELSKRVG-L----SPTPCLERVRRLERQGFIQG   59 (163)
T ss_dssp             HHHHHHHHHHHC---SSCCTTGGGTSSS-C----CTTTSSSTHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEE
Confidence            455667766652   6889999999999 9    78888889999999999873

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=86.49  E-value=0.8  Score=29.37  Aligned_cols=50  Identities=12%  Similarity=0.196  Sum_probs=40.1

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhC--------CCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQL--------PATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~--------~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +--.++-|...|.+    +|++..||++.+        + +    ++..|+++|+-|...|++....
T Consensus        39 ~g~~~~~IL~~L~~----~~~~gyeI~~~l~~~~~~~~~-i----s~gtLy~~L~rLE~~GlI~~~~   96 (145)
T 1xma_A           39 RGYVDTIILSLLIE----GDSYGYEISKNIRIKTDELYV-I----KETTLYSAFARLEKNGYIKSYY   96 (145)
T ss_dssp             GGTHHHHHHHHHHH----CCEEHHHHHHHHHHHHTTSCC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCcHHHHHHHHHHh----CCCCHHHHHHHHHHhhCCccC-c----ChhHHHHHHHHHHHCCCEEEEE
Confidence            34456677777865    689999988887        5 6    7889999999999999998653

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=86.37  E-value=1.5  Score=25.94  Aligned_cols=40  Identities=10%  Similarity=0.179  Sum_probs=30.1

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      +.+.|.++-.+.++|+++||+.++ .    .+..|.|+++.....
T Consensus         8 ~~~~i~~~~~~~~~~~~~lA~~~~-~----S~~~l~r~fk~~~G~   47 (107)
T 2k9s_A            8 ACQYISDHLADSNFDIASVAQHVC-L----SPSRLSHLFRQQLGI   47 (107)
T ss_dssp             HHHHHHHTSSCSSCCHHHHHHHTT-S----CHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHhccCCCCHHHHHHHHC-C----CHHHHHHHHHHHHCc
Confidence            455566543126899999999999 9    999999998765543

>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=86.35  E-value=0.61  Score=29.15  Aligned_cols=37  Identities=19%  Similarity=0.306  Sum_probs=32.9

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    +...+++-++.|...|++....
T Consensus        35 G~~LPser~La~~~g-V----Sr~tVReAl~~L~~eGlv~~~~   72 (134)
T 4ham_A           35 GEKILSIREFASRIG-V----NPNTVSKAYQELERQEVIITVK   72 (134)
T ss_dssp             TCEECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEEEc
Confidence            4667 8999999999 9    9999999999999999997543

>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=86.34  E-value=0.54  Score=30.90  Aligned_cols=31  Identities=26%  Similarity=0.333  Sum_probs=28.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      -|+|-++||..+| +    .+..+.|+++.|...|+
T Consensus       177 l~~t~~~iA~~lg-~----sr~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          177 LPYDKMLIAGRLG-M----KPESLSRAFSRLKAAGV  207 (237)
T ss_dssp             CCSCTHHHHHHTT-C----CHHHHHHHHHHHGGGTE
T ss_pred             ecCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCe
Confidence            3678999999999 9    99999999999999996

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=86.30  E-value=1  Score=26.64  Aligned_cols=39  Identities=10%  Similarity=0.031  Sum_probs=29.9

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      +.+.|.++- ..++|+++||+.++ .    .+..|.|+++.....
T Consensus         7 ~~~~i~~~~-~~~~~~~~lA~~~~-~----s~~~l~r~fk~~~G~   45 (108)
T 3mn2_A            7 VEEYIEANW-MRPITIEKLTALTG-I----SSRGIFKAFQRSRGY   45 (108)
T ss_dssp             HHHHHHHHT-TSCCCHHHHHHHHT-C----CHHHHHHHHHHHTSS
T ss_pred             HHHHHHHcc-cCCCCHHHHHHHHC-C----CHHHHHHHHHHHhCc
Confidence            445565543 26899999999999 9    899999998866543

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=86.07  E-value=3.1  Score=25.26  Aligned_cols=56  Identities=14%  Similarity=0.109  Sum_probs=40.8

Q ss_pred             HHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCC--CCC-CCCc-chHHHHHHHHhccCceeeec
Q 045477           26 MKAVINLGLFEIIAKAGPGAKLSASEIAAQLPA--TKN-KDAP-TMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        26 L~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~--~~~-~~d~-~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++-..++-|...|.+    +|++..||++.+..  ... ..++ ..|++.|+-|...|++....
T Consensus        10 ~~~~~~~~IL~~L~~----~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~   69 (118)
T 2esh_A           10 RGWWLASTILLLVAE----KPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEW   69 (118)
T ss_dssp             HHHHHHHHHHHHHHH----SCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEE
T ss_pred             ccchHHHHHHHHHHc----CCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEe
Confidence            344466667777876    68999999998841  101 0167 89999999999999998654

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=86.01  E-value=0.75  Score=28.39  Aligned_cols=37  Identities=19%  Similarity=0.178  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .|.++.|++..++ .    ++..+.++++.|+..|.+.....
T Consensus        19 ~p~~~~~la~~~~-~----~~~~~~~~l~~l~~~G~l~~i~~   55 (121)
T 2pjp_A           19 EPWWVRDLAKETG-T----DEQAMRLTLRQAAQQGIITAIVK   55 (121)
T ss_dssp             SCEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEET
T ss_pred             CCCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEecC
Confidence            5779999999999 9    99999999999999998876543

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

Probab=85.96  E-value=1.8  Score=26.65  Aligned_cols=52  Identities=19%  Similarity=0.132  Sum_probs=40.9

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhC------CCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQL------PATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~------~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .++-.+++-|.-+|.+    +|++--||.+.+      + +    ++..|+++|+-|...|+++...
T Consensus         9 l~~g~l~~~IL~lL~~----~p~~Gyei~~~l~~~g~~~-i----s~gtlY~~L~rLe~~GlI~~~~   66 (116)
T 3hhh_A            9 LLKGILEGLVLAIIQR----KETYGYEITKILNDQGFTE-I----VEGTVYTILLRLEKNQWVIAEK   66 (116)
T ss_dssp             HHTTHHHHHHHHHHHH----SCBCHHHHHHHHHTTSCSS-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHhhhHHHHHHHHHhc----CCCCHHHHHHHHHHcCCCC-C----CccHHHHHHHHHHHCCCEEEEe
Confidence            3444455566667775    699999999987      4 5    7889999999999999998653

>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=85.70  E-value=1.1  Score=30.26  Aligned_cols=34  Identities=12%  Similarity=0.189  Sum_probs=30.3

Q ss_pred             CCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           47 LSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..+||+.++ .    ++..+.|+++.|...|++....
T Consensus        25 ~~~~~La~~l~-v----s~~tvs~~l~~Le~~GlV~r~~   58 (230)
T 1fx7_A           25 PLRARIAERLD-Q----SGPTVSQTVSRMERDGLLRVAG   58 (230)
T ss_dssp             CCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             CcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEEeC
Confidence            34599999999 9    9999999999999999998654

>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=85.42  E-value=1.2  Score=26.32  Aligned_cols=40  Identities=8%  Similarity=0.088  Sum_probs=30.6

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      +.+.|.++- ..++|+++||+.++ +    .+..|.|+++......
T Consensus        10 ~~~~i~~~~-~~~~~~~~lA~~~~-~----S~~~l~r~fk~~~G~s   49 (108)
T 3oou_A           10 VLSYITEHF-SEGMSLKTLGNDFH-I----NAVYLGQLFQKEMGEH   49 (108)
T ss_dssp             HHHHHHHHT-TSCCCHHHHHHHHT-S----CHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHh-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence            445565543 26899999999999 9    9999999998765443

>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=85.34  E-value=0.48  Score=23.39  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=23.5

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      ++|..|||+.++ +    ....++|.++.....|
T Consensus        21 g~s~~~IA~~lg-i----s~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C           21 NVSLHEMSRKIS-R----SRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             TCCHHHHHHHHT-C----CHHHHHHHHHCSTTTT
T ss_pred             CCCHHHHHHHHC-c----CHHHHHHHHhhHHhcC
Confidence            589999999999 9    8889999887544433

>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60

Probab=85.16  E-value=0.38  Score=31.97  Aligned_cols=45  Identities=18%  Similarity=0.228  Sum_probs=37.6

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      |.+..+|+-+   +|+|-.||++..| .    +   ...++|.|...|++.+.++.
T Consensus        97 LEtLaiIay~---qPiTR~eI~~irG-v----~---~~~~v~~L~e~glI~e~g~~  141 (162)
T 1t6s_A           97 LEVLAVVAWH---QPVTKGEIQQIRG-A----S---PDYSIDRLLARGLIEVRGRA  141 (162)
T ss_dssp             HHHHHHHHHH---CSEEHHHHHHHHT-C----C---CCSHHHHHHHTTSEEEEEEC
T ss_pred             HHHHHHHHHc---CCcCHHHHHHHHC-C----C---HHHHHHHHHHCCCEEEcccc
Confidence            4578888875   6999999999999 8    4   55689999999999987653

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=84.66  E-value=0.77  Score=30.66  Aligned_cols=45  Identities=16%  Similarity=0.141  Sum_probs=39.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -.|.++|. .   |+.|..+||+.+| .    .-....=+++.|...|++.+..
T Consensus        14 ~~ILE~Lk-~---G~~~t~~Iak~LG-l----Shg~aq~~Ly~LeREG~V~~Vk   58 (165)
T 2vxz_A           14 RDILALLA-D---GCKTTSLIQQRLG-L----SHGRAKALIYVLEKEGRVTRVA   58 (165)
T ss_dssp             HHHHHHHT-T---CCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHH-h---CCccHHHHHHHhC-C----cHHHHHHHHHHHHhcCceEEEE
Confidence            35677787 3   7999999999999 9    8889999999999999999875

>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=84.24  E-value=1.6  Score=31.47  Aligned_cols=48  Identities=19%  Similarity=0.220  Sum_probs=39.4

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +-.|.+.|.+++ +.++|.+|||+.++ +    ....+.+-++.|...|+.-+.
T Consensus         5 ~~~iL~~L~~~~-g~~~Sg~eLa~~lg-v----Sr~aV~k~i~~L~~~G~~i~~   52 (323)
T 3rkx_A            5 SQDVLQLLYKNK-PNYISGQSIAESLN-I----SRTAVKKVIDQLKLEGCKIDS   52 (323)
T ss_dssp             HHHHHHHHHHHT-TSCBCHHHHHHHHT-S----CHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHhCC-CCccCHHHHHHHHC-C----CHHHHHHHHHHHHhcCCeEEE
Confidence            346788886543 26999999999999 9    999999999999999985543

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=83.92  E-value=1.4  Score=26.31  Aligned_cols=40  Identities=15%  Similarity=0.144  Sum_probs=30.7

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      +.+.|.++- ..++|+++||+.++ .    .+..|.|+++......
T Consensus        12 ~~~~i~~~~-~~~~~~~~lA~~~~-~----S~~~l~r~fk~~~G~s   51 (113)
T 3oio_A           12 AVSLMEANI-EEPLSTDDIAYYVG-V----SRRQLERLFKQYLGTV   51 (113)
T ss_dssp             HHHHHHTCS-SSCCCHHHHHHHHT-S----CHHHHHHHHHHHTSSC
T ss_pred             HHHHHHhhh-cCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence            445666552 26899999999999 9    9999999988765443

>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=83.51  E-value=0.22  Score=35.99  Aligned_cols=42  Identities=10%  Similarity=0.176  Sum_probs=0.0

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      .|...|...   +++|..|||+.++ +    ++..++|.+..|...|+++
T Consensus        24 ~iL~~l~~~---~~~t~~eLa~~l~-v----s~~Tv~r~l~~Le~~Glv~   65 (345)
T 2o0m_A           24 QILRNIYWM---QPIGRRSLSETMG-I----TERVLRTETDVLKQLNLIE   65 (345)
T ss_dssp             --------------------------------------------------
T ss_pred             HHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEE
Confidence            455666553   6899999999999 9    9999999999999999996

