Psyllid ID: psy5744

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------
Protein Sequence
MSTSDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEEEEccccEEEEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccccccHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHcHHHHHHHHHHHHHHHcccccEEEEEHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHccEEEEEEEEEcccccccEEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHccccccccccEcccccccccHHHHHHHccccccEEcc
Coil and Loop (DISEMBL)
mstsdegyvhtevptsLKQLSRLVVRGFYSIEDSLIIDMlvrnpcmkedDICELLKFERKMLRARISTLKNDKIIQTRLRMetgldgkaqKVNYYFINYQTFVNIVKYKLDVMRKRMEmeerdatsrssfkcprclktftdlepclLVLWCACPCKR
Flexible Loop (DISEMBL)
mstsdegyvhtevptslkqlsrLVVRGFYSIEDsliidmlvrnpCMKEDDICELLKFERKMLRaristlkndkiiqtrlrmetgldgkaQKVNYYFINYQTFVNIVKYKLDVMRKRMEMeerdatsrssfkcprcLKTFTDLEPCLLVLWCACPCKR
Low Complexity Region (SEG)
MSTSDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR
Disordered region (IsUnstruct)
************VPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR***************FKCPRCLKTFTDLEPCLLVLWCACPC**
Disordered Region (DISOPRED)
************VPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT**************VNYYFINYQTFVNIVKYKLDVMRK***********RSSFKCPRCLKTFTDLEPCLLVLWCACPCK*
Disordered Region (DISEMBL)
*************PTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRM************FKCPRCLKTFTDLEPCLLVLWCACPCKR
Disordered Region (DISPRO)
******GYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTSDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR
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	157	2.2.26 [Sep-21-2011]
Q5R8H5	439	General transcription fac	yes	N/A	0.859	0.307	0.614	1e-46
A6QLI8	438	General transcription fac	yes	N/A	0.859	0.308	0.614	2e-46
P29083	439	General transcription fac	yes	N/A	0.859	0.307	0.607	1e-45
Q9D0D5	440	General transcription fac	no	N/A	0.859	0.306	0.607	3e-45
P36100	482	Transcription initiation	yes	N/A	0.840	0.273	0.272	1e-11
Q557M8	456	General transcription fac	yes	N/A	0.834	0.287	0.318	8e-11
Q9P3W1	434	Transcription initiation	yes	N/A	0.872	0.315	0.221	3e-06

>sp|Q5R8H5|T2EA_PONAB General transcription factor IIE subunit 1 OS=Pongo abelii GN=GTF2E1 PE=2 SV=1

 Score =  185 bits (469), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query: 9   VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
           V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct: 6   VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query: 69  LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
           LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct: 66  LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query: 129 SFKCPRCLKTFTDLE 143
           SFKCP C  TFTDLE
Sbjct: 126 SFKCPVCSSTFTDLE 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.
Pongo abelii (taxid: 9601)

>sp|A6QLI8|T2EA_BOVIN General transcription factor IIE subunit 1 OS=Bos taurus GN=GTF2E1 PE=2 SV=1

 Score =  184 bits (468), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query: 9   VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
           V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct: 6   VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query: 69  LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
           LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct: 66  LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query: 129 SFKCPRCLKTFTDLE 143
           SFKCP C  TFTDLE
Sbjct: 126 SFKCPVCSSTFTDLE 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

Bos taurus (taxid: 9913)

>sp|P29083|T2EA_HUMAN General transcription factor IIE subunit 1 OS=Homo sapiens GN=GTF2E1 PE=1 SV=2

 Score =  181 bits (460), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 82/135 (60%), Positives = 110/135 (81%)

Query: 9   VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
           V TEVP +LK+L++ V+RGFY IE +L +D+L+RN C+KE+D+ ELLKF+RK LR+ ++ 
Sbjct: 6   VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNSCVKEEDMLELLKFDRKQLRSVLNN 65

Query: 69  LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
           LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct: 66  LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query: 129 SFKCPRCLKTFTDLE 143
           SFKCP C  TFTDLE
Sbjct: 126 SFKCPVCSSTFTDLE 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

Homo sapiens (taxid: 9606)

>sp|Q9D0D5|T2EA_MOUSE General transcription factor IIE subunit 1 OS=Mus musculus GN=Gtf2e1 PE=2 SV=1

 Score =  180 bits (456), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 82/135 (60%), Positives = 110/135 (81%)

Query: 9   VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
           V TEVP +LK+L++ V+RGFY IE  L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct: 6   VLTEVPAALKRLAKYVIRGFYGIEHVLALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query: 69  LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
           LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ER++T+R+
Sbjct: 66  LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERNSTNRA 125

Query: 129 SFKCPRCLKTFTDLE 143
           SFKCP C  TFTDLE
Sbjct: 126 SFKCPVCCSTFTDLE 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

Mus musculus (taxid: 10090)

>sp|P36100|T2EA_YEAST Transcription initiation factor IIE subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TFA1 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/132 (27%), Positives = 73/132 (55%)

Query: 17  LKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ 76
           +K L + VVRGFY     L++D ++ +  + EDD+ +LL   +  L   I+ L++D++I 
Sbjct: 9   VKNLLKFVVRGFYGGSFVLVLDAILFHSVLAEDDLKQLLSINKTELGPLIARLRSDRLIS 68

Query: 77  TRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCL 136
              + E   + K+ +  YY++ Y   ++ +K+K+  + +R++ +    +  + + CP CL
Sbjct: 69  IHKQREYPPNSKSVERVYYYVKYPHAIDAIKWKVHQVVQRLKDDLDKNSEPNGYMCPICL 128

Query: 137 KTFTDLEPCLLV 148
             +T LE   L+
Sbjct: 129 TKYTQLEAVQLL 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

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

>sp|Q557M8|T2EA_DICDI General transcription factor IIE subunit 1 OS=Dictyostelium discoideum GN=gtf2e1-1 PE=3 SV=1

 Score = 66.2 bits (160), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 80/135 (59%), Gaps = 4/135 (2%)

Query: 17  LKQLSRLVVRGFYSIEDSLIIDMLVRNPC-MKEDDICELLKFERKMLRARISTLKNDKII 75
           L  L ++V+R FY  E ++IID L+R    +K++D+   L+ ++K +R  +  LK D ++
Sbjct: 11  LDDLVKMVIRAFYPDEYAVIIDGLLREKKRIKDEDLALRLRIQQKYVRKILMDLKGDSMV 70

Query: 76  QTR-LRMET-GLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCP 133
           ++  +++E  G + +      ++I+Y+  ++IVKYKL + RK+ME  +       ++KC 
Sbjct: 71  KSSDVKVEAKGPNERGSTHLLWYIDYKHIIDIVKYKLYMFRKKMESVKVQKIDVQTYKCQ 130

Query: 134 RCLKTFTDLE-PCLL 147
            C K +T L+ P LL
Sbjct: 131 TCHKVYTALDIPKLL 145

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9P3W1|T2EA_SCHPO Transcription initiation factor IIE subunit alpha OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tfa1 PE=1 SV=3

 Score = 51.2 bits (121), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 31/140 (22%), Positives = 71/140 (50%), Gaps = 3/140 (2%)

Query: 11  TEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70
           +  P  +++L ++++R FY     + +D ++R+  + ++    L+    K  R     L+
Sbjct: 2   SNAPEIVQRLIKMIMRAFYETRHIIFMDAILRHSALTDEQTALLMGIPIKECRFIAGKLR 61

Query: 71  NDKI--IQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
            D++  IQ+R  M+ G   +     Y++I++ + ++ +K+++  + K +E   R+     
Sbjct: 62  EDRLLAIQSRTEMKEGQQ-RQYHTTYFYIDFCSTIDSIKWRMHQLVKTVEDRMRNDFDSK 120

Query: 129 SFKCPRCLKTFTDLEPCLLV 148
            + CP C K F+ L+   LV
Sbjct: 121 GYVCPFCNKKFSSLDVLSLV 140

Recruits TFIIH to the initiation complex and stimulates the RNA polymerase II C-terminal domain kinase and DNA-dependent ATPase activities of TFIIH. Both TFIIH and TFIIE are required for promoter clearance by RNA polymerase.

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
357613512	413	hypothetical protein KGM_03878 [Danaus p	0.847	0.322	0.879	5e-65
91082005	404	PREDICTED: similar to transcription init	0.891	0.346	0.842	6e-65
307178158	420	General transcription factor IIE subunit	0.847	0.316	0.879	7e-65
242010384	408	predicted protein [Pediculus humanus cor	0.878	0.338	0.841	1e-64
332017143	418	General transcription factor IIE subunit	0.847	0.318	0.879	1e-64
350408250	419	PREDICTED: general transcription factor	0.891	0.334	0.842	5e-64
340720120	419	PREDICTED: general transcription factor	0.891	0.334	0.842	5e-64
66517504	419	PREDICTED: general transcription factor	0.891	0.334	0.842	5e-64
383847090	419	PREDICTED: general transcription factor	0.891	0.334	0.835	1e-63
312373741	435	hypothetical protein AND_17055 [Anophele	0.885	0.319	0.821	7e-63

>gi|357613512|gb|EHJ68554.1| hypothetical protein KGM_03878 [Danaus plexippus]

 Score =  251 bits (642), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 117/133 (87%), Positives = 128/133 (96%)

Query: 11  TEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70
           TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLRARI+TLK
Sbjct: 8   TEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLRARIATLK 67

Query: 71  NDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSF 130
           NDK IQ RL+METGLDGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERDATSR+SF
Sbjct: 68  NDKFIQVRLKMETGLDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERDATSRASF 127

Query: 131 KCPRCLKTFTDLE 143
           KCP C KTFTDLE
Sbjct: 128 KCPSCGKTFTDLE 140

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91082005|ref|XP_969623.1| PREDICTED: similar to transcription initiation factor IIE subunit alpha [Tribolium castaneum] gi|270007311|gb|EFA03759.1| hypothetical protein TcasGA2_TC013870 [Tribolium castaneum]

 Score =  251 bits (642), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 118/140 (84%), Positives = 132/140 (94%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
           S+E  + TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   SNEERLVTEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLR 61

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARI+TLKNDK IQ RLRMETG+D KAQKVNYYFINY+TFVN+VKYKLD+MRKR+E EERD
Sbjct: 62  ARIATLKNDKFIQVRLRMETGVDSKAQKVNYYFINYKTFVNVVKYKLDLMRKRLETEERD 121

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKCP CLKTFTDLE
Sbjct: 122 ATSRASFKCPGCLKTFTDLE 141

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307178158|gb|EFN66966.1| General transcription factor IIE subunit 1 [Camponotus floridanus]

 Score =  251 bits (641), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 117/133 (87%), Positives = 128/133 (96%)

Query: 11  TEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70
           TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLRARISTL+
Sbjct: 9   TEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLRARISTLR 68

Query: 71  NDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSF 130
           NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERDATSR+SF
Sbjct: 69  NDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERDATSRASF 128

Query: 131 KCPRCLKTFTDLE 143
           KCP CLKTFTDLE
Sbjct: 129 KCPSCLKTFTDLE 141

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242010384|ref|XP_002425948.1| predicted protein [Pediculus humanus corporis] gi|212509931|gb|EEB13210.1| predicted protein [Pediculus humanus corporis]

 Score =  250 bits (639), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 117/139 (84%), Positives = 132/139 (94%), Gaps = 1/139 (0%)

Query: 5   DEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRA 64
           +E YV TE+P+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR+
Sbjct: 2   EEQYV-TEIPSSLKQLARLVVRGFYNIEDALIVDMLVRNPCMKEDDICELLKFERKMLRS 60

Query: 65  RISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDA 124
           +I+TLKNDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERDA
Sbjct: 61  KIATLKNDKFIQVRLKMETGFDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERDA 120

Query: 125 TSRSSFKCPRCLKTFTDLE 143
           TSR+SFKCP CLKTFTDLE
Sbjct: 121 TSRASFKCPNCLKTFTDLE 139

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332017143|gb|EGI57942.1| General transcription factor IIE subunit 1 [Acromyrmex echinatior]

 Score =  250 bits (639), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 117/133 (87%), Positives = 128/133 (96%)

Query: 11  TEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70
           TEVP+SLK+L+RLVVRGFYSIED+LI+DMLVRNPCMKEDDICELLKFERKMLRARISTL+
Sbjct: 9   TEVPSSLKKLARLVVRGFYSIEDALIVDMLVRNPCMKEDDICELLKFERKMLRARISTLR 68

Query: 71  NDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSF 130
           NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERDATSR+SF
Sbjct: 69  NDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERDATSRASF 128

Query: 131 KCPRCLKTFTDLE 143
           KCP CLKTFTDLE
Sbjct: 129 KCPSCLKTFTDLE 141

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350408250|ref|XP_003488350.1| PREDICTED: general transcription factor IIE subunit 1-like [Bombus impatiens]

 Score =  248 bits (634), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 118/140 (84%), Positives = 130/140 (92%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
           S E  + TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   SGEERLVTEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLR 61

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARISTL+NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERD
Sbjct: 62  ARISTLRNDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERD 121

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKC  CLKTFTDLE
Sbjct: 122 ATSRASFKCTNCLKTFTDLE 141

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340720120|ref|XP_003398491.1| PREDICTED: general transcription factor IIE subunit 1-like [Bombus terrestris]

 Score =  248 bits (634), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 118/140 (84%), Positives = 130/140 (92%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
           S E  + TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   SGEERLVTEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLR 61

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARISTL+NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERD
Sbjct: 62  ARISTLRNDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERD 121

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKC  CLKTFTDLE
Sbjct: 122 ATSRASFKCTNCLKTFTDLE 141

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66517504|ref|XP_395253.2| PREDICTED: general transcription factor IIE subunit 1 [Apis mellifera] gi|380027214|ref|XP_003697324.1| PREDICTED: general transcription factor IIE subunit 1-like [Apis florea]

 Score =  248 bits (634), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 118/140 (84%), Positives = 130/140 (92%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
           S E  + TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   SGEERLVTEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLR 61

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARISTL+NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERD
Sbjct: 62  ARISTLRNDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERD 121

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKC  CLKTFTDLE
Sbjct: 122 ATSRASFKCTNCLKTFTDLE 141

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847090|ref|XP_003699188.1| PREDICTED: general transcription factor IIE subunit 1-like [Megachile rotundata]

 Score =  247 bits (630), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 117/140 (83%), Positives = 130/140 (92%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
           S E  + TEVP+SLKQL+RLVVRGFY+IED+LI+DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   SGEERLVTEVPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDICELLKFERKMLR 61

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARISTL+NDK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+M+KRME EERD
Sbjct: 62  ARISTLRNDKFIQVRLKMETGSDGKAQKVNYYFINYKTFVNVVKYKLDLMKKRMETEERD 121

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKC  CLKTFTDLE
Sbjct: 122 ATSRASFKCTNCLKTFTDLE 141

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312373741|gb|EFR21432.1| hypothetical protein AND_17055 [Anopheles darlingi]

 Score =  244 bits (624), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 115/140 (82%), Positives = 129/140 (92%), Gaps = 1/140 (0%)

Query: 4   SDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLR 63
            D+ YV TE+P+SLKQL+RLVVRGFY+IED+L++DMLVRNPCMKEDDICELLKFERKMLR
Sbjct: 2   GDQRYV-TEIPSSLKQLARLVVRGFYTIEDALVVDMLVRNPCMKEDDICELLKFERKMLR 60

Query: 64  ARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD 123
           ARIS L+NDK +Q RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD MRKRME EERD
Sbjct: 61  ARISILRNDKFLQVRLKMETGPDGKAQKVNYYFINYKTFVNVVKYKLDHMRKRMETEERD 120

Query: 124 ATSRSSFKCPRCLKTFTDLE 143
           ATSR+SFKCP C KTFTDLE
Sbjct: 121 ATSRASFKCPSCNKTFTDLE 140

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
FB|FBgn0015828	429	TfIIEalpha "Transcription fact	0.859	0.314	0.823	6.8e-56
UNIPROTKB|F1NTL4	442	GTF2E1 "Uncharacterized protei	0.859	0.305	0.622	8.1e-44
UNIPROTKB|A6QLI8	438	GTF2E1 "General transcription	0.859	0.308	0.614	1.3e-43
UNIPROTKB|F1MGT5	439	GTF2E1 "General transcription	0.859	0.307	0.614	1.3e-43
UNIPROTKB|E2R3P2	460	GTF2E1 "Uncharacterized protei	0.859	0.293	0.614	1.3e-43
UNIPROTKB|I3LMA9	438	LOC100624061 "Uncharacterized	0.859	0.308	0.614	1.3e-43
MGI|MGI:1921447	440	Gtf2e1 "general transcription	0.859	0.306	0.607	7.3e-43
UNIPROTKB|G3V992	438	Gtf2e1 "General transcription	0.859	0.308	0.607	7.3e-43
UNIPROTKB|P29083	439	GTF2E1 "General transcription	0.859	0.307	0.607	9.3e-43
ZFIN|ZDB-GENE-041210-221	447	gtf2e1 "general transcription	0.847	0.297	0.609	1.2e-42

FB|FBgn0015828 TfIIEalpha "Transcription factor IIEalpha" [Drosophila melanogaster (taxid:7227)]

 Score = 576 (207.8 bits), Expect = 6.8e-56, P = 6.8e-56
 Identities = 112/136 (82%), Positives = 125/136 (91%)

Query:     8 YVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS 67
             YV TEVP+SLKQL+RLVVRGFYS+ED+LIIDMLVRNPCMKEDDI ELL+FE+K LRARI+
Sbjct:    20 YV-TEVPSSLKQLARLVVRGFYSLEDALIIDMLVRNPCMKEDDIGELLRFEKKQLRARIT 78

Query:    68 TLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSR 127
             TL+ DK IQ RL+METG DGKAQKVNYYFINY+TFVN+VKYKLD+MRKRME EERDATSR
Sbjct:    79 TLRTDKFIQIRLKMETGPDGKAQKVNYYFINYKTFVNVVKYKLDLMRKRMETEERDATSR 138

Query:   128 SSFKCPRCLKTFTDLE 143
             +SFKC  C KTFTDLE
Sbjct:   139 ASFKCSSCSKTFTDLE 154

GO:0005634 "nucleus" evidence=IDA

GO:0005673 "transcription factor TFIIE complex" evidence=ISS;IPI

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

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

UNIPROTKB|F1NTL4 GTF2E1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 84/135 (62%), Positives = 111/135 (82%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ VVRGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++T
Sbjct:     7 VLTEVPAALKRLAKYVVRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNT 66

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+  VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    67 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRLLVNVVKYKLDHMRRRIETDERDSTNRA 126

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   127 SFKCPICFSTFTDLE 141

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|A6QLI8 GTF2E1 "General transcription factor IIE subunit 1" [Bos taurus (taxid:9913)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCSSTFTDLE 140

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|F1MGT5 GTF2E1 "General transcription factor IIE subunit 1" [Bos taurus (taxid:9913)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCSSTFTDLE 140

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

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

UNIPROTKB|E2R3P2 GTF2E1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCSSTFTDLE 140

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

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

UNIPROTKB|I3LMA9 LOC100624061 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 83/135 (61%), Positives = 111/135 (82%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE +L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCSSTFTDLE 140

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

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

MGI|MGI:1921447 Gtf2e1 "general transcription factor II E, polypeptide 1 (alpha subunit)" [Mus musculus (taxid:10090)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 82/135 (60%), Positives = 110/135 (81%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE  L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHVLALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ER++T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERNSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCCSTFTDLE 140

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|G3V992 Gtf2e1 "General transcription factor II E, polypeptide 1 (Alpha subunit)" [Rattus norvegicus (taxid:10116)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 82/135 (60%), Positives = 110/135 (81%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE  L +D+L+RNPC+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHVLALDILIRNPCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ER++T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERNSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCCSTFTDLE 140

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|P29083 GTF2E1 "General transcription factor IIE subunit 1" [Homo sapiens (taxid:9606)]

 Score = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 82/135 (60%), Positives = 110/135 (81%)

Query:     9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST 68
             V TEVP +LK+L++ V+RGFY IE +L +D+L+RN C+KE+D+ ELLKF+RK LR+ ++ 
Sbjct:     6 VLTEVPAALKRLAKYVIRGFYGIEHALALDILIRNSCVKEEDMLELLKFDRKQLRSVLNN 65

Query:    69 LKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRS 128
             LK DK I+ R+R+ET  DGK  + NYYFINY+T VN+VKYKLD MR+R+E +ERD+T+R+
Sbjct:    66 LKGDKFIKCRMRVETAADGKTTRHNYYFINYRTLVNVVKYKLDHMRRRIETDERDSTNRA 125

Query:   129 SFKCPRCLKTFTDLE 143
             SFKCP C  TFTDLE
Sbjct:   126 SFKCPVCSSTFTDLE 140

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0019048 "virus-host interaction" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

ZFIN|ZDB-GENE-041210-221 gtf2e1 "general transcription factor IIE, polypeptide 1, alpha" [Danio rerio (taxid:7955)]

 Score = 451 (163.8 bits), Expect = 1.2e-42, P = 1.2e-42
 Identities = 81/133 (60%), Positives = 110/133 (82%)

Query:    11 TEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK 70
             TEVP SLK+L++ VVRGFY IE +L +D+L+RNPC++E+D+ ELLKF+RK LR+ ++TLK
Sbjct:     8 TEVPASLKRLAKQVVRGFYGIEHALALDVLIRNPCVREEDMLELLKFDRKQLRSVLNTLK 67

Query:    71 NDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSF 130
              DK ++ R+R+ET  DGK  + NYYFINY+  VN+VKYKLD MR+R+E +ERD+T+R+SF
Sbjct:    68 ADKFVKCRMRVETAPDGKTTRHNYYFINYRLLVNVVKYKLDHMRRRIETDERDSTNRASF 127

Query:   131 KCPRCLKTFTDLE 143
             +CP C  TFTDLE
Sbjct:   128 RCPCCTNTFTDLE 140

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

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P29083	T2EA_HUMAN	No assigned EC number	0.6074	0.8598	0.3075	yes	N/A
A6QLI8	T2EA_BOVIN	No assigned EC number	0.6148	0.8598	0.3082	yes	N/A
Q5R8H5	T2EA_PONAB	No assigned EC number	0.6148	0.8598	0.3075	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	157
smart00531	147	smart00531, TFIIE, Transcription initiation factor	4e-36
pfam02002	105	pfam02002, TFIIE_alpha, TFIIE alpha subunit	5e-21
COG1675	176	COG1675, TFA1, Transcription initiation factor IIE	5e-04

>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE

 Score =  121 bits (306), Expect = 4e-36
 Identities = 45/113 (39%), Positives = 71/113 (62%)

Query: 31  IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQ 90
            E  L++D L+RN C+ E+D+ ELL  ++K LR  +  L ++K+I+   + E   + K  
Sbjct: 1   GEAFLVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTW 60

Query: 91  KVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE 143
              Y++INY T +++VKYKLD MRKR+E +  D T+ + +KCP C   +T LE
Sbjct: 61  YRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLE 113

Length = 147

>gnl|CDD|216839 pfam02002, TFIIE_alpha, TFIIE alpha subunit

 Score = 81.6 bits (202), Expect = 5e-21
 Identities = 36/103 (34%), Positives = 61/103 (59%), Gaps = 3/103 (2%)

Query: 24  VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET 83
           VVRGF+  E  L++D L+R   + E+D+ ELL  +   LR  +  L + ++++ R R + 
Sbjct: 6   VVRGFFGDEAVLVLDALLRKGEVTEEDLAELLGIDLNELRKLLYRLYDARLVKYRRRRD- 64

Query: 84  GLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATS 126
             D       Y++INY+  +N+VKYKLD MR+++E +    T+
Sbjct: 65  --DETGWYRYYWYINYEKLLNVVKYKLDHMRQKLEKDLEFETN 105

The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the pre-initiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Archaeoglobus fulgidus tfe. Length = 105

>gnl|CDD|224589 COG1675, TFA1, Transcription initiation factor IIE, alpha subunit [Transcription]

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 22/113 (19%), Positives = 54/113 (47%), Gaps = 3/113 (2%)

Query: 35  LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY 94
           L++D L+    + ++++ ELL  ++  +R  +  L  D +I  R   +   +    +   
Sbjct: 22  LVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYR---KKRDEESGWEEYT 78

Query: 95  YFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLL 147
           ++INY+  + ++K K   + ++++ +    T  + + CP C   ++  E   L
Sbjct: 79  WYINYEKVLEVLKGKKRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAMEL 131