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=83.46  E-value=1.5  Score=29.67  Aligned_cols=36  Identities=14%  Similarity=0.198  Sum_probs=31.5

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+.+..+||+.++ .    ++..+.++++.|...|++....
T Consensus        23 ~~~~~~~la~~l~-v----s~~tvs~~l~~Le~~GlV~r~~   58 (226)
T 2qq9_A           23 VTPLRARIAERLE-Q----SGPTVSQTVARMERDGLVVVAS   58 (226)
T ss_dssp             CCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeC
Confidence            3456799999999 9    9999999999999999998653

>3sxy_A Transcriptional regulator, GNTR family; transcription factor, metal-binding, structur genomics, PSI-2, protein structure initiative; 1.65A {Thermotoga maritima} PDB: 3dbw_A 3fms_A*

Probab=83.27  E-value=0.82  Score=30.47  Aligned_cols=39  Identities=28%  Similarity=0.301  Sum_probs=34.7

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|..+|-.+||+..| +    ....++.-|+.|.+.|++.-...
T Consensus        32 pG~~L~e~~La~~lg-V----SRtpVREAL~~L~~eGlv~~~~~   70 (218)
T 3sxy_A           32 LGEKLNVRELSEKLG-I----SFTPVRDALLQLATEGLVKVVPR   70 (218)
T ss_dssp             TTCEECHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEETT
T ss_pred             CCCEeCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeCC
Confidence            457899999999999 9    99999999999999999986543

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=83.07  E-value=0.98  Score=31.34  Aligned_cols=44  Identities=11%  Similarity=0.138  Sum_probs=36.9

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .-|.-.|.+    ++.|..+||..++ .    .+..+.-.|+.|+..|++...
T Consensus       168 ~~l~~~l~~----~~~t~~~la~~~~-l----~~~~V~~~l~~L~~~~~v~~~  211 (232)
T 2qlz_A          168 AILHYLLLN----GRATVEELSDRLN-L----KEREVREKISEMARFVPVKII  211 (232)
T ss_dssp             HHHHHHHHS----SEEEHHHHHHHHT-C----CHHHHHHHHHHHTTTSCEEEE
T ss_pred             HHHHHHHhc----CCCCHHHHHHHhC-c----CHHHHHHHHHHHHhcCCeEEe
Confidence            444445554    7999999999999 9    899999999999999999743

>2fq3_A Transcription regulatory protein SWI3; four-helix bundle; 1.40A {Saccharomyces cerevisiae} SCOP: a.4.1.18

Probab=82.95  E-value=3.9  Score=25.27  Aligned_cols=54  Identities=9%  Similarity=0.087  Sum_probs=44.2

Q ss_pred             HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      .-+...+.=.|.+.+...+ ..-+|.++....+. .    |...+.||.++|...|++..
T Consensus        46 pe~Yl~iRN~iI~~yr~nP-~~yLT~t~~r~~l~-g----Dv~~i~RVh~FLe~wGLIN~   99 (104)
T 2fq3_A           46 PEVYMRYRNFMVNSYRLNP-NEYFSVTTARRNVS-G----DAAALFRLHKFLTKWGLINY   99 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHCT-TSCCCHHHHHHHSC-S----CHHHHHHHHHHHHHTTSSSS
T ss_pred             HHHHHHHHHHHHHHHHhCC-ceeeeHHHHHHHcc-c----cHHHHHHHHHHHHHcCeecc
Confidence            3455666667778887764 37899999999887 7    99999999999999999874

>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=82.88  E-value=0.24  Score=32.38  Aligned_cols=34  Identities=21%  Similarity=0.286  Sum_probs=0.0

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-++||..+| +    .+..+.|+++.|...|+++..
T Consensus       164 ~~t~~~lA~~lg-~----sr~tvsR~l~~L~~~G~I~~~  197 (213)
T 1o5l_A          164 PVTLEELSRLFG-C----ARPALSRVFQELEREGYIEKH  197 (213)
T ss_dssp             ---------------------------------------
T ss_pred             CCCHHHHHHHhC-C----CHHHHHHHHHHHHHCCeEEEc
Confidence            789999999999 9    899999999999999998754

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=82.39  E-value=2.7  Score=29.10  Aligned_cols=50  Identities=18%  Similarity=0.138  Sum_probs=39.0

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.-.|.+.+.++|- .|-.+.||+..++ .    ++..+..+|+.|+..|.+....
T Consensus       142 ~~~~i~~~~~~~g~-~pp~~~dl~~~l~-~----~~~~~~~~l~~l~~~g~lv~l~  191 (258)
T 1lva_A          142 LLKDLEDKYRVSRW-QPPSFKEVAGSFN-L----DPSELEELLHYLVREGVLVKIN  191 (258)
T ss_dssp             HHHHHHHHHHHHTT-SCCBHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEESS
T ss_pred             HHHHHHHHHHHCCC-CCCCHHHHHhHhC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence            33455666655432 4778999999999 9    9999999999999999877654

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=82.28  E-value=1.8  Score=26.48  Aligned_cols=48  Identities=13%  Similarity=0.191  Sum_probs=37.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCC-----CCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLP-----ATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~-----~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +++-|.-+|.+    +|++--||++.+.     .+    ++..|+++|+-|...|++....
T Consensus        10 l~~~IL~~L~~----~~~~Gyei~~~l~~~~~~~i----s~gtlY~~L~rLe~~GlI~~~~   62 (115)
T 4esb_A           10 LEGCILYIISQ----EEVYGYELSTKLNKHGFTFV----SEGSIYPLLLRMQKEKLIEGTL   62 (115)
T ss_dssp             HHHHHHHHHHH----SCEEHHHHHHHHHHTTCTTC----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHHHcCCCCC----CcChHHHHHHHHHHCCCeEEEe
Confidence            34445666765    6899999998873     15    7889999999999999998653

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

Probab=81.91  E-value=0.32  Score=30.38  Aligned_cols=37  Identities=16%  Similarity=0.157  Sum_probs=31.8

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    +...+++.++.|...|++....
T Consensus        32 G~~lPs~~~La~~~~-v----Sr~tvr~Al~~L~~~G~i~~~~   69 (126)
T 3ic7_A           32 EGRIPSVREYASIVE-V----NANTVMRSYEYLQSQEVIYNKR   69 (126)
T ss_dssp             TSEECCTTTTTTCC--C----CSGGGHHHHHHHHTTTSEEEET
T ss_pred             CCcCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCcEEEEc
Confidence            3567 8999999999 9    8999999999999999997654

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=81.88  E-value=2  Score=25.89  Aligned_cols=36  Identities=19%  Similarity=0.310  Sum_probs=28.4

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHH
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGL   74 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~   74 (89)
                      .+.+.|.++- ..++|+++||+.++ +    .+..|.|+++.
T Consensus        11 ~~~~~i~~~~-~~~~~~~~lA~~~~-~----S~~~l~r~fk~   46 (120)
T 3mkl_A           11 RVCTVINNNI-AHEWTLARIASELL-M----SPSLLKKKLRE   46 (120)
T ss_dssp             HHHHHHHTST-TSCCCHHHHHHHTT-C----CHHHHHHHHHH
T ss_pred             HHHHHHHHhc-cCCCCHHHHHHHHC-c----CHHHHHHHHHH
Confidence            3455666553 26899999999999 9    89999998875

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=80.89  E-value=1.3  Score=30.18  Aligned_cols=39  Identities=26%  Similarity=0.448  Sum_probs=34.6

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|..++-.+||+..| +    ....++.-|+.|.+.|++.-...
T Consensus        48 pG~~L~e~~La~~lg-V----SRtpVREAL~~L~~eGlv~~~~~   86 (239)
T 2hs5_A           48 PGARLSEPDICAALD-V----SRNTVREAFQILIEDRLVAHELN   86 (239)
T ss_dssp             TTCEECHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CcCEeCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeCC
Confidence            457899999999999 9    89999999999999999986543

>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=80.82  E-value=1.9  Score=26.38  Aligned_cols=39  Identities=13%  Similarity=0.124  Sum_probs=30.3

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhcc
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASY   78 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~   78 (89)
                      +.+.|.++- ..++|+++||+.++ .    .+..|.|+++.....
T Consensus        16 ~~~~i~~~~-~~~~sl~~lA~~~~-~----S~~~l~r~fk~~~G~   54 (129)
T 1bl0_A           16 ILDWIEDNL-ESPLSLEKVSERSG-Y----SKWHLQRMFKKETGH   54 (129)
T ss_dssp             HHHHHHTTT-TSCCCCHHHHHHSS-S----CHHHHHHHHHHHHSS
T ss_pred             HHHHHHHcc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCc
Confidence            455666542 26799999999999 9    999999998876544

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=80.81  E-value=1.2  Score=27.27  Aligned_cols=43  Identities=16%  Similarity=0.098  Sum_probs=30.7

Q ss_pred             HHhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           30 INLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        30 v~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      .+-.|.+.|-++.. -..+|+.|||+.++ +    .+..+.|+.|.|=-
T Consensus        22 ~e~~ia~yil~~~~~~~~~si~elA~~~~-v----S~aTv~Rf~kklG~   65 (111)
T 2o3f_A           22 SERKLADYILAHPHXAIESTVNEISALAN-S----SDAAVIRLCXSLGL   65 (111)
T ss_dssp             HHHHHHHHHHHCHHHHHTCCHHHHHHHTT-C----CHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHChHHHHhcCHHHHHHHHC-C----CHHHHHHHHHHcCC
Confidence            35566776655320 02589999999999 9    88888888876643

---

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	89
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	4e-27
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	5e-26
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	1e-11
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	1e-07
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	3e-05

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 110

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 93.3 bits (232), Expect = 4e-27
 Identities = 38/88 (43%), Positives = 53/88 (60%), Gaps = 2/88 (2%)

Query: 4  EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAG-PGAKLSASEIAAQLPA-TKN 61
          +  D     A  +T   V    + A I+L LFEIIAKA  PGA +S SEIA++LPA T++
Sbjct: 1  QTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQH 60

Query: 62 KDAPTMLDRILGLLASYGIVECSVDDVD 89
           D P  LDR+L LLASY ++  +   ++
Sbjct: 61 SDLPNRLDRMLRLLASYSVLTSTTRTIE 88

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 107

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 90.3 bits (224), Expect = 5e-26
 Identities = 44/83 (53%), Positives = 56/83 (67%), Gaps = 1/83 (1%)

Query: 7  DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPT 66
          +E   +A ++   SVL M +K+ + L L EIIAKAGPGA++S  EIA+QLP T N DAP 
Sbjct: 5  EEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLP-TTNPDAPV 63

Query: 67 MLDRILGLLASYGIVECSVDDVD 89
          MLDR+L LLA Y I+ CSV    
Sbjct: 64 MLDRMLRLLACYIILTCSVRTQQ 86

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 101

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 53.4 bits (128), Expect = 1e-11
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 4/77 (5%)

Query: 11 AYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDR 70
          A  ++     +  M++K  + + +  II   G    +S S + + L           + R
Sbjct: 11 ALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKP--ISLSNLVSILQV--PSSKIGNVRR 66

Query: 71 ILGLLASYGIVECSVDD 87
          ++  LA  G  E    +
Sbjct: 67 LMRYLAHNGFFEIITKE 83

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

 Score = 43.2 bits (102), Expect = 1e-07
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 9/84 (10%)

Query: 4  EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKD 63
          E  D++     +     V  M ++    L L + +  AG     + + +A +        
Sbjct: 2  EPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLL-AGA---DTLAGLADRTDTH---- 53

Query: 64 APTMLDRILGLLASYGIVECSVDD 87
           P  L R++  L   G++E     
Sbjct: 54 -PQALSRLVRHLTVVGVLEGGEKQ 76

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]} Length = 85

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

 Score = 36.3 bits (84), Expect = 3e-05
 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 9/71 (12%)

Query: 18 MGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS 77
                M ++    L L + I         +   +AA+         P  L R++  L +
Sbjct: 10 GSLHTPMVVRTAATLRLVDHILAG----ARTVKALAARTDT-----RPEALLRLIRHLVA 60

Query: 78 YGIVECSVDDV 88
           G++E      
Sbjct: 61 IGLLEEDAPGE 71

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	89
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.89
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.89
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.87
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.74
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.74
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	98.11
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.63
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.4
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.3
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	97.27
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	97.24
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	97.14
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.13
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	97.07
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	97.03
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	97.02
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.93
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.92
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	96.88
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.86
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	96.57
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.53
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.5
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.48
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.46
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	96.45
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	96.38
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	96.37
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.37
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	96.29
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	96.27
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.16
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	96.08
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	96.06
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	96.06
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	96.05
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	95.98
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.96
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.89
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	95.89
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.88
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	95.83
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.81
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	95.7
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	95.67
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.65
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	95.54
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.45
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	95.38
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	95.11
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	94.34
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	94.34
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.25
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	94.23
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	94.23
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	93.97
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.79
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	93.57
d1okra_	120	Methicillin resistance regulatory protein MecI {St	93.24
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	93.06
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	92.94
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	92.79
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.55
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	92.06
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	92.02
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	91.85
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	91.79
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	91.49
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	91.24
d2fq3a1	85	Transcription regulatory protein swi3 {Baker's yea	90.88
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	90.71
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	90.46
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	88.79
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	88.5
d2dw4a1	102	Lysine-specific histone demethylase 1, LSD1 {Human	88.37
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	88.12
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	87.23
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	86.69
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	85.41
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	84.79
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	84.6
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	83.71
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	83.44
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	83.34
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	81.76
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	80.55
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	80.13

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.89  E-value=9.7e-24  Score=133.44  Aligned_cols=82  Identities=54%  Similarity=0.807  Sum_probs=75.3

Q ss_pred             hHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477            4 EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus         4 ~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      -++++.+.+.++++++++.|++||+|++|||||+|+++|++.++|+.||+.+++ ..||+.+..|+||||+|+++|+|++
T Consensus         2 ~~dee~~l~a~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~-~~~p~~~~~L~RilR~Las~~vf~~   80 (107)
T d1kyza1           2 ISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLP-TTNPDAPVMLDRMLRLLACYIILTC   80 (107)
T ss_dssp             CCHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSS-CCCTTHHHHHHHHHHHHHHTTSEEE
T ss_pred             cccHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcC-CCCCcchHHHHHHHHHHHhcCceEE
Confidence            367888899999999999999999999999999999998778999999999999 8888888899999999999999997


Q ss_pred             ecc
Q 045477           84 SVD   86 (89)
Q Consensus        84 ~~~   86 (89)
                      +.+
T Consensus        81 ~~~   83 (107)
T d1kyza1          81 SVR   83 (107)
T ss_dssp             EEE
T ss_pred             eee
Confidence            643

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.89  E-value=1.7e-23  Score=130.90  Aligned_cols=81  Identities=17%  Similarity=0.225  Sum_probs=73.1

Q ss_pred             hhHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477            3 NEARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus         3 ~~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      ..+..+++..+|++++||+.+++|++|++|||||+|+++|  +|+|++|||++++ + +|.++..|.|+||+|++.|+|+
T Consensus         3 ~~e~~qaq~~l~~~~~gf~~s~aL~~aveLgi~d~l~~~~--~p~t~~eLa~~~~-~-~~~~~~~L~RlLR~L~~~gi~~   78 (101)
T d1fp2a1           3 PSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHG--KPISLSNLVSILQ-V-PSSKIGNVRRLMRYLAHNGFFE   78 (101)
T ss_dssp             STHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHT--SCEEHHHHHHHHT-C-CGGGHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcHHHHHHcC--CCCCHHHHHHHcC-C-CCccchHHHHHHHHHHhCCcee
Confidence            4677889999999999999999999999999999999876  8999999999999 8 5556678999999999999998


Q ss_pred             eeccc
Q 045477           83 CSVDD   87 (89)
Q Consensus        83 e~~~~   87 (89)
                      ++..+
T Consensus        79 ~~~~~   83 (101)
T d1fp2a1          79 IITKE   83 (101)
T ss_dssp             EEESS
T ss_pred             eecCC
Confidence            86543

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.87  E-value=9.5e-23  Score=129.38  Aligned_cols=82  Identities=44%  Similarity=0.648  Sum_probs=72.5

Q ss_pred             hHhhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcC-CCCCCCHHHHHhhCCCC--CCCCCcchHHHHHHHHhccCc
Q 045477            4 EARDENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAG-PGAKLSASEIAAQLPAT--KNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus         4 ~~~~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g-~~~~~t~~eLA~~~~~~--~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      +++++.+.++++++++++.|++||+||+|||||+|+++| +++++|++||+++++ +  +||+.+..|+||||+|+++|+
T Consensus         1 ~~~~~~~l~a~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp-~~~~~p~~~~~L~RiLRlLas~~v   79 (110)
T d1fp1d1           1 QTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLP-ASTQHSDLPNRLDRMLRLLASYSV   79 (110)
T ss_dssp             CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSC-GGGCCTTHHHHHHHHHHHHHHTTS
T ss_pred             CchHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCC-CCCCCccHHHHHHHHHHHHHHcCc
Confidence            357889999999999999999999999999999999986 346799999999998 5  367667789999999999999


Q ss_pred             eeeecc
Q 045477           81 VECSVD   86 (89)
Q Consensus        81 ~~e~~~   86 (89)
                      |+++..
T Consensus        80 f~~~~~   85 (110)
T d1fp1d1          80 LTSTTR   85 (110)
T ss_dssp             EEEEEE
T ss_pred             cccccc
Confidence            987643

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=99.74  E-value=2.7e-18  Score=103.69  Aligned_cols=65  Identities=20%  Similarity=0.233  Sum_probs=58.9

Q ss_pred             HHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           13 AFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        13 ~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+....+|+.+++|++|++|||||+|++    ||+|++|||++++ +    ++..+.|+||+|++.|+|+|+++
T Consensus         5 ~l~~l~~~~~~~aL~~av~L~ifd~l~~----gp~s~~eLA~~~g-~----~~~~l~rlLr~l~a~gl~~e~~~   69 (85)
T d1tw3a1           5 TLIRLGSLHTPMVVRTAATLRLVDHILA----GARTVKALAARTD-T----RPEALLRLIRHLVAIGLLEEDAP   69 (85)
T ss_dssp             HHHHHHCSHHHHHHHHHHHTTHHHHHHT----TCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEET
T ss_pred             HHHHHHchHHHHHHHHHHHcCcHHHhcc----CCCCHHHHHHHhC-c----ChhHHHHHHHHHHHCCCeEecCC
Confidence            3445578999999999999999999974    7999999999999 9    99999999999999999998754

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=99.74  E-value=1.9e-18  Score=105.99  Aligned_cols=71  Identities=18%  Similarity=0.273  Sum_probs=65.3

Q ss_pred             hHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477            7 DENFAYAFEVTMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus         7 ~~~~~~~~~l~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .+....+++++.+|+.+++|++|++|||||+|++    ||+|++|||++++ +    ++..+.|+||+|++.|+|++...
T Consensus         5 d~~~d~ll~~~~~~~~~~~L~~aveL~ifd~L~~----gp~t~~eLA~~~g-~----~~~~l~rLlr~L~a~gll~~~~d   75 (92)
T d1qzza1           5 DQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLA----GADTLAGLADRTD-T----HPQALSRLVRHLTVVGVLEGGEK   75 (92)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHHT----TCCSHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEECCCC
T ss_pred             chhHHHHHHHHHchHHHHHHHHHHHcCchHHHhC----CCCCHHHHHHHHC-c----CchHHHHHHHHHHHCCCeeeecC
Confidence            3566778999999999999999999999999975    7999999999999 9    99999999999999999998653

>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=98.11  E-value=2.2e-06  Score=49.14  Aligned_cols=47  Identities=21%  Similarity=0.277  Sum_probs=42.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.|.+.+++++  +|+|++|||+.++ .    ++..++|++..|+..|++.++.
T Consensus         8 l~IL~~~a~~~--~~~s~~eia~~~~-~----~~st~~rll~tL~~~g~l~~~~   54 (75)
T d1mkma1           8 FEILDFIVKNP--GDVSVSEIAEKFN-M----SVSNAYKYMVVLEEKGFVLRKK   54 (75)
T ss_dssp             HHHHHHHHHCS--SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEECC
Confidence            46788898876  7999999999999 9    9999999999999999999864

>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=97.63  E-value=5.4e-05  Score=42.41  Aligned_cols=51  Identities=14%  Similarity=0.252  Sum_probs=44.2

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |-.-...|+.+|..+   +|+|..|||+.++ .    .+..+.++++.|...|++.+.+
T Consensus         4 r~~N~~~Il~~l~~~---g~~sr~eLa~~~g-l----S~~Tv~~~l~~L~~~Glv~e~~   54 (71)
T d1z05a1           4 KQINAGRVYKLIDQK---GPISRIDLSKESE-L----APASITKITRELIDAHLIHETT   54 (71)
T ss_dssp             HHHHHHHHHHHHHHH---CSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHHHc---CCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEec
Confidence            334455789999876   5999999999999 9    9999999999999999998764

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=97.40  E-value=7.8e-05  Score=44.54  Aligned_cols=48  Identities=15%  Similarity=0.230  Sum_probs=39.6

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      ..|+..|..++  +|+|.+|||..++ .    ++..+.|+++.|...|++.....
T Consensus        24 ~~iL~~L~~~~--~~~t~~eLa~~~~-i----~~~tvs~~l~~L~~~GlV~r~~~   71 (109)
T d2d1ha1          24 VAVLLKMVEIE--KPITSEELADIFK-L----SKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             HHHHHHHHHHC--SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHcC--CCCCHHHHHHHHC-c----cHhHHHHHHHHHHHCCCEEEeec
Confidence            34555554444  7999999999999 9    99999999999999999986644

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=97.30  E-value=0.00013  Score=45.19  Aligned_cols=51  Identities=18%  Similarity=0.167  Sum_probs=42.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ..|+-.|..++  +|+|..|||+.++ .    ++..+++.++.|...|++..+.+.+|
T Consensus        29 ~~i~~~L~~~~--~plt~~ela~~l~-v----sk~~vs~~l~~L~~~GlV~r~~~~~d   79 (151)
T d1ku9a_          29 GAVYAILYLSD--KPLTISDIMEELK-I----SKGNVSMSLKKLEELGFVRKVWIKGE   79 (151)
T ss_dssp             HHHHHHHHHCS--SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEECCTTC
T ss_pred             HHHHHHHHhCC--CCcCHHHHHHHhC-C----CcchHHHHHHHHHHCCCEEEEEcCCC
Confidence            35666676554  7999999999999 9    99999999999999999987765543

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=97.27  E-value=0.00022  Score=39.21  Aligned_cols=45  Identities=27%  Similarity=0.324  Sum_probs=40.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .|+..|.+    +|+|-.|||+.++ .    .+..+.++++.|...|++.|.+.
T Consensus         3 ~Il~~i~~----~pisr~eLa~~~g-l----s~~TVs~~v~~L~~~GlV~e~~~   47 (62)
T d2hoea1           3 RILKRIMK----SPVSRVELAEELG-L----TKTTVGEIAKIFLEKGIVVEEKD   47 (62)
T ss_dssp             CSHHHHHH----SCBCHHHHHHHHT-C----CHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHH----CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEECCC
Confidence            57788876    6899999999999 9    89999999999999999998754

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.24  E-value=0.00034  Score=39.09  Aligned_cols=50  Identities=12%  Similarity=0.172  Sum_probs=43.2