Length = 176

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
KOG2593|consensus	436		100.0
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	100.0
smart00531	147	TFIIE Transcription initiation factor IIE.	100.0
PRK06266	178	transcription initiation factor E subunit alpha; V	100.0
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	99.97
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	99.96
COG3355	126	Predicted transcriptional regulator [Transcription	98.5
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	98.06
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.79
KOG2587|consensus	551		97.77
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	97.75
PHA02943	165	hypothetical protein; Provisional	97.7
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.6
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.39
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	97.38
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	97.36
COG2345	218	Predicted transcriptional regulator [Transcription	97.25
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	97.25
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	97.15
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	97.01
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.97
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.89
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.88
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.88
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.87
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.86
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.83
KOG2587|consensus	551		96.67
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.66
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	96.55
PRK11014	141	transcriptional repressor NsrR; Provisional	96.54
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.54
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.46
PHA00738	108	putative HTH transcription regulator	96.35
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.31
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.2
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.19
COG1959	150	Predicted transcriptional regulator [Transcription	96.19
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	96.14
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	96.12
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	96.08
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.08
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	95.98
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	95.98
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	95.97
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.97
PRK06474	178	hypothetical protein; Provisional	95.96
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.95
PRK03837	241	transcriptional regulator NanR; Provisional	95.95
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.94
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	95.94
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	95.84
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	95.8
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.65
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	95.64
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	95.6
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	95.57
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.51
PRK10870	176	transcriptional repressor MprA; Provisional	95.48
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.43
COG1378	247	Predicted transcriptional regulators [Transcriptio	95.38
TIGR03338	212	phnR_burk phosphonate utilization associated trans	95.3
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	95.3
PRK11169	164	leucine-responsive transcriptional regulator; Prov	95.25
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	95.25
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.23
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	95.22
PF03428	177	RP-C: Replication protein C N-terminal domain; Int	95.18
PF13730	55	HTH_36: Helix-turn-helix domain	95.17
COG2512	258	Predicted membrane-associated trancriptional regul	95.16
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	95.12
PRK14999	241	histidine utilization repressor; Provisional	95.11
PHA03103	183	double-strand RNA-binding protein; Provisional	95.05
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	94.99
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	94.96
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	94.94
PRK04984	239	fatty acid metabolism regulator; Provisional	94.91
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	94.88
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	94.86
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	94.8
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	94.8
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	94.74
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	94.73
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	94.72
PRK13509	251	transcriptional repressor UlaR; Provisional	94.68
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	94.66
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	94.64
COG1846	126	MarR Transcriptional regulators [Transcription]	94.57
PF09824	160	ArsR: ArsR transcriptional regulator; InterPro: IP	94.56
PRK11050	152	manganese transport regulator MntR; Provisional	94.5
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	94.48
PF04423	54	Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IP	94.45
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	94.44
PRK03573	144	transcriptional regulator SlyA; Provisional	94.43
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	94.39
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	94.35
PRK10079	241	phosphonate metabolism transcriptional regulator P	94.35
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	94.35
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	94.29
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	94.29
COG5625	113	Predicted transcription regulator containing HTH d	94.22
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	94.15
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	94.14
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	94.1
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	93.95
PRK13777	185	transcriptional regulator Hpr; Provisional	93.94
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	93.94
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	93.9
PRK03902	142	manganese transport transcriptional regulator; Pro	93.87
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	93.86
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	93.79
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	93.64
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.61
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	93.59
COG1414	246	IclR Transcriptional regulator [Transcription]	93.58
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	93.48
COG1802	230	GntR Transcriptional regulators [Transcription]	93.45
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	93.43
PRK09954	362	putative kinase; Provisional	93.42
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	93.39
COG1777	217	Predicted transcriptional regulators [Transcriptio	93.35
COG2188	236	PhnF Transcriptional regulators [Transcription]	93.24
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	93.2
PF03962	188	Mnd1: Mnd1 family; InterPro: IPR005647 This family	93.14
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	93.11
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	92.93
PF13814	191	Replic_Relax: Replication-relaxation	92.92
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	92.84
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	92.81
COG4190	144	Predicted transcriptional regulator [Transcription	92.73
PF13894	24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	92.71
COG1654	79	BirA Biotin operon repressor [Transcription]	92.65
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	92.55
COG1725	125	Predicted transcriptional regulators [Transcriptio	92.54
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	92.51
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	92.5
PRK09462	148	fur ferric uptake regulator; Provisional	92.38
PRK09391	230	fixK transcriptional regulator FixK; Provisional	92.29
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	92.28
PF13465	26	zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A	92.25
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	92.19
PRK11569	274	transcriptional repressor IclR; Provisional	92.19
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	92.19
PHA02768	55	hypothetical protein; Provisional	92.16
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.09
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	92.09
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	91.92
TIGR03337	231	phnR transcriptional regulator protein. This famil	91.85
PRK13824	404	replication initiation protein RepC; Provisional	91.78
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	91.59
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	91.43
COG2186	241	FadR Transcriptional regulators [Transcription]	91.43
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	91.42
PRK14165	217	winged helix-turn-helix domain-containing protein/	91.17
COG0640	110	ArsR Predicted transcriptional regulators [Transcr	91.09
COG4189	308	Predicted transcriptional regulator [Transcription	90.98
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	90.85
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	90.72
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	90.72
COG2901	98	Fis Factor for inversion stimulation Fis, transcri	90.39
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	90.35
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	90.35
COG1510	177	Predicted transcriptional regulators [Transcriptio	90.3
PRK10046	225	dpiA two-component response regulator DpiA; Provis	90.21
PF13912	27	zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9	90.13
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	89.93
PF11994	72	DUF3489: Protein of unknown function (DUF3489); In	89.67
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	89.53
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	89.17
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	88.71
PRK05638	442	threonine synthase; Validated	88.63
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	88.43
COG4738	124	Predicted transcriptional regulator [Transcription	88.38
COG3388	101	Predicted transcriptional regulator [Transcription	88.37
PRK09334	86	30S ribosomal protein S25e; Provisional	88.29
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	88.23
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.19
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	88.06
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	87.66
PRK12423	202	LexA repressor; Provisional	87.59
COG3888	321	Predicted transcriptional regulator [Transcription	87.41
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	87.19
COG1733	120	Predicted transcriptional regulators [Transcriptio	87.15
PRK15418	318	transcriptional regulator LsrR; Provisional	86.94
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	86.74
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	86.68
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	86.43
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	86.43
COG4860	170	Uncharacterized protein conserved in archaea [Func	86.4
COG1497	260	Predicted transcriptional regulator [Transcription	86.4
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	86.38
COG5124	209	Protein predicted to be involved in meiotic recomb	86.31
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	86.05
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	85.7
PHA02591	83	hypothetical protein; Provisional	85.42
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	85.1
TIGR01714	119	phage_rep_org_N phage replisome organizer, putativ	85.01
PHA00626	59	hypothetical protein	84.89
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	84.82
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	84.8
PF12171	27	zf-C2H2_jaz: Zinc-finger double-stranded RNA-bindi	84.71
KOG2907|consensus	116		84.38
COG2865	467	Predicted transcriptional regulator containing an	84.37
COG1592	166	Rubrerythrin [Energy production and conversion]	84.21
COG5340	269	Predicted transcriptional regulator [Transcription	84.12
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	84.1
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	84.06
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	83.91
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	83.84
TIGR02844	80	spore_III_D sporulation transcriptional regulator	83.79
PF03551	75	PadR: Transcriptional regulator PadR-like family;	83.77
PHA00616	44	hypothetical protein	83.69
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	83.21
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	83.13
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	83.11
PF05043	87	Mga: Mga helix-turn-helix domain; InterPro: IPR007	83.04
COG4049	65	Uncharacterized protein containing archaeal-type C	82.99
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	82.55
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	82.53
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	82.46
cd08324	85	CARD_NOD1_CARD4 Caspase activation and recruitment	82.4
KOG3623|consensus	1007		82.38
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	82.07
PF13913	25	zf-C2HC_2: zinc-finger of a C2HC-type	81.93
PRK00215	205	LexA repressor; Validated	81.65
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	81.63
COG4565	224	CitB Response regulator of citrate/malate metaboli	81.56
PRK13239	206	alkylmercury lyase; Provisional	81.41
PF13518	52	HTH_28: Helix-turn-helix domain	81.37
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	81.19
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	81.18
PF10668	60	Phage_terminase: Phage terminase small subunit; In	81.09
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	81.01
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	80.91
COG5647	773	Cullin, a subunit of E3 ubiquitin ligase [Posttran	80.49
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	80.28
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	80.12

>KOG2593|consensus

Probab=100.00  E-value=4.6e-43  Score=297.73  Aligned_cols=148  Identities=45%  Similarity=0.779  Sum_probs=143.3

Q ss_pred             ccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCc
Q psy5744           9 VHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGK   88 (157)
Q Consensus         9 ~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk   88 (157)
                      .+.++|..+++|+++|||.||+.+|++|+|+|+|++|++|||||++|+|+.|++|++|.+|++|+||+.++|.|..+||+
T Consensus         7 ~~~~~~~~~~~l~k~vvr~fy~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr   86 (436)
T KOG2593|consen    7 VVYDIPTALNDLLKKVVRGFYGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGR   86 (436)
T ss_pred             EeecCcHHHHHHHHHHHHhcccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999989998


Q ss_pred             eeE-EEEEEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCC--CCcccC
Q psy5744          89 AQK-VNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLW--CACPCK  156 (157)
Q Consensus        89 ~~~-~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~--~~F~C~  156 (157)
                      +.. ++||||||.+++||||||||+|+++|+.++++.++..+|+||.|+++||.|||++|+|+  +.|+|-
T Consensus        87 ~~~~~~YyyInY~~~idvVKyKlh~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~  157 (436)
T KOG2593|consen   87 AVDKHTYYYINYAQVIDVVKYKLHQMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCE  157 (436)
T ss_pred             ceeeeEEEEeehHHHHHHHHHHHHHHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEe
Confidence            874 79999999999999999999999999999999999999999999999999999999996  799995

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=100.00  E-value=5.3e-40  Score=250.78  Aligned_cols=132  Identities=20%  Similarity=0.208  Sum_probs=124.0

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      .||+.+++.|||++++.|+|+|++++++||||||+.||++.|+||++|++|+++|||+++++. + ++ ++|..|||+||
T Consensus         2 ~~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r-~-~~-~gw~~Y~w~i~   78 (158)
T TIGR00373         2 ELLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRK-D-DE-TGWYEYTWRIN   78 (158)
T ss_pred             hHHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeee-e-cC-CCcEEEEEEeC
Confidence            478999999999999999999999999999999999999999999999999999999977543 3 23 46899999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744          99 YQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR  157 (157)
Q Consensus        99 y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~  157 (157)
                      |+.++++|+||++++.++|++++++++++.+|+||+|+.+|||+||++    .+|.||+
T Consensus        79 ~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~----~~F~Cp~  133 (158)
T TIGR00373        79 YEKALDVLKRKLEETAKKLREKLEFETNNMFFICPNMCVRFTFNEAME----LNFTCPR  133 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEECCCCCcEeeHHHHHH----cCCcCCC
Confidence            999999999999999999999999999999999999999999999998    7999995

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.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=100.00  E-value=1.5e-39  Score=245.52  Aligned_cols=127  Identities=38%  Similarity=0.640  Sum_probs=117.5

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHH
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKL  110 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl  110 (157)
                      .+|++|||+|+++++++|||||+.|||+.|+||++|++|++||++....+.+..+++++|.++||||||+.++++|+||+
T Consensus         1 ~e~~~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~   80 (147)
T smart00531        1 GEAFLVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKL   80 (147)
T ss_pred             CcEEeehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHH
Confidence            36899999999999999999999999999999999999999999877766665566567999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCC-CcccCC
Q psy5744         111 DVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWC-ACPCKR  157 (157)
Q Consensus       111 ~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~-~F~C~~  157 (157)
                      ++|+++|+++++.+.++.+|+||+||.+|+++||+.+.|++ .|.||.
T Consensus        81 ~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~  128 (147)
T smart00531       81 DKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPR  128 (147)
T ss_pred             HHHHHHHHHHHhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCC
Confidence            99999999999999999999999999999999999998764 599984

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=100.00  E-value=2.4e-36  Score=234.60  Aligned_cols=134  Identities=13%  Similarity=0.190  Sum_probs=121.5

Q ss_pred             HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEE
Q psy5744          15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY   94 (157)
Q Consensus        15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~y   94 (157)
                      +.++.|++.+++  .++.++.|||+|.++|++||+|||+.||++.+.||++|++|+++|||.+++.++.   +++|+.+|
T Consensus         8 ~~v~~~l~~~~~--~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~---~~Gr~~y~   82 (178)
T PRK06266          8 PLVQKVLFEIME--GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDE---ETNWYTYT   82 (178)
T ss_pred             HHHHHHHHHHhc--CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeecc---CCCcEEEE
Confidence            345667777776  3777999999999999999999999999999999999999999999998754432   35699999


Q ss_pred             EEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744          95 YFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR  157 (157)
Q Consensus        95 w~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~  157 (157)
                      |++|++.++++|+||++++.++|+++++.+.++++|+||+|+++|||+||+.    .+|.||+
T Consensus        83 w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~----~~F~Cp~  141 (178)
T PRK06266         83 WKPELEKLPEIIKKKKMEELKKLKEQLEEEENNMFFFCPNCHIRFTFDEAME----YGFRCPQ  141 (178)
T ss_pred             EEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCEEECCCCCcEEeHHHHhh----cCCcCCC
Confidence            9999999999999999999999999999999999999999999999999997    7999995

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

Probab=99.97  E-value=2.7e-31  Score=205.07  Aligned_cols=134  Identities=20%  Similarity=0.395  Sum_probs=124.8

Q ss_pred             hHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEE
Q psy5744          14 PTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVN   93 (157)
Q Consensus        14 p~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~   93 (157)
                      .+.+..++..|++   |++++.|+|+|+.+|.++||+||..+|+.+++||++|+.|+++|+|++++..+. +  +.|.+|
T Consensus         4 ~~~~~~~~~~i~~---g~~~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~-~--~~~~~y   77 (176)
T COG1675           4 DPVLQELLKSIVR---GDEAVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE-E--SGWEEY   77 (176)
T ss_pred             cHHHHHHHHHHcc---CchhhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc-C--CCcEEE
Confidence            3567888888888   999999999999989999999999999999999999999999999999866543 2  359999


Q ss_pred             EEEecchhHHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744          94 YYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLWCACPCKR  157 (157)
Q Consensus        94 yw~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~  157 (157)
                      ||++||+.+.++|+++++++.++|+..++.++++.+|+||.|+.+||++||..    .+|.||.
T Consensus        78 ~w~~~~~~v~~~l~~~~~~~le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~----~~F~Cp~  137 (176)
T COG1675          78 TWYINYEKVLEVLKGKKRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAME----LGFTCPK  137 (176)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeCCCCCCcccHHHHHH----hCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999    7899995

>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=99.96  E-value=1.3e-30  Score=186.17  Aligned_cols=105  Identities=26%  Similarity=0.504  Sum_probs=61.9

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      +||+.|+|+|||++|++|||+|+++++++|||||+.+|+++|+||++|++|+++|||+++++.+   ++++|+.+|||||
T Consensus         1 ~L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d---~~~~~~~~yw~i~   77 (105)
T PF02002_consen    1 ELLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKD---DERGWTRYYWYID   77 (105)
T ss_dssp             -----HHHTTS-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE-----------EEEEE-T
T ss_pred             ChHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEc---CCCcEEEEEEEEc
Confidence            4899999999999999999999999999999999999999999999999999999999986654   2367999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy5744          99 YQTFVNIVKYKLDVMRKRMEMEERDATS  126 (157)
Q Consensus        99 y~~~~~vik~rl~~m~~~L~~~~~~~~~  126 (157)
                      |+.++++|+||+++|.++|++++++++|
T Consensus        78 ~~~~~~~ik~r~~~~~~~l~~~l~~e~n  105 (105)
T PF02002_consen   78 YDQIIDVIKYRIYKMREKLKKRLEFEEN  105 (105)
T ss_dssp             HHHH------------------SSS--S
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999999999988754

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=98.50  E-value=3e-06  Score=62.52  Aligned_cols=101  Identities=16%  Similarity=0.186  Sum_probs=81.1

Q ss_pred             HHHHHHHcCCC--chHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEE-EEE
Q psy5744          21 SRLVVRGFYSI--EDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVN-YYF   96 (157)
Q Consensus        21 v~~v~R~Fy~~--e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~-yw~   96 (157)
                      +..+.+-+||=  -.+-++-+|+ .++.++-||||+.|+.+...+.+.|++|.+.|||..++..-  +.|  .+.| |--
T Consensus        15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~--~~G--gy~yiY~~   90 (126)
T COG3355          15 CEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL--KGG--GYYYLYKP   90 (126)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc--CCC--ceeEEEec
Confidence            45667777873  3577888888 69999999999999999999999999999999999874432  233  4455 447


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHHHHhhcC
Q psy5744          97 INYQTFVNIVKYKLDVMRKRMEMEERDAT  125 (157)
Q Consensus        97 I~y~~~~~vik~rl~~m~~~L~~~~~~~~  125 (157)
                      ++++.+.+.++..+..--+++++-++...
T Consensus        91 i~~ee~k~~i~~~l~~w~~~~~~~i~~~~  119 (126)
T COG3355          91 IDPEEIKKKILKDLDEWYDKMKQLIEEFE  119 (126)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999888888887766543

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

Probab=98.06  E-value=1.3e-05  Score=52.23  Aligned_cols=56  Identities=16%  Similarity=0.314  Sum_probs=43.1

Q ss_pred             HHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          36 IIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        36 IlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      |+++|-. ++.++-.|||+.+|++..++|.+|..|+++|.|...   .   -|++.. +||.++
T Consensus         5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~---~---~~rG~~-~~W~l~   61 (62)
T PF04703_consen    5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS---P---VRRGKS-TYWRLN   61 (62)
T ss_dssp             HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE---S----SSSSS--EEEES
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---c---CCCCcc-eeeeec
Confidence            6778777 889999999999999999999999999999999743   1   122222 489987

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

Probab=97.79  E-value=6.2e-05  Score=49.60  Aligned_cols=45  Identities=11%  Similarity=0.155  Sum_probs=41.0

Q ss_pred             HHHHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -.|+.+|-+++.  ++-.|||+.+|++.+.|+++|+.|.++|+|...
T Consensus         9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~   55 (68)
T smart00550        9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ   55 (68)
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            468888888876  999999999999999999999999999999754

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

>KOG2587|consensus

Probab=97.77  E-value=0.00012  Score=64.78  Aligned_cols=86  Identities=14%  Similarity=0.231  Sum_probs=73.4

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHhCCCcC-HHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744          19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMK-EDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI   97 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~-dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I   97 (157)
                      +|-..++-.|+|+-.-.|+.+|+++|.++ +.-++...||+.+.||++|..|-++++|+|..-  +.++|   ..++|+-
T Consensus         7 elc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~--~~~~g---~vt~Y~~   81 (551)
T KOG2587|consen    7 ELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVH--TRNSG---KVTTYEA   81 (551)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEe--cCCCC---ceEEEEe
Confidence            36777888999999889999999999988 999999999999999999999999999999833  33444   5666777


Q ss_pred             cchhHHHHHHHH
Q psy5744          98 NYQTFVNIVKYK  109 (157)
Q Consensus        98 ~y~~~~~vik~r  109 (157)
                      .++.+..+++|=
T Consensus        82 ~~~ei~hilry~   93 (551)
T KOG2587|consen   82 QCSEILHILRYP   93 (551)
T ss_pred             hhhHHHHHHhcc
Confidence            778888888875

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

Probab=97.75  E-value=8.2e-05  Score=48.30  Aligned_cols=60  Identities=12%  Similarity=0.196  Sum_probs=53.3

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          19 QLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +|...++...||+-.-.|.+.|+++|..|=.+|+..+++++++||+.|..|-+.++|.+.
T Consensus         1 ~L~~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~   60 (62)
T PF08221_consen    1 ELCTLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYF   60 (62)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeee
Confidence            366778889999999999999999999999999999999999999999999999999986

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.

>PHA02943 hypothetical protein; Provisional

Probab=97.70  E-value=0.00055  Score=52.11  Aligned_cols=83  Identities=16%  Similarity=0.304  Sum_probs=62.6

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHH
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR  114 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~  114 (157)
                      -|+..| ..|+.|-.+||+.||++-.+++=+|..|+.+|.|...   +-      ...+||+++.+...+.    +..+.
T Consensus        15 eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV---~~------G~~tyw~l~~day~~~----v~~~~   80 (165)
T PHA02943         15 KTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKV---EI------GRAAIWCLDEDAYTNL----VFEIK   80 (165)
T ss_pred             HHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEE---ee------cceEEEEEChHHHHHH----HHHHH
Confidence            466666 7899999999999999999999999999999999874   22      2368999998766666    55555


Q ss_pred             HHHHHHHhhcCCCCeeecC
Q psy5744         115 KRMEMEERDATSRSSFKCP  133 (157)
Q Consensus       115 ~~L~~~~~~~~~~~~Y~Cp  133 (157)
                      +.|..-++.  ++--|+-|
T Consensus        81 Relwrlv~s--~~~kfi~p   97 (165)
T PHA02943         81 RELWRLVCN--SRLKFITP   97 (165)
T ss_pred             HHHHHHHHh--ccccccCh
Confidence            555554443  34455554

>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=97.60  E-value=0.0002  Score=43.54  Aligned_cols=44  Identities=20%  Similarity=0.428  Sum_probs=38.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      ..-|+.+|..++.+|-.+||+.+|++...+++++..|.++|+|+
T Consensus         5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence            45688999999999999999999999999999999999999985

...

>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=97.39  E-value=0.00033  Score=45.63  Aligned_cols=46  Identities=15%  Similarity=0.305  Sum_probs=41.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-|.-+|+.++.++-+|||+.+|++...|+++|..|.+.|||...
T Consensus        10 E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~   55 (68)
T PF01978_consen   10 EAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE   55 (68)
T ss_dssp             HHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3556677778999999999999999999999999999999999865

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.

>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=97.38  E-value=0.00092  Score=42.70  Aligned_cols=56  Identities=14%  Similarity=0.244  Sum_probs=49.5

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+.+++-++--.-|++.|..++.++=.+||+.+|+++..+..-|..|.+.|||..+
T Consensus         2 ~i~~aL~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~   57 (61)
T PF12840_consen    2 EIFKALSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE   57 (61)
T ss_dssp             HHHHHHTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHhCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            35677777777889999967899999999999999999999999999999999976

...

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=97.36  E-value=0.0051  Score=44.83  Aligned_cols=68  Identities=15%  Similarity=0.178  Sum_probs=56.6

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      .+.+++-++--.-|++.|..++.++=-|||+.+|+++..|-+.|..|++.|||..++      +|   ...||++|.
T Consensus         8 ~~fkaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r------~G---r~~~Y~l~~   75 (117)
T PRK10141          8 QLFKILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRK------QG---KWVHYRLSP   75 (117)
T ss_pred             HHHHHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEE------Ec---CEEEEEECc
Confidence            566677777778899998877889999999999999999999999999999999762      12   246788885

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=97.25  E-value=0.00093  Score=53.68  Aligned_cols=60  Identities=15%  Similarity=0.375  Sum_probs=48.6

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      .|+-.|.+++.+|-+|||+.||++..-+|+-|..|..+|+|..+..    +.|+++....|++-
T Consensus        15 ~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~----~~g~GRP~~~y~Lt   74 (218)
T COG2345          15 RILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQ----QGGRGRPAKLYRLT   74 (218)
T ss_pred             HHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeec----cCCCCCCceeeeec
Confidence            4566666799999999999999999999999999999999998822    23345666666664

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

Probab=97.25  E-value=0.0046  Score=39.22  Aligned_cols=66  Identities=15%  Similarity=0.424  Sum_probs=50.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc-hhHHHHHH
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY-QTFVNIVK  107 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y-~~~~~vik  107 (157)
                      ....|++.+..++ ++-.+||+.+|++...++++|..|.+.|++....   .   +   ...+|.++. +.+.+.++
T Consensus         8 ~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~---~---~---~~~~~~~~~g~~~~~~~~   74 (78)
T cd00090           8 TRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR---E---G---RRVYYSLTDAERLLALLE   74 (78)
T ss_pred             HHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE---e---c---cEEEEEeCCchHHHHHHH
Confidence            3467888888777 9999999999999999999999999999998641   1   1   245666664 44544443

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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=97.15  E-value=0.0042  Score=38.37  Aligned_cols=62  Identities=16%  Similarity=0.419  Sum_probs=47.0

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK  107 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik  107 (157)
                      |+..|. ++.++-.+|++.+|++...++++|..|.++|++....      +|+   ..+|+++.+...+++.
T Consensus         2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~------~~~---~~~~~~~~~~~~~~~~   63 (66)
T smart00418        2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR------EGK---RVYYSLTDEKVADLLE   63 (66)
T ss_pred             HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee------cCC---EEEEEEchHHHHHHHH
Confidence            455555 7778999999999999999999999999999998441      111   3557777665555544

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

Probab=97.01  E-value=0.0089  Score=40.52  Aligned_cols=74  Identities=14%  Similarity=0.186  Sum_probs=52.8

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHH
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR  114 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~  114 (157)
                      -||-.|...+.++=.+|.+.+|++.-.+.+.|.+|+++|+|+.+..  .  .| ...++||.|-- .=..+++..+..++
T Consensus         4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~--~--~~-~~p~t~~~lT~-~Gr~~~~~~~~~L~   77 (80)
T PF13601_consen    4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKE--F--EG-RRPRTWYSLTD-KGREAFERYVAALR   77 (80)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-----SS-S--EEEEEE-H-HHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEe--c--cC-CCCeEEEEECH-HHHHHHHHHHHHHH
Confidence            4777788788999999999999999999999999999999998732  2  22 35688999884 34455555444444

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.97  E-value=0.0027  Score=49.89  Aligned_cols=44  Identities=16%  Similarity=0.314  Sum_probs=40.5

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -||..|..++.++-.+||+.+|+++.-|++.|..|.++|||...
T Consensus         5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~   48 (203)
T TIGR02702         5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE   48 (203)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence            47778888888999999999999999999999999999999865

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.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=96.89  E-value=0.0031  Score=40.00  Aligned_cols=44  Identities=14%  Similarity=0.309  Sum_probs=40.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|++.|-.++.++-+|||+.+|++...+|+=|..|.+.|++...
T Consensus         4 ~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    4 QILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            47888888999999999999999999999999999999998865

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

>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=96.88  E-value=0.0025  Score=39.40  Aligned_cols=45  Identities=13%  Similarity=0.241  Sum_probs=39.8

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+-||++|..+ +.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus         5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            46799999975 5589999999999999999999999999999975

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.

>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=96.88  E-value=0.0032  Score=42.65  Aligned_cols=45  Identities=27%  Similarity=0.389  Sum_probs=36.0

Q ss_pred             HHHHHHHHhCC---CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNP---CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~---~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-+|-.|..++   .++=++||+.+|+++..+++++..|.+.|||...
T Consensus        11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~   58 (83)
T PF02082_consen   11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS   58 (83)
T ss_dssp             HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence            44555555432   3999999999999999999999999999999875

(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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.87  E-value=0.0048  Score=37.07  Aligned_cols=44  Identities=16%  Similarity=0.380  Sum_probs=40.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|++.|.+++.++-.+||+.+|++...+++.|..|.+.|+|...
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~   47 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV   47 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            47788888888999999999999999999999999999999754

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.86  E-value=0.023  Score=38.33  Aligned_cols=61  Identities=8%  Similarity=0.153  Sum_probs=48.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      ...||..|..++.++-.+||+.++++...+.+++..|.+.|+|....   .+   +.....++.+.-
T Consensus        12 ~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~---~~---~~~r~~~~~lT~   72 (101)
T smart00347       12 QFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP---SP---EDRRSVLVSLTE   72 (101)
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC---CC---CCCCeEEEEECH
Confidence            56788888878889999999999999999999999999999998651   11   123345677764

>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=96.83  E-value=0.0033  Score=38.14  Aligned_cols=43  Identities=12%  Similarity=0.294  Sum_probs=37.2

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +-|+.+|. ++..+=.|||+.+|+++..|.+.|..|.+.|+|.+
T Consensus         5 ~~Il~~L~-~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    5 LRILKLLS-EGPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHHHT-TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHH-hCCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence            45677766 48899999999999999999999999999999975

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 ....

>KOG2587|consensus

Probab=96.67  E-value=0.032  Score=49.80  Aligned_cols=103  Identities=10%  Similarity=0.105  Sum_probs=83.3

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      ..|++.=||+.++=++-.|..++.+.++.++..--|+.|+.|..|++|-++|.|.-.....+..-+-+++-+.|+.|...
T Consensus       388 E~vI~~rfG~rAiRl~R~l~~k~~veekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~psrtF~L~~v~~~~  467 (551)
T KOG2587|consen  388 ESVIQERFGSRAIRLFRLLLQKKHVEEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAPSRTFYLYTVNILR  467 (551)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcccchHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCCcceEEEEEeccHH
Confidence            45667778889999999998888999999999999999999999999999999986543333212345677899999888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhc
Q psy5744         102 FVNIVKYKLDVMRKRMEMEERDA  124 (157)
Q Consensus       102 ~~~vik~rl~~m~~~L~~~~~~~  124 (157)
                      ...-+.-.+++...+|=.+++.+
T Consensus       468 a~~~lld~ly~~iaNL~~R~~~e  490 (551)
T KOG2587|consen  468 AYRMLLDELYKSIANLIERLRHE  490 (551)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888888888777776666554

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.66  E-value=0.0065  Score=41.04  Aligned_cols=45  Identities=11%  Similarity=0.196  Sum_probs=41.2

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+.|++.|..+ +.++-.|||+.+|++...++++|..|.+.|+|..
T Consensus         7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~   52 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ   52 (91)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence            46789998876 7899999999999999999999999999999975

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

Probab=96.55  E-value=0.0073  Score=37.76  Aligned_cols=47  Identities=19%  Similarity=0.309  Sum_probs=41.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+|..|-.++.++-.+||+.++++..-+-+++..|.+.|+|....
T Consensus         5 q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    5 QFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence            46678888888889999999999999999999999999999999873

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 ....

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=96.54  E-value=0.0029  Score=46.98  Aligned_cols=36  Identities=11%  Similarity=0.134  Sum_probs=33.6

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ..++.++||+.+|++..-||++|..|..+|||...+
T Consensus        24 ~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~   59 (141)
T PRK11014         24 RMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR   59 (141)
T ss_pred             CccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence            468999999999999999999999999999999873

>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=96.54  E-value=0.0087  Score=37.60  Aligned_cols=48  Identities=13%  Similarity=0.313  Sum_probs=41.9

Q ss_pred             CchHHHHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+.-||-+|..++.  ++-.|||+.+++++.-+.+++..|.+.|+|..+
T Consensus         5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~   54 (62)
T PF12802_consen    5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE   54 (62)
T ss_dssp             HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            345678888888766  999999999999999999999999999999876

...