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -.-...|+..|..+   +|+|-.|||+.++ .    .+..+.++++.|...|++.|.+
T Consensus         4 ~~N~~~Il~~i~~~---g~~sr~eLa~~~g-L----S~~Tvs~iv~~L~~~glv~e~g   53 (70)
T d1z6ra1           4 QTNAGAVYRLIDQL---GPVSRIDLSRLAQ-L----APASITKIVHEMLEAHLVQELE   53 (70)
T ss_dssp             HHHHHHHHHHHHSS---CSCCHHHHHHHTT-C----CHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCEEeeC
Confidence            34455688999875   6999999999999 9    8999999999999999999864

>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=97.14  E-value=0.00029  Score=42.13  Aligned_cols=46  Identities=20%  Similarity=0.372  Sum_probs=39.2

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ..|+-.|.+.   +++|+.|||+.++ .    +...+++++.-|...|++....
T Consensus        23 ~~v~~~L~~~---g~~t~~eia~~~~-i----~~~~v~~~l~~L~~~GlV~r~~   68 (109)
T d1sfxa_          23 VRIYSLLLER---GGMRVSEIARELD-L----SARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHHHH---CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHhc---CCCCHHHHHHHhC-C----CcchHHHHHHHHHhCCCEEEEe
Confidence            3455666665   5999999999999 9    9999999999999999998653

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.13  E-value=0.00026  Score=41.43  Aligned_cols=49  Identities=24%  Similarity=0.332  Sum_probs=42.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++.|..+|...   +++|..|||+.++ .    .+..+.|.++.|...|+++....
T Consensus        17 ~r~~IL~~L~~~---~~~~~~eLa~~l~-i----s~~~vs~~l~~L~~~glV~~~~~   65 (100)
T d1ub9a_          17 VRLGIMIFLLPR---RKAPFSQIQKVLD-L----TPGNLDSHIRVLERNGLVKTYKV   65 (100)
T ss_dssp             HHHHHHHHHHHH---SEEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHhccC---CCeeHHHHHHHHh-h----ccccccHHHHHHhhhceeEEEEc
Confidence            467788889765   5899999999999 9    99999999999999999986544

>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=97.07  E-value=0.00046  Score=41.98  Aligned_cols=54  Identities=6%  Similarity=0.183  Sum_probs=43.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .+..|...|..++ ++++|..|||+.++ .    +...+.|++..|...|++....+.+|
T Consensus        30 ~q~~vL~~l~~~~-~~~it~~ela~~~~-~----~~~~vs~~l~~L~~~g~v~r~~~~~D   83 (135)
T d3broa1          30 TQMTIIDYLSRNK-NKEVLQRDLESEFS-I----KSSTATVLLQRMEIKKLLYRKVSGKD   83 (135)
T ss_dssp             HHHHHHHHHHHTT-TSCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             HHHHHHHHHHHcC-CCCCCHHHHHHHHC-c----CHhHHHHHHHHHHHHHHHHHHhhhhh
Confidence            3445566677654 37899999999999 9    99999999999999999987765543

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=97.03  E-value=0.00045  Score=42.25  Aligned_cols=42  Identities=26%  Similarity=0.420  Sum_probs=35.7

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .-.|+.+   +++|.++||+.++ +    ++..+++||+.|...|+++-.
T Consensus        10 L~~la~~---~~~ss~~IA~~~~-~----~~~~v~kIl~~L~~aglV~s~   51 (127)
T d1xd7a_          10 LSLISMD---EKTSSEIIADSVN-T----NPVVVRRMISLLKKADILTSR   51 (127)
T ss_dssp             HHHHHTC---SCCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHhcC---CCCCHHHHHHHhC-c----CHHHHHHHHHHHHHhCccccc
Confidence            3445543   6899999999999 9    999999999999999999744

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=97.02  E-value=0.00056  Score=37.76  Aligned_cols=49  Identities=20%  Similarity=0.213  Sum_probs=41.8

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .|-+++.++| -.|-++.||+..++ .    ++..+..+|+.|+..|.+....++
T Consensus        11 ~I~~~~~~~g-~~PP~vrdl~~~l~-~----~e~~~~~lL~~l~~~G~lvkI~~d   59 (64)
T d1lvaa3          11 DLEDKYRVSR-WQPPSFKEVAGSFN-L----DPSELEELLHYLVREGVLVKINDE   59 (64)
T ss_dssp             HHHHHHHHHT-TSCCBHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEESSSS
T ss_pred             HHHHHHHHcC-CCCCcHHHHHHHhC-C----CHHHHHHHHHHHHHCCCEEEeccc
Confidence            4566677665 37999999999999 9    999999999999999999877543

>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=96.93  E-value=0.00093  Score=41.16  Aligned_cols=52  Identities=23%  Similarity=0.277  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      .+..+...|...+  |++|..+||+.++ .    ++..+.|++.-|...|++......+
T Consensus        35 ~q~~vL~~L~~~~--g~~t~~~La~~~~-~----~~~~vs~~i~~L~~~glv~r~~~~~   86 (145)
T d2hr3a1          35 SQLVVLGAIDRLG--GDVTPSELAAAER-M----RSSNLAALLRELERGGLIVRHADPQ   86 (145)
T ss_dssp             HHHHHHHHHHHTT--SCBCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEC---
T ss_pred             HHHHHHHHHHHcC--CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHcCCeEeeeCcc
Confidence            3455556676554  7899999999999 9    9999999999999999998665433

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=96.92  E-value=0.00083  Score=41.08  Aligned_cols=52  Identities=27%  Similarity=0.287  Sum_probs=43.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .+.-|...|.++   +++|..+||+.++ .    ++..+.|+++.|...|++....+..|
T Consensus        33 ~q~~iL~~l~~~---~~~t~~~La~~l~-i----~~~~vs~~v~~L~~~gli~r~~~~~D   84 (140)
T d2etha1          33 TELYAFLYVALF---GPKKMKEIAEFLS-T----TKSNVTNVVDSLEKRGLVVREMDPVD   84 (140)
T ss_dssp             HHHHHHHHHHHH---CCBCHHHHHHHTT-S----CHHHHHHHHHHHHHTTSEEEEECTTT
T ss_pred             HHHHHHHHHHHc---CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeeeeecccc
Confidence            345566677776   5899999999999 9    99999999999999999997766554

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=96.88  E-value=0.00061  Score=42.13  Aligned_cols=44  Identities=18%  Similarity=0.353  Sum_probs=36.7

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .-.|+.++ +.++|+++||+.++ +    ++..|+|+|+.|+..|++.-.
T Consensus        13 L~~la~~~-~~~vss~~IA~~~~-i----~~~~l~kil~~L~~aGlv~S~   56 (138)
T d1ylfa1          13 LSILKNNP-SSLCTSDYMAESVN-T----NPVVIRKIMSYLKQAGFVYVN   56 (138)
T ss_dssp             HHHHHHSC-GGGCCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHhCC-CCcCcHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEee
Confidence            34455443 37899999999999 9    999999999999999999754

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=96.86  E-value=0.0041  Score=37.91  Aligned_cols=49  Identities=18%  Similarity=0.274  Sum_probs=40.7

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|...|...   +|+|..+||+.++ .    ++..+.|++.-|...|++....+..|
T Consensus        39 ~iL~~l~~~---~~~t~~~la~~~~-i----~~~~vs~~l~~L~~~glv~r~~~~~D   87 (143)
T d1s3ja_          39 FVLASLKKH---GSLKVSEIAERME-V----KPSAVTLMADRLEQKNLIARTHNTKD   87 (143)
T ss_dssp             HHHHHHHHH---SEEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             HHHHHHHHC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHhhhheeeeecCC
Confidence            355566665   5899999999999 9    99999999999999999987655443

>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=96.57  E-value=0.0015  Score=41.99  Aligned_cols=52  Identities=15%  Similarity=0.276  Sum_probs=43.7

Q ss_pred             HHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           24 MTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        24 ~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .+|.--..+.|+++|.+    +|+|+.|||+.+| .    .+..+++-|+.|...|++...
T Consensus        14 ~~l~~p~R~~Il~~L~~----~~~s~~ela~~lg-~----s~~~v~~hl~~L~~~glv~~~   65 (190)
T d1ulya_          14 KVMLEDTRRKILKLLRN----KEMTISQLSEILG-K----TPQTIYHHIEKLKEAGLVEVK   65 (190)
T ss_dssp             HHHHSHHHHHHHHHHTT----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHhCCHHHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            34444567788888864    7999999999999 9    899999999999999999643

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.53  E-value=0.0019  Score=39.14  Aligned_cols=46  Identities=24%  Similarity=0.244  Sum_probs=38.8

Q ss_pred             HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|..++  +++|.++||..++ .    ++..+.|+++-|...|++....+.+|
T Consensus        36 ~l~~~~--~~~t~~~la~~~~-~----~~~~vs~~v~~L~~~gli~r~~~~~D   81 (137)
T d2fbha1          36 HLARHR--DSPTQRELAQSVG-V----EGPTLARLLDGLESQGLVRRLAVAED   81 (137)
T ss_dssp             HHHHCS--SCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEECCBTT
T ss_pred             HHHHcC--CCCcHHHHHHHHC-C----CHHHHHHHHHHHHHcCCccccCCCCC
Confidence            455444  5789999999999 9    99999999999999999997766544

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.50  E-value=0.0021  Score=39.40  Aligned_cols=49  Identities=14%  Similarity=0.264  Sum_probs=40.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|.-.|.+.   +++|..|||..++ .    ++..+.|+++.|+..|++....+..|
T Consensus        40 ~vL~~l~~~---~~~t~~~la~~l~-~----~~~~vsr~l~~L~~~G~v~r~~~~~D   88 (141)
T d1lnwa_          40 HVLKLIDEQ---RGLNLQDLGRQMC-R----DKALITRKIRELEGRNLVRRERNPSD   88 (141)
T ss_dssp             HHHHHHHSS---TTCBHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEECSSS
T ss_pred             HHHHHHHHC---CCCCHHHHHHHHC-c----cHhHHHHHHHHHHHhhceeeeccCCC
Confidence            344455543   5799999999999 9    99999999999999999987765543

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.48  E-value=0.0018  Score=39.38  Aligned_cols=49  Identities=10%  Similarity=0.243  Sum_probs=40.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|...|...   +|+|..|||..++ .    ++..+.|+++-|...|++....+..|
T Consensus        38 ~vL~~i~~~---~~~t~~~la~~l~-~----~~~~~s~~l~~L~~~Gli~r~~~~~D   86 (136)
T d2bv6a1          38 LVLTILWDE---SPVNVKKVVTELA-L----DTGTVSPLLKRMEQVDLIKRERSEVD   86 (136)
T ss_dssp             HHHHHHHHS---SEEEHHHHHHHTT-C----CTTTHHHHHHHHHHTTSEEEEECSSS
T ss_pred             HHHHHHHcC---CCCCHHHHHHHHC-C----CHhHHHHHHHHHHHCCCEEEeecCCc
Confidence            344556654   5899999999999 9    89999999999999999987765544

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=96.46  E-value=0.0018  Score=39.53  Aligned_cols=49  Identities=16%  Similarity=0.211  Sum_probs=40.1

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      -+.-.|...   +|.|.+|||..++ .    ++..+.|++.-|...|++....+.+|
T Consensus        34 ~iL~~i~~~---~~~t~~~la~~l~-i----~~~tvs~~l~~L~~~gli~r~~~~~D   82 (139)
T d2a61a1          34 DILQKIYFE---GPKRPGELSVLLG-V----AKSTVTGLVKRLEADGYLTRTPDPAD   82 (139)
T ss_dssp             HHHHHHHHH---CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             HHHHHHHHc---CCCCHHHHHHHhC-C----CcccchHHHHHHHhcCeeeeeeccCC
Confidence            344455554   5899999999999 9    99999999999999999987765443

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.45  E-value=0.0015  Score=39.68  Aligned_cols=53  Identities=13%  Similarity=0.133  Sum_probs=42.8

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +..|...|...+ ++++|..|||..++ .    ++..+.|+++.|...|++....+..|
T Consensus        36 q~~iL~~l~~~~-~~~~t~~eia~~~~-~----~~~~vs~~l~~L~~~g~v~r~~~~~D   88 (125)
T d1p4xa1          36 EFILLTYLFHQQ-ENTLPFKKIVSDLC-Y----KQSDLVQHIKVLVKHSYISKVRSKID   88 (125)
T ss_dssp             HHHHHHHHHSCS-CSEEEHHHHHHHSS-S----CGGGTHHHHHHHHHTTSCEEEECSSS
T ss_pred             HHHHHHHHHHhc-cCCcCHHHHHHHhC-C----CcchHHHHHHHHHHCCCceeecccCC
Confidence            344455565543 37899999999999 9    99999999999999999998876654

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.38  E-value=0.0014  Score=39.34  Aligned_cols=49  Identities=10%  Similarity=0.149  Sum_probs=40.4

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ..+|...+ ++++|..|||..++ .    ++..+.|+++.|...|++....+..|
T Consensus        39 L~~l~~~~-~~~~t~~~la~~l~-~----~~~tvs~~i~~Le~~gli~r~~~~~D   87 (115)
T d2frha1          39 LTYISENK-EKEYYLKDIINHLN-Y----KQPQVVKAVKILSQEDYFDKKRNEHD   87 (115)
T ss_dssp             HHHHHHTC-CSEEEHHHHHHHSS-S----HHHHHHHHHHHHHHTTSSCCBCCSSS
T ss_pred             HHHHHcCC-CCCCCHHHHHHHHC-C----CHhHHHHHHHHHHhhhhheeeecccC
Confidence            34455543 37899999999999 9    99999999999999999998766554

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.37  E-value=0.0018  Score=39.40  Aligned_cols=49  Identities=18%  Similarity=0.219  Sum_probs=40.7

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|...|...   +++|..|||..++ +    ++..+.|+++-|...|++....+..|
T Consensus        34 ~vL~~l~~~---~~~t~~~la~~~~-i----~~~~vs~~i~~L~~~gli~r~~~~~D   82 (136)
T d2fbia1          34 RVIRILRQQ---GEMESYQLANQAC-I----LRPSMTGVLARLERDGIVRRWKAPKD   82 (136)
T ss_dssp             HHHHHHHHH---CSEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred             HHHHHHHHc---CCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEeecCcc
Confidence            345556665   5899999999999 9    99999999999999999987755443

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.37  E-value=0.0021  Score=37.74  Aligned_cols=52  Identities=19%  Similarity=0.281  Sum_probs=43.9

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +|.--..+.|...|.+    +++++.||++.++ .    ....+.+=|+.|...|++....
T Consensus        14 aL~d~~Rl~Il~~L~~----~~~~v~el~~~l~-~----s~~~vS~HL~~L~~~glv~~~r   65 (94)
T d1r1ua_          14 ALGDYNRIRIMELLSV----SEASVGHISHQLN-L----SQSNVSHQLKLLKSVHLVKAKR   65 (94)
T ss_dssp             HTCSHHHHHHHHHHHH----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HhCCHHHHHHHHHHHc----CCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCceEEEE
Confidence            3444466778888886    6899999999999 9    8889999999999999998653

>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=96.29  E-value=0.0028  Score=38.03  Aligned_cols=55  Identities=15%  Similarity=0.127  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           22 LHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        22 ~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ...+|.--..+.|+..|...   +++++.||++.++ .    .+..+.+-|+.|...|++...
T Consensus        24 ~~kaLadp~Rl~Il~~L~~~---~~~~v~ela~~l~-~----s~s~vS~HL~~L~~aGlv~~~   78 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQD---EELCVCDIANILG-V----TIANASHHLRTLYKQGVVNFR   78 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHHS---SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHhCCHHHHHHHHHHHhC---CCccHHHHHHHHc-c----ChhHHHHHHHHHHHCCeeEEE
Confidence            34566777889999999763   6899999999999 9    899999999999999999854

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.27  E-value=0.0036  Score=35.98  Aligned_cols=50  Identities=18%  Similarity=0.224  Sum_probs=45.0

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      .-|+++|.++|. .++...+|-.+++ .    ....+.|+|+.|.+.+++.++.+.
T Consensus        16 ~lVY~~I~~ag~-~GIW~~dir~ktn-L----~~~~l~K~LK~Lesk~lIK~VksV   65 (78)
T d2dk5a1          16 KLVYQIIEDAGN-KGIWSRDVRYKSN-L----PLTEINKILKNLESKKLIKAVKSV   65 (78)
T ss_dssp             HHHHHHHHHHCT-TCEEHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHccc-cceeHHHHHHHcC-C----CHHHHHHHHHHHHhcCCceeeccc
Confidence            347889998884 8999999999999 9    899999999999999999998765

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=96.16  E-value=0.0027  Score=37.37  Aligned_cols=51  Identities=16%  Similarity=0.300  Sum_probs=43.6

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|.--..+.|...|.+    +|+++.||++.++ .    ....+.+-|+.|...|++...
T Consensus        19 aL~~p~Rl~Il~~L~~----~~~~v~ela~~l~-i----s~stvS~HL~~L~~aglV~~~   69 (98)
T d1r1ta_          19 VLADPNRLRLLSLLAR----SELCVGDLAQAIG-V----SESAVSHQLRSLRNLRLVSYR   69 (98)
T ss_dssp             HHCCHHHHHHHHHHTT----CCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCCHHHHHHHHHHHc----CCcCHHHHHHHHC-c----CHHHHHHHHHHHHHCCceEEE
Confidence            4444567788888864    6899999999999 9    899999999999999999864

>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=96.08  E-value=0.0036  Score=38.16  Aligned_cols=51  Identities=14%  Similarity=0.108  Sum_probs=41.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|...|...+ ++++|..|||+.++ .    ++..+.|+++-|...|++....+.+|
T Consensus        37 ~vL~~l~~~~-~~~~~~~~ia~~l~-~----~~~~vs~~v~~L~~~glV~r~~~~~D   87 (125)
T d1p4xa2          37 TILAIITSQN-KNIVLLKDLIETIH-H----KYPQTVRALNNLKKQGYLIKERSTED   87 (125)
T ss_dssp             HHHHHHHTTT-TCCEEHHHHHHHSS-S----CHHHHHHHHHHHHHHTSSEEEECSSS
T ss_pred             HHHHHHHHcc-CCCccHHHHHHHHC-C----CcchHHHHHHHHHhccCEeeeecCCC
Confidence            3455665543 36899999999999 9    99999999999999999987766554

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.06  E-value=0.0029  Score=38.44  Aligned_cols=49  Identities=18%  Similarity=0.179  Sum_probs=37.1

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +.-.|.+.+  +++|..+||+.++ +    ++..+.|+++.|...|++....+.+|
T Consensus        36 ~L~~l~~~~--~~~t~~~la~~l~-i----~~~~vs~~l~~L~~~glI~~~~~~~D   84 (140)
T d3deua1          36 TLHNIHQLP--PDQSQIQLAKAIG-I----EQPSLVRTLDQLEDKGLISRQTCASD   84 (140)
T ss_dssp             HHHHHHHSC--SSEEHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEC-----
T ss_pred             HHHHHHHcC--CCccHHHHHHHHC-C----CHhHHHHHHHHHHhCCCEEecccCCC
Confidence            333455433  5799999999999 9    99999999999999999987765543

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.06  E-value=0.0031  Score=37.75  Aligned_cols=50  Identities=20%  Similarity=0.228  Sum_probs=40.4

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      +...|..+. ++++|..|||+.++ .    ++..+.|++..|...|++....+.+|
T Consensus        37 vL~~l~~~~-~~~~t~~ela~~l~-~----~~~~vs~~i~~Le~~gli~r~~~~~D   86 (115)
T d1hsja1          37 ILNHILRSE-SNEISSKEIAKCSE-F----KPYYLTKALQKLKDLKLLSKKRSLQD   86 (115)
T ss_dssp             HHHHHHTCS-CSEEEHHHHHHSSC-C----CHHHHHHHHHHHHTTTTSCCEECCSS
T ss_pred             HHHHHHccC-CCCcCHHHHHHHHC-C----ChhhHHHHHHHHHHcCCeEEEeecCC
Confidence            344455332 36899999999999 9    99999999999999999997766554

>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=96.05  E-value=0.0043  Score=40.09  Aligned_cols=46  Identities=17%  Similarity=0.260  Sum_probs=40.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..+.|.+.|.+    +|+|+.|||+.++ +    .+..++|-|+.|...|++...
T Consensus        16 ~R~~Il~~L~~----~~~~~~ela~~l~-~----s~~~v~~HL~~L~~~Glv~~~   61 (194)
T d2p4wa1          16 TRRRILFLLTK----RPYFVSELSRELG-V----GQKAVLEHLRILEEAGLIESR   61 (194)
T ss_dssp             HHHHHHHHHHH----SCEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEEE
Confidence            45667788875    6999999999999 9    899999999999999999854

>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=95.98  E-value=0.004  Score=38.25  Aligned_cols=46  Identities=15%  Similarity=0.172  Sum_probs=39.0

Q ss_pred             HHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           36 EIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        36 d~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      -.|.++   +|+|..|||+.++ +    ++..+.|+++-|...|++....+.+|
T Consensus        36 ~~i~~~---~~~t~~~la~~l~-i----~~~tvs~~l~~L~~~glI~r~~~~~D   81 (144)
T d1lj9a_          36 VRVCEN---PGIIQEKIAELIK-V----DRTTAARAIKRLEEQGFIYRQEDASN   81 (144)
T ss_dssp             HHHHHS---TTEEHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECSSC
T ss_pred             HHHHhC---CCCCHHHHHHHHC-c----cHhhHHHHHHHHHhhhcccccCCCCC
Confidence            345554   4799999999999 9    99999999999999999997766554

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=95.96  E-value=0.0031  Score=38.33  Aligned_cols=47  Identities=15%  Similarity=0.244  Sum_probs=39.8

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ...|...   +++|.+|||..++ .    ++..+.|++..|...|++....+.+|
T Consensus        39 L~~l~~~---~~~t~~~La~~~~-i----~~~~vsr~i~~L~~~glv~r~~~~~D   85 (137)
T d1z91a1          39 LLLLWEH---ETLTVKKMGEQLY-L----DSGTLTPMLKRMEQQGLITRKRSEED   85 (137)
T ss_dssp             HHHHHHH---SEEEHHHHHHTTT-C----CHHHHHHHHHHHHHHTSEECCBCSSC
T ss_pred             HHHHHcC---CCCCHHHHHHHHC-c----CHHHHHHHHHHHhhccceEEeecCCC
Confidence            4455554   5899999999999 9    99999999999999999997766554

>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=95.89  E-value=0.0087  Score=32.50  Aligned_cols=46  Identities=15%  Similarity=0.261  Sum_probs=39.1

Q ss_pred             HHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCc
Q 045477           28 AVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGI   80 (89)
Q Consensus        28 ~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi   80 (89)
                      .--...|...|.++.  +++|++|||+.++ +    ....++|=+..|...|+
T Consensus         6 ~eR~~~Il~~L~~~~--~~vs~~~La~~l~-V----S~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           6 QERLKSIVRILERSK--EPVSGAQLAEELS-V----SRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHHHCS--SCBCHHHHHHHHT-S----CHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcC--CCCcHHHHHHHHC-C----CHHHHHHHHHHHHHCCC
Confidence            333456788887754  7899999999999 9    99999999999999986

>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=95.89  E-value=0.0078  Score=36.55  Aligned_cols=50  Identities=26%  Similarity=0.236  Sum_probs=40.3

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      ..+.-.|...   +++|.+|||..++ .    ++..+.|++..|...|+++.....+|
T Consensus        37 ~~vL~~l~~~---~~~t~~ela~~~~-i----~~~~vs~~v~~L~~~glv~r~~~~~D   86 (138)
T d1jgsa_          37 FKVLCSIRCA---ACITPVELKKVLS-V----DLGALTRMLDRLVCKGWVERLPNPND   86 (138)
T ss_dssp             HHHHHHHHHH---SSBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECTTC
T ss_pred             HHHHHhHHhC---cCCCHHHHHHHHC-C----CHhHHHHHHHHHhhCCCEEEeeccCC
Confidence            3344455554   5899999999999 9    99999999999999999987655443