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.46  E-value=0.0055  Score=37.81  Aligned_cols=36  Identities=22%  Similarity=0.420  Sum_probs=32.4

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.+ +..+||+.+|++...||+++..|.++|+|...
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4456 89999999999999999999999999999754

>PHA00738 putative HTH transcription regulator

Probab=96.35  E-value=0.018  Score=41.39  Aligned_cols=60  Identities=15%  Similarity=0.192  Sum_probs=48.9

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF  102 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~  102 (157)
                      .-||+.|..++.++=-||++.++|.+.-|-+-|..|++.|||..+  + .   |   ...||+|+.+.-
T Consensus        15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr--K-~---G---r~vyY~Ln~~~~   74 (108)
T PHA00738         15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELY--K-E---G---RTLYAKIRENSK   74 (108)
T ss_pred             HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE--E-E---C---CEEEEEECCCcc
Confidence            568888887777889999999999999999999999999999976  1 1   2   245778876543

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.31  E-value=0.15  Score=36.27  Aligned_cols=83  Identities=14%  Similarity=0.184  Sum_probs=57.4

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc--hhHHHHHHHH
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY--QTFVNIVKYK  109 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y--~~~~~vik~r  109 (157)
                      ....||..|..++.++-.+||+.+|++...+-+++..|.++|+|.....   ..|   ....++++.-  ..+...+...
T Consensus        29 ~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~---~~D---~R~~~v~LT~~G~~~~~~~~~~  102 (118)
T TIGR02337        29 QQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKA---SND---QRRVYISLTPKGQALYASLSPQ  102 (118)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccC---CCC---CCeeEEEECHhHHHHHHHhhHH
Confidence            3567888888888999999999999999999999999999999997521   123   2345566664  2333444444


Q ss_pred             HHHHHHHHHHH
Q psy5744         110 LDVMRKRMEME  120 (157)
Q Consensus       110 l~~m~~~L~~~  120 (157)
                      .......+.+.
T Consensus       103 ~~~~~~~~~~~  113 (118)
T TIGR02337       103 IEEIYAAIEER  113 (118)
T ss_pred             HHHHHHHHHHH
Confidence            44444444333

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.

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

Probab=96.20  E-value=0.0095  Score=33.76  Aligned_cols=30  Identities=23%  Similarity=0.461  Sum_probs=26.0

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      ++-+|||..+|.....|-++|.+|+++|++
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            677899999999999999999999999986

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 ....

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.19  E-value=0.051  Score=37.93  Aligned_cols=46  Identities=13%  Similarity=0.325  Sum_probs=42.0

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-|+.+|.+++.++-.+||+.+|++...+++.+..|.+.|+|...
T Consensus         5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~   50 (108)
T smart00344        5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY   50 (108)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence            4568888888899999999999999999999999999999999843

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

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=96.19  E-value=0.012  Score=44.42  Aligned_cols=36  Identities=14%  Similarity=0.197  Sum_probs=33.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR   80 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~   80 (157)
                      .++=++||+..|+++..++|++..|.+.|||++++.
T Consensus        25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG   60 (150)
T COG1959          25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG   60 (150)
T ss_pred             cccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence            688999999999999999999999999999999843

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

Probab=96.14  E-value=0.034  Score=38.75  Aligned_cols=36  Identities=22%  Similarity=0.291  Sum_probs=33.9

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...++..+||+.+|++...|.++|..|++.|+|...
T Consensus        45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~   80 (95)
T TIGR01610        45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ   80 (95)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            568999999999999999999999999999999865

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

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=96.12  E-value=0.047  Score=40.31  Aligned_cols=46  Identities=9%  Similarity=0.149  Sum_probs=41.1

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..||-.|..++.++-.+||+.+++++..+-+++..|++.|+|...
T Consensus        42 q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~   87 (144)
T PRK11512         42 QFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   87 (144)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            4567767766788999999999999999999999999999999965

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=96.08  E-value=0.02  Score=42.20  Aligned_cols=45  Identities=13%  Similarity=0.093  Sum_probs=37.4

Q ss_pred             HHHHHHHHh---CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVR---NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~---~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-+|-.|..   ++.++-++||+.++++.+.++++|..|.+.|||.+.
T Consensus        11 l~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~   58 (135)
T TIGR02010        11 VTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV   58 (135)
T ss_pred             HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence            444545553   246999999999999999999999999999999864

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

>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=96.08  E-value=0.038  Score=35.18  Aligned_cols=47  Identities=15%  Similarity=0.289  Sum_probs=38.1

Q ss_pred             chHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+..||..|. .++.++-.+||+.++++...+.+++.+|.+.|+|...
T Consensus         4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~   51 (68)
T PF13463_consen    4 PQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE   51 (68)
T ss_dssp             HHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            3567788877 6788999999999999999999999999999999654

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=95.98  E-value=0.017  Score=43.69  Aligned_cols=37  Identities=11%  Similarity=0.097  Sum_probs=33.9

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .+.++=.+||+..|++.+.|+||+..|.+.|||.+.+
T Consensus        22 ~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r   58 (153)
T PRK11920         22 GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVR   58 (153)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            3458899999999999999999999999999999873

>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=95.98  E-value=0.04  Score=35.27  Aligned_cols=35  Identities=20%  Similarity=0.400  Sum_probs=30.9

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+ ++.+||+.+|++...+|++|..|.++|+|...
T Consensus        22 ~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~   57 (64)
T PF00392_consen   22 DRLPSERELAERYGVSRTTVREALRRLEAEGLIERR   57 (64)
T ss_dssp             SBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence            467 99999999999999999999999999999865

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 ....

>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=95.97  E-value=0.069  Score=35.75  Aligned_cols=59  Identities=24%  Similarity=0.441  Sum_probs=44.9

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      |+..|. +++.|=|+|-+.+|++.+.+-..|..|++.|+|...-+.   -+|+....  |++-|+
T Consensus        10 IL~~ls-~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~---~~gkk~R~--YclK~~   68 (72)
T PF05584_consen   10 ILIILS-KRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK---FGGKKYRE--YCLKYK   68 (72)
T ss_pred             HHHHHH-hccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE---ecCeEEEE--EEecch
Confidence            444555 449999999999999999999999999999999976333   24433333  777664

>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=95.97  E-value=0.017  Score=36.64  Aligned_cols=37  Identities=16%  Similarity=0.364  Sum_probs=34.2

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+..++-.|||+.+|++...+.++|..|.++|+|...
T Consensus        22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~   58 (67)
T cd00092          22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR   58 (67)
T ss_pred             ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            3567999999999999999999999999999999865

>PRK06474 hypothetical protein; Provisional

Probab=95.96  E-value=0.041  Score=42.69  Aligned_cols=73  Identities=16%  Similarity=0.246  Sum_probs=54.9

Q ss_pred             HHHcCCCchHHHHHHHHhCCC-cCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          25 VRGFYSIEDSLIIDMLVRNPC-MKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        25 ~R~Fy~~e~ivIlD~L~~~~~-i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      +.++-.+.-..|++.|..++. ++-.+|+..+ +++...|-+.|..|.+.|||........    ++....||.++...
T Consensus         5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~----~~~~ek~y~~~~~~   79 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKV----RSVSEKYYAINEED   79 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccc----cCceeEEEEeccce
Confidence            344445556789999987665 9999999999 7999999999999999999997632211    23445677777643

>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=95.95  E-value=0.027  Score=36.15  Aligned_cols=37  Identities=14%  Similarity=0.228  Sum_probs=34.0

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+.++--|||+.||+++--+-..+.+|.++|||.+.
T Consensus        19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~   55 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE   55 (60)
T ss_dssp             CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            4688999999999999999999999999999999976

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 ....

>PRK03837 transcriptional regulator NanR; Provisional

Probab=95.95  E-value=0.036  Score=43.98  Aligned_cols=53  Identities=15%  Similarity=0.327  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHcCCCchHHHHHHHHhCCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          15 TSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        15 ~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....|...+..+.|.+           ...+ ++.+||+.+|++..-||.+|..|..+|||..+
T Consensus        17 ~v~~~l~~~I~~g~l~p-----------G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~   70 (241)
T PRK03837         17 EVEERLEQMIRSGEFGP-----------GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS   70 (241)
T ss_pred             HHHHHHHHHHHhCCCCC-----------CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34455555555555554           4467 89999999999999999999999999999986

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

Probab=95.94  E-value=0.028  Score=35.24  Aligned_cols=33  Identities=21%  Similarity=0.427  Sum_probs=30.1

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+..+||..+|++...|++.+.+|.+.|+|...
T Consensus        26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377          26 PSERELAEELGVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            359999999999999999999999999998743

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

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=95.94  E-value=0.019  Score=34.00  Aligned_cols=34  Identities=21%  Similarity=0.435  Sum_probs=31.4

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-.|||+.+|++...++++|..|.++|++...
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4788999999999999999999999999999753

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=95.84  E-value=0.035  Score=43.68  Aligned_cols=36  Identities=11%  Similarity=0.152  Sum_probs=33.4

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++++||+.+|++..-||.+|..|..+|||...
T Consensus        32 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~   67 (221)
T PRK11414         32 GARLITKNLAEQLGMSITPVREALLRLVSVNALSVA   67 (221)
T ss_pred             CCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec
Confidence            457889999999999999999999999999999865

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=95.80  E-value=0.028  Score=40.73  Aligned_cols=45  Identities=18%  Similarity=0.173  Sum_probs=37.5

Q ss_pred             HHHHHHHHhC---CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRN---PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~---~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-+|-.|.++   +.++-++||+.+|++...|++++..|.+.|+|.+.
T Consensus        11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            4455555532   37999999999999999999999999999999864

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.

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

Probab=95.65  E-value=0.028  Score=36.72  Aligned_cols=43  Identities=14%  Similarity=0.152  Sum_probs=37.2

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |.++|-.++.++-.|||..+++++..|+..|..|...|-|...
T Consensus         5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~   47 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV   47 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            6677778999999999999999999999999999999999976

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

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=95.64  E-value=0.027  Score=44.11  Aligned_cols=48  Identities=15%  Similarity=0.154  Sum_probs=42.9

Q ss_pred             CchHHHHHHHHhCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.-.|+|+|-++| .++--+||.+|||+..+|++.|++|.+.+.|...
T Consensus         4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~   52 (183)
T PHA02701          4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCE   52 (183)
T ss_pred             hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence            33568999999887 6999999999999999999999999999999653

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

Probab=95.60  E-value=0.13  Score=36.25  Aligned_cols=78  Identities=18%  Similarity=0.316  Sum_probs=58.2

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK  107 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik  107 (157)
                      ..|+++|.. ++.+|-+||.+.+     +++...|=++|..|.+.|+|...   +. ++|    .++|..+-        
T Consensus         4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~---~~-~~~----~~~y~~~~--------   67 (116)
T cd07153           4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREI---EL-GDG----KARYELNT--------   67 (116)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEE---Ee-CCC----ceEEEeCC--------
Confidence            468899886 4679999999999     69999999999999999999965   22 232    12332331        


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         108 YKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       108 ~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                      ......++|-.||+.+.+..
T Consensus        68 ----------------~~~h~H~~C~~Cg~i~~~~~   87 (116)
T cd07153          68 ----------------DEHHHHLICTKCGKVIDFED   87 (116)
T ss_pred             ----------------CCCCCceEeCCCCCEEEecC
Confidence                            02345799999999998744

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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=95.57  E-value=0.039  Score=40.14  Aligned_cols=46  Identities=15%  Similarity=0.268  Sum_probs=39.2

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-+|..|..+  +.++-.+||..+|+++..|+++|..|.+.|+|...
T Consensus        11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            45566666643  56999999999999999999999999999999764

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.

>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=95.51  E-value=0.034  Score=34.32  Aligned_cols=39  Identities=21%  Similarity=0.375  Sum_probs=33.7

Q ss_pred             HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744          35 LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus        35 vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      -|+.+|.. ++.+|-++||+.+|++.+.|++.+..|.+.+
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            46777865 4569999999999999999999999999999

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 ....

>PRK10870 transcriptional repressor MprA; Provisional

Probab=95.48  E-value=0.17  Score=39.03  Aligned_cols=71  Identities=13%  Similarity=0.034  Sum_probs=53.2

Q ss_pred             cccccchHHHHHHHHHHHHHcC------------CCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744           8 YVHTEVPTSLKQLSRLVVRGFY------------SIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus         8 ~~~~~ip~~~~~Lv~~v~R~Fy------------~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      ...|..+-.+..|.+.+.|.+.            ...+..||-.|..  ++.++-.|||+.++++...+-+++..|.+.|
T Consensus        20 ~~~~~~~~~~~~l~~~~~~~l~~~~~~~l~~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG   99 (176)
T PRK10870         20 EDFPYQEILLTRLCMHMQSKLLENRNKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG   99 (176)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            4455555556666666665431            1225677777764  4579999999999999999999999999999


Q ss_pred             ceeee
Q psy5744          74 IIQTR   78 (157)
Q Consensus        74 Lv~~~   78 (157)
                      ||...
T Consensus       100 lV~R~  104 (176)
T PRK10870        100 WIERR  104 (176)
T ss_pred             CEEec
Confidence            99975

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.43  E-value=0.049  Score=40.22  Aligned_cols=70  Identities=13%  Similarity=0.189  Sum_probs=53.3

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeee-cCCCceeEEEEEEecchh
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMET-GLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~-~~~gk~~~~~yw~I~y~~  101 (157)
                      +-..-|+..|-+++-++-.+||+.+|+++..+++.+.+|.++|+++...-.-. ..-|.... .+.-++...
T Consensus         8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~-a~v~v~~~~   78 (154)
T COG1522           8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLT-AFVEVKLER   78 (154)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEE-EEEEEEecC
Confidence            34567899999999999999999999999999999999999999987643211 01132222 667777665

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=95.38  E-value=0.27  Score=40.10  Aligned_cols=83  Identities=12%  Similarity=0.188  Sum_probs=70.0

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHH
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDV  112 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~  112 (157)
                      ..-+--+|+..|..|-.||++..|++...|=.+|..|+..|+|...       .  +....|..++.+.+++.++.++..
T Consensus        18 Ea~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~-------~--g~P~~y~av~p~~~i~~~~~~~~~   88 (247)
T COG1378          18 EAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVI-------E--GRPKKYRAVPPEELIERIKEELQE   88 (247)
T ss_pred             HHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEee-------C--CCCceEEeCCHHHHHHHHHHHHHH
Confidence            4566678888999999999999999999999999999999999854       1  244678889999999999999988


Q ss_pred             HHHHHHHHHhhc
Q psy5744         113 MRKRMEMEERDA  124 (157)
Q Consensus       113 m~~~L~~~~~~~  124 (157)
                      ....++..+...
T Consensus        89 ~~~~~~~~~~~~  100 (247)
T COG1378          89 LLRELESELEEL  100 (247)
T ss_pred             HHHHHHHHHHHh
Confidence            777777765443

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=95.30  E-value=0.058  Score=41.99  Aligned_cols=36  Identities=19%  Similarity=0.347  Sum_probs=33.5

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||.+|..|..+|||...
T Consensus        32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~   67 (212)
T TIGR03338        32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNE   67 (212)
T ss_pred             CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence            556899999999999999999999999999999865

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.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=95.30  E-value=0.05  Score=42.66  Aligned_cols=50  Identities=12%  Similarity=0.209  Sum_probs=44.8

Q ss_pred             CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++....|+..|.+++.++-.+||+.+|+++..+++.|..|++.|+|...
T Consensus       141 ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~  190 (203)
T TIGR01884       141 LSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQK  190 (203)
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            34556788888888888999999999999999999999999999999976

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=95.25  E-value=0.049  Score=41.37  Aligned_cols=46  Identities=15%  Similarity=0.225  Sum_probs=42.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -.-||.+|.+++-++-.+||+.+|++..-|++-+.+|.++|++...
T Consensus        16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~   61 (164)
T PRK11169         16 DRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGY   61 (164)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4578999999999999999999999999999999999999999743

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=95.25  E-value=0.09  Score=37.21  Aligned_cols=63  Identities=21%  Similarity=0.288  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHHHcC-CCchHHHHHHHH----hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          16 SLKQLSRLVVRGFY-SIEDSLIIDMLV----RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        16 ~~~~Lv~~v~R~Fy-~~e~ivIlD~L~----~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++.+-+.+...+- +.....||..|.    .++.++-.+||..+++++..|-+++..|++.|+|...
T Consensus         9 ~~~~~~~~l~~~~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~   76 (109)
T TIGR01889         9 YIKSLKRYLKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE   76 (109)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEecc
Confidence            34455555554321 233567787777    4578999999999999999999999999999999976

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.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=95.23  E-value=0.01  Score=35.96  Aligned_cols=24  Identities=25%  Similarity=0.494  Sum_probs=18.9

Q ss_pred             CeeecCCCCCccchhhhhhccCCCCcccC
Q psy5744         128 SSFKCPRCLKTFTDLEPCLLVLWCACPCK  156 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~  156 (157)
                      ..|.||+||..+++.+...     .+.||
T Consensus         2 ~~y~C~~CG~~~~~~~~~~-----~~~Cp   25 (46)
T PRK00398          2 AEYKCARCGREVELDEYGT-----GVRCP   25 (46)
T ss_pred             CEEECCCCCCEEEECCCCC-----ceECC
Confidence            4699999999998877664     56776

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=95.22  E-value=0.038  Score=45.15  Aligned_cols=62  Identities=18%  Similarity=0.277  Sum_probs=49.2

Q ss_pred             HHHHHHHHHH-cCCC-chH-HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          18 KQLSRLVVRG-FYSI-EDS-LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        18 ~~Lv~~v~R~-Fy~~-e~i-vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +..|++.+.. -|++ ++| .|++.|-. ++-+++.+||+++|++..-+|..+.+|+..|++..+.
T Consensus       167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            3455664443 3443 343 48888887 5899999999999999999999999999999999874

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.

>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []

Probab=95.18  E-value=0.15  Score=39.80  Aligned_cols=86  Identities=16%  Similarity=0.235  Sum_probs=62.1

Q ss_pred             hHHHHHHHHHHHHHcCC-CchHHHHHHHHh-CC------------CcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          14 PTSLKQLSRLVVRGFYS-IEDSLIIDMLVR-NP------------CMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        14 p~~~~~Lv~~v~R~Fy~-~e~ivIlD~L~~-~~------------~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.+-.+++.....|-= +-.+-+|++|+. ..            +.|-..||..+ ||+...||+.+..|.+.|||..+
T Consensus        25 k~~ll~~l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rr  104 (177)
T PF03428_consen   25 KWQLLRALKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIVRR  104 (177)
T ss_pred             HHHHHHHHHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeec
Confidence            34567777776666654 446789999995 21            34568999999 99999999999999999999975


Q ss_pred             EeeeecCCCce--------eEEEEEEecchhHH
Q psy5744          79 LRMETGLDGKA--------QKVNYYFINYQTFV  103 (157)
Q Consensus        79 ~~~e~~~~gk~--------~~~~yw~I~y~~~~  103 (157)
                          +.|+||-        ....-|=||...++
T Consensus       105 ----DS~NgkRy~~R~~~G~I~~A~GfdLsPL~  133 (177)
T PF03428_consen  105 ----DSPNGKRYARRDRGGRIVEAFGFDLSPLI  133 (177)
T ss_pred             ----cCCCCCccCccCCCCCEEeEeCcCHHHHH
Confidence                2355531        23446678865544

They may be involved in plasmid replication and stabilisation functions.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=95.17  E-value=0.035  Score=34.21  Aligned_cols=31  Identities=16%  Similarity=0.326  Sum_probs=28.7

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      +-+-+.||+.+|++.+.|++++..|++.|++
T Consensus        25 ~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   25 FPSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            3579999999999999999999999999985

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=95.16  E-value=0.046  Score=45.01  Aligned_cols=48  Identities=10%  Similarity=0.282  Sum_probs=43.5

Q ss_pred             CchHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++..-|||+|..| |.++..||.+.+|++.-.+-++|.+|++.|+|...
T Consensus       195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~  243 (258)
T COG2512         195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKE  243 (258)
T ss_pred             HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEE
Confidence            4467799999976 56999999999999999999999999999999976

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=95.12  E-value=0.062  Score=41.22  Aligned_cols=35  Identities=17%  Similarity=0.181  Sum_probs=33.2

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.++-++||+.+|++.+.++++|..|.+.|||.+.
T Consensus        24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~   58 (164)
T PRK10857         24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV   58 (164)
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            47999999999999999999999999999999974

>PRK14999 histidine utilization repressor; Provisional

Probab=95.11  E-value=0.1  Score=41.76  Aligned_cols=35  Identities=11%  Similarity=0.232  Sum_probs=32.2

Q ss_pred             Cc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          45 CM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        45 ~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .+ +|.+||+.+|++...||++|..|.++|+|..++
T Consensus        35 ~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   70 (241)
T PRK14999         35 RIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ   70 (241)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            35 899999999999999999999999999998763

>PHA03103 double-strand RNA-binding protein; Provisional

Probab=95.05  E-value=0.039  Score=43.23  Aligned_cols=43  Identities=12%  Similarity=0.187  Sum_probs=39.5

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++|.|-.++.++--+||.+||++.++|.+.|++|.+.|.|...
T Consensus        18 ~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~   60 (183)
T PHA03103         18 EVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMS   60 (183)
T ss_pred             HHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecC
Confidence            6777777899999999999999999999999999999999754

>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=94.99  E-value=0.058  Score=35.16  Aligned_cols=34  Identities=21%  Similarity=0.492  Sum_probs=32.1

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|++...|.++|..|+++|+|...
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~   61 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVK   61 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence            5889999999999999999999999999999864

...

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=94.96  E-value=0.06  Score=40.39  Aligned_cols=47  Identities=17%  Similarity=0.268  Sum_probs=43.4

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -..-|+++|.+++-.+=.+||+.+|++...|++-+.+|.+.|++...
T Consensus        10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~   56 (153)
T PRK11179         10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT   56 (153)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence            35679999999999999999999999999999999999999999854

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=94.94  E-value=0.037  Score=43.80  Aligned_cols=34  Identities=18%  Similarity=0.289  Sum_probs=31.9

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      =+|.+||+.+|++...||++|..|.++|+|..++
T Consensus        33 PsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   66 (238)
T TIGR02325        33 PAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ   66 (238)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            3799999999999999999999999999999764

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

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=94.91  E-value=0.096  Score=41.56  Aligned_cols=36  Identities=22%  Similarity=0.403  Sum_probs=33.1

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~   64 (239)
T PRK04984         28 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   64 (239)
T ss_pred             CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3457 79999999999999999999999999999976

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=94.88  E-value=0.098  Score=41.97  Aligned_cols=36  Identities=19%  Similarity=0.359  Sum_probs=33.3

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~   67 (254)
T PRK09464         31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR   67 (254)
T ss_pred             CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4457 89999999999999999999999999999976

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=94.86  E-value=0.1  Score=41.38  Aligned_cols=36  Identities=22%  Similarity=0.403  Sum_probs=33.4

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~   63 (235)
T TIGR02812        27 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   63 (235)
T ss_pred             CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4568 79999999999999999999999999999976

Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=94.80  E-value=0.11  Score=40.85  Aligned_cols=36  Identities=11%  Similarity=0.177  Sum_probs=33.3

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||.+|..|..+|||...
T Consensus        28 G~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~   63 (224)
T PRK11534         28 DEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVV   63 (224)
T ss_pred             CCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEe
Confidence            456899999999999999999999999999999865

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=94.80  E-value=0.061  Score=43.82  Aligned_cols=47  Identities=13%  Similarity=0.320  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-.|++.|-+++.++-.|||+.++++...+|+-|..|.++|++...
T Consensus         6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            35678999988999999999999999999999999999999999764

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=94.74  E-value=0.12  Score=41.61  Aligned_cols=37  Identities=22%  Similarity=0.415  Sum_probs=33.7

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+.
T Consensus        30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~   67 (257)
T PRK10225         30 GERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR   67 (257)
T ss_pred             CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4568 699999999999999999999999999998763

>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=94.73  E-value=0.058  Score=37.68  Aligned_cols=43  Identities=16%  Similarity=0.323  Sum_probs=34.6

Q ss_pred             HHHHHHHHh----CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          34 SLIIDMLVR----NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        34 ivIlD~L~~----~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      -.|+++|-.    ..-++=++|++.|+++.++||++|..|-++|.|=
T Consensus        50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY   96 (102)
T PF08784_consen   50 DKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY   96 (102)
T ss_dssp             HHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence            345665553    3458899999999999999999999999999883

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.

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=94.72  E-value=0.046  Score=43.36  Aligned_cols=33  Identities=18%  Similarity=0.259  Sum_probs=31.4

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +|.+||+.+|++.-.||++|..|.++|+|..++
T Consensus        26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   58 (233)
T TIGR02404        26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQ   58 (233)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            699999999999999999999999999999764

subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=94.68  E-value=0.063  Score=43.64  Aligned_cols=47  Identities=13%  Similarity=0.260  Sum_probs=43.2

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-.|++.|-+++.++=.|||+.+|++...+|+-|..|.+.|++...
T Consensus         6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~   52 (251)
T PRK13509          6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV   52 (251)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            45678999999999999999999999999999999999999999764

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=94.66  E-value=0.05  Score=43.14  Aligned_cols=33  Identities=12%  Similarity=0.279  Sum_probs=31.4

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +|.+||+.+|++...||++|..|.++|+|..++
T Consensus        27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~   59 (230)
T TIGR02018        27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQ   59 (230)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            899999999999999999999999999999764

This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=94.64  E-value=0.05  Score=43.42  Aligned_cols=35  Identities=23%  Similarity=0.379  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      -=+|.+||+.+|++.-.||++|..|.++|+|..++
T Consensus        33 LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   67 (241)
T PRK11402         33 IPTENELCTQYNVSRITIRKAISDLVADGVLIRWQ   67 (241)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            45799999999999999999999999999999763

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=94.57  E-value=0.1  Score=36.17  Aligned_cols=50  Identities=12%  Similarity=0.210  Sum_probs=44.0

Q ss_pred             CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .......++..|..++..+..+||+.+++++..+-+++.+|.+.|+|...
T Consensus        20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~   69 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERL   69 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence            45667788888887776666999999999999999999999999999976

>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family

Probab=94.56  E-value=0.05  Score=41.59  Aligned_cols=95  Identities=19%  Similarity=0.239  Sum_probs=67.1

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCce---eEE------EE
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKA---QKV------NY   94 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~---~~~------~y   94 (157)
                      +..+|-++.|--|.|.|. .+|+|+++|.+.+|-+.   ++.|..|+.-|||..+=|+-+ |.++.   +..      -=
T Consensus        10 ll~~f~s~~~kkV~~~Ls-~~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP~-pG~kPeKEYhtsYs~vqaN   84 (160)
T PF09824_consen   10 LLQTFNSEVYKKVYDELS-KGWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMPE-PGEKPEKEYHTSYSKVQAN   84 (160)
T ss_pred             HHHHhCCHHHHHHHHHHH-hccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccCC-CCCCchHHHHhhHhheeee
Confidence            457899999999999998 77999999999999877   999999999999998755532 32221   111      12


Q ss_pred             EEecchhHHHHHH------HHHHHHHHHHHHHHhh
Q psy5744          95 YFINYQTFVNIVK------YKLDVMRKRMEMEERD  123 (157)
Q Consensus        95 w~I~y~~~~~vik------~rl~~m~~~L~~~~~~  123 (157)
                      ++.....+-++|.      -.+..+.++|++.++.
T Consensus        85 Fqcs~~DLsdii~i~f~~deel~~~~e~i~~~v~~  119 (160)
T PF09824_consen   85 FQCSMEDLSDIIYIAFMSDEELRDYVEKIEKEVEA  119 (160)
T ss_pred             eEeeHHHHHHHHheeecCHHHHHHHHHHHHHHHHc
Confidence            3333444555543      3566666777777666

>PRK11050 manganese transport regulator MntR; Provisional

Probab=94.50  E-value=0.12  Score=38.95  Aligned_cols=44  Identities=20%  Similarity=0.331  Sum_probs=38.4

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+.++..++.++-.+||+.+++++..|++.+..|++.|+|..+
T Consensus        41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45556656788999999999999999999999999999999754

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=94.48  E-value=0.032  Score=36.63  Aligned_cols=44  Identities=14%  Similarity=0.061  Sum_probs=34.0

Q ss_pred             HHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+++|-..+  ..+.-.+|..|+++.++|.++|+.|+..|.|...
T Consensus         8 ~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~   53 (66)
T PF02295_consen    8 KILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKE   53 (66)
T ss_dssp             HHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeC
Confidence            5788888655  4556666667777799999999999999999753

5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....