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=95.88  E-value=0.0083  Score=32.52  Aligned_cols=46  Identities=26%  Similarity=0.498  Sum_probs=40.9

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +|..|.++|.+.   +.+|..|||+.+| .    .+..+.+=++-|...|++..
T Consensus         6 ~D~~IL~~L~~n---~r~s~~~iA~~lg-i----s~~tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1           6 IDLNIIEELKKD---SRLSMRELGRKIK-L----SPPSVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             HHHHHHHHHHHC---SCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeee
Confidence            577888999874   6899999999999 9    88899999999999999974

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.83  E-value=0.0033  Score=39.95  Aligned_cols=47  Identities=17%  Similarity=0.231  Sum_probs=37.2

Q ss_pred             HHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccC
Q 045477           37 IIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDV   88 (89)
Q Consensus        37 ~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~   88 (89)
                      .|...|+..++|..|||+.++ +    ++..+.|++.-|...|++....+..
T Consensus        70 ~L~~~~~~~~lt~~eLa~~l~-i----~~~tvsr~l~~Le~~GlV~r~~~~~  116 (172)
T d2fbka1          70 TLYRSAPPEGLRPTELSALAA-I----SGPSTSNRIVRLLEKGLIERREDER  116 (172)
T ss_dssp             HHHHHCCSSCBCHHHHHHHCS-C----CSGGGSSHHHHHHHHTSEECCC---
T ss_pred             HHHhhCCCCCcCHHHHHHHHC-c----CHhHHHHHHHHHHhCCCeeeecccc
Confidence            344454335699999999999 9    9999999999999999999776544

>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=95.81  E-value=0.0055  Score=33.30  Aligned_cols=45  Identities=18%  Similarity=0.364  Sum_probs=38.6

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      .++.|..+|.+ +  +.+|.+|||+.++ +    ....++|-+..|...|+.-
T Consensus         6 ~~~~iL~~L~~-~--~~~s~~eLa~~l~-v----S~~ti~r~i~~L~~~G~~I   50 (63)
T d1biaa1           6 VPLKLIALLAN-G--EFHSGEQLGETLG-M----SRAAINKHIQTLRDWGVDV   50 (63)
T ss_dssp             HHHHHHHHHTT-S--SCBCHHHHHHHHT-S----CHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHH-C--CcCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCcE
Confidence            45678888865 2  6899999999999 9    9999999999999999743

>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=95.70  E-value=0.0076  Score=32.24  Aligned_cols=46  Identities=17%  Similarity=0.258  Sum_probs=40.7

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +|..|...|.+.   +.+|..|||++++ .    .+..+.+=++.|...|++..
T Consensus         4 ~D~~Il~~L~~n---~r~s~~eiA~~l~-l----s~~~v~~Ri~~L~~~giI~~   49 (60)
T d2cyya1           4 IDKKIIKILQND---GKAPLREISKITG-L----AESTIHERIRKLRESGVIKK   49 (60)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHC-S----CHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEe
Confidence            578899999884   6899999999999 9    89899999999999998874

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.67  E-value=0.0073  Score=36.53  Aligned_cols=53  Identities=13%  Similarity=0.105  Sum_probs=44.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|+.|.++|.+.|  +|+|+.||.+.++ -..|-....+..+|+-|+..|++....
T Consensus         8 ~E~~IM~~lW~~g--~~~t~~eI~~~l~-~~~~~~~sTV~T~L~rL~~Kg~l~~~~   60 (122)
T d2g9wa1           8 LERAVMDHLWSRT--EPQTVRQVHEALS-ARRDLAYTTVMAVLQRLAKKNLVLQIR   60 (122)
T ss_dssp             HHHHHHHHHHTCS--SCEEHHHHHHHHT-TTCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHcCC--CCccHHHHHHHHh-ccCCCcHHHHHHHHHHHHHCCCEEEee
Confidence            5778899999876  7999999999998 644446778999999999999998653

>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=95.65  E-value=0.0097  Score=32.13  Aligned_cols=47  Identities=19%  Similarity=0.369  Sum_probs=41.2

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      +|..|...|.+.   +.+|..|||++++ .    .+..+.+=++.|...|++...
T Consensus         6 ~D~~IL~~L~~~---~r~s~~eiA~~l~-l----s~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           6 LDRGILEALMGN---ARTAYAELAKQFG-V----SPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHHC---TTSCHHHHHHHHT-S----CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEeE
Confidence            577888999875   5899999999999 9    888999999999999998743

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.54  E-value=0.0097  Score=34.82  Aligned_cols=49  Identities=24%  Similarity=0.390  Sum_probs=41.2

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      +.|++.|-+.+  +.+|=.+||+.++ .    ....++|+|-.|-..|++......
T Consensus        21 ~~v~~~L~~~~--~evtDe~iA~~tg-i----~in~VRk~Ly~L~~~~L~~y~R~k   69 (88)
T d1q1ha_          21 IDVLRILLDKG--TEMTDEEIANQLN-I----KVNDVRKKLNLLEEQGFVSYRKTR   69 (88)
T ss_dssp             HHHHHHHHHHC--SCBCHHHHHHTTT-S----CHHHHHHHHHHHHHHTSCEEEEEC
T ss_pred             HHHHHHHHhcc--CcCCHHHHHHHhC-C----cHHHHHHHHHHHHhCCceEEEEee
Confidence            35788776654  6899999999999 9    999999999999999998765443

>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=95.45  E-value=0.012  Score=31.47  Aligned_cols=46  Identities=28%  Similarity=0.354  Sum_probs=40.3

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVEC   83 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e   83 (89)
                      +|..|...|.+.   +.+|..|||+.+| .    ++..+.+=++.|...|++..
T Consensus         4 ~D~kIl~~L~~n---~r~s~~~lA~~~g-l----s~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1           4 RDKIILEILEKD---ARTPFTEIAKKLG-I----SETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHHHC---TTCCHHHHHHHHT-S----CHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHHC-c----CHHHHHHHHHHHHHCCCeEe
Confidence            467888889874   6899999999999 9    89999999999999998864

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=95.38  E-value=0.0078  Score=38.08  Aligned_cols=49  Identities=20%  Similarity=-0.007  Sum_probs=39.6

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecccCC
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDDVD   89 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~~~   89 (89)
                      .|..+|...   +++|..+||..++ .    +...+.|++.-|...|++....+.+|
T Consensus        45 ~vL~~l~~~---~~~t~~~la~~~~-l----~~~tvs~~i~rL~~~gli~r~~~~~D   93 (162)
T d2fxaa1          45 HILWIAYQL---NGASISEIAKFGV-M----HVSTAFNFSKKLEERGYLRFSKRLND   93 (162)
T ss_dssp             HHHHHHHHH---TSEEHHHHHHHTT-C----CHHHHHHHHHHHHHHTSEEEECC---
T ss_pred             HHHhhhccC---CCcCHHHHHHHHc-C----CchhhHHHHHHHHHCCCceeeccccc
Confidence            355566665   5899999999999 9    99999999999999999997765443

>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=95.11  E-value=0.019  Score=31.04  Aligned_cols=44  Identities=16%  Similarity=0.268  Sum_probs=35.8

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+....+.   ++.+..+||+.++ +    .+..+...++-|...|++....
T Consensus        12 I~~l~~~~---~~v~~~~iA~~L~-v----s~~SVs~mikrL~~~GlV~~~~   55 (61)
T d2ev0a1          12 IYMLIEEK---GYARVSDIAEALA-V----HPSSVTKMVQKLDKDEYLIYEK   55 (61)
T ss_dssp             HHHHHHHH---SSCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHhcC---CCccHHHHHHHhC-C----CchhHHHHHHHHHHCCCEEEcc
Confidence            45544443   6899999999999 9    8889999999999999998654

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.34  E-value=0.052  Score=30.09  Aligned_cols=51  Identities=12%  Similarity=0.206  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ....||++|.......+++..||++++++.    ...-+...+..|+.-|.+=.+
T Consensus         7 ~q~~V~~~i~s~~~~eGi~~~el~~~l~~~----~~~~i~~aid~L~~eG~IYsT   57 (69)
T d1dpua_           7 AQNQVLNLIKACPRPEGLNFQDLKNQLKHM----SVSSIKQAVDFLSNEGHIYST   57 (69)
T ss_dssp             HHHHHHHHHHHCCCTTTEEHHHHHHHSTTS----CHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHhCCCccCcCHHHHHHHccCC----CHHHHHHHHHHHHhCCceecc
Confidence            345678888765545789999999998328    788999999999999987643

>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=94.34  E-value=0.01  Score=33.91  Aligned_cols=36  Identities=25%  Similarity=0.258  Sum_probs=33.2

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++++|..|||+.++ .    ++..+.|++.-|...|++...
T Consensus        19 ~~~lt~~eLa~~l~-i----~~~~vs~~l~~Le~~GlV~r~   54 (85)
T d3ctaa1          19 RAYLTSSKLADMLG-I----SQQSASRIIIDLEKNGYITRT   54 (85)
T ss_dssp             EEECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCeeee
Confidence            36899999999999 9    999999999999999999853

>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=94.25  E-value=0.061  Score=29.55  Aligned_cols=42  Identities=29%  Similarity=0.427  Sum_probs=35.1

Q ss_pred             HHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           38 IAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        38 l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      +.++|  -|-|..||++.+| .+   .+..+.+.|..|...|+++...
T Consensus        18 ~~~~G--~~Ps~rei~~~~g-~~---S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          18 ISQTG--MPPTRAEIAQRLG-FR---SPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             HHHHS--SCCCHHHHHHHTT-CS---SHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHhC--CCCCHHHHHHHcC-CC---CHHHHHHHHHHHHHCcCeecCC
Confidence            44555  7899999999999 83   4668999999999999998764

>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=94.23  E-value=0.031  Score=30.91  Aligned_cols=36  Identities=19%  Similarity=0.076  Sum_probs=32.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      -|+|-+|||..+| +    .+..+.|+|+.|...|+++...
T Consensus        28 ~~lt~~eLA~~~G-~----sretvsr~L~~l~~~glI~~~~   63 (81)
T d2gaua1          28 IYLSREELATLSN-M----TVSNAIRTLSTFVSERMLALDG   63 (81)
T ss_dssp             CCCCHHHHHHHTT-S----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ecCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEecC
Confidence            3789999999999 9    8999999999999999998543

>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=94.23  E-value=0.051  Score=29.44  Aligned_cols=36  Identities=11%  Similarity=0.181  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++.+..+||+.++ +    .+..+.+.++-|...|++....
T Consensus        22 ~~v~~~~iA~~L~-v----s~~SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          22 VTPLRARIAERLD-Q----SGPTVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             CCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCcHHHHHHHhC-C----CchhHHHHHHHHHHCCCEEEcC
Confidence            7899999999999 9    8999999999999999998654

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.97  E-value=0.04  Score=33.30  Aligned_cols=56  Identities=16%  Similarity=0.204  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCC-CCCcchHHHHHHHHhccCceeeeccc
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKN-KDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~-~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      -..-|++.|.+++ +.|+|+.||-+.+. -.. .-+...++|.|..|+..|++.+....
T Consensus        17 qR~~Il~~L~~~~-~~h~sa~ei~~~l~-~~~~~i~~aTVYR~L~~l~e~gli~~~~~~   73 (134)
T d1mzba_          17 PRVKILQMLDSAE-QRHMSAEDVYKALM-EAGEDVGLATVYRVLTQFEAAGLVVRHNFD   73 (134)
T ss_dssp             HHHHHHHHHHCC--CCSBCHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHHTSEEEECSS
T ss_pred             HHHHHHHHHHhCC-CCCCCHHHHHHHHH-HhCCCccHHHHHHHHHHHHhccEEEEEeec
Confidence            4556888887653 25999999998875 321 11667899999999999999977543

>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=93.79  E-value=0.027  Score=30.49  Aligned_cols=35  Identities=20%  Similarity=0.334  Sum_probs=32.1

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+|-+|||..+| +    ....+.|+|+.|...|+++-..
T Consensus        29 ~lt~~~lA~~~G-~----sRetvsr~L~~l~~~glI~~~~   63 (69)
T d1i5za1          29 KITRQEIGQIVG-C----SRETVGRILKMLEDQNLISAHG   63 (69)
T ss_dssp             ECCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEcC
Confidence            589999999999 9    8999999999999999998553

>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=93.57  E-value=0.029  Score=31.12  Aligned_cols=34  Identities=18%  Similarity=0.227  Sum_probs=31.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      |+|-+|||..+| +    ....+.|+|+.|...|+++-.
T Consensus        30 ~~t~~eiA~~lG-~----sretvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1          30 DFTVEEIANLIG-S----SRQTTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             CCCHHHHHHHHC-S----CHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEEC
Confidence            789999999999 9    999999999999999999754

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.24  E-value=0.017  Score=34.41  Aligned_cols=52  Identities=15%  Similarity=0.226  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .+..|..+|.+.   +|+|+.||.+.+. ...+-++..+.++|+-|...|++....
T Consensus         8 ~E~~VM~~lW~~---~~~t~~ei~~~l~-~~~~~~~sTv~t~L~rL~~Kg~l~r~~   59 (120)
T d1okra_           8 AEWEVMNIIWMK---KYASANNIIEEIQ-MQKDWSPKTIRTLITRLYKKGFIDRKK   59 (120)
T ss_dssp             HHHHHHHHHHHH---SSEEHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHcC---CCCCHHHHHHHHh-cccCccHHhHHHHHHHHHHCCCeEEEe
Confidence            467788888876   5899999988874 322227789999999999999998643

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=92.94  E-value=0.051  Score=27.89  Aligned_cols=43  Identities=12%  Similarity=0.115  Sum_probs=35.5

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCce
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIV   81 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~   81 (89)
                      .+.+.|.++- ..|+|+++||+.++ .    .+..+.|+.+......+.
T Consensus         7 ~v~~yI~~~~-~~~~tl~~lA~~~~-~----s~~~l~r~Fk~~~g~tp~   49 (54)
T d1bl0a1           7 SILDWIEDNL-ESPLSLEKVSERSG-Y----SKWHLQRMFKKETGHSLG   49 (54)
T ss_dssp             HHHHHHHTTT-TSCCCCHHHHHHSS-S----CHHHHHHHHHHHHSSCHH
T ss_pred             HHHHHHHhcc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcCHH
Confidence            4567787764 38999999999999 9    999999999988776543

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=92.79  E-value=0.074  Score=30.25  Aligned_cols=49  Identities=24%  Similarity=0.262  Sum_probs=38.0

Q ss_pred             ChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeeccc
Q 045477           33 GLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVDD   87 (89)
Q Consensus        33 gIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~~   87 (89)
                      -++++-.+. +++|.|+..|+++.+ +    .=..|+|.|-.|.+-|+..-+-++
T Consensus        12 ~L~eA~~e~-~g~~WSLaklsKra~-~----PMS~LRR~LTqL~~aGl~~t~~~e   60 (81)
T d2obpa1          12 VLREAGIEN-GATPWSLPKIAKRAQ-L----PMSVLRRVLTQLQAAGLADVSVEA   60 (81)
T ss_dssp             HHHHHTSST-TCCCCBHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             HHHHHhccC-CCCCccHHHHHhhcC-C----cHHHHHHHHHHHhhcCceeeeecc
Confidence            344444333 358999999999999 8    677899999999999998755443

>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=92.55  E-value=0.05  Score=29.99  Aligned_cols=34  Identities=21%  Similarity=0.331  Sum_probs=31.3

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ++|-+|||+.+| +    ....+.|.|+.|...|+++..
T Consensus        27 ~lt~~elA~~lg-~----sr~tvsr~l~~l~~~g~I~~~   60 (73)
T d1zyba1          27 KVKMDDLARCLD-D----TRLNISKTLNELQDNGLIELH   60 (73)
T ss_dssp             ECCHHHHHHHHT-S----CHHHHHHHHHHHHHTTSCEEE
T ss_pred             ecCHHHHHHHHC-C----CHHHHHHHHHHHHHCCCEEec
Confidence            579999999999 9    999999999999999999743

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=92.06  E-value=0.12  Score=28.50  Aligned_cols=37  Identities=24%  Similarity=0.309  Sum_probs=33.4

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    ....+++.++.|+..|++....
T Consensus        19 G~~LPse~~La~~~~-v----Sr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          19 GDKLPVLETLMAQFE-V----SKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             TCBCCCHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCCcCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEEEc
Confidence            4678 8999999999 9    9999999999999999998654

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=92.02  E-value=0.069  Score=28.97  Aligned_cols=38  Identities=24%  Similarity=0.393  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           44 GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        44 ~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      |..++..+||+..+ +    ....+++-|+.|+..|++.....
T Consensus        23 G~~l~~~~La~~~~-v----Sr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1          23 GARLSEPDICAALD-V----SRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             TCEECHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cCccCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEEEcC
Confidence            46789999999999 9    99999999999999999986543

>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=91.85  E-value=0.076  Score=29.24  Aligned_cols=35  Identities=20%  Similarity=0.208  Sum_probs=31.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      -|+|-+|||..+| +    ....+.|+|..|...|+++..
T Consensus        29 ~~lt~~elA~~~g-~----sretvsr~l~~l~~~glI~~~   63 (80)
T d3e5ua1          29 MPLSQKSIGEITG-V----HHVTVSRVLASLKRENILDKK   63 (80)
T ss_dssp             SCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEC-
T ss_pred             eCCCHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEec
Confidence            4789999999999 9    999999999999999998754

>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=91.79  E-value=0.092  Score=28.97  Aligned_cols=39  Identities=26%  Similarity=0.355  Sum_probs=34.3

Q ss_pred             CCCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      +|..+ |..|||+..+ +    ....+++-++.|+..|++.....
T Consensus        23 ~G~~LPs~~eLa~~~~-v----Sr~tvr~Al~~L~~~G~i~~~~g   62 (74)
T d1hw1a1          23 PGTILPAERELSELIG-V----TRTTLREVLQRLARDGWLTIQHG   62 (74)
T ss_dssp             TTSBCCCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CcCCCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEEEeC
Confidence            34678 8999999999 9    99999999999999999986543

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.49  E-value=0.11  Score=31.14  Aligned_cols=52  Identities=15%  Similarity=0.218  Sum_probs=42.4

Q ss_pred             HHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           29 VINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        29 av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ..|+.|.++|.+.   +|.|+.||.+.++ -..|-.+..+.-+|+-|+..|+++..
T Consensus         6 ~~E~~VM~~lW~~---~~~t~~ei~~~l~-~~~~~~~tTv~T~L~rL~~Kg~l~~~   57 (122)
T d1sd4a_           6 MAEWDVMNIIWDK---KSVSANEIVVEIQ-KYKEVSDKTIRTLITRLYKKEIIKRY   57 (122)
T ss_dssp             HHHHHHHHHHHHS---SSEEHHHHHHHHH-TTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcC---CCCCHHHHHHHhh-ccCCCcHhHHHHHHHHHHhhhceeee
Confidence            3577888999885   5999999999987 53444677899999999999999754

>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=91.24  E-value=0.15  Score=26.02  Aligned_cols=42  Identities=17%  Similarity=0.098  Sum_probs=34.7

Q ss_pred             hChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           32 LGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        32 LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      -++.+.|.++- .+|+|+++||+..+ .    .+..+.|+.+.-....
T Consensus         6 ~~i~~yi~~~~-~~~itl~~lA~~~~-~----S~~~l~r~Fk~~~g~t   47 (54)
T d1d5ya1           6 RDLLIWLEGHL-DQPLSLDNVAAKAG-Y----SKWHLQRMFKDVTGHA   47 (54)
T ss_dssp             HHHHHHHHTTS-SSSCCCHHHHTTTS-S----CHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHcc-CCCCCHHHHHHHHC-c----CHHHHHHHHHHHHCcC
Confidence            35677888764 38999999999999 9    9999999998776554

>d2fq3a1 a.4.1.18 (A:311-395) Transcription regulatory protein swi3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Transcription regulatory protein swi3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.88  E-value=0.36  Score=27.33  Aligned_cols=52  Identities=10%  Similarity=0.109  Sum_probs=44.0

Q ss_pred             HHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           25 TMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        25 aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      -....+.=.|...+...+ ...+|.++....+. .    |..++.|+.++|...|++.
T Consensus        31 ~~Yl~iRN~Il~~w~~np-~~~Lt~~~~~~~~~-~----d~~~~~ri~~FL~~~G~IN   82 (85)
T d2fq3a1          31 EVYMRYRNFMVNSYRLNP-NEYFSVTTARRNVS-G----DAAALFRLHKFLTKWGLIN   82 (85)
T ss_dssp             HHHHHHHHHHHHHHHHCT-TSCCCHHHHHHHSC-S----CHHHHHHHHHHHHHTTSSS
T ss_pred             HHHHHHHHHHHHHHHhCC-CeeeeHHHHHhhcc-C----CHHHHHHHHHHHHHcCccC
Confidence            456667778888887764 48999999998988 8    9999999999999999875

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.71  E-value=0.26  Score=28.07  Aligned_cols=37  Identities=8%  Similarity=0.045  Sum_probs=31.5

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      .|.+..+|++..+ .+  -.+..++-.|..|...|++...
T Consensus        22 ~Pv~s~~i~~~~~-l~--~S~aTIRn~m~~LE~~G~l~~~   58 (87)
T d1stza1          22 KPVSSQRVLEVSN-IE--FSSATIRNDMKKLEYLGYIYQP   58 (87)
T ss_dssp             SCBCHHHHHHHSC-CC--SCHHHHHHHHHHHHHTTSEECC
T ss_pred             CccCHHHHHHHhC-CC--CCHHHHHHHHHHHHHCCcccCC
Confidence            8999999999976 50  0477999999999999999864

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=90.46  E-value=0.069  Score=30.12  Aligned_cols=52  Identities=17%  Similarity=0.296  Sum_probs=40.5

Q ss_pred             HHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           30 INLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        30 v~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      .|+.|.++|.+.   +|+|+.||.+.+. -..+-....+..+|+-|+..|++....
T Consensus        10 ~E~~IM~~lW~~---~~~t~~ei~~~l~-~~~~~~~tTv~T~L~rL~~KG~l~~~k   61 (82)
T d1p6ra_          10 AELEVMKVIWKH---SSINTNEVIKELS-KTSTWSPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHHHTS---SSEEHHHHHHHHH-HHSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHhC---CCCCHHHHHHHhc-cccCCcHhHHHHHHHHHHHCCCeEEEe
Confidence            577888999874   6899999988876 322225667999999999999998543

>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=88.79  E-value=0.29  Score=28.42  Aligned_cols=35  Identities=17%  Similarity=0.214  Sum_probs=30.7

Q ss_pred             CCCHHHHHhhCCCCCCCCCc-chHHHHHHHHhccCceeeec
Q 045477           46 KLSASEIAAQLPATKNKDAP-TMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~-~~l~RlLR~L~s~gi~~e~~   85 (89)
                      ++|-+|||..+| +    .+ ..+.|+|+.|...|+++...
T Consensus        31 ~lTqeeLA~~lG-~----s~ReTVsR~L~~L~~~GlI~~~~   66 (100)
T d2bgca1          31 NLTMQELGYSSG-I----AHSSAVSRIISKLKQEKVIVYKN   66 (100)
T ss_dssp             CCCHHHHHHHTT-C----CCHHHHHHHHHHHHHTTSEEEET
T ss_pred             ccCHHHHHHHhC-C----chHHHHHHHHHHHHHCCCEEEcC
Confidence            589999999999 8    64 68999999999999998543

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=88.50  E-value=0.42  Score=27.34  Aligned_cols=45  Identities=11%  Similarity=0.122  Sum_probs=36.4