>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association

Probab=94.45  E-value=0.06  Score=33.62  Aligned_cols=38  Identities=11%  Similarity=0.188  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhhccC
Q psy5744         111 DVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCLLVL  149 (157)
Q Consensus       111 ~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d  149 (157)
                      +.....+++.+....+... .||-|++.++......|+.
T Consensus         3 ~~~~~~~~k~i~~l~~~~~-~CPlC~r~l~~e~~~~li~   40 (54)
T PF04423_consen    3 KSEIEELKKYIEELKEAKG-CCPLCGRPLDEEHRQELIK   40 (54)
T ss_dssp             HHHHHHHHHHHHHHTT-SE-E-TTT--EE-HHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCCC-cCCCCCCCCCHHHHHHHHH
Confidence            3344445555555556667 9999999999999887763

The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.

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

Probab=94.44  E-value=0.34  Score=34.55  Aligned_cols=79  Identities=19%  Similarity=0.343  Sum_probs=56.7

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK  107 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik  107 (157)
                      ..|+++|.. .+.+|-++|...|     +++...|=+.|..|.+.|+|...   .. ++|    ..+|..+.        
T Consensus        11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~---~~-~~~----~~~Y~~~~--------   74 (120)
T PF01475_consen   11 LAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI---EF-GDG----ESRYELST--------   74 (120)
T ss_dssp             HHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE---EE-TTS----EEEEEESS--------
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE---Ec-CCC----cceEeecC--------
Confidence            578999996 4689999999988     67788999999999999999975   22 233    33444442        


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhh
Q psy5744         108 YKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       108 ~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda  144 (157)
                                      ......++|..||+.+.+.+-
T Consensus        75 ----------------~~~h~h~iC~~Cg~v~~~~~~   95 (120)
T PF01475_consen   75 ----------------CHHHHHFICTQCGKVIDLDDP   95 (120)
T ss_dssp             ----------------SSSCEEEEETTTS-EEEE-GH
T ss_pred             ----------------CCcceEEEECCCCCEEEecch
Confidence                            234668999999999876553

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 ....

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.43  E-value=0.44  Score=34.93  Aligned_cols=46  Identities=11%  Similarity=0.208  Sum_probs=40.8

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..||..|..+ +.++-.|||+.+|+++..|-+++..|.+.|+|...
T Consensus        33 q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~   79 (144)
T PRK03573         33 HWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ   79 (144)
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence            56778887764 56899999999999999999999999999999976

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=94.39  E-value=0.031  Score=32.25  Aligned_cols=29  Identities=21%  Similarity=0.479  Sum_probs=20.8

Q ss_pred             eeecCCCCCccchhhhhhccCCCCcccCC
Q psy5744         129 SFKCPRCLKTFTDLEPCLLVLWCACPCKR  157 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~~  157 (157)
                      .+.||+|++.|...++..--+...+.|++
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~   30 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGK   30 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCC
Confidence            46899999999988776322234788874

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=94.35  E-value=0.15  Score=40.76  Aligned_cols=37  Identities=32%  Similarity=0.580  Sum_probs=33.9

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+.
T Consensus        28 G~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~   65 (251)
T PRK09990         28 GQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQ   65 (251)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            4568 899999999999999999999999999999763

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=94.35  E-value=0.062  Score=42.94  Aligned_cols=34  Identities=24%  Similarity=0.316  Sum_probs=31.7

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      =+|.+||+.+|++...||++|..|.++|+|..++
T Consensus        36 PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~   69 (241)
T PRK10079         36 PAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ   69 (241)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            3799999999999999999999999999999764

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=94.35  E-value=0.015  Score=34.79  Aligned_cols=23  Identities=26%  Similarity=0.534  Sum_probs=13.4

Q ss_pred             eecCCCCCccchhhhhhccCCCCcccC
Q psy5744         130 FKCPRCLKTFTDLEPCLLVLWCACPCK  156 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~~L~d~~~F~C~  156 (157)
                      |+||.||.+....|..+    +.+.|+
T Consensus         1 m~Cp~Cg~~~~~~D~~~----g~~vC~   23 (43)
T PF08271_consen    1 MKCPNCGSKEIVFDPER----GELVCP   23 (43)
T ss_dssp             ESBTTTSSSEEEEETTT----TEEEET
T ss_pred             CCCcCCcCCceEEcCCC----CeEECC
Confidence            56777777665444333    455554

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>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=94.29  E-value=0.13  Score=30.67  Aligned_cols=37  Identities=22%  Similarity=0.316  Sum_probs=30.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      .-|+..|-.++-.+-.+||+.+|++...|++=+.+|+
T Consensus         6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence            4588898999999999999999999999999888875

...

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=94.29  E-value=0.17  Score=40.73  Aligned_cols=36  Identities=19%  Similarity=0.268  Sum_probs=33.0

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~   65 (253)
T PRK11523         29 GDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVR   65 (253)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4567 59999999999999999999999999999876

>COG5625 Predicted transcription regulator containing HTH domain [Transcription]

Probab=94.22  E-value=0.4  Score=34.24  Aligned_cols=105  Identities=15%  Similarity=0.153  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHcCCCchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEE
Q psy5744          16 SLKQLSRLVVRGFYSIEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNY   94 (157)
Q Consensus        16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~y   94 (157)
                      .++.|...+.-.=.-...|.|-..|+. .+.|.-.+|+.+++++...+|-.+..|...||++.+-.     + ++|.-|-
T Consensus         6 ~l~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relv-----q-kgWvGYi   79 (113)
T COG5625           6 RLRKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELV-----Q-KGWVGYI   79 (113)
T ss_pred             HHHHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHH-----h-ccceeeE
Confidence            345555555444455566888888886 45699999999999999999999999999999986522     1 3566553


Q ss_pred             E-EecchhHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy5744          95 Y-FINYQTFVNIVKYKLDVMRKRMEMEERDATS  126 (157)
Q Consensus        95 w-~I~y~~~~~vik~rl~~m~~~L~~~~~~~~~  126 (157)
                      | -.....++.-|+..+.+-.+.|++..++++.
T Consensus        80 ya~~~P~k~leei~~~i~keiEelEk~~k~es~  112 (113)
T COG5625          80 YATTPPPKPLEEIEEEIMKEIEELEKEFKNESQ  112 (113)
T ss_pred             ecCCCCchHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            3 3667789999999999999999998877643

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=94.15  E-value=0.18  Score=40.47  Aligned_cols=36  Identities=19%  Similarity=0.337  Sum_probs=33.0

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~   59 (253)
T PRK10421         23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR   59 (253)
T ss_pred             CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3467 69999999999999999999999999999875

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=94.14  E-value=0.075  Score=42.51  Aligned_cols=35  Identities=14%  Similarity=0.270  Sum_probs=32.3

Q ss_pred             Cc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          45 CM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        45 ~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .+ +|.+||+.+|++...||++|..|.++|+|..++
T Consensus        28 ~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~   63 (240)
T PRK09764         28 ALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ   63 (240)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            45 799999999999999999999999999999763

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=94.10  E-value=0.13  Score=39.05  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=36.7

Q ss_pred             HHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          39 MLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        39 ~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-..+.++=-|||+.||+++..|.+.+.+|.+.|+|.+..
T Consensus        18 l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~   58 (154)
T COG1321          18 LLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP   58 (154)
T ss_pred             HHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence            33357889999999999999999999999999999999863

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=93.95  E-value=0.17  Score=41.20  Aligned_cols=46  Identities=17%  Similarity=0.255  Sum_probs=41.3

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-||++|..+ +.++-.|||+.+|++...+.++|..|.+.|+|...
T Consensus        13 al~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~   59 (263)
T PRK09834         13 GLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRS   59 (263)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            46799999865 46999999999999999999999999999999854

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=93.94  E-value=0.25  Score=38.69  Aligned_cols=46  Identities=7%  Similarity=-0.046  Sum_probs=41.3

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||-.|..++.++-.|||+.++++...+-+++.+|++.|+|...
T Consensus        47 q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~   92 (185)
T PRK13777         47 EHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS   92 (185)
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence            4467777777889999999999999999999999999999999965

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=93.94  E-value=0.13  Score=41.93  Aligned_cols=49  Identities=8%  Similarity=0.206  Sum_probs=44.2

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +..-.|++.|-.++.++=.|||+.+|++.--+|+=|..|+++|+|...+
T Consensus         5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~   53 (256)
T PRK10434          5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY   53 (256)
T ss_pred             HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            3456799999999999999999999999999999999999999997653

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=93.90  E-value=0.13  Score=32.55  Aligned_cols=39  Identities=13%  Similarity=0.410  Sum_probs=34.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN   71 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~   71 (157)
                      .+-++..|+.+++++=++||+.+|++.+.+|.-+..|.+
T Consensus         7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~~   45 (59)
T PF08280_consen    7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELNE   45 (59)
T ss_dssp             HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999984

; PDB: 2WTE_A 3SQN_A.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=93.87  E-value=0.17  Score=37.35  Aligned_cols=37  Identities=16%  Similarity=0.240  Sum_probs=34.4

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++.++-.+||..+++++..|++.|.+|.+.|+|.+.
T Consensus        19 ~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         19 EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            4688899999999999999999999999999999864

>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=93.86  E-value=0.62  Score=30.90  Aligned_cols=49  Identities=14%  Similarity=0.291  Sum_probs=42.2

Q ss_pred             chHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744          32 EDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR   80 (157)
Q Consensus        32 e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~   80 (157)
                      .+..+|..+.+  ...++--||+..+|++++.+-.++.+|.+.|||.....
T Consensus         3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~   53 (75)
T PF04182_consen    3 IQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV   53 (75)
T ss_pred             hHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence            35667778775  45688899999999999999999999999999998755

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.

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=93.79  E-value=0.16  Score=41.02  Aligned_cols=45  Identities=9%  Similarity=0.090  Sum_probs=41.2

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-||++|..++.++=.|||+.+|++...+.++|..|.+.|+|.+.
T Consensus        17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~   61 (257)
T PRK15090         17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE   61 (257)
T ss_pred             HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            578999887778999999999999999999999999999999853

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

Probab=93.64  E-value=0.27  Score=34.44  Aligned_cols=49  Identities=16%  Similarity=0.125  Sum_probs=41.2

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +.+.-|+-.|-+.+.=.---||..++++..+|+.+|.+|++.|||....
T Consensus         7 ~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~   55 (92)
T PF10007_consen    7 PLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVE   55 (92)
T ss_pred             hhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            3355677777766777778899999999999999999999999999864

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.61  E-value=0.17  Score=40.91  Aligned_cols=45  Identities=18%  Similarity=0.423  Sum_probs=40.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .--|++.|-+++.++=.|||+.+|++...+|+-|..|.+.|++..
T Consensus         6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r   50 (240)
T PRK10411          6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR   50 (240)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            345888888899999999999999999999999999999988864

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=93.59  E-value=0.17  Score=41.59  Aligned_cols=47  Identities=17%  Similarity=0.254  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-.|++.|-.++.++-.|||+.+|++..-+|+=|..|+++|++...
T Consensus        18 R~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~   64 (269)
T PRK09802         18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRA   64 (269)
T ss_pred             HHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEE
Confidence            35678999988999999999999999999999999999999999854

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=93.58  E-value=0.17  Score=41.04  Aligned_cols=46  Identities=17%  Similarity=0.306  Sum_probs=41.2

Q ss_pred             hHHHHHHHHhCCC-cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPC-MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~-i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-|||+|-+++. ++=.|||+.+|++...++++|..|.+.|+|.+.
T Consensus         6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d   52 (246)
T COG1414           6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQD   52 (246)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEc
Confidence            4679999997644 789999999999999999999999999999864

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=93.48  E-value=0.23  Score=32.07  Aligned_cols=43  Identities=16%  Similarity=0.241  Sum_probs=36.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+..|. ++.++-.+||+.+|++...|++.+..|.++|+.-..
T Consensus         4 ~il~~L~-~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~   46 (69)
T TIGR00122         4 RLLALLA-DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLT   46 (69)
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            3455544 667899999999999999999999999999996543

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.

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=93.45  E-value=0.28  Score=38.78  Aligned_cols=36  Identities=17%  Similarity=0.386  Sum_probs=34.0

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++++||+.+|++.--||.+|..|..+|||...
T Consensus        37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~   72 (230)
T COG1802          37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE   72 (230)
T ss_pred             CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec
Confidence            557999999999999999999999999999999976

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=93.43  E-value=0.04  Score=27.99  Aligned_cols=16  Identities=38%  Similarity=0.864  Sum_probs=13.6

Q ss_pred             eecCCCCCccchhhhh
Q psy5744         130 FKCPRCLKTFTDLEPC  145 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~  145 (157)
                      |.||.|++.|+....+
T Consensus         1 y~C~~C~~~f~~~~~l   16 (23)
T PF00096_consen    1 YKCPICGKSFSSKSNL   16 (23)
T ss_dssp             EEETTTTEEESSHHHH
T ss_pred             CCCCCCCCccCCHHHH
Confidence            7999999999977654

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....

>PRK09954 putative kinase; Provisional

Probab=93.42  E-value=0.15  Score=43.06  Aligned_cols=44  Identities=27%  Similarity=0.489  Sum_probs=40.8

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ..|+..|.+++.++=.+||+.||++...|++.|.+|+++|++..
T Consensus         6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~   49 (362)
T PRK09954          6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKG   49 (362)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCC
Confidence            45889999999999999999999999999999999999999853

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=93.39  E-value=0.13  Score=38.97  Aligned_cols=34  Identities=18%  Similarity=0.305  Sum_probs=32.1

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+....|-++|.+|+++|+|+..
T Consensus       143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~  176 (193)
T TIGR03697       143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH  176 (193)
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            3789999999999999999999999999999875

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.

>COG1777 Predicted transcriptional regulators [Transcription]

Probab=93.35  E-value=0.11  Score=41.49  Aligned_cols=43  Identities=21%  Similarity=0.403  Sum_probs=36.2

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|+-+|.+.+ -.=-+|...+|+.++-|=+.|..|.++|||.++
T Consensus        19 ~Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~   61 (217)
T COG1777          19 RILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERAGLVESR   61 (217)
T ss_pred             HHHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhh
Confidence            4666777655 345679999999999999999999999999985

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=93.24  E-value=0.14  Score=41.04  Aligned_cols=35  Identities=20%  Similarity=0.317  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      -=+|.+||+.+|++.-.|||+|..|.++|+|..++
T Consensus        31 LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~   65 (236)
T COG2188          31 LPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQ   65 (236)
T ss_pred             CCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEe
Confidence            34699999999999999999999999999999875

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=93.20  E-value=0.12  Score=40.29  Aligned_cols=47  Identities=11%  Similarity=0.256  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-.|++.|-.++.++-+|||+.+|++..-+|+=|..|.++|+|..-
T Consensus         8 R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424          8 RQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence            45678999999999999999999999999999999999999999763

>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast)

Probab=93.14  E-value=0.65  Score=36.40  Aligned_cols=74  Identities=12%  Similarity=0.210  Sum_probs=50.5

Q ss_pred             HHHHHh-CCCcCHHHHHHH----hCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHH
Q psy5744          37 IDMLVR-NPCMKEDDICEL----LKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLD  111 (157)
Q Consensus        37 lD~L~~-~~~i~dedLa~~----l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~  111 (157)
                      ++++.. +...+--||.+.    -||.+-.|.-+|..|-+||||...    .    =+++.+||.+... .....+.++.
T Consensus         2 l~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E----K----iGssn~YWsFps~-~~~~~~~~~~   72 (188)
T PF03962_consen    2 LEIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE----K----IGSSNYYWSFPSQ-AKQKRQNKLE   72 (188)
T ss_pred             hHHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh----h----ccCeeEEEecChH-HHHHHHHHHH
Confidence            444443 455665565554    599999999999999999999864    2    1356889999864 4455555555


Q ss_pred             HHHHHHHH
Q psy5744         112 VMRKRMEM  119 (157)
Q Consensus       112 ~m~~~L~~  119 (157)
                      ++.+.++.
T Consensus        73 ~l~~~~~~   80 (188)
T PF03962_consen   73 KLQKEIEE   80 (188)
T ss_pred             HHHHHHHH
Confidence            55554443

The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].

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

Probab=93.11  E-value=0.91  Score=33.96  Aligned_cols=49  Identities=8%  Similarity=0.232  Sum_probs=41.9

Q ss_pred             CCchHHHHHHHHhC-CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRN-PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~-~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+.-..|+++|..+ +.+|-+||=..+     ++++-.|-++|..|.+.|||...
T Consensus        20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~   74 (145)
T COG0735          20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRL   74 (145)
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEE
Confidence            45567899999964 679999988877     48899999999999999999965

>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=92.93  E-value=0.3  Score=31.81  Aligned_cols=38  Identities=16%  Similarity=0.213  Sum_probs=31.2

Q ss_pred             HhCC-CcCHHHHHHHhCCC-hHHHHHHHHHHhhCcceeee
Q psy5744          41 VRNP-CMKEDDICELLKFE-RKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        41 ~~~~-~i~dedLa~~l~i~-~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++| .-|-.|||+.+|++ ++-|...|..|++.|+|...
T Consensus        20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~   59 (65)
T PF01726_consen   20 EENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRD   59 (65)
T ss_dssp             HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred             HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCC
Confidence            3455 36789999999998 99999999999999999864

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.

>PF13814 Replic_Relax: Replication-relaxation

Probab=92.92  E-value=0.31  Score=37.17  Aligned_cols=62  Identities=19%  Similarity=0.247  Sum_probs=48.1

Q ss_pred             HHHHhCCCcCHHHHHHHhCCChH---HHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          38 DMLVRNPCMKEDDICELLKFERK---MLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        38 D~L~~~~~i~dedLa~~l~i~~k---~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      ..|-++..+|-++|+..++.+.+   .+++.|.+|++.|+|......-  +.+..+..+.|++....
T Consensus         2 ~~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~--~~~~g~~~~vy~Lt~~G   66 (191)
T PF13814_consen    2 RLLARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRV--GARGGSQPYVYYLTPAG   66 (191)
T ss_pred             hhHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccc--cccCCCcceEEEECHHH
Confidence            45667899999999999999998   7999999999999998764321  12234556788888654

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=92.84  E-value=0.43  Score=37.56  Aligned_cols=33  Identities=15%  Similarity=0.182  Sum_probs=31.0

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-+|||..+|+.+..|.++|.+|+++|+|...
T Consensus       170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~  202 (226)
T PRK10402        170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS  202 (226)
T ss_pred             chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence            578999999999999999999999999999865

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

Probab=92.81  E-value=0.23  Score=40.42  Aligned_cols=48  Identities=13%  Similarity=0.293  Sum_probs=44.4

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .+-.|++.|-+++.++=+|||+.+|++.-.+|+=|..|.+.|++....
T Consensus         6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h   53 (253)
T COG1349           6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH   53 (253)
T ss_pred             HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence            466799999999999999999999999999999999999999999754

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=92.73  E-value=1.1  Score=33.57  Aligned_cols=49  Identities=16%  Similarity=0.233  Sum_probs=44.3

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +|...-++..+-.++..|-.|||++.|=+.+.|.+.|..|.+-|+|..+
T Consensus        63 sp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe  111 (144)
T COG4190          63 SPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFE  111 (144)
T ss_pred             ChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEe
Confidence            5666778888777899999999999999999999999999999999976

>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A

Probab=92.71  E-value=0.066  Score=26.80  Aligned_cols=17  Identities=35%  Similarity=0.749  Sum_probs=12.6

Q ss_pred             eecCCCCCccchhhhhh
Q psy5744         130 FKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~~  146 (157)
                      |.||.|+.+|+..++..
T Consensus         1 ~~C~~C~~~~~~~~~l~   17 (24)
T PF13894_consen    1 FQCPICGKSFRSKSELR   17 (24)
T ss_dssp             EE-SSTS-EESSHHHHH
T ss_pred             CCCcCCCCcCCcHHHHH
Confidence            78999999999887654

...

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=92.65  E-value=0.31  Score=33.11  Aligned_cols=35  Identities=14%  Similarity=0.250  Sum_probs=31.9

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      ....+|=++||+.||++..-|-|.+..|+++|+=-
T Consensus        16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I   50 (79)
T COG1654          16 TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDI   50 (79)
T ss_pred             CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence            35689999999999999999999999999999854

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=92.55  E-value=0.19  Score=38.54  Aligned_cols=34  Identities=15%  Similarity=0.347  Sum_probs=31.6

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|+..
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~  201 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH  201 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            4677999999999999999999999999999865

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=92.54  E-value=0.19  Score=37.07  Aligned_cols=37  Identities=11%  Similarity=0.175  Sum_probs=32.8

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR   80 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~   80 (157)
                      ..-|=.+||..+|+++|.|+|+...|+++|+|...++
T Consensus        34 kLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg   70 (125)
T COG1725          34 KLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG   70 (125)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            3456789999999999999999999999999998743

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=92.51  E-value=0.61  Score=33.02  Aligned_cols=62  Identities=16%  Similarity=0.215  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHhC--C------CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          17 LKQLSRLVVRGFYSIEDSLIIDMLVRN--P------CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~~--~------~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+|+..+.++=......-|+.++.|.  |      .|+..++|+.+|++...|.+.+..|.+.|++...
T Consensus        18 aNelld~l~~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~   87 (100)
T PF04492_consen   18 ANELLDALLRADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRD   87 (100)
T ss_pred             HHHHHHHHHhccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            345556665544444445777777764  2      6999999999999999999999999999999654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=92.50  E-value=0.23  Score=33.98  Aligned_cols=47  Identities=15%  Similarity=0.252  Sum_probs=36.6

Q ss_pred             chHHHHHHH---Hh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDML---VR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L---~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.-|+.++   .+ |++|+.+.|+...|++...+.+.|..|...+||.+.
T Consensus         7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~   57 (82)
T PF09202_consen    7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRR   57 (82)
T ss_dssp             HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCcccc
Confidence            344444444   44 689999999999999999999999999999999984

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>PRK09462 fur ferric uptake regulator; Provisional

Probab=92.38  E-value=1.6  Score=32.40  Aligned_cols=78  Identities=13%  Similarity=0.239  Sum_probs=56.9

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI  105 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v  105 (157)
                      -..|++.|..+  +.+|-++|-+.+     +++...|=++|..|.+.|||...   +. ++|..    +|-++       
T Consensus        19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~---~~-~~~~~----~y~~~-------   83 (148)
T PRK09462         19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH---NF-EGGKS----VFELT-------   83 (148)
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE---Ec-CCCcE----EEEeC-------
Confidence            46799999853  589999998888     57889999999999999999865   22 23321    22221       


Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchh
Q psy5744         106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDL  142 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~l  142 (157)
                                       ....-..++|..||+.+.+.
T Consensus        84 -----------------~~~~H~H~iC~~Cg~i~~i~  103 (148)
T PRK09462         84 -----------------QQHHHDHLICLDCGKVIEFS  103 (148)
T ss_pred             -----------------CCCCCCceEECCCCCEEEeC
Confidence                             01234579999999998874

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=92.29  E-value=0.47  Score=37.55  Aligned_cols=33  Identities=21%  Similarity=0.359  Sum_probs=31.0

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+.+..|-++|.+|+++|+|...
T Consensus       180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~  212 (230)
T PRK09391        180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLS  212 (230)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence            678999999999999999999999999999864

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

Probab=92.28  E-value=0.32  Score=32.44  Aligned_cols=42  Identities=19%  Similarity=0.321  Sum_probs=32.4

Q ss_pred             HHHHHHH--hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          35 LIIDMLV--RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        35 vIlD~L~--~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      +|+|.|-  .++..+=.+|+...|++.+.+.++|..|.+.|||+
T Consensus         7 Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~   50 (77)
T PF14947_consen    7 IIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK   50 (77)
T ss_dssp             HHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee
Confidence            4555554  27889999999999999999999999999999994

>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A

Probab=92.25  E-value=0.12  Score=27.41  Aligned_cols=17  Identities=41%  Similarity=0.958  Sum_probs=13.8

Q ss_pred             cCCCCeeecCCCCCccc
Q psy5744         124 ATSRSSFKCPRCLKTFT  140 (157)
Q Consensus       124 ~~~~~~Y~Cp~C~~~Ys  140 (157)
                      -++...|.||.|+++|+
T Consensus         9 H~~~k~~~C~~C~k~F~   25 (26)
T PF13465_consen    9 HTGEKPYKCPYCGKSFS   25 (26)
T ss_dssp             HSSSSSEEESSSSEEES
T ss_pred             cCCCCCCCCCCCcCeeC
Confidence            34556799999999986

...

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

Probab=92.19  E-value=0.33  Score=40.55  Aligned_cols=43  Identities=16%  Similarity=0.187  Sum_probs=38.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      .-|++.|..+..++-.+||+.+|++..-|++.+..|.+.|++-
T Consensus         7 ~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i   49 (319)
T PRK11886          7 LQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDI   49 (319)
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence            4578888777889999999999999999999999999999943

>PRK11569 transcriptional repressor IclR; Provisional

Probab=92.19  E-value=0.39  Score=39.31  Aligned_cols=44  Identities=5%  Similarity=0.198  Sum_probs=40.5

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +-||++|.+ ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~   75 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQ   75 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            679999986 46799999999999999999999999999999974

>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=92.19  E-value=0.93  Score=30.87  Aligned_cols=45  Identities=22%  Similarity=0.367  Sum_probs=38.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...|+..|.. +..+=.||.+.+ |++++.+.+-|..|.++|||...
T Consensus         7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~   52 (90)
T PF01638_consen    7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERR   52 (90)
T ss_dssp             HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcc
Confidence            3567777774 889999999999 99999999999999999999865

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.

>PHA02768 hypothetical protein; Provisional

Probab=92.16  E-value=0.057  Score=34.33  Aligned_cols=20  Identities=15%  Similarity=0.567  Sum_probs=17.3

Q ss_pred             CeeecCCCCCccchhhhhhc
Q psy5744         128 SSFKCPRCLKTFTDLEPCLL  147 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda~~L  147 (157)
                      -+|.||.||++|+..+++..
T Consensus         4 ~~y~C~~CGK~Fs~~~~L~~   23 (55)
T PHA02768          4 LGYECPICGEIYIKRKSMIT   23 (55)
T ss_pred             cccCcchhCCeeccHHHHHH
Confidence            47999999999999998753

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.09  E-value=0.12  Score=29.77  Aligned_cols=28  Identities=14%  Similarity=0.369  Sum_probs=20.6

Q ss_pred             eeecCCCCCccchhhhhhccCC-CCcccCC
Q psy5744         129 SFKCPRCLKTFTDLEPCLLVLW-CACPCKR  157 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~~L~d~-~~F~C~~  157 (157)
                      ...||+|+++|...|.. |-.. ....|++
T Consensus         2 ~i~Cp~C~~~y~i~d~~-ip~~g~~v~C~~   30 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDEK-IPPKGRKVRCSK   30 (36)
T ss_pred             EEECCCCCCEEeCCHHH-CCCCCcEEECCC
Confidence            35799999999999887 4443 3677763

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

Probab=92.09  E-value=0.4  Score=38.46  Aligned_cols=44  Identities=18%  Similarity=0.206  Sum_probs=40.2

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      .+-||++|-. .+.++=.|||+.+|++...+.++|..|.+.|+|.
T Consensus        11 al~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~   55 (248)
T TIGR02431        11 GLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT   55 (248)
T ss_pred             HHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            3679999886 5679999999999999999999999999999996

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.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=91.92  E-value=0.23  Score=37.97  Aligned_cols=34  Identities=15%  Similarity=0.246  Sum_probs=31.6

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~  182 (202)
T PRK13918        149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG  182 (202)
T ss_pred             cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence            3689999999999999999999999999999854

>TIGR03337 phnR transcriptional regulator protein

Probab=91.85  E-value=0.26  Score=38.79  Aligned_cols=34  Identities=21%  Similarity=0.281  Sum_probs=31.7

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      =+|.+||+.+|++.-.+|++|..|.++|+|..++
T Consensus        26 PsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~   59 (231)
T TIGR03337        26 PSERDLGERFNTTRVTIREALQQLEAEGLIYRED   59 (231)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC
Confidence            3799999999999999999999999999999764

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 Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.

>PRK13824 replication initiation protein RepC; Provisional

Probab=91.78  E-value=1.1  Score=39.18  Aligned_cols=104  Identities=12%  Similarity=0.110  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHHHHcCC-CchHHHHHHHHh-CC------------CcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeE
Q psy5744          15 TSLKQLSRLVVRGFYS-IEDSLIIDMLVR-NP------------CMKEDDICELL-KFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        15 ~~~~~Lv~~v~R~Fy~-~e~ivIlD~L~~-~~------------~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      -.+-.+++.....|-= +-.+-|||+|+. ++            +-|-..|+..+ ||+...||+.|..|.+.|||..+ 
T Consensus        38 w~l~r~l~~a~~~lGl~~~~l~vL~aLlsf~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGLI~rr-  116 (404)
T PRK13824         38 WKLFRDLCEARALLGVSDRALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIRR-  116 (404)
T ss_pred             HHHHHHHHHHHHhcCCChhHHHHHHHHHhhCCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEee-
Confidence            3456666666666544 446789999994 33            34567899985 99999999999999999999965 


Q ss_pred             eeeecCCCce--------eEEEEEEecchhH--------------------HHHHHHHHHHHHHHHHHHHh
Q psy5744          80 RMETGLDGKA--------QKVNYYFINYQTF--------------------VNIVKYKLDVMRKRMEMEER  122 (157)
Q Consensus        80 ~~e~~~~gk~--------~~~~yw~I~y~~~--------------------~~vik~rl~~m~~~L~~~~~  122 (157)
                        + .||||-        ....-|=||...+                    ...++.++-.++..|.+.+.
T Consensus       117 --D-SpNGKRyarr~~~G~i~~AfGfDLsPL~~R~~El~~~A~~~~ae~~~~r~lr~~it~~rRdi~~li~  184 (404)
T PRK13824        117 --D-SPNGKRYARKGRGGEIEEAFGFDLAPLLARAEEFEALAEQVAAERKALRRLRERLTLCRRDIAKLIE  184 (404)
T ss_pred             --c-CCCCcccceeCCCCceeeeeccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              2 356532        1234555665332                    44556666666665555443

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=91.59  E-value=0.12  Score=29.93  Aligned_cols=27  Identities=22%  Similarity=0.472  Sum_probs=19.5

Q ss_pred             eecCCCCCccchhhhhhccC-CCCcccCC
Q psy5744         130 FKCPRCLKTFTDLEPCLLVL-WCACPCKR  157 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~~L~d-~~~F~C~~  157 (157)
                      -.||+|+++|...|.. |-. .....|++
T Consensus         3 i~CP~C~~~f~v~~~~-l~~~~~~vrC~~   30 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDK-LPAGGRKVRCPK   30 (37)
T ss_pred             EECCCCCceEEcCHHH-cccCCcEEECCC
Confidence            4799999999988876 333 34777764

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=91.43  E-value=0.075  Score=29.65  Aligned_cols=20  Identities=30%  Similarity=0.426  Sum_probs=7.5

Q ss_pred             ecCCCCCccchhhhhhccCCCCcccC
Q psy5744         131 KCPRCLKTFTDLEPCLLVLWCACPCK  156 (157)
Q Consensus       131 ~Cp~C~~~Ys~lda~~L~d~~~F~C~  156 (157)
                      .||.|+..|+.      .|...|.||
T Consensus         4 ~Cp~C~se~~y------~D~~~~vCp   23 (30)
T PF08274_consen    4 KCPLCGSEYTY------EDGELLVCP   23 (30)
T ss_dssp             --TTT-----E------E-SSSEEET
T ss_pred             CCCCCCCccee------ccCCEEeCC
Confidence            47777777776      444566665

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=91.43  E-value=0.25  Score=39.84  Aligned_cols=33  Identities=18%  Similarity=0.419  Sum_probs=31.2

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          47 KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +|.+||+.+|++...||.+|..|..+|||..++
T Consensus        36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~r~   68 (241)
T COG2186          36 SERELAERFGVSRTVVREALKRLEAKGLVEIRQ   68 (241)
T ss_pred             CHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecC
Confidence            499999999999999999999999999999874

>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=91.42  E-value=0.51  Score=30.76  Aligned_cols=44  Identities=18%  Similarity=0.340  Sum_probs=36.2

Q ss_pred             HHHHHHHhC-CCcCHHHHHHHh---CCCh--HHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRN-PCMKEDDICELL---KFER--KMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~-~~i~dedLa~~l---~i~~--k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .||+.|-.+ +.++-.+|++.+   |.+.  ..||+.|..|.++|++...
T Consensus         2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~   51 (66)
T PF08461_consen    2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV   51 (66)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc
Confidence            578888864 679999999999   4554  7899999999999988743

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

Probab=91.17  E-value=0.5  Score=37.96  Aligned_cols=36  Identities=8%  Similarity=0.099  Sum_probs=33.4

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..+|-.+||+.+++++..+.++|..|++.|+|...
T Consensus        19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~   54 (217)
T PRK14165         19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRT   54 (217)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            456899999999999999999999999999999865

>COG0640 ArsR Predicted transcriptional regulators [Transcription]

Probab=91.09  E-value=2.9  Score=27.16  Aligned_cols=75  Identities=11%  Similarity=0.260  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744          18 KQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI   97 (157)
Q Consensus        18 ~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I   97 (157)
                      ..-+..+..+.-++.-..|+..|.+....+-.+|+..++++...+...|..|.+.|+|..+  .    +|+.   .+|.+
T Consensus        12 ~~~~~~~~~~l~~~~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~--~----~~~~---~~~~l   82 (110)
T COG0640          12 SEEVAEILKALADPTRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELR--R----EGRL---RLYRL   82 (110)
T ss_pred             hHHHHHHHHHhCCHHHHHHHHHHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEE--e----cccE---EEEec
Confidence            3344455556666667778888876667889999999999999999999999999999973  1    2212   56667


Q ss_pred             cchh
Q psy5744          98 NYQT  101 (157)
Q Consensus        98 ~y~~  101 (157)
                      +...
T Consensus        83 ~~~~   86 (110)
T COG0640          83 ADEK   86 (110)
T ss_pred             CcHH
Confidence            7655

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=90.98  E-value=0.86  Score=37.46  Aligned_cols=49  Identities=22%  Similarity=0.343  Sum_probs=44.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM   81 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~   81 (157)
                      -+-|+..|.+.+.+.=.+||+.+|+++..+-.-+..|++.||+..++++
T Consensus        25 Rv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~k   73 (308)
T COG4189          25 RVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVK   73 (308)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeec
Confidence            4778999999999999999999999999999999999999999988654

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=90.85  E-value=0.67  Score=37.88  Aligned_cols=44  Identities=14%  Similarity=0.121  Sum_probs=40.0

Q ss_pred             HHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +-||++|-.+ +.++=.|||+.+|++...+.++|..|.+.|+|.+
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~   72 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ   72 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5789998865 5799999999999999999999999999999965

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=90.72  E-value=0.37  Score=37.78  Aligned_cols=34  Identities=12%  Similarity=0.293  Sum_probs=31.8

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-++||..+|+....|.++|.+|+++|+|...
T Consensus       184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            3788999999999999999999999999999965

>TIGR00498 lexA SOS regulatory protein LexA

Probab=90.72  E-value=0.34  Score=37.56  Aligned_cols=45  Identities=9%  Similarity=0.166  Sum_probs=36.8

Q ss_pred             HHHHHHHHh----CC-CcCHHHHHHHhCCC-hHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVR----NP-CMKEDDICELLKFE-RKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~----~~-~i~dedLa~~l~i~-~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      --|+++|..    ++ ..+-.|||+.+|++ ..-+++.|..|.+.|+|...
T Consensus         9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~   59 (199)
T TIGR00498         9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD   59 (199)
T ss_pred             HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence            345666653    22 37789999999999 99999999999999999865

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.

>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]

Probab=90.39  E-value=0.78  Score=32.02  Aligned_cols=68  Identities=12%  Similarity=0.307  Sum_probs=46.9

Q ss_pred             CCCCcccccch-HHHHHHHHHHHHHcCCC----c------------hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHH
Q psy5744           4 SDEGYVHTEVP-TSLKQLSRLVVRGFYSI----E------------DSLIIDMLVRNPCMKEDDICELLKFERKMLRARI   66 (157)
Q Consensus         4 ~~~~~~~~~ip-~~~~~Lv~~v~R~Fy~~----e------------~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL   66 (157)
                      ..-+.+.+.|+ .++.+.|+.+.+-+|.+    +            ...++|..+.+..=...--|..|||+...+||-|
T Consensus        13 ~s~~~t~~~~~~~plRdsV~~~L~~Y~~~L~G~~v~~lY~mVL~evE~PLL~~vM~~~~gNQtrAa~mLGinR~TLRKKL   92 (98)
T COG2901          13 VSTPNSQDQITQKPLRDSVKQALKNYFADLNGQDVNDLYEMVLAEVEQPLLDMVMQYTRGNQTRAALMLGINRGTLRKKL   92 (98)
T ss_pred             ccccccCCccccccHHHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhHHHHHHHHHhcccHHHHHHHHcccHHHHHHHH
Confidence            34456677777 77888877777777653    2            3457777776544456677889999999999854


Q ss_pred             HHHhhCcc
Q psy5744          67 STLKNDKI   74 (157)
Q Consensus        67 ~~L~~d~L   74 (157)
                         ++.||
T Consensus        93 ---kqygl   97 (98)
T COG2901          93 ---KKYGL   97 (98)
T ss_pred             ---HHhCC
Confidence               44444

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

Probab=90.35  E-value=0.43  Score=32.36  Aligned_cols=30  Identities=17%  Similarity=0.340  Sum_probs=28.1

Q ss_pred             HHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          49 DDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+||+.+|+++.-+++++..|.+.|+|...
T Consensus         3 ~ela~~l~is~stvs~~l~~L~~~glI~r~   32 (96)
T smart00529        3 SEIAERLNVSPPTVTQMLKKLEKDGLVEYE   32 (96)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence            489999999999999999999999999865

iron dependent repressor

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=90.35  E-value=1.2  Score=34.98  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=39.4

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI   97 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I   97 (157)
                      ..++-++||+.|+++.+.||+.+..|.+-|++..+..-  +.-||.  .++|.+
T Consensus       177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~--~~~~~~--~~~~~~  226 (239)
T PRK10430        177 YEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHY--GVTGRP--VYRYRL  226 (239)
T ss_pred             CCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeec--cCCCCC--Ceeeec
Confidence            67899999999999999999999999999999876432  234444  455544

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=90.30  E-value=1.3  Score=34.45  Aligned_cols=67  Identities=9%  Similarity=0.052  Sum_probs=54.6

Q ss_pred             cchHHHHHHHHHHHHHcCCCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          12 EVPTSLKQLSRLVVRGFYSIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        12 ~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-+.+-..+-..++.|.-+..|--+-+++-  .+.++-+||++.+||+...|-..+.+|.+-+||...
T Consensus         6 qak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~   74 (177)
T COG1510           6 QAKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV   74 (177)
T ss_pred             HHHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence            3445566666667777877887776666663  578999999999999999999999999999999875

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=90.21  E-value=1.1  Score=34.86  Aligned_cols=52  Identities=15%  Similarity=0.298  Sum_probs=40.1

Q ss_pred             HHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCcee
Q psy5744          36 IIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQ   90 (157)
Q Consensus        36 IlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~   90 (157)
                      |+..+. .+  ..+-.+||+.||++.+.|++.+..|...|+++....=  +.-||..
T Consensus       167 Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~--~~~grp~  220 (225)
T PRK10046        167 VRKLFK-EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH--GKVGRPQ  220 (225)
T ss_pred             HHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec--CCCCCcC
Confidence            455444 33  4789999999999999999999999999999976432  2345554

>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B

Probab=90.13  E-value=0.16  Score=26.76  Aligned_cols=17  Identities=41%  Similarity=0.823  Sum_probs=15.2

Q ss_pred             eecCCCCCccchhhhhh
Q psy5744         130 FKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~~  146 (157)
                      |.|+.|++.|+..++..
T Consensus         2 ~~C~~C~~~F~~~~~l~   18 (27)
T PF13912_consen    2 FECDECGKTFSSLSALR   18 (27)
T ss_dssp             EEETTTTEEESSHHHHH
T ss_pred             CCCCccCCccCChhHHH
Confidence            89999999999988764

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

Probab=89.93  E-value=0.56  Score=33.50  Aligned_cols=44  Identities=11%  Similarity=0.133  Sum_probs=37.7

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      |.+-..+..++|-..||..+||+...-|++|..|++.|.|.-..
T Consensus        50 i~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvs   93 (107)
T COG4901          50 IRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVS   93 (107)
T ss_pred             HHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeec
Confidence            34444456799999999999999999999999999999998763

>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised

Probab=89.67  E-value=0.99  Score=30.21  Aligned_cols=47  Identities=26%  Similarity=0.360  Sum_probs=40.0

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHH--hhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTL--KNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L--~~d~Lv~~~   78 (157)
                      ..-.|+++|-+-+..+-++|++.+|+++-.+|-.|.-+  +..||.-..
T Consensus        11 Kqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s   59 (72)
T PF11994_consen   11 KQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTITS   59 (72)
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEe
Confidence            34678899888888899999999999999999999988  666776543

This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=89.53  E-value=8  Score=29.72  Aligned_cols=98  Identities=13%  Similarity=0.098  Sum_probs=64.7

Q ss_pred             HHHcCCCc-hHHHHHHHHhC-CCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeeeEe-----eee----c-------
Q psy5744          25 VRGFYSIE-DSLIIDMLVRN-PCMKEDDICELL--KFERKMLRARISTLKNDKIIQTRLR-----MET----G-------   84 (157)
Q Consensus        25 ~R~Fy~~e-~ivIlD~L~~~-~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~~~-----~e~----~-------   84 (157)
                      ...||+.= |.+|..++--. +.-..+.||+.+  +++..++|+.|..|.+-||++....     .+.    +       
T Consensus        17 ~~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~a   96 (171)
T PF14394_consen   17 EFEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEA   96 (171)
T ss_pred             HHHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHH
Confidence            34455554 45555544433 344899999999  9999999999999999999986321     000    0       


Q ss_pred             --------------------CCCceeEEEEEEecchhHHHHHHHHHHHHHHHHHHHHhh
Q psy5744          85 --------------------LDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERD  123 (157)
Q Consensus        85 --------------------~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~~L~~~~~~  123 (157)
                                          ++.|..+...--|+ +.-..-|+..|...++++-...+.
T Consensus        97 vr~~h~q~~~lA~~al~~~p~~~R~~s~~T~~vs-~~~~~ki~~~i~~fRk~i~~i~~~  154 (171)
T PF14394_consen   97 VRSYHKQMLELAQEALDRVPPEERDFSGLTMSVS-REDYEKIKKEIREFRKKIIAIAEE  154 (171)
T ss_pred             HHHHHHHHHHHHHHHHHhCCccccceeeeEEEeC-HHHHHHHHHHHHHHHHHHHHHHhc
Confidence                                12133334455666 345566777888888888877666

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=89.17  E-value=0.44  Score=31.27  Aligned_cols=29  Identities=14%  Similarity=0.193  Sum_probs=22.8

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhC
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKND   72 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d   72 (157)
                      ..-++++||+.|||+.++|+.++.....-
T Consensus        19 r~Pt~eEiA~~lgis~~~v~~~l~~~~~~   47 (78)
T PF04539_consen   19 REPTDEEIAEELGISVEEVRELLQASRRP   47 (78)
T ss_dssp             S--BHHHHHHHHTS-HHHHHHHHHHHSCC
T ss_pred             CCCCHHHHHHHHcccHHHHHHHHHhCCCC
Confidence            46789999999999999999999876543

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

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

Probab=88.71  E-value=0.72  Score=39.15  Aligned_cols=37  Identities=14%  Similarity=0.310  Sum_probs=34.3

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +..++-.|||++||++.-.|++.|.+.++.|+|+-.-
T Consensus        24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i   60 (321)
T COG2390          24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISI   60 (321)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEe
Confidence            4589999999999999999999999999999999763

>PRK05638 threonine synthase; Validated

Probab=88.63  E-value=1.5  Score=38.48  Aligned_cols=60  Identities=20%  Similarity=0.288  Sum_probs=47.3

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhC--CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLK--FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~--i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      ...||..|. ++.++=.||++.++  ++...|++.|..|+++|||..+.+     +|+   +.||.|+-..
T Consensus       373 r~~IL~~L~-~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~-----~g~---~~~Y~Lt~~g  434 (442)
T PRK05638        373 KLEILKILS-EREMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYR-----KGR---RVYYKLTEKG  434 (442)
T ss_pred             HHHHHHHHh-hCCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeec-----CCC---cEEEEECcHH
Confidence            466887766 55789999999998  899999999999999999987511     232   5588888543

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=88.43  E-value=0.3  Score=28.19  Aligned_cols=18  Identities=28%  Similarity=0.645  Sum_probs=14.7

Q ss_pred             eeecCCCCCccchhhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~~  146 (157)
                      .|.|+.||..|+.....+
T Consensus         5 ~y~C~~Cg~~fe~~~~~~   22 (41)
T smart00834        5 EYRCEDCGHTFEVLQKIS   22 (41)
T ss_pred             EEEcCCCCCEEEEEEecC
Confidence            689999999998776543

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>COG4738 Predicted transcriptional regulator [Transcription]

Probab=88.38  E-value=8  Score=28.25  Aligned_cols=105  Identities=14%  Similarity=0.181  Sum_probs=72.0

Q ss_pred             CCCCCcccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeee
Q psy5744           3 TSDEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRME   82 (157)
Q Consensus         3 ~~~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e   82 (157)
                      |.+.+.++++....+.++++.   .=..-.-...+-+|....+++--+|....|+-+-+|--++..|++.|-|..+.  +
T Consensus         2 ~~~~~~~l~E~e~~~ie~L~~---lgi~R~vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~--e   76 (124)
T COG4738           2 MEDNDMVLTEKEYEIIELLRI---LGIPRNVATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDERE--E   76 (124)
T ss_pred             CcccccccchhHHHHHHHHHH---cCCCchHHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccchHH--h
Confidence            344555666666666555543   33333334455566667899999999999999999999999999999999873  3


Q ss_pred             ecCCCceeEEEEEEec--chhHHHHHHHHHHHH
Q psy5744          83 TGLDGKAQKVNYYFIN--YQTFVNIVKYKLDVM  113 (157)
Q Consensus        83 ~~~~gk~~~~~yw~I~--y~~~~~vik~rl~~m  113 (157)
                      . ..|+++...+|.+.  .+.|++.+-..+.+=
T Consensus        77 K-KkGKGRPik~Y~Lt~~~~eIvs~iee~~~ke  108 (124)
T COG4738          77 K-KKGKGRPIKLYRLTVPFDEIVSEIEEEIIKE  108 (124)
T ss_pred             c-ccCCCCCceEEEecCcHHHHHHHHHHHHHHH
Confidence            3 25677777777754  555665555444433

>COG3388 Predicted transcriptional regulator [Transcription]

Probab=88.37  E-value=1.5  Score=30.93  Aligned_cols=78  Identities=12%  Similarity=0.174  Sum_probs=59.9

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeee-ecCCCceeEEEEEEecchhHHHHHHHHH
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRME-TGLDGKAQKVNYYFINYQTFVNIVKYKL  110 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e-~~~~gk~~~~~yw~I~y~~~~~vik~rl  110 (157)
                      .|+.|++.+++++.+-=--|+..+||+--.||=-|..|++.++++..+.-- .+++            ...++.-++-++
T Consensus        15 RHl~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~~iI~PS~~GAi~td~------------~~e~ie~i~~dl   82 (101)
T COG3388          15 RHLSVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQENIISPSRQGAILTDD------------FPEFIEEIIGDL   82 (101)
T ss_pred             HHHHHHHHHHHhCCceeEeechhcCCchhhhhhhhhhhhhcCccCccccCCccCcc------------HHHHHHHHHHHH
Confidence            388999999998877777899999999999999999999999998653110 1223            246777777888


Q ss_pred             HHHHHHHHHHH
Q psy5744         111 DVMRKRMEMEE  121 (157)
Q Consensus       111 ~~m~~~L~~~~  121 (157)
                      .++.++.++-.
T Consensus        83 ~ei~e~~~~i~   93 (101)
T COG3388          83 SEINEEAENIE   93 (101)
T ss_pred             HHHHHHHHHHH
Confidence            77777666543

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=88.29  E-value=1  Score=31.09  Aligned_cols=37  Identities=3%  Similarity=0.089  Sum_probs=34.4

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||-..|++++++...--|++|..|.+.|+++..
T Consensus        38 ~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V   74 (86)
T PRK09334         38 KEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY   74 (86)
T ss_pred             cCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence            4578999999999999999999999999999999865

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=88.23  E-value=1.5  Score=39.14  Aligned_cols=47  Identities=9%  Similarity=0.134  Sum_probs=41.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ..-||..|-.++.++-.+||+.+|++...|-+++..|...|||....
T Consensus         8 e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~   54 (489)
T PRK04172          8 EKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEE   54 (489)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEe
Confidence            45677787777889999999999999999999999999999999763

>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=88.19  E-value=1.5  Score=29.79  Aligned_cols=35  Identities=14%  Similarity=0.217  Sum_probs=32.8

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ...|.-.+||+.+++++--||-.+..|++.|||..
T Consensus        21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~   55 (78)
T PF03444_consen   21 GEPVGSKTIAEELGRSPATIRNEMADLEELGLVES   55 (78)
T ss_pred             CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence            46799999999999999999999999999999974

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

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

Probab=88.06  E-value=0.9  Score=27.14  Aligned_cols=31  Identities=13%  Similarity=0.160  Sum_probs=19.5

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      ..+..++|+.+|++.+.|++++....+.|+-
T Consensus        17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~   47 (50)
T PF13384_consen   17 GWSIREIAKRLGVSRSTVYRWIKRYREEGLE   47 (50)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHT--------
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHccccccc
Confidence            7899999999999999999999988887764

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=87.66  E-value=7.3  Score=26.97  Aligned_cols=80  Identities=11%  Similarity=0.133  Sum_probs=51.9

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FV  103 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~  103 (157)
                      ..||-.|. .+.++=-+|++.+        .++...+-.+|.+|+++|+|...... . ++  ...+.+|.|.-..  ..
T Consensus         7 ~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~-~-~~--~~~rk~y~iT~~Gr~~l   81 (100)
T TIGR03433         7 LLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGE-S-EN--NRRAKFYRLTAAGRKQL   81 (100)
T ss_pred             HHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeee-c-CC--CCCceEEEECHHHHHHH
Confidence            45565555 4567777777775        68888999999999999999986222 1 22  2335788888532  34


Q ss_pred             HHHHHHHHHHHHHHH
Q psy5744         104 NIVKYKLDVMRKRME  118 (157)
Q Consensus       104 ~vik~rl~~m~~~L~  118 (157)
                      +....+...+.+.+.
T Consensus        82 ~~~~~~~~~~~~~i~   96 (100)
T TIGR03433        82 AAETESWARLSAAIA   96 (100)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            444444444444444

Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein

>PRK12423 LexA repressor; Provisional

Probab=87.59  E-value=1.5  Score=34.33  Aligned_cols=33  Identities=18%  Similarity=0.345  Sum_probs=30.5

Q ss_pred             cCHHHHHHHhCC-ChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKF-ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i-~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|..|||+.+|+ ++.-+|+.|..|.+.|+|...
T Consensus        26 Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~   59 (202)
T PRK12423         26 PSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV   59 (202)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence            599999999995 889999999999999999874

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=87.41  E-value=1.9  Score=36.01  Aligned_cols=44  Identities=23%  Similarity=0.390  Sum_probs=37.3

Q ss_pred             HHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          36 IIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        36 IlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-.|-+.+.  +..-+|.+++|++...|-.+|..|++.|+|+.++
T Consensus         9 lir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rrk   54 (321)
T COG3888           9 LIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRK   54 (321)
T ss_pred             HHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeee
Confidence            3444555444  8999999999999999999999999999999875

>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins

Probab=87.19  E-value=1  Score=27.95  Aligned_cols=32  Identities=13%  Similarity=0.250  Sum_probs=24.2

Q ss_pred             HHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHH
Q psy5744          35 LIIDMLVRN--PCMKEDDICELLKFERKMLRARI   66 (157)
Q Consensus        35 vIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL   66 (157)
                      -+|..|...  ..++=.+||+.+|+++.+|||=|
T Consensus        16 r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl   49 (50)
T PF06971_consen   16 RYLEQLKEEGVERVSSQELAEALGITPAQVRKDL   49 (50)
T ss_dssp             HHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence            456666654  46999999999999999999854

These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=87.15  E-value=3.7  Score=29.84  Aligned_cols=48  Identities=19%  Similarity=0.245  Sum_probs=41.7

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhC-CChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLK-FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~-i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.=.++|+-.|.. +...=.+|...++ |+++.+-+-|..|+++|||...
T Consensus        22 ~kW~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~   70 (120)
T COG1733          22 GKWTLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERV   70 (120)
T ss_pred             CccHHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEee
Confidence            3345778877775 8889999999998 9999999999999999999976

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=86.94  E-value=1.5  Score=36.97  Aligned_cols=46  Identities=17%  Similarity=0.234  Sum_probs=40.8

Q ss_pred             HHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          20 LSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        20 Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |+-.+++.+|.+             .++-.|||++||++.-.|-|+|..=++.|+|+-.
T Consensus        17 l~~~vA~lYY~~-------------g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~   62 (318)
T PRK15418         17 LVARIAWFYYHD-------------GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQ   62 (318)
T ss_pred             HHHHHHHHHHhc-------------CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEE
Confidence            566777777755             7899999999999999999999999999999875

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=86.74  E-value=0.53  Score=28.41  Aligned_cols=22  Identities=14%  Similarity=0.255  Sum_probs=16.2

Q ss_pred             eeecCCCCCccchhhhhhccCCCCcccC
Q psy5744         129 SFKCPRCLKTFTDLEPCLLVLWCACPCK  156 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~  156 (157)
                      .|+|..||..++..      +.....||
T Consensus         2 ~Y~C~~Cg~~~~~~------~~~~irC~   23 (44)
T smart00659        2 IYICGECGRENEIK------SKDVVRCR   23 (44)
T ss_pred             EEECCCCCCEeecC------CCCceECC
Confidence            69999999998865      23456665

present in RNA polymerase I, II and III

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=86.68  E-value=2.3  Score=31.18  Aligned_cols=46  Identities=9%  Similarity=0.161  Sum_probs=37.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHH----hCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICEL----LKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~----l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-||..|-.++.++=.||.+.    .|+..+-|+.+|..|.+.|+|..+
T Consensus         6 E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~   55 (130)
T TIGR02698         6 EWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE   55 (130)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence            4568888887777887775554    489999999999999999999754

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.