Q ss_pred             hHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           34 LFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        34 Ifd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+|+|..-.  ++.+...|...++ .    +...+.+.+..|...|++.+..
T Consensus         8 i~DIL~~~~--~g~~kT~i~~~aN-L----s~~~~~kyl~~L~~~GLI~~~~   52 (90)
T d1r7ja_           8 IQAILEACK--SGSPKTRIMYGAN-L----SYALTGRYIKMLMDLEIIRQEG   52 (90)
T ss_dssp             HHHHHHHHT--TCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHh--CCCCccHHHHHcC-C----CHHHHHHHHHHHHHCCCeeecC
Confidence            466665433  3457899999999 9    9999999999999999997643

>d2dw4a1 a.4.1.18 (A:172-273) Lysine-specific histone demethylase 1, LSD1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Lysine-specific histone demethylase 1, LSD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.37  E-value=0.81  Score=26.60  Aligned_cols=64  Identities=13%  Similarity=0.170  Sum_probs=49.5

Q ss_pred             HHhHHHHHHHHHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           17 TMGSVLHMTMKAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        17 ~~~~~~~~aL~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      +.+..........+.=.|...+.... ...+|.++....+. ...-.|..++.|+.++|..+|++.
T Consensus        29 ~~~~~~~~~~Yl~iRN~Il~~w~~np-~~~Lt~~~~~~~l~-~~~~~d~~li~ri~~FL~~~G~IN   92 (102)
T d2dw4a1          29 ISGPQQTQKVFLFIRNRTLQLWLDNP-KIQLTFEATLQQLE-APYNSDTVLVHRVHSYLERHGLIN   92 (102)
T ss_dssp             HTSCHHHHHHHHHHHHHHHHHHHHCT-TBCCCHHHHHHHSC-TTGGGCHHHHHHHHHHHHHTTSSS
T ss_pred             hcCCCCCHHHHHHHHHHHHHHHHhCC-CeeeeHHHHHhhcc-ccccccHHHHHHHHHHHHHcCcee
Confidence            33444556678888989999998865 48899999888876 422236789999999999998875

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.12  E-value=0.41  Score=25.22  Aligned_cols=45  Identities=11%  Similarity=0.254  Sum_probs=37.3

Q ss_pred             HhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCcee
Q 045477           31 NLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVE   82 (89)
Q Consensus        31 ~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~   82 (89)
                      |-+|...|.++|  +|.-+.+|+..++ +    ....|.|+|-.|-..+=+.
T Consensus         3 EQkILQVL~dag--spvk~~ql~k~cq-V----pkk~lNqVL~rlkke~kVs   47 (57)
T d1j75a_           3 EQKILQVLSDDG--GPVKIGQLVKKCQ-V----PKKTLNQVLYRLKKEDRVS   47 (57)
T ss_dssp             HHHHHHHHHHHC--SCEEHHHHHHHHC-S----CHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHC-C----CHHHHHHHHHHHHhccccc
Confidence            457888999987  8999999999999 9    7778999988776655444

>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=87.23  E-value=0.56  Score=25.86  Aligned_cols=39  Identities=13%  Similarity=0.083  Sum_probs=33.0

Q ss_pred             CCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeecc
Q 045477           43 PGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSVD   86 (89)
Q Consensus        43 ~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~~   86 (89)
                      .++..|+.+||.++| .    ...-+.|.|=.|...|.+.....
T Consensus        21 ~~~~~tA~~LAk~Lg-~----~Kk~VNr~LY~L~~~G~v~~~~~   59 (70)
T d1sfua_          21 TNDYTTAISLSNRLK-I----NKKKINQQLYKLQKEDTVKMVPS   59 (70)
T ss_dssp             TTCEECHHHHHHHTT-C----CHHHHHHHHHHHHHTTSEEEECC
T ss_pred             CCCCchHHHHHHHhC-C----CHHHHHHHHHHHHHCCCeecCCC
Confidence            347899999999999 9    78889999988888888876543

>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=86.69  E-value=0.3  Score=24.57  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=21.6

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      .++++.+||.+++ +    ....++|+|-
T Consensus        17 ~G~gat~IAk~lg-I----~R~SVYR~L~   40 (43)
T d1gdta1          17 QGLGASHISKTMN-I----ARSTVYKVIN   40 (43)
T ss_dssp             TTCCHHHHHHHHT-C----CHHHHHHHHH
T ss_pred             cCCCHHHHHHHHC-C----CHHHHHHHHh
Confidence            5789999999999 9    9999999984

>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=85.41  E-value=0.29  Score=26.03  Aligned_cols=23  Identities=9%  Similarity=0.190  Sum_probs=18.1

Q ss_pred             CCCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           46 KLSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        46 ~~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      ++|+.|||+.+| +    .+..+.|+|+
T Consensus         2 ~~Ti~diA~~ag-v----S~sTVSr~l~   24 (59)
T d1efaa1           2 PVTLYDVAEYAG-V----SYQTVSRVVN   24 (59)
T ss_dssp             CCCHHHHHHTTT-S----CHHHHHHHHT
T ss_pred             CCCHHHHHHHHC-C----CHHHHHHHHC
Confidence            678999999999 8    7777776664

>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=84.79  E-value=0.33  Score=27.88  Aligned_cols=37  Identities=35%  Similarity=0.477  Sum_probs=33.1

Q ss_pred             CCCC-CHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           44 GAKL-SASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        44 ~~~~-t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |..+ |..+||+..+ +    +...+++-++.|...|++....
T Consensus        30 G~~LPs~r~La~~~~-v----Sr~tvr~Al~~L~~~Gli~~~~   67 (100)
T d1v4ra1          30 GDTLPSVADIRAQFG-V----AAKTVSRALAVLKSEGLVSSRG   67 (100)
T ss_dssp             TSBCCCHHHHHHHSS-S----CTTHHHHHTTTTTTSSCCEEET
T ss_pred             cCCCccHHHHHHHHC-C----CHHHHHHHHHHHHHCCcEEEec
Confidence            4677 9999999999 9    8999999999999999988653

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.60  E-value=1.4  Score=23.31  Aligned_cols=45  Identities=22%  Similarity=0.395  Sum_probs=35.6

Q ss_pred             HHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeee
Q 045477           35 FEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECS   84 (89)
Q Consensus        35 fd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~   84 (89)
                      ...|.+-|++...|+.+||.+++ +    ...-+.|+|=.|...|-+...
T Consensus         5 l~~l~~lg~~~~~tA~~LA~kl~-v----pKk~iNr~LYsL~~kgkl~k~   49 (59)
T d2gxba1           5 LKFLEELGEGKATTAHDLSGKLG-T----PKKEINRVLYSLAKKGKLQKE   49 (59)
T ss_dssp             HHHHHHHCTTCCBCHHHHHHHHT-C----CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHhcCCccchhHHHHHHHhC-C----cHHHHHHHHHHHHHccchhhc
Confidence            33444434457899999999999 9    888999999999998877643

>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=83.71  E-value=0.88  Score=24.02  Aligned_cols=23  Identities=13%  Similarity=0.183  Sum_probs=17.5

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHH
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRIL   72 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlL   72 (89)
                      ..+|-.|+|+.+| +    .+..+.++.
T Consensus        18 ~gltq~elA~~~g-v----~~~~is~ie   40 (69)
T d2a6ca1          18 SGLTQFKAAELLG-V----TQPRVSDLM   40 (69)
T ss_dssp             TTCCHHHHHHHHT-S----CHHHHHHHH
T ss_pred             cCCCHHHHHHHHH-c----CHhHHHHHH
Confidence            6899999999999 8    555544443

>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=83.44  E-value=0.91  Score=26.57  Aligned_cols=42  Identities=14%  Similarity=0.185  Sum_probs=35.9

Q ss_pred             HHHHHhChHHHHHhcCCCCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhc
Q 045477           27 KAVINLGLFEIIAKAGPGAKLSASEIAAQLPATKNKDAPTMLDRILGLLAS   77 (89)
Q Consensus        27 ~~av~LgIfd~l~~~g~~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s   77 (89)
                      ..+-.+.|+..|.+    |.+|-.||++.+| +    ....+.|+=|.|-.
T Consensus        43 ~la~R~~ia~~L~~----G~~s~reI~~~~g-v----s~aTItR~s~~Lk~   84 (101)
T d1jhga_          43 ALGTRVRIIEELLR----GEMSQRELKNELG-A----GIATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHHH----CCSCHHHHHHHHC-C----CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc----CCcCHHHHHHHhC-C----ChHHHHHHHHHHHh
Confidence            45678889998987    6799999999999 9    88899999888863

>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=83.34  E-value=0.41  Score=25.27  Aligned_cols=22  Identities=18%  Similarity=0.200  Sum_probs=16.9

Q ss_pred             CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           47 LSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      +|+.|||+.+| +    .+..+.|+|.
T Consensus         1 vTl~diA~~ag-v----S~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAG-V----SRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHT-S----CTTHHHHHHH
T ss_pred             CCHHHHHHHHC-c----CHHHHHHHHc
Confidence            57889999988 8    6667777664

>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=81.76  E-value=0.52  Score=26.29  Aligned_cols=44  Identities=18%  Similarity=0.141  Sum_probs=30.8

Q ss_pred             HhChHHHHHhcCC-CCCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccC
Q 045477           31 NLGLFEIIAKAGP-GAKLSASEIAAQLPATKNKDAPTMLDRILGLLASYG   79 (89)
Q Consensus        31 ~LgIfd~l~~~g~-~~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~g   79 (89)
                      +..|.+.|-++.. -..+|+.|||+.++ +    .+..+.|+.+.|=-.|
T Consensus        20 e~~ia~yil~~~~~~~~~si~~lA~~~~-v----S~sTi~Rf~kklG~~g   64 (83)
T d2o3fa1          20 ERKLADYILAHPHKAIESTVNEISALAN-S----SDAAVIRLCKSLGLKG   64 (83)
T ss_dssp             HHHHHHHHHHCHHHHHTCCHHHHHHHTT-C----CHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHcCHHHHHHccHHHHHHHHC-C----CHHHHHHHHHHhCCCC
Confidence            3355666554320 13589999999999 9    8889999888764444

>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=80.55  E-value=0.54  Score=24.66  Aligned_cols=22  Identities=9%  Similarity=0.306  Sum_probs=16.3

Q ss_pred             CCHHHHHhhCCCCCCCCCcchHHHHHH
Q 045477           47 LSASEIAAQLPATKNKDAPTMLDRILG   73 (89)
Q Consensus        47 ~t~~eLA~~~~~~~~~~d~~~l~RlLR   73 (89)
                      +|+.|||+..| +    .+..+.|+|+
T Consensus         2 vTi~dvA~~ag-v----S~~TVSr~Ln   23 (57)
T d2hsga1           2 VTIYDVAREAS-V----SMATVSRVVN   23 (57)
T ss_dssp             CCHHHHHHHTT-S----CHHHHHHHHT
T ss_pred             cCHHHHHHHHC-c----CHHHHHHHhC
Confidence            57888888888 8    6666666665

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.13  E-value=1.6  Score=26.56  Aligned_cols=36  Identities=19%  Similarity=0.141  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhCCCCCCCCCcchHHHHHHHHhccCceeeec
Q 045477           45 AKLSASEIAAQLPATKNKDAPTMLDRILGLLASYGIVECSV   85 (89)
Q Consensus        45 ~~~t~~eLA~~~~~~~~~~d~~~l~RlLR~L~s~gi~~e~~   85 (89)
                      |+....||.+.+| +    .+..|.+=|+.|...|++....
T Consensus        32 G~~rf~el~~~lg-i----s~~vLs~rL~~L~~~gLv~r~~   67 (142)
T d2f2ea1          32 GLTRFGEFQKSLG-L----AKNILAARLRNLVEHGVMVAVP   67 (142)
T ss_dssp             TCCSHHHHHHHHC-C----CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHhh-c----cHHHHHHHHHHHHHhcceeeec
Confidence            7999999999999 9    8889999999999999998643