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

Probab=86.43  E-value=1.7  Score=37.79  Aligned_cols=34  Identities=15%  Similarity=0.189  Sum_probs=32.1

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      .+.++.++|++.++++...++++|..|.+.|+|.
T Consensus       308 g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~  341 (412)
T PRK04214        308 GKALDVDEIRRLEPMGYDELGELLCELARIGLLR  341 (412)
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE
Confidence            3578999999999999999999999999999997

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=86.43  E-value=0.47  Score=25.11  Aligned_cols=12  Identities=33%  Similarity=0.794  Sum_probs=9.9

Q ss_pred             CCCeeecCCCCC
Q psy5744         126 SRSSFKCPRCLK  137 (157)
Q Consensus       126 ~~~~Y~Cp~C~~  137 (157)
                      ....|.||+||.
T Consensus        13 ~~v~f~CPnCG~   24 (24)
T PF07754_consen   13 QAVPFPCPNCGF   24 (24)
T ss_pred             cCceEeCCCCCC
Confidence            367899999984

It is likely to bind zinc via its four well-conserved cysteine residues.

>COG4860 Uncharacterized protein conserved in archaea [Function unknown]

Probab=86.40  E-value=8.1  Score=29.39  Aligned_cols=97  Identities=13%  Similarity=0.162  Sum_probs=66.1

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCC-ceeE--EE-------
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDG-KAQK--VN-------   93 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~g-k~~~--~~-------   93 (157)
                      +.++|-++-+-.++++|. .||+|--+|.+..|-   +-|+.|..|+..|++...=+.  +.+| +...  ++       
T Consensus        17 ifh~~~set~rKl~~aLs-tgW~T~~eiee~iG~---eg~RaL~iLkkagmlEtqWr~--p~~G~kPeKeYHtsYt~Vqi   90 (170)
T COG4860          17 IFHAADSETKRKLLLALS-TGWITLPEIEEKIGK---EGRRALLILKKAGMLETQWRT--PSNGQKPEKEYHTSYTNVQI   90 (170)
T ss_pred             HHHHcccHHHHHHHHHHh-hcceeHHHHHHHhch---hhHHHHHHHHhhcchhheeec--cCCCCCchhhhhhheeeEEE
Confidence            457888888899999988 889999999999994   557799999999999876443  2233 2111  11       


Q ss_pred             EEEecchhHHHHHH------HHHHHHHHHHHHHHhhcCC
Q psy5744          94 YYFINYQTFVNIVK------YKLDVMRKRMEMEERDATS  126 (157)
Q Consensus        94 yw~I~y~~~~~vik------~rl~~m~~~L~~~~~~~~~  126 (157)
                      =+++....+.|+|-      -.+....++|+..++....
T Consensus        91 Nf~~Sl~dL~dii~~~f~sdeev~ey~~ei~~l~e~g~t  129 (170)
T COG4860          91 NFMGSLSDLADIIYAAFLSDEEVKEYEDEIKALMEEGNT  129 (170)
T ss_pred             EEEEeHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCCc
Confidence            23444566666653      3455566667776665433

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=86.40  E-value=1.9  Score=35.44  Aligned_cols=46  Identities=22%  Similarity=0.421  Sum_probs=39.5

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEe
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLR   80 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~   80 (157)
                      ++...-.+++.++..|||..||+.+.-|--.+..|.++|+|..+-|
T Consensus        15 IL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR   60 (260)
T COG1497          15 ILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGR   60 (260)
T ss_pred             HHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCC
Confidence            3444445789999999999999999999999999999999987543

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=86.38  E-value=0.29  Score=35.40  Aligned_cols=25  Identities=20%  Similarity=0.550  Sum_probs=21.7

Q ss_pred             HHHHHhhcCCCCeeecCCCCCccch
Q psy5744         117 MEMEERDATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       117 L~~~~~~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      ++.+..++....||.|.+||.+|.+
T Consensus        88 ~QtRsaDEp~T~Fy~C~~Cg~~wre  112 (113)
T COG1594          88 LQTRSADEPETRFYKCTRCGYRWRE  112 (113)
T ss_pred             eehhccCCCceEEEEecccCCEeec
Confidence            5677788889999999999999875

>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]

Probab=86.31  E-value=2.8  Score=32.93  Aligned_cols=44  Identities=9%  Similarity=0.160  Sum_probs=35.0

Q ss_pred             HHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          49 DDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      |.|+..-||=.+.|.-+|+.|-+||+|+.+    .    =+++.+||.+...
T Consensus        32 EkLGSKK~IVl~tVKd~lQqlVDDgvV~~E----K----~GtsN~YWsF~s~   75 (209)
T COG5124          32 EKLGSKKQIVLMTVKDLLQQLVDDGVVSVE----K----CGTSNIYWSFKSQ   75 (209)
T ss_pred             HHhccccccHHHHHHHHHHHHhhcCceeee----e----eccceeEEecchH
Confidence            556677788889999999999999999965    2    1255889998864

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

Probab=86.05  E-value=1.7  Score=29.51  Aligned_cols=37  Identities=11%  Similarity=0.301  Sum_probs=26.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      +.++..|.....++-++||..+|.+..+|+.+|..+-
T Consensus        27 r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p   63 (77)
T PF12324_consen   27 RPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP   63 (77)
T ss_dssp             HHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence            4466666666789999999999999999999998774

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.

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=85.70  E-value=0.41  Score=29.69  Aligned_cols=20  Identities=20%  Similarity=0.424  Sum_probs=15.2

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|+|-+||+.++.+.+.
T Consensus         3 ~~~~Y~C~~Cg~~~~~~~~~   22 (49)
T COG1996           3 AMMEYKCARCGREVELDQET   22 (49)
T ss_pred             ceEEEEhhhcCCeeehhhcc
Confidence            35689999999999555444

>PHA02591 hypothetical protein; Provisional

Probab=85.42  E-value=2  Score=29.23  Aligned_cols=41  Identities=20%  Similarity=0.203  Sum_probs=30.3

Q ss_pred             HHcCCCc--hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744          26 RGFYSIE--DSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS   67 (157)
Q Consensus        26 R~Fy~~e--~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~   67 (157)
                      |-|.+.+  -+-+.-.|. ...+|-++||..||++.+.||+.|.
T Consensus        39 ryfi~~~dd~~~vA~eL~-eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         39 RYFVESEDDLISVTHELA-RKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             EEEEeccchHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4555533  334444444 5578999999999999999999985

>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=85.10  E-value=2.2  Score=25.38  Aligned_cols=30  Identities=17%  Similarity=0.213  Sum_probs=22.1

Q ss_pred             HHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744          37 IDMLVRNPCMKEDDICELLKFERKMLRARIS   67 (157)
Q Consensus        37 lD~L~~~~~i~dedLa~~l~i~~k~vRkiL~   67 (157)
                      +-.|...| ++-.+||+.+|++...|.++|.
T Consensus        14 i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   14 IKELYAEG-MSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence            33455577 9999999999999999999875

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 ....

>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region

Probab=85.01  E-value=1.4  Score=32.15  Aligned_cols=55  Identities=9%  Similarity=0.177  Sum_probs=41.2

Q ss_pred             HHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          20 LSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        20 Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++.++.+ ...++.+.++   .+-..++|.||..++-+...||.+|..|.+-|||..-
T Consensus        30 ~lkLll~s-~n~~G~L~~~---~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~   84 (119)
T TIGR01714        30 WLKLLLLS-LNDGGCIYLN---ELAPYNAEMLATMFNRNVGDIRITLQTLESLGLIEKK   84 (119)
T ss_pred             HHHHHHHH-hcCCCEEEEc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34555555 5555554443   2335689999999999999999999999999999853

This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.

>PHA00626 hypothetical protein

Probab=84.89  E-value=0.53  Score=30.03  Aligned_cols=16  Identities=13%  Similarity=0.237  Sum_probs=14.1

Q ss_pred             CCeeecCCCCCccchh
Q psy5744         127 RSSFKCPRCLKTFTDL  142 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~l  142 (157)
                      +..|+||.||-.||-+
T Consensus        21 snrYkCkdCGY~ft~~   36 (59)
T PHA00626         21 SDDYVCCDCGYNDSKD   36 (59)
T ss_pred             CcceEcCCCCCeechh
Confidence            5789999999999864

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=84.82  E-value=0.64  Score=28.83  Aligned_cols=9  Identities=67%  Similarity=1.364  Sum_probs=5.7

Q ss_pred             eeecCCCCC
Q psy5744         129 SFKCPRCLK  137 (157)
Q Consensus       129 ~Y~Cp~C~~  137 (157)
                      .|.||-|++
T Consensus         2 ~f~CP~C~~   10 (54)
T PF05605_consen    2 SFTCPYCGK   10 (54)
T ss_pred             CcCCCCCCC
Confidence            456666666

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

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

Probab=84.80  E-value=2.5  Score=31.30  Aligned_cols=43  Identities=7%  Similarity=0.122  Sum_probs=38.4

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |+++.=.||-+|-.|++..+|.+.+.+++.+..|.+.|-|-.+
T Consensus        17 IvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~   59 (127)
T PF06163_consen   17 IVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRH   59 (127)
T ss_pred             HHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence            6666566999999999999999999999999999999988654

>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length

Probab=84.71  E-value=0.58  Score=24.76  Aligned_cols=17  Identities=29%  Similarity=0.534  Sum_probs=14.9

Q ss_pred             eecCCCCCccchhhhhh
Q psy5744         130 FKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~~  146 (157)
                      |.|+.|++.|+...+..
T Consensus         2 ~~C~~C~k~f~~~~~~~   18 (27)
T PF12171_consen    2 FYCDACDKYFSSENQLK   18 (27)
T ss_dssp             CBBTTTTBBBSSHHHHH
T ss_pred             CCcccCCCCcCCHHHHH
Confidence            78999999999988765

The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.

>KOG2907|consensus

Probab=84.38  E-value=0.5  Score=34.27  Aligned_cols=27  Identities=22%  Similarity=0.668  Sum_probs=20.6

Q ss_pred             HHHHHHHhhcCCCCeeecCCCCCccch
Q psy5744         115 KRMEMEERDATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       115 ~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      ..++-|-.+|....||.||+|+.+|+.
T Consensus        88 ~T~QlRSADEGQTVFYTC~kC~~k~~e  114 (116)
T KOG2907|consen   88 HTLQLRSADEGQTVFYTCPKCKYKFTE  114 (116)
T ss_pred             hhhhcccccCCceEEEEcCccceeeec
Confidence            345556667777889999999998875

>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]

Probab=84.37  E-value=1.6  Score=39.03  Aligned_cols=59  Identities=17%  Similarity=0.400  Sum_probs=47.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +-.++.++..++.+|-.+|++.+|++.+.+++.|..|...|++++.     ++.|    .-+|||...
T Consensus       404 ~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~-----g~~~----~g~~~v~~~  462 (467)
T COG2865         404 QEKILELIKENGKVTARELREILGISSETIRRRIANLVKRGLLKQL-----GSSG----RGTWYVKGE  462 (467)
T ss_pred             HHHHHHHHhhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHh-----CcCC----CCcEEecCC
Confidence            3567777778899999999999999999999999999999999864     2222    346777654

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=84.21  E-value=2.2  Score=32.95  Aligned_cols=37  Identities=16%  Similarity=0.176  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhhh
Q psy5744         106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +..+-.++-+++.++++   ++..|+||.||...-- ++..
T Consensus       114 ~Ek~H~~~~~~~Le~~~---~~~~~vC~vCGy~~~g-e~P~  150 (166)
T COG1592         114 AEKRHAEMFRGLLERLE---EGKVWVCPVCGYTHEG-EAPE  150 (166)
T ss_pred             HHHHHHHHHHHHHHhhh---cCCEEEcCCCCCcccC-CCCC
Confidence            33444444455555443   4449999999977665 5543

>COG5340 Predicted transcriptional regulator [Transcription]

Probab=84.12  E-value=0.81  Score=37.28  Aligned_cols=35  Identities=20%  Similarity=0.286  Sum_probs=33.1

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      |+.+|=+|.|+.+|+++|.+|++++.|++.|.+..
T Consensus        28 hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeR   62 (269)
T COG5340          28 HKIITIRDVAETLEVAPNTLRELASRLEKKGWLER   62 (269)
T ss_pred             CceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhh
Confidence            68999999999999999999999999999999864

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=84.10  E-value=0.76  Score=28.06  Aligned_cols=15  Identities=27%  Similarity=0.804  Sum_probs=12.1

Q ss_pred             eeecCCCCCccchhh
Q psy5744         129 SFKCPRCLKTFTDLE  143 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~ld  143 (157)
                      .|.|+.||.+|..+.
T Consensus         5 ey~C~~Cg~~fe~~~   19 (52)
T TIGR02605         5 EYRCTACGHRFEVLQ   19 (52)
T ss_pred             EEEeCCCCCEeEEEE
Confidence            588999998888763

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=84.06  E-value=0.33  Score=28.62  Aligned_cols=21  Identities=14%  Similarity=0.445  Sum_probs=16.5

Q ss_pred             HHhhcCCCCeeecCCCCCccc
Q psy5744         120 EERDATSRSSFKCPRCLKTFT  140 (157)
Q Consensus       120 ~~~~~~~~~~Y~Cp~C~~~Ys  140 (157)
                      +-.++....+|+|.+|+.+|.
T Consensus        19 RsaDE~mT~fy~C~~C~~~w~   39 (40)
T smart00440       19 RSADEPMTVFYVCTKCGHRWR   39 (40)
T ss_pred             cCCCCCCeEEEEeCCCCCEeC
Confidence            344666778999999999875

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=83.91  E-value=3.5  Score=37.04  Aligned_cols=49  Identities=8%  Similarity=0.110  Sum_probs=42.1

Q ss_pred             hHHHHHHHHhCCC-cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744          33 DSLIIDMLVRNPC-MKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM   81 (157)
Q Consensus        33 ~ivIlD~L~~~~~-i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~   81 (157)
                      ..-||..|..++. ++-++||+.+|++...|..++..|...|+|....+.
T Consensus         5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~   54 (492)
T PLN02853          5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIK   54 (492)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence            3567788876664 899999999999999999999999999999987544

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=83.84  E-value=0.95  Score=27.20  Aligned_cols=28  Identities=29%  Similarity=0.462  Sum_probs=17.4

Q ss_pred             CCCCeeecCCCCCccchhhhhhccCCCCcccC
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPCLLVLWCACPCK  156 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~~L~d~~~F~C~  156 (157)
                      .=..+++||.||.+    .+..|-+...|.|.
T Consensus        14 RW~~g~~CP~Cg~~----~~~~~~~~~~~~C~   41 (46)
T PF12760_consen   14 RWPDGFVCPHCGST----KHYRLKTRGRYRCK   41 (46)
T ss_pred             cCCCCCCCCCCCCe----eeEEeCCCCeEECC
Confidence            34556899999985    33333334566664

It may be a zinc-binding beta ribbon domain that could bind DNA.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=83.79  E-value=1.6  Score=29.75  Aligned_cols=36  Identities=6%  Similarity=0.059  Sum_probs=32.4

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHH
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARIS   67 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~   67 (157)
                      +.+..|++.|.. +.++=.|||+..|++...|++.|.
T Consensus         6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~   41 (80)
T TIGR02844         6 ERVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT   41 (80)
T ss_pred             HHHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence            356789999999 999999999999999999999773

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

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles

Probab=83.77  E-value=7.2  Score=25.31  Aligned_cols=40  Identities=23%  Similarity=0.347  Sum_probs=30.5

Q ss_pred             CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          56 KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        56 ~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      .++...|-.+|.+|.++|+|.......  ++  ...+.+|.|.-
T Consensus        28 ~i~~g~lY~~L~~Le~~gli~~~~~~~--~~--~~~rk~Y~iT~   67 (75)
T PF03551_consen   28 KISPGSLYPALKRLEEEGLIESRWEEE--GN--GRPRKYYRITE   67 (75)
T ss_dssp             ETTHHHHHHHHHHHHHTTSEEEEEEEE--TT--SSEEEEEEESH
T ss_pred             ccChhHHHHHHHHHHhCCCEEEeeecc--CC--CCCCEEEEECH
Confidence            577889999999999999999884432  23  35567888764

In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....

>PHA00616 hypothetical protein

Probab=83.69  E-value=0.27  Score=29.80  Aligned_cols=13  Identities=31%  Similarity=0.797  Sum_probs=11.1

Q ss_pred             eecCCCCCccchh
Q psy5744         130 FKCPRCLKTFTDL  142 (157)
Q Consensus       130 Y~Cp~C~~~Ys~l  142 (157)
                      |.||+||..|...
T Consensus         2 YqC~~CG~~F~~~   14 (44)
T PHA00616          2 YQCLRCGGIFRKK   14 (44)
T ss_pred             CccchhhHHHhhH
Confidence            8899999998754

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=83.21  E-value=7.3  Score=30.42  Aligned_cols=30  Identities=10%  Similarity=0.169  Sum_probs=27.7

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      ++-+|||..+|+....|.++|.+|++.|+.
T Consensus       174 ~t~~~iA~~lG~tretvsR~l~~L~~~gl~  203 (236)
T PRK09392        174 YEKRVLASYLGMTPENLSRAFAALASHGVH  203 (236)
T ss_pred             CCHHHHHHHhCCChhHHHHHHHHHHhCCeE
Confidence            457899999999999999999999999974

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

Probab=83.13  E-value=4.1  Score=24.13  Aligned_cols=28  Identities=11%  Similarity=0.334  Sum_probs=24.6

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKN   71 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~   71 (157)
                      +.++..++|+.+|++.+.|+..+..+..
T Consensus        14 ~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170          14 EGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4579999999999999999999987654

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

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=83.11  E-value=2.5  Score=34.85  Aligned_cols=44  Identities=9%  Similarity=0.018  Sum_probs=39.0

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|.|.|- .+..|-++||+.+|+++.-++++|..|..-|++...
T Consensus        13 Lglfd~L~-~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~   56 (306)
T TIGR02716        13 LDLFSHMA-EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLE   56 (306)
T ss_pred             cCcHHHHh-cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEec
Confidence            34788876 578999999999999999999999999999999853

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.

>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=83.04  E-value=2.2  Score=28.52  Aligned_cols=41  Identities=20%  Similarity=0.314  Sum_probs=33.9

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN   71 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~   71 (157)
                      .....++..|+.++.++=+++|+.++++...+++.+..+.+
T Consensus        16 s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~   56 (87)
T PF05043_consen   16 SLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNK   56 (87)
T ss_dssp             SHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44678898999899999999999999999999999998875

The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.

>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]

Probab=82.99  E-value=0.36  Score=30.92  Aligned_cols=19  Identities=32%  Similarity=0.754  Sum_probs=14.2

Q ss_pred             hcCCCCeeecCCCCCccch
Q psy5744         123 DATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       123 ~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      ......++.||+|+.-|..
T Consensus        11 ~RDGE~~lrCPRC~~~FR~   29 (65)
T COG4049          11 DRDGEEFLRCPRCGMVFRR   29 (65)
T ss_pred             ccCCceeeeCCchhHHHHH
Confidence            3345679999999987753

>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins

Probab=82.55  E-value=2.6  Score=27.07  Aligned_cols=35  Identities=14%  Similarity=0.321  Sum_probs=28.9

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.+.-..+|.+.|+....+-.+|.+|+..|++.++
T Consensus         3 g~lvas~iAd~~GiTRSvIVNALRKleSaGvIesr   37 (61)
T PF08222_consen    3 GRLVASKIADRVGITRSVIVNALRKLESAGVIESR   37 (61)
T ss_dssp             EEE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             ceehHHHHHHHhCccHHHHHHHHHHHHhcCceeec
Confidence            34667789999999999999999999999999976

CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=82.53  E-value=1.6  Score=30.43  Aligned_cols=26  Identities=31%  Similarity=0.612  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHhhcCCCCeeecCCCCCcc
Q psy5744         109 KLDVMRKRMEMEERDATSRSSFKCPRCLKTF  139 (157)
Q Consensus       109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Y  139 (157)
                      .+.++.++++....     ..|.||.||+.=
T Consensus        20 slRK~vkkie~~q~-----~ky~Cp~Cgk~~   45 (90)
T PF01780_consen   20 SLRKRVKKIEISQH-----AKYTCPFCGKTS   45 (90)
T ss_dssp             HHHHHHHHHHHHHH-----S-BEESSSSSSE
T ss_pred             HHHHHHHHHHHHHh-----CCCcCCCCCCce
Confidence            35566666666553     479999998753

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>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=82.46  E-value=3.3  Score=29.35  Aligned_cols=46  Identities=13%  Similarity=0.213  Sum_probs=39.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||+.|-.++.++=.||.+.++    +..+.|+.+|..|.+.|+|+..
T Consensus         5 E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~   54 (115)
T PF03965_consen    5 ELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTRE   54 (115)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEe
Confidence            467999999887899999988885    5699999999999999999975

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 ....

>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1

Probab=82.40  E-value=3.6  Score=28.37  Aligned_cols=39  Identities=13%  Similarity=0.206  Sum_probs=31.0

Q ss_pred             HHHHHHHhCCCcCHHHHH--HHhCCChHHHHHHHHHHhhCc
Q psy5744          35 LIIDMLVRNPCMKEDDIC--ELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa--~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      .++|.|+.++.+++||.-  ..-.-++..+|+++.-+..-|
T Consensus        19 plLD~Ll~n~~it~E~y~~V~a~~T~qdkmRkLld~v~akG   59 (85)
T cd08324          19 CLVDNLLKNDYFSTEDAEIVCACPTQPDKVRKILDLVQSKG   59 (85)
T ss_pred             HHHHHHhccCCccHHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence            589999999999988754  445889999999998655443

Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom

>KOG3623|consensus

Probab=82.38  E-value=0.88  Score=42.69  Aligned_cols=35  Identities=26%  Similarity=0.573  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccch
Q psy5744         102 FVNIVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       102 ~~~vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      .-.+.|||     ..|++-++--.+..-|.||+|++|||-
T Consensus       287 CgKAFKfK-----HHLKEHlRIHSGEKPfeCpnCkKRFSH  321 (1007)
T KOG3623|consen  287 CGKAFKFK-----HHLKEHLRIHSGEKPFECPNCKKRFSH  321 (1007)
T ss_pred             cchhhhhH-----HHHHhhheeecCCCCcCCccccccccc
Confidence            33455555     457888888888899999999999974

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=82.07  E-value=4.6  Score=36.37  Aligned_cols=49  Identities=18%  Similarity=0.320  Sum_probs=41.9

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM   81 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~   81 (157)
                      ...||..|-. .+.++-++||+.+|++...|..++..|...|+|....+.
T Consensus         8 e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~   57 (494)
T PTZ00326          8 ENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKK   57 (494)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence            3457777776 467889999999999999999999999999999987543

>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type

Probab=81.93  E-value=0.84  Score=24.08  Aligned_cols=15  Identities=27%  Similarity=0.600  Sum_probs=11.5

Q ss_pred             eecCCCCCccchhhh
Q psy5744         130 FKCPRCLKTFTDLEP  144 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda  144 (157)
                      ..||.||++|...-.
T Consensus         3 ~~C~~CgR~F~~~~l   17 (25)
T PF13913_consen    3 VPCPICGRKFNPDRL   17 (25)
T ss_pred             CcCCCCCCEECHHHH
Confidence            469999999965543

>PRK00215 LexA repressor; Validated

Probab=81.65  E-value=4.1  Score=31.62  Aligned_cols=34  Identities=12%  Similarity=0.241  Sum_probs=31.5

Q ss_pred             CcCHHHHHHHhCC-ChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKF-ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i-~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+-.|||+.+|+ +..-+.++|..|.+.|+|...
T Consensus        23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~   57 (205)
T PRK00215         23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRD   57 (205)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeC
Confidence            5789999999999 999999999999999999754

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=81.63  E-value=2.3  Score=28.52  Aligned_cols=33  Identities=12%  Similarity=0.112  Sum_probs=29.4

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      ...+|=.|||+.||++.+.|+..+..+.+.|.+
T Consensus        30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~   62 (73)
T TIGR03879        30 EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL   62 (73)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence            367899999999999999999999998877654

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

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

Probab=81.56  E-value=6.9  Score=31.65  Aligned_cols=43  Identities=14%  Similarity=0.304  Sum_probs=36.8

Q ss_pred             HHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |+++|-. ....|-|++|+.+|++.-.+||.|..|...+++..+
T Consensus       163 i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~  206 (224)
T COG4565         163 VREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE  206 (224)
T ss_pred             HHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence            4444442 467999999999999999999999999999999876

>PRK13239 alkylmercury lyase; Provisional

Probab=81.41  E-value=3  Score=33.34  Aligned_cols=38  Identities=8%  Similarity=0.156  Sum_probs=33.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      ++-|+..|.+...++-++||..+|.+..+|+++|..|-
T Consensus        24 ~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~   61 (206)
T PRK13239         24 LVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP   61 (206)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence            46688888877889999999999999999999999875

>PF13518 HTH_28: Helix-turn-helix domain

Probab=81.37  E-value=4.9  Score=23.75  Aligned_cols=41  Identities=12%  Similarity=0.211  Sum_probs=33.1

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |+.... ++. +=.++|..+|++...|++.+....+.|+..-.
T Consensus         5 iv~~~~-~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~   45 (52)
T PF13518_consen    5 IVELYL-EGE-SVREIAREFGISRSTVYRWIKRYREGGIEGLK   45 (52)
T ss_pred             HHHHHH-cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhc
Confidence            444444 455 99999999999999999999999998875443

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=81.19  E-value=1.1  Score=25.12  Aligned_cols=14  Identities=29%  Similarity=0.736  Sum_probs=9.1

Q ss_pred             eecCCCCCccchhh
Q psy5744         130 FKCPRCLKTFTDLE  143 (157)
Q Consensus       130 Y~Cp~C~~~Ys~ld  143 (157)
                      |+|+.||-.|+..+
T Consensus         2 ~~C~~CGy~y~~~~   15 (33)
T cd00350           2 YVCPVCGYIYDGEE   15 (33)
T ss_pred             EECCCCCCEECCCc
Confidence            67777776666544

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=81.18  E-value=4.1  Score=31.22  Aligned_cols=49  Identities=16%  Similarity=0.267  Sum_probs=39.6

Q ss_pred             CCchHHHHHHHHhC----C--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRN----P--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~----~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |....-|+-+|+.+    +  .++..+||+.+|++...|.+.+..|.+.+++...
T Consensus        54 g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~  108 (165)
T PF05732_consen   54 GNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI  108 (165)
T ss_pred             chhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence            44556666666643    2  4789999999999999999999999999999753

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>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=81.09  E-value=2.5  Score=27.27  Aligned_cols=23  Identities=30%  Similarity=0.322  Sum_probs=21.2

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHH
Q psy5744          43 NPCMKEDDICELLKFERKMLRAR   65 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRki   65 (157)
                      +|.++--|||+.||++.+.||+=
T Consensus        20 ~g~i~lkdIA~~Lgvs~~tIr~W   42 (60)
T PF10668_consen   20 NGKIKLKDIAEKLGVSESTIRKW   42 (60)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHH
Confidence            68999999999999999999974

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 [].

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=81.01  E-value=0.79  Score=34.04  Aligned_cols=17  Identities=24%  Similarity=0.530  Sum_probs=12.5

Q ss_pred             CCeeecCCCCCccchhh
Q psy5744         127 RSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~ld  143 (157)
                      ...|.|+.||..|+..+
T Consensus        68 p~~~~C~~CG~~~~~~~   84 (135)
T PRK03824         68 EAVLKCRNCGNEWSLKE   84 (135)
T ss_pred             ceEEECCCCCCEEeccc
Confidence            35678888888887764

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=80.91  E-value=2.3  Score=36.54  Aligned_cols=36  Identities=14%  Similarity=0.173  Sum_probs=32.4

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .-+ ++.+||+.+|++...||+++..|..+|+|..+.
T Consensus        27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~   63 (431)
T PRK15481         27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQG   63 (431)
T ss_pred             CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            445 789999999999999999999999999998753

>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=80.49  E-value=6.4  Score=36.97  Aligned_cols=73  Identities=19%  Similarity=0.271  Sum_probs=55.3

Q ss_pred             CCCcccccchHHHHHHHHHHHHHcCCCc------------------------------------hHHHHHHHHhCCCcCH
Q psy5744           5 DEGYVHTEVPTSLKQLSRLVVRGFYSIE------------------------------------DSLIIDMLVRNPCMKE   48 (157)
Q Consensus         5 ~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e------------------------------------~ivIlD~L~~~~~i~d   48 (157)
                      .++.+...+|+.+...+...-. ||...                                    ..+|++.+-.+.+++=
T Consensus       547 sp~~~~~~lP~~l~p~le~f~~-~Y~sKhngRkL~W~~hLg~~evkarf~~~~~~~~is~~s~~q~~vfll~n~~e~lt~  625 (773)
T COG5647         547 SPEEVSIRLPKELVPILEGFKK-FYSSKHNGRKLKWYWHLGSGEVKARFNEGQKYLEISTFSVYQLLVFLLFNDHEELTF  625 (773)
T ss_pred             CccccccCCChHHHHHHHHHHH-HHHHhccCceEEeeeccccEEEEeeccCCccceehhHHHHHHHHHHHHhcCccceeH
Confidence            4567777888877776666543 33322                                    2335555456789999


Q ss_pred             HHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          49 DDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        49 edLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |+|.+.++++..++-.+|+.|...+++.-.
T Consensus       626 eei~e~T~l~~~dl~~~L~sl~~ak~~~l~  655 (773)
T COG5647         626 EEILELTKLSTDDLKRVLQSLSCAKLVVLL  655 (773)
T ss_pred             HHHHhhcCCChhhHHHHHHHHHhhheeeec
Confidence            999999999999999999999999998765

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=80.28  E-value=1.7  Score=28.68  Aligned_cols=35  Identities=9%  Similarity=0.125  Sum_probs=25.9

Q ss_pred             CCcCHHHH---HHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCMKEDDI---CELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i~dedL---a~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++++=-+|   .+.+|++.+-+|-.|..|..+|++...
T Consensus        19 ~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~   56 (70)
T PF07848_consen   19 GWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESE   56 (70)
T ss_dssp             S-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             CceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeee
Confidence            45555544   455699999999999999999999976

PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=80.12  E-value=1.1  Score=33.60  Aligned_cols=14  Identities=29%  Similarity=0.819  Sum_probs=11.8

Q ss_pred             CCCeeecCCCCCcc
Q psy5744         126 SRSSFKCPRCLKTF  139 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Y  139 (157)
                      ...||.||.||+-|
T Consensus       121 ~~~f~~C~~C~kiy  134 (147)
T PF01927_consen  121 YDEFWRCPGCGKIY  134 (147)
T ss_pred             CCeEEECCCCCCEe
Confidence            45699999999987

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	157
1vd4_A	62	Solution Structure Of The Zinc Finger Domain Of Tfi		3e-05

>pdb|1VD4|A Chain A, Solution Structure Of The Zinc Finger Domain Of Tfiie Alpha Length = 62

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/28 (67%), Positives = 24/28 (85%)
Query: 116 RMEMEERDATSRSSFKCPRCLKTFTDLE 143
           R+E +ERD+T+R+SFKCP C  TFTDLE
Sbjct: 1   RIETDERDSTNRASFKCPVCSSTFTDLE 28

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	157
1vd4_A	62	Transcription initiation factor IIE, alpha subunit	2e-07

>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 62

 Score = 44.9 bits (106), Expect = 2e-07
 Identities = 19/28 (67%), Positives = 24/28 (85%)

Query: 116 RMEMEERDATSRSSFKCPRCLKTFTDLE 143
           R+E +ERD+T+R+SFKCP C  TFTDLE
Sbjct: 1   RIETDERDSTNRASFKCPVCSSTFTDLE 28

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
2xub_A	534	DNA-directed RNA polymerase III subunit RPC3; tran	99.26
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	99.08
3r0a_A	123	Putative transcriptional regulator; structural gen	98.09
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.92
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.87
2kko_A	108	Possible transcriptional regulatory protein (possi	97.8
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.74
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.72
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	97.72
3jth_A	98	Transcription activator HLYU; transcription factor	97.72
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	97.7
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.65
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	97.64
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	97.54
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.49
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.44
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	97.39
2nnn_A	140	Probable transcriptional regulator; structural gen	97.38
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.31
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.3
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	97.28
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	97.28
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	97.2
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.19
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	97.17
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.15
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.05
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.04
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.02
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	97.01
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	97.0
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.98
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.98
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	96.96
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	96.95
2xub_A	534	DNA-directed RNA polymerase III subunit RPC3; tran	96.92
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.9
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.89
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.88
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.87
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.87
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.85
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.84
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.79
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	96.78
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.76
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.74
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.74
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.71
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.68
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	96.66
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.65
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	96.64
2vn2_A	128	DNAD, chromosome replication initiation protein; D	96.64
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.64
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.61
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.58
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.54
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.53
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.51
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.44
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.43
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.43
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.42
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.42
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	96.4
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	96.4
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.4
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.4
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.38
2w25_A	150	Probable transcriptional regulatory protein; trans	96.37
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.35
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.34
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	96.33
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	96.29
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.28
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	96.22
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.22
1ylf_A	149	RRF2 family protein; structural genomics, transcri	96.21
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	96.2
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.19
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	96.19
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.18
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	96.18
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.18
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.17
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.13
3nqo_A	189	MARR-family transcriptional regulator; structural	96.13
3k69_A	162	Putative transcription regulator; putative transcr	96.05
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.05
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.05
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.0
3f3x_A	144	Transcriptional regulator, MARR family, putative;	96.0
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	95.99
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.99
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.98
3bja_A	139	Transcriptional regulator, MARR family, putative;	95.98
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	95.98
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.94
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.92
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.87
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.86
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.83
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	95.79
1xd7_A	145	YWNA; structural genomics, protein structure initi	95.78
2e72_A	49	POGO transposable element with ZNF domain; zinc fi	95.76
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	95.75
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.74
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	95.72
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.7
2h09_A	155	Transcriptional regulator MNTR; transcription regu	95.68
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.67
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	95.65
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	95.61
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.59
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	95.54
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	95.54
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	95.54
4g6q_A	182	Putative uncharacterized protein; structural genom	95.53
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.51
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.51
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.48
3by6_A	126	Predicted transcriptional regulator; structural ge	95.45
2fxa_A	207	Protease production regulatory protein HPR; protea	95.44
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.43
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	95.43
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	95.41
3c7j_A	237	Transcriptional regulator, GNTR family; structural	95.39
1xma_A	145	Predicted transcriptional regulator; southea colla	95.36
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	95.31
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	95.3
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	95.3
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	95.23
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.2
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	95.17
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	95.15
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	95.12
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	95.03
3qph_A	342	TRMB, A global transcription regulator; transcript	94.95
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	94.91
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	94.82
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	94.79
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.78
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	94.75
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	94.72
4esf_A	117	PADR-like transcriptional regulator; PADR family,	94.7
2pg4_A	95	Uncharacterized protein; structural genomics, join	94.68
3eet_A	272	Putative GNTR-family transcriptional regulator; st	94.6
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	94.54
2w57_A	150	Ferric uptake regulation protein; gene regulation,	94.53
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	94.51
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	94.47
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	94.46
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	94.46
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	94.42
1okr_A	123	MECI, methicillin resistance regulatory protein ME	94.21
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	94.19
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	94.19
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	93.97
1hsj_A	487	Fusion protein consisting of staphylococcus access	93.94
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.82
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	93.82
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	93.79
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	93.76
1vd4_A	62	Transcription initiation factor IIE, alpha subunit	93.71
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	93.69
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	93.66
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	93.65
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	93.59
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	93.58
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	93.55
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	93.52
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	93.48
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.34
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.3
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	93.29
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	93.21
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	93.05
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	93.03
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	93.01
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	92.97
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	92.96
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	92.92
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	92.9
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	92.81
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	92.75
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	92.65
1bia_A	321	BIRA bifunctional protein; transcription regulatio	92.58
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	92.58
3b02_A	195	Transcriptional regulator, CRP family; structural	92.53
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	92.51
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	92.51
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	92.5
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	92.4
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	92.35
2dql_A	115	PEX protein; circadian clock associated protein, c	92.1
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	92.04
3elk_A	117	Putative transcriptional regulator TA0346; structu	92.02
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	91.99
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	91.97
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	91.82
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	91.75
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	91.75
2k9l_A	76	RNA polymerase sigma factor RPON; protein, transcr	91.67
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	91.67
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	91.58
1ft9_A	222	Carbon monoxide oxidation system transcription reg	91.47
2g7u_A	257	Transcriptional regulator; ICLR family, structural	91.41
2o0m_A	345	Transcriptional regulator, SORC family; structural	91.4
1z05_A	429	Transcriptional regulator, ROK family; structural	91.32
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	91.25
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	91.24
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	91.22
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	91.17
2obp_A	96	Putative DNA-binding protein; structural genomics,	91.13
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	91.1
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	90.96
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	90.85
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	90.84
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	90.62
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	90.57
1bja_A	95	Transcription regulatory protein MOTA; activation	90.55
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	90.37
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	90.19
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	90.1
3mjh_B	34	Early endosome antigen 1; protein-zinc finger comp	90.08
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	90.0
2ra5_A	247	Putative transcriptional regulator; beta structure	89.95
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	89.72
2kvh_A	27	Zinc finger and BTB domain-containing protein 32;	89.57
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	89.56
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	89.46
2i5o_A	39	DNA polymerase ETA; zinc finger, DNA polymerase,PO	89.37
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	89.36
1znf_A	27	31ST zinc finger from XFIN; zinc finger DNA bindin	89.12
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	89.11
2kvf_A	28	Zinc finger and BTB domain-containing protein 32;	89.11
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	89.07
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	88.82
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	88.6
2kvg_A	27	Zinc finger and BTB domain-containing protein 32;	88.47
1p7a_A	37	BF3, BKLF, kruppel-like factor 3; classical zinc f	88.42
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	88.35
2m0d_A	30	Zinc finger and BTB domain-containing protein 17;	88.09
1ard_A	29	Yeast transcription factor ADR1; transcription reg	88.03
1rik_A	29	E6APC1 peptide; E6-binding domain, zinc finger, hu	88.0
2el5_A	42	Zinc finger protein 268; alternative splicing, DNA	87.93
2eof_A	44	Zinc finger protein 268; ZF-C2H2, structural genom	87.73
2elx_A	35	Zinc finger protein 406; ZFAT zinc finger 1, struc	87.68
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	87.6
2m0f_A	29	Zinc finger and BTB domain-containing protein 17;	87.58
2lvu_A	26	Zinc finger and BTB domain-containing protein 17;	87.41
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	87.37
2emb_A	44	Zinc finger protein 473; ZF-C2H2, structural genom	87.36
2eoj_A	44	Zinc finger protein 268; ZF-C2H2, structural genom	87.31
2en3_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	87.29
2els_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	86.97
2ytp_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	86.86
1srk_A	35	Zinc finger protein ZFPM1; classical zinc finger,	86.65
2eor_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	86.64
2elm_A	37	Zinc finger protein 406; ZFAT zinc finger 1, struc	86.53
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	86.51
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	86.46
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	86.27
2elo_A	37	Zinc finger protein 406; ZFAT zinc finger 1, struc	86.22
2eon_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	86.19
2en7_A	44	Zinc finger protein 268; ZF-C2H2, structural genom	86.12
2elt_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	86.12
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	86.1
2m0e_A	29	Zinc finger and BTB domain-containing protein 17;	85.96
1paa_A	30	Yeast transcription factor ADR1; transcription reg	85.95
2elv_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	85.9
2emg_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	85.86
2eoz_A	46	Zinc finger protein 473; ZF-C2H2, structural genom	85.84
2elq_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	85.83
2elr_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	85.81
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	85.8
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	85.78
2en9_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	85.5
2ytf_A	46	Zinc finger protein 268; ZF-C2H2, structural genom	85.44
2epc_A	42	Zinc finger protein 32; zinc finger domain, C2H2,	85.32
2ema_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	85.24
1rim_A	33	E6APC2 peptide; E6-binding domain, zinc finger, hu	85.22
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	85.19
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	85.18
2lvt_A	29	Zinc finger and BTB domain-containing protein 17;	85.35
2ytg_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	85.02
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	85.01
2ytn_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	84.98
2yti_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	84.93
2eq1_A	46	Zinc finger protein 347; C2H2, zinc finger domain,	84.92
2elp_A	37	Zinc finger protein 406; ZFAT zinc finger 1, struc	84.9
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	84.88
2kfq_A	32	FP1; protein, de novo protein; NMR {Synthetic}	84.77
2eou_A	44	Zinc finger protein 473; ZF-C2H2, structural genom	84.62
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	84.58
2yte_A	42	Zinc finger protein 473; ZF-C2H2, structural genom	84.54
2eq3_A	46	Zinc finger protein 347; C2H2, zinc finger domain,	84.53
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	84.44
1klr_A	30	Zinc finger Y-chromosomal protein; transcription;	84.41
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	84.41
2ytb_A	42	Zinc finger protein 32; zinc-finger domain, C2H2,	84.32
2lvr_A	30	Zinc finger and BTB domain-containing protein 17;	84.58
2en2_A	42	B-cell lymphoma 6 protein; ZF-C2H2, structural gen	84.07
2ysp_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	83.84
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	83.82
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	83.81
2adr_A	60	ADR1; transcription regulation, zinc finger,; NMR	83.78
1fv5_A	36	First zinc finger of U-shaped; CCHC, protein inter	83.77
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	83.76
1bbo_A	57	Human enhancer-binding protein MBP-1; DNA-binding	83.49
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	83.42
2epu_A	45	Zinc finger protein 32; C2H2, zinc finger domain,	83.41
1njq_A	39	Superman protein; zinc-finger, peptide-zinc comple	83.34
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	83.31
2emi_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	83.29
2en6_A	46	Zinc finger protein 268; ZF-C2H2, structural genom	83.15
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	83.14
2enf_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	83.02
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	82.94
2eos_A	42	B-cell lymphoma 6 protein; ZF-C2H2, structural gen	82.87
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	82.74
2ept_A	41	Zinc finger protein 32; C2H2, zinc finger domain,	82.73
2em0_A	46	Zinc finger protein 224; DNA-binding, metal-bindin	82.71
1x4s_A	59	Protein FON, zinc finger HIT domain containing pro	82.69
2eow_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	82.59
3uk3_C	57	Zinc finger protein 217; transcription factor, DNA	82.46
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	82.44
1bm9_A	122	RTP, TER, replication terminator protein; DNA-bind	82.42
2epv_A	44	Zinc finger protein 268; C2H2, zinc finger domain,	82.4
3eqx_A	373	FIC domain containing transcriptional regulator; F	82.36
2eoy_A	46	Zinc finger protein 473; ZF-C2H2, structural genom	82.26
2ep3_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	82.21
2yu5_A	44	Zinc finger protein 473; ZF-C2H2 domain, structura	82.15
2yto_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.97
2yts_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.97
2emj_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	81.94
2yrj_A	46	Zinc finger protein 473; C2H2-type zinc finger, st	81.75
2ene_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	81.71
2ytj_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.7
2eml_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	81.69
2emh_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.69
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	81.56
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	81.53
2em4_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	81.47
2eme_A	46	Zinc finger protein 473; ZF-C2H2, structural genom	81.45
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	81.37
2emx_A	44	Zinc finger protein 268; ZF-C2H2, structural genom	81.31
2eoo_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	81.31
2ep2_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.27
1f2i_G	73	Fusion of N-terminal 17-MER peptide extension to Z	81.24
2em7_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	81.24
1x6e_A	72	Zinc finger protein 24; ZNF24, KOX17, ZNF191, zsca	81.21
2emf_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	81.01
2eq0_A	46	Zinc finger protein 347; C2H2, zinc finger domain,	80.91
2eov_A	46	Zinc finger protein 484; ZF-C2H2, structural genom	80.87
2qm3_A	373	Predicted methyltransferase; putative methyltransf	80.85
2em3_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	80.83
2epw_A	46	Zinc finger protein 268; C2H2, zinc finger domain,	80.73
2em9_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.73
2el4_A	46	Zinc finger protein 268; alternative splicing, DNA	80.64
2em6_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.58
2eox_A	44	Zinc finger protein 473; ZF-C2H2, structural genom	80.52
2em5_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	80.46
2yu8_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	80.39
2ytk_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	80.32
1x5w_A	70	Zinc finger protein 64, isoforms 1; ZNF338, nuclea	80.16
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	80.15
2eop_A	46	Zinc finger protein 268; ZF-C2H2, structural genom	80.15
2yth_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.07

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S

Probab=99.26  E-value=9.5e-12  Score=109.43  Aligned_cols=111  Identities=7%  Similarity=0.076  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744          18 KQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI   97 (157)
Q Consensus        18 ~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I   97 (157)
                      ...+..++..-||++++-|+..|..++.++|++||+..+|+.|++|++|++|.++|+|.++....+...+.+|+.|+|++
T Consensus       347 ~~~ie~ii~~~~G~~a~RI~r~L~~~~~l~d~~ia~~a~i~~k~vR~~Ly~L~~~g~v~~qevp~~~d~~~~~~~ylW~~  426 (534)
T 2xub_A          347 TATLESVVQERFGSRCARIFRLVLQKKHIEQKQVEDFAMIPAKEAKDMLYKMLSENFMSLQEIPKTPDHAPSRTFYLYTV  426 (534)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHHC---CHHHHHHHHCSCHHHHHHHHHHHHHTTCC---------------------C
T ss_pred             HHHHHHHHHHHhChHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEccCCCCCCCcceEEEEEE
Confidence            45566778888999999999999999999999999999999999999999999999999985433222235688999999


Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy5744          98 NYQTFVNIVKYKLDVMRKRMEMEERDATSRS  128 (157)
Q Consensus        98 ~y~~~~~vik~rl~~m~~~L~~~~~~~~~~~  128 (157)
                      |.+.+...+..++.+...+|..+++.+.++.
T Consensus       427 ~~~~~~~~l~~~~~k~l~nl~~Rl~~E~~~~  457 (534)
T 2xub_A          427 NILSAARMLLHRCYKSIANLIERRQFETKEN  457 (534)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999988875543

>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=99.08  E-value=2.6e-10  Score=79.81  Aligned_cols=102  Identities=12%  Similarity=0.190  Sum_probs=67.4

Q ss_pred             HHHHHHHHcCCCchHHHHHHHHhCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          20 LSRLVVRGFYSIEDSLIIDMLVRNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        20 Lv~~v~R~Fy~~e~ivIlD~L~~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      .+..++...+++...-|+..|...| .++..+||+.+|++...||++|..|.++|+|...... . ++ +++..++|.++
T Consensus         7 ~~~~~~~~~~~~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~~~~-~-~~-~g~~v~~~~~~   83 (110)
T 1q1h_A            7 LFINLAKSLLGDDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTR-D-KD-SGWFIYYWKPN   83 (110)
T ss_dssp             HHHHHHHTTSCSTTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC------CCCCEEEEECT
T ss_pred             HHHHHHHHHcChHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecc-c-CC-CceEEEEeecC
Confidence            4567788888988899999998655 7999999999999999999999999999999876432 2 33 45667789999


Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHhhc
Q psy5744          99 YQTFVNIVKYKLDVMRKRMEMEERDA  124 (157)
Q Consensus        99 y~~~~~vik~rl~~m~~~L~~~~~~~  124 (157)
                      .+.+.+.+..++.+..+++..++..+
T Consensus        84 ~~~i~~~~~~~~~~~~e~l~~~l~~e  109 (110)
T 1q1h_A           84 IDQINEILLNRKRLILDKLKTRLEYE  109 (110)
T ss_dssp             HHHHC---------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999999998887664

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

Probab=98.09  E-value=7.1e-05  Score=53.22  Aligned_cols=91  Identities=18%  Similarity=0.291  Sum_probs=69.5

Q ss_pred             CchHHHHHHHHhCCC--cCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHH
Q psy5744          31 IEDSLIIDMLVRNPC--MKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKY  108 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~--i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~  108 (157)
                      +....|+.+|..++.  ++-.+||+.+|++...|.+.|..|.+.|+|......   .+++.....|.-.+...+...++.
T Consensus        26 ~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~~~---~d~~~~~~~y~~~~~~~~~~~i~~  102 (123)
T 3r0a_A           26 KADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRSQQN---LDGGGYVYIYKIYSKNQIRNIIQK  102 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEE---CTTSCEEEEEEECCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeCCc---cCCCcceEEEecCCHHHHHHHHHH
Confidence            445778999997765  999999999999999999999999999999976332   232233333445677778888888


Q ss_pred             HHHHHHHHHHHHHhhc
Q psy5744         109 KLDVMRKRMEMEERDA  124 (157)
Q Consensus       109 rl~~m~~~L~~~~~~~  124 (157)
                      .+....+.+.+.++.-
T Consensus       103 ~~~~~~~~~~~~l~~~  118 (123)
T 3r0a_A          103 IVQSWADRLGQELKEW  118 (123)
T ss_dssp             HHHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            8888777777766544

>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=97.92  E-value=0.00028  Score=47.40  Aligned_cols=87  Identities=16%  Similarity=0.168  Sum_probs=62.2

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHH
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYK  109 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~r  109 (157)
                      ++....|+..|..++.++-.+||+.+|++...|.++|..|.+.|+|.....    ++++ ....+-...-..+...+...
T Consensus        19 ~~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~----~~~r-~~~~~~t~~g~~~~~~~~~~   93 (109)
T 1sfx_A           19 KPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV----EKGW-VGYIYSAEKPEKVLKEFKSS   93 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE----ESSS-EEEEEEECCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee----cCCc-eEEEEecCcHHHHHHHHHHH
Confidence            555678899988888899999999999999999999999999999986522    1322 22223333445566666666


Q ss_pred             HHHHHHHHHHHH
Q psy5744         110 LDVMRKRMEMEE  121 (157)
Q Consensus       110 l~~m~~~L~~~~  121 (157)
                      +..+.+.+.+.+
T Consensus        94 ~~~~~~~~~~~l  105 (109)
T 1sfx_A           94 ILGEIERIEKMF  105 (109)
T ss_dssp             HHHHHHHHHTTS
T ss_pred             HHHHHHHHHHhc
Confidence            666665555443

>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=97.87  E-value=3.2e-05  Score=51.75  Aligned_cols=43  Identities=9%  Similarity=0.095  Sum_probs=40.4

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChH-HHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERK-MLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k-~vRkiL~~L~~d~Lv~~   77 (157)
                      .|+++|..++..+-.+||+.||++.. .||+.|+.|+++|+|..
T Consensus        15 ~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~   58 (79)
T 1xmk_A           15 KICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYR   58 (79)
T ss_dssp             HHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEe
Confidence            57888889999999999999999998 99999999999999984

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=97.80  E-value=0.00032  Score=48.57  Aligned_cols=83  Identities=17%  Similarity=0.213  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEE
Q psy5744          17 LKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYF   96 (157)
Q Consensus        17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~   96 (157)
                      .-.-+..+.+++-++--.-|+.+|. ++.++-.|||+.+|+++..|.+.|..|++.|+|..+.      +|+   ..||+
T Consensus        11 ~~~~~~~~~~al~~~~r~~IL~~L~-~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~------~gr---~~~y~   80 (108)
T 2kko_A           11 LLDQVARVGKALANGRRLQILDLLA-QGERAVEAIATATGMNLTTASANLQALKSGGLVEARR------EGT---RQYYR   80 (108)
T ss_dssp             HHHHHHHHHHHHTTSTTHHHHHHHT-TCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE------ETT---EEEEE
T ss_pred             hHHHHHHHHHHhCCHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE------eCC---EEEEE
Confidence            3334555677777777778888876 5788999999999999999999999999999998752      232   35788


Q ss_pred             ecchhHHHHHHHH
Q psy5744          97 INYQTFVNIVKYK  109 (157)
Q Consensus        97 I~y~~~~~vik~r  109 (157)
                      ++.+.+..++.+=
T Consensus        81 l~~~~~~~l~~~l   93 (108)
T 2kko_A           81 IAGEDVARLFALV   93 (108)
T ss_dssp             ESCHHHHHHHHHH
T ss_pred             EChHHHHHHHHHH
Confidence            9987665555443

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

Probab=97.74  E-value=0.00025  Score=47.32  Aligned_cols=73  Identities=14%  Similarity=0.293  Sum_probs=57.2

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHH
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFV  103 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~  103 (157)
                      +.+++.++...-|+..|..++.++-.|||+.+|+++..|.+.|..|.+.|+|....      +|+   ..+|.++.+.+.
T Consensus        17 ~~~~l~~~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~------~~r---~~~y~l~~~~~~   87 (99)
T 3cuo_A           17 LLKAMSHPKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQR------DAQ---RILYSIKNEAVN   87 (99)
T ss_dssp             HHHHHCSHHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE------CSS---CEEEEECCHHHH
T ss_pred             HHHHhCChHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe------cCC---EEEEEEChHHHH
Confidence            34455666678899888777789999999999999999999999999999998651      233   457788866544


Q ss_pred             HH
Q psy5744         104 NI  105 (157)
Q Consensus       104 ~v  105 (157)
                      .+
T Consensus        88 ~l   89 (99)
T 3cuo_A           88 AI   89 (99)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=97.72  E-value=5.6e-05  Score=50.64  Aligned_cols=45  Identities=16%  Similarity=0.184  Sum_probs=40.8

Q ss_pred             HHHHHHHHhCC---CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNP---CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~---~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      --|+++|..++   .++-.+||+.||++.+.|++.|++|+++|+|...
T Consensus        13 ~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~   60 (81)
T 1qbj_A           13 QRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   60 (81)
T ss_dssp             HHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            34788888888   8999999999999999999999999999999754

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=97.72  E-value=0.00023  Score=47.88  Aligned_cols=83  Identities=13%  Similarity=0.219  Sum_probs=56.8

Q ss_pred             CchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHH
Q psy5744          31 IEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYK  109 (157)
Q Consensus        31 ~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~r  109 (157)
                      +....++..|+. ++.++-.|||+.+|++...|+++|..|.+.|+|......   .++.+....+|.++. .+...+.-.
T Consensus        21 ~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~~---~~~~gr~~~~~~l~~-~~~~~~~~~   96 (109)
T 2d1h_A           21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE---GKKIGRPKYYYSISS-NILEKIRND   96 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC----------CCEEEEECT-THHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeeccc---cCCCCCCCeeeecCH-HHHHHHHHH
Confidence            445566666665 788999999999999999999999999999999875321   232233346677775 555555555


Q ss_pred             HHHHHHHH
Q psy5744         110 LDVMRKRM  117 (157)
Q Consensus       110 l~~m~~~L  117 (157)
                      +....+.+
T Consensus        97 ~~~~~~~~  104 (109)
T 2d1h_A           97 LLNCAKRM  104 (109)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55544443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=97.72  E-value=0.00017  Score=48.64  Aligned_cols=77  Identities=17%  Similarity=0.372  Sum_probs=60.1

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +..+.+++-++-...|+..|.. +.++=.|||+.+|+++..|.+.|..|.+.|+|..+      .+|+   ..||.++.+
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~------~~g~---~~~y~l~~~   82 (98)
T 3jth_A           13 AVVLLKAMANERRLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTR------KEAQ---TVYYTLKSE   82 (98)
T ss_dssp             HHHHHHHHCSHHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE------CCTT---CCEEEECCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE------EeCC---EEEEEECHH
Confidence            4455677777777889988775 88999999999999999999999999999999865      1233   357888876


Q ss_pred             hHHHHHH
Q psy5744         101 TFVNIVK  107 (157)
Q Consensus       101 ~~~~vik  107 (157)
                      .+...+.
T Consensus        83 ~~~~l~~   89 (98)
T 3jth_A           83 EVKAMIK   89 (98)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5544443

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=97.70  E-value=0.00023  Score=53.06  Aligned_cols=94  Identities=10%  Similarity=0.059  Sum_probs=75.8

Q ss_pred             CCCcccccchHHHHHHHHHHHHHcCCCchHHHHHHHHhCC--CcCHHHHHHHhC-CChHHHHHHHHHHhhCcceeeeEee
Q psy5744           5 DEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNP--CMKEDDICELLK-FERKMLRARISTLKNDKIIQTRLRM   81 (157)
Q Consensus         5 ~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~--~i~dedLa~~l~-i~~k~vRkiL~~L~~d~Lv~~~~~~   81 (157)
                      ++++.-++.+..|.. .+....++-++--..|+..|+.++  ..+-++|++.++ +++.-|++.|..|.+.|||......
T Consensus         4 ~~~~~~~~~~~~f~~-~~~~~~~l~~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~~   82 (151)
T 3u1d_A            4 MATQDRGERPNGFGD-ELERRRFVLHETRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVDELVDRGIVEKIPVP   82 (151)
T ss_dssp             CCSCBTTBCCTTHHH-HHHHHHHHCCHHHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             cccccCCCCchhHHH-HHHHHHHhcchHHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeecC
Confidence            344556677888988 888888999998899999999864  488899999999 9999999999999999999987432


Q ss_pred             eecCCCceeEEEEEEecch
Q psy5744          82 ETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        82 e~~~~gk~~~~~yw~I~y~  100 (157)
                      . +..++.....||.+.-.
T Consensus        83 ~-~~~~rGrP~k~Y~LT~~  100 (151)
T 3u1d_A           83 R-AKSVDDPPTTFYAVTGE  100 (151)
T ss_dssp             C-CTTSSSCCCEEEEECHH
T ss_pred             c-CcccCCCCceEEEECHH
Confidence            2 22335677889999854

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=97.65  E-value=0.00033  Score=47.59  Aligned_cols=77  Identities=13%  Similarity=0.211  Sum_probs=60.8

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +..+.+++-++-...|+..|. ++.++=.|||+.+|+++..|.+.|..|.+.|||..+.      +|+   ..||.++.+
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~-~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~------~g~---~~~y~l~~~   82 (102)
T 3pqk_A           13 VANLLKTLSHPVRLMLVCTLV-EGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRR------NIK---QIFYRLTEA   82 (102)
T ss_dssp             HHHHHHHHCSHHHHHHHHHHH-TCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEEC------SSS---CCEEEECSS
T ss_pred             HHHHHHHcCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE------eCC---EEEEEECcH
Confidence            344567777777888999885 5779999999999999999999999999999998651      333   358889987


Q ss_pred             hHHHHHH
Q psy5744         101 TFVNIVK  107 (157)
Q Consensus       101 ~~~~vik  107 (157)
                      .+..++.
T Consensus        83 ~~~~~~~   89 (102)
T 3pqk_A           83 KAAQLVN   89 (102)
T ss_dssp             THHHHHH
T ss_pred             HHHHHHH
Confidence            5555443

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=97.64  E-value=0.00084  Score=46.06  Aligned_cols=78  Identities=12%  Similarity=0.208  Sum_probs=61.0

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +..+.+++-++-..-|+..|. ++.++-.|||+.+|+++..|.+.|..|++.|+|..++   .   |+   ..||.++.+
T Consensus        16 ~~~~~~~l~~~~r~~IL~~L~-~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~---~---gr---~~~y~l~~~   85 (106)
T 1r1u_A           16 VTEIFKALGDYNRIRIMELLS-VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR---Q---GQ---SMIYSLDDI   85 (106)
T ss_dssp             HHHHHHHTCSHHHHHHHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE---E---TT---EEEEEESSH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE---e---CC---EEEEEEChH
Confidence            334566776666778888887 6778999999999999999999999999999998752   2   32   468889977


Q ss_pred             hHHHHHHH
Q psy5744         101 TFVNIVKY  108 (157)
Q Consensus       101 ~~~~vik~  108 (157)
                      .+...+..
T Consensus        86 ~~~~~~~~   93 (106)
T 1r1u_A           86 HVATMLKQ   93 (106)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            66555543

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=97.54  E-value=0.00038  Score=49.21  Aligned_cols=80  Identities=15%  Similarity=0.203  Sum_probs=62.2

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +..+.+++-++-..-|+..|..++.++=.+||+.+|+++..|.+.|..|++.|+|..+      .+|+   ..||.++.+
T Consensus        32 ~~~~~~al~~~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~------~~gr---~~~y~l~~~  102 (122)
T 1u2w_A           32 VSQILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR------KEGK---LALYSLGDE  102 (122)
T ss_dssp             HHHHHHHHHSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-------------CCEEEESCH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE------EECC---EEEEEECHH
Confidence            3455666666666789998887888999999999999999999999999999999864      1232   458889987


Q ss_pred             hHHHHHHHH
Q psy5744         101 TFVNIVKYK  109 (157)
Q Consensus       101 ~~~~vik~r  109 (157)
                      .+...+.+=
T Consensus       103 ~~~~~~~~l  111 (122)
T 1u2w_A          103 HIRQIMMIA  111 (122)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            776666553

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

Probab=97.49  E-value=0.0012  Score=45.17  Aligned_cols=73  Identities=11%  Similarity=0.094  Sum_probs=57.2

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      ..+.+++-++-...|+..| .++.++-.|||+.+|+++..|.+.|..|.+.|+|....   .   |+   ..+|.+....
T Consensus        12 ~~~~~~l~~~~r~~IL~~L-~~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~---~---gr---~~~y~l~~~~   81 (114)
T 2oqg_A           12 ASVFAALSDETRWEILTEL-GRADQSASSLATRLPVSRQAIAKHLNALQACGLVESVK---V---GR---EIRYRALGAE   81 (114)
T ss_dssp             HHHHHHTTCHHHHHHHHHH-HHSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEE---E---TT---EEEEEECSHH
T ss_pred             HHHHHHhCChHHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEe---c---CC---EEEEEechHH
Confidence            3455666566667888888 67789999999999999999999999999999998651   1   33   5678888765


Q ss_pred             HHH
Q psy5744         102 FVN  104 (157)
Q Consensus       102 ~~~  104 (157)
                      +..
T Consensus        82 ~~~   84 (114)
T 2oqg_A           82 LNK   84 (114)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

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

Probab=97.44  E-value=0.00023  Score=46.75  Aligned_cols=44  Identities=23%  Similarity=0.256  Sum_probs=40.3

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+++|..++.++-.|||+.+|++...|++.|..|.+.|+|...
T Consensus         4 ~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            4 EILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            47788887888999999999999999999999999999999854

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=97.39  E-value=0.00012  Score=49.29  Aligned_cols=44  Identities=9%  Similarity=0.187  Sum_probs=39.5

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      --|+++|.+++ ++=.+||+.||++...||+.|++|+++|+|.+.
T Consensus        20 ~~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           20 CEAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            34777777677 999999999999999999999999999999874

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

Probab=97.38  E-value=0.0032  Score=43.89  Aligned_cols=93  Identities=11%  Similarity=0.065  Sum_probs=59.0

Q ss_pred             CCCCCCCcccccchHHHHHHHHHH---HHHcC----CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744           1 MSTSDEGYVHTEVPTSLKQLSRLV---VRGFY----SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus         1 ~~~~~~~~~~~~ip~~~~~Lv~~v---~R~Fy----~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      |.+++.......+...+..+.+.+   ....+    +.....||..|..++.++-.+||+.+|++...|.+++..|.+.|
T Consensus         1 mp~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~g   80 (140)
T 2nnn_A            1 MSRTTPYRLDDQIGFILRQANQRYAALFANGIGNGLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRG   80 (140)
T ss_dssp             ------CCGGGCHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTT
T ss_pred             CCCCcccchhhhHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            444444444444444444433322   22222    23357788888888899999999999999999999999999999


Q ss_pred             ceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          74 IIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        74 Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      +|....   . +.  .....++.+.-
T Consensus        81 lv~r~~---~-~~--d~R~~~~~lT~  100 (140)
T 2nnn_A           81 LIQRSA---D-PD--DGRRLLVSLSP  100 (140)
T ss_dssp             CEEEEE---E-TT--EEEEEEEEECH
T ss_pred             CEEeeC---C-CC--CCCeeeeEECH
Confidence            998641   2 21  23345666664

>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=97.31  E-value=0.00022  Score=47.02  Aligned_cols=45  Identities=16%  Similarity=0.184  Sum_probs=40.7

Q ss_pred             HHHHHHHHhCC---CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNP---CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~---~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -.|+++|..++   .+|-.+||+.+|++...|++.|++|+++|+|...
T Consensus        17 ~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~   64 (77)
T 1qgp_A           17 QRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   64 (77)
T ss_dssp             HHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            45778888777   8999999999999999999999999999999754

>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=97.30  E-value=0.0022  Score=42.58  Aligned_cols=70  Identities=14%  Similarity=0.022  Sum_probs=55.4

Q ss_pred             HHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          26 RGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        26 R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      +++-++-...|+..|..++.++-.+||+.+|+++..|.+.|..|.+.|+|.....  . .+|   ...+|.+....
T Consensus        11 ~~l~~~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~--~-~~~---r~~~~~lt~~g   80 (100)
T 1ub9_A           11 HILGNPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKV--I-ADR---PRTVVEITDFG   80 (100)
T ss_dssp             HHHHSHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEE--C-SSS---CEEEEEECHHH
T ss_pred             cccCChHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec--C-CCc---ceEEEEECHHH
Confidence            4555666788999988788899999999999999999999999999999987521  1 232   25677787553

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=97.28  E-value=0.0011  Score=46.46  Aligned_cols=76  Identities=12%  Similarity=0.163  Sum_probs=60.3

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      ..+.+++-++--.-|+..|. ++.++-.|||+.+|+++..|.+.|..|.+.|||..+.   .   |   ...||.++.+.
T Consensus         9 ~~~~~al~~~~R~~Il~~L~-~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~---~---g---r~~~y~l~~~~   78 (118)
T 3f6o_A            9 NGIFQALADPTRRAVLGRLS-RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHK---Q---G---RVRTCAIEKEP   78 (118)
T ss_dssp             HHHHHHHTSHHHHHHHHHHH-TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEE---E---T---TEEEEEECSHH
T ss_pred             HHHHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEe---c---C---CEEEEEECHHH
Confidence            34566777777788999887 6788999999999999999999999999999999752   1   2   24678899766


Q ss_pred             HHHHHH
Q psy5744         102 FVNIVK  107 (157)
Q Consensus       102 ~~~vik  107 (157)
                      +..+..
T Consensus        79 ~~~l~~   84 (118)
T 3f6o_A           79 FTAVEA   84 (118)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555443

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=97.28  E-value=0.00099  Score=45.30  Aligned_cols=75  Identities=16%  Similarity=0.320  Sum_probs=58.9

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF  102 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~  102 (157)
                      .+.+++-++-..-|+..|+.++.++=.|||+.+|+++..+.+.|..|++. +|..++      +|+   ..||.++.+.+
T Consensus        19 ~~~~aL~~~~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~------~gr---~~~y~l~~~~~   88 (99)
T 2zkz_A           19 ELLKTMAHPMRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNR------QGL---EIYYSINNPKV   88 (99)
T ss_dssp             HHHHHHCSHHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEE------ETT---EEEEECCCHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheE------eCc---EEEEEEChHHH
Confidence            34455556666778888887888999999999999999999999999999 998651      233   36889998776


Q ss_pred             HHHHH
Q psy5744         103 VNIVK  107 (157)
Q Consensus       103 ~~vik  107 (157)
                      ...+.
T Consensus        89 ~~~~~   93 (99)
T 2zkz_A           89 EGIIK   93 (99)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65554

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=97.20  E-value=0.0051  Score=43.43  Aligned_cols=82  Identities=12%  Similarity=0.221  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEE
Q psy5744          17 LKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYF   96 (157)
Q Consensus        17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~   96 (157)
                      ...-+..+.+++.++...-|+..|. ++.++=.+||+.+|+++..|.+.|..|++.|+|..++   .   |+   ..||.
T Consensus        32 ~~~~~~~~~kaL~~~~rl~IL~~L~-~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~---~---gr---~~~y~  101 (122)
T 1r1t_A           32 VAQSLAEFFAVLADPNRLRLLSLLA-RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK---Q---GR---HVYYQ  101 (122)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE---E---TT---EEEEE
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE---e---CC---EEEEE
Confidence            3344566777887777778888876 5778999999999999999999999999999998752   2   32   35788


Q ss_pred             ecchhHHHHHHH
Q psy5744          97 INYQTFVNIVKY  108 (157)
Q Consensus        97 I~y~~~~~vik~  108 (157)
                      ++-+.+...++.
T Consensus       102 l~~~~l~~~~~~  113 (122)
T 1r1t_A          102 LQDHHIVALYQN  113 (122)
T ss_dssp             ESSHHHHHHHHH
T ss_pred             EChHHHHHHHHH
Confidence            887765555443

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

Probab=97.19  E-value=0.0062  Score=43.80  Aligned_cols=47  Identities=11%  Similarity=0.174  Sum_probs=43.2

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        53 ~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   99 (162)
T 3cjn_A           53 AKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRRE   99 (162)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            36778888888889999999999999999999999999999999865

>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=97.15  E-value=0.0011  Score=44.50  Aligned_cols=55  Identities=18%  Similarity=0.205  Sum_probs=47.6

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+.+++.++-...|+++|  ++.++-.|||+.+|++...|++.|..|.+.|+|...
T Consensus        22 ~~~~~~l~~~~r~~Il~~L--~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~   76 (96)
T 1y0u_A           22 KRYNYAVTNPVRRKILRML--DKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERV   76 (96)
T ss_dssp             HHHHHHHSCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHhCCHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3466677777777899988  567999999999999999999999999999999854

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

Probab=97.05  E-value=0.0082  Score=43.78  Aligned_cols=46  Identities=11%  Similarity=0.117  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        47 ~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   92 (168)
T 2nyx_A           47 QFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRL   92 (168)
T ss_dssp             HHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            5678888888889999999999999999999999999999999865

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

Probab=97.04  E-value=0.00084  Score=42.86  Aligned_cols=43  Identities=14%  Similarity=0.199  Sum_probs=38.6

Q ss_pred             HHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -||++|-.+ +.++-.|||+.+|++...|.++|..|+++|+|..
T Consensus        14 ~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           14 KILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            588888765 5799999999999999999999999999999864

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

Probab=97.02  E-value=0.0044  Score=43.87  Aligned_cols=46  Identities=2%  Similarity=0.132  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        44 ~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   89 (150)
T 2rdp_A           44 QFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARV   89 (150)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            5778888888889999999999999999999999999999999865

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=97.01  E-value=0.0052  Score=42.13  Aligned_cols=72  Identities=14%  Similarity=0.156  Sum_probs=55.5

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ..+...+-+.-.+.||..|. ++.++=.|||+.+ |+++..+-+.|..|++.|||..+.  .. .|   ....+|++.-.
T Consensus         5 ~~~l~~l~~~~~~~IL~~L~-~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~--~~-~d---~r~~~y~LT~~   77 (107)
T 2hzt_A            5 EATLEVIGGKWKXVILXHLT-HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIV--YN-QV---PPKVEYELSEY   77 (107)
T ss_dssp             HHHHHHHCSTTHHHHHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEE--EC-SS---SCEEEEEECTT
T ss_pred             HHHHHHHcCccHHHHHHHHH-hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee--cC-CC---CCeEEEEECcc
Confidence            44566666666777888876 7889999999999 999999999999999999999652  11 23   23456677654

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

Probab=97.00  E-value=0.0015  Score=46.26  Aligned_cols=46  Identities=15%  Similarity=0.195  Sum_probs=39.6

Q ss_pred             hHHHHHHHHhC---CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN---PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~---~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.||..|..+   +.++-++||+.+|+++..|+++|..|.+.|||.+.
T Consensus        11 al~iL~~la~~~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           11 GLTIMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             HHHHHHHHHHTTTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEec
Confidence            45566666653   57999999999999999999999999999999865

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

Probab=96.98  E-value=0.0056  Score=43.72  Aligned_cols=48  Identities=13%  Similarity=0.231  Sum_probs=43.2

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        43 ~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~   90 (155)
T 3cdh_A           43 VPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRV   90 (155)
T ss_dssp             HHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            336778888888889999999999999999999999999999999864

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=96.98  E-value=0.01  Score=43.06  Aligned_cols=109  Identities=10%  Similarity=-0.037  Sum_probs=68.8

Q ss_pred             HHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744          26 RGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI  105 (157)
Q Consensus        26 R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v  105 (157)
                      ..+-+.-.+.||..|. ++.++=.||++.+|+++..|.+.|..|+++|||..+.   . ++  .. ..+|++.-..  ..
T Consensus        19 ~~l~~~w~l~IL~~L~-~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~---~-~~--d~-~~~y~LT~~G--~~   88 (146)
T 2f2e_A           19 DVIGDGWSMLIVRDAF-EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVP---A-ES--GS-HQEYRLTDKG--RA   88 (146)
T ss_dssp             HHHCSSSHHHHHHHHH-TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE---C-SS--SS-CEEEEECHHH--HT
T ss_pred             HHhCCchHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEe---c-CC--CC-eEEEEECchH--HH
Confidence            3334444567777775 7889999999999999999999999999999999652   1 22  12 4567777532  11


Q ss_pred             HHHHHHHHHHHHHHHHhhc-C-------------CCCeeecCCCCCccchhhh
Q psy5744         106 VKYKLDVMRKRMEMEERDA-T-------------SRSSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~-~-------------~~~~Y~Cp~C~~~Ys~lda  144 (157)
                      +.-.+..+.+-.++-+... .             -...+.|..||..-+..|+
T Consensus        89 l~~~l~~l~~w~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~g~~~~~~~~  141 (146)
T 2f2e_A           89 LFPLLVAIRQWGEDYFFAPDESHVRLVERDSGQPVPRLQVRAGDGSPLAAEDT  141 (146)
T ss_dssp             THHHHHHHHHHHHHHSSCTTCCCCEEEETTTCCBCCCCCCBCTTSCBCCGGGE
T ss_pred             HHHHHHHHHHHHHHhhccccCCcceeeeCCCCCCCCceEEECCCcCCCCHHHe
Confidence            2223334433333332211 1             1135677777777666554

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=96.96  E-value=0.0041  Score=46.28  Aligned_cols=83  Identities=17%  Similarity=0.202  Sum_probs=64.8

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHH
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMR  114 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~  114 (157)
                      -|++.|. +|+++=.+||+.||++--+++=+|+.|+.+|+|....+         ....||+++-.   +... ++.-+.
T Consensus        15 ~ILE~Lk-~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~---------GK~ayw~L~~s---~y~~-kV~dil   80 (165)
T 2vxz_A           15 DILALLA-DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAF---------GNVALVCLSMD---QYRQ-LVDGMI   80 (165)
T ss_dssp             HHHHHHT-TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEE---------TTEEEEESCHH---HHHH-HHHHHH
T ss_pred             HHHHHHH-hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEE---------ccEEEEEecHH---HHHH-HHHHHH
Confidence            4777777 99999999999999999999999999999999986522         23679999854   3333 777787


Q ss_pred             HHHHHHHhhcCCCCeeecC
Q psy5744         115 KRMEMEERDATSRSSFKCP  133 (157)
Q Consensus       115 ~~L~~~~~~~~~~~~Y~Cp  133 (157)
                      +.+..-++.  .+..|+-|
T Consensus        81 rel~~~l~s--~gvk~i~p   97 (165)
T 2vxz_A           81 REVERLVTT--NKLKFISP   97 (165)
T ss_dssp             HHHHHHHHH--TTCSEECH
T ss_pred             HHHHHHHHH--cCCeeeCc
Confidence            777777755  45556554

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=96.95  E-value=0.019  Score=39.54  Aligned_cols=81  Identities=11%  Similarity=0.179  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEE
Q psy5744          16 SLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYY   95 (157)
Q Consensus        16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw   95 (157)
                      ..-.-+..+.+++.++....|+..|.. +.++-.+||+.+|+++.-|.+.|..|++.|+|...+   .   |+   ..+|
T Consensus        17 ~~~~~~~~~~~~l~~~~~~~il~~L~~-~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~---~---~r---~~~~   86 (119)
T 2lkp_A           17 QAAAQVASTLQALATPSRLMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDR---A---GR---SIVY   86 (119)
T ss_dssp             HHHHHHHHHHHHHCCHHHHHHHHHHHH-CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEE---E---TT---EEEE
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe---c---CC---EEEE
Confidence            344455667788888888889998887 789999999999999999999999999999998652   2   22   3467


Q ss_pred             EecchhHHHHH
Q psy5744          96 FINYQTFVNIV  106 (157)
Q Consensus        96 ~I~y~~~~~vi  106 (157)
                      .+.-..+...+
T Consensus        87 ~~~~~~~~~~~   97 (119)
T 2lkp_A           87 SLYDTHVAQLL   97 (119)
T ss_dssp             EESCHHHHHHH
T ss_pred             EEchHHHHHHH
Confidence            77755444433

>2xub_A DNA-directed RNA polymerase III subunit RPC3; transcription, winged helix; 2.80A {Homo sapiens} PDB: 2xv4_S

Probab=96.92  E-value=0.0014  Score=57.40  Aligned_cols=78  Identities=13%  Similarity=0.091  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEE
Q psy5744          17 LKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYF   96 (157)
Q Consensus        17 ~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~   96 (157)
                      -.+|.-.++..-||+-.-.|.+.|+++|..+=.+|+..+++++++||..|..|-++++|.+.  .+  ++|    .+||.
T Consensus         5 ~~~L~~~li~~~FG~~~~~V~~~Ll~~G~ltL~~I~~~t~L~~~~Vk~~L~vLIQh~lV~~~--~~--~~~----~~~Y~   76 (534)
T 2xub_A            5 EIKLCSLLLQEHFGEIVEKIGVHLIRTGSQPLRVIAHDTGTSLDQVKKALCVLVQHNLVSYQ--VH--KRG----VVEYE   76 (534)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--EE--TTT----EEEEE
T ss_pred             HHHHHHHHHHHhcChHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhcCCeeEE--eC--CCC----cEEEE
Confidence            45788899999999999999999999999999999999999999999999999999999886  22  233    48888


Q ss_pred             ecchhH
Q psy5744          97 INYQTF  102 (157)
Q Consensus        97 I~y~~~  102 (157)
                      +|.+.+
T Consensus        77 ~~~~~i   82 (534)
T 2xub_A           77 AQCSRV   82 (534)
T ss_dssp             ECHHHH
T ss_pred             EChhhH
Confidence            885443

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

Probab=96.90  E-value=0.0018  Score=42.89  Aligned_cols=44  Identities=18%  Similarity=0.189  Sum_probs=41.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+++|-.++.++=.|||+.++++.-.||+-|..|.+.|+|...
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            47888888999999999999999999999999999999999765

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

Probab=96.89  E-value=0.0031  Score=46.37  Aligned_cols=72  Identities=13%  Similarity=0.226  Sum_probs=58.2

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF  102 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~  102 (157)
                      .+.+++-++--.-||..|. ++.++=.+||+.+|+++..|.+.|..|++.|||..++      +|+.   .||.++.+.+
T Consensus        50 ~~l~aL~~p~R~~IL~~L~-~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~------~Gr~---~~y~lt~~~~  119 (151)
T 3f6v_A           50 DQLEVAAEPTRRRLVQLLT-SGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRK------DGRF---RYYRLDPQGL  119 (151)
T ss_dssp             CHHHHHTSHHHHHHHHHGG-GCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEE------ETTE---EEEEECHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe------cCCE---EEEEEChHHH
Confidence            4567777777788998887 6789999999999999999999999999999999752      2332   7888986544


Q ss_pred             HH
Q psy5744         103 VN  104 (157)
Q Consensus       103 ~~  104 (157)
                      ..
T Consensus       120 ~~  121 (151)
T 3f6v_A          120 AQ  121 (151)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

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

Probab=96.88  E-value=0.02  Score=39.84  Aligned_cols=48  Identities=15%  Similarity=0.192  Sum_probs=43.6

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        36 ~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~   83 (142)
T 2fbi_A           36 EQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRW   83 (142)
T ss_dssp             HHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            446778888888888999999999999999999999999999999865

>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=96.87  E-value=0.012  Score=41.99  Aligned_cols=71  Identities=13%  Similarity=0.072  Sum_probs=53.0

Q ss_pred             cccccchHHHHHHHHHHHHHcCC------------CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744           8 YVHTEVPTSLKQLSRLVVRGFYS------------IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus         8 ~~~~~ip~~~~~Lv~~v~R~Fy~------------~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      ...+..+..+-.++..+.+.+..            .....||..|..++.++-.+||+.+|++...|.+++..|.+.|+|
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli   88 (154)
T 2eth_A            9 HHHHMDALEIFKTLFSLVMRFSSYLPSNEEISDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLV   88 (154)
T ss_dssp             ---CCCHHHHHHHHHHHHHHHHTTSCCCHHHHHSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSE
T ss_pred             hhhcccHHHHHHHHHHHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            34444445555555555555433            125678888888889999999999999999999999999999999


Q ss_pred             eee
Q psy5744          76 QTR   78 (157)
Q Consensus        76 ~~~   78 (157)
                      ...
T Consensus        89 ~r~   91 (154)
T 2eth_A           89 VRE   91 (154)
T ss_dssp             EEE
T ss_pred             Eee
Confidence            865

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

Probab=96.87  E-value=0.0019  Score=43.76  Aligned_cols=45  Identities=13%  Similarity=0.152  Sum_probs=41.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      .|+++|-.++.++=.|||+.+|++.--||+-|..|.+.|+|...+
T Consensus         6 ~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            478888889999999999999999999999999999999999764

>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=96.85  E-value=0.003  Score=42.88  Aligned_cols=49  Identities=12%  Similarity=0.206  Sum_probs=44.5

Q ss_pred             CCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++...|+..|-.  +..++-.|||..++++...|.++|..|++.|||+..
T Consensus        19 t~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~   69 (91)
T 2dk5_A           19 DNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   69 (91)
T ss_dssp             CSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3567889999987  558999999999999999999999999999999976

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

Probab=96.84  E-value=0.015  Score=40.65  Aligned_cols=48  Identities=10%  Similarity=0.155  Sum_probs=43.3

Q ss_pred             CchHHHHHHH-HhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDML-VRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L-~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..| ..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        37 ~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~   85 (146)
T 2fbh_A           37 QARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRL   85 (146)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeec
Confidence            4467888888 56789999999999999999999999999999999865

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

Probab=96.79  E-value=0.0022  Score=45.32  Aligned_cols=48  Identities=8%  Similarity=0.270  Sum_probs=40.4

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        37 ~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           37 PPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeec
Confidence            346789989888899999999999999999999999999999999865

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=96.78  E-value=0.0056  Score=44.39  Aligned_cols=63  Identities=5%  Similarity=-0.075  Sum_probs=51.2

Q ss_pred             HHHHHHHHHcCCCchHHHHHHHHh-----CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEee
Q psy5744          19 QLSRLVVRGFYSIEDSLIIDMLVR-----NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRM   81 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e~ivIlD~L~~-----~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~   81 (157)
                      -|++......-++...+++=.|..     +...+-++||+.+|+++++|.++|..|.+.|++....+.
T Consensus        20 ~LL~~y~~LgLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~~~~   87 (135)
T 2v79_A           20 LLLTHYKQLGLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECE   87 (135)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEEEEE
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEe
Confidence            356666677777777666666665     466899999999999999999999999999999987554

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

Probab=96.76  E-value=0.0085  Score=42.19  Aligned_cols=46  Identities=11%  Similarity=0.208  Sum_probs=42.5

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|.. ++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        37 ~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~   83 (147)
T 2hr3_A           37 QLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH   83 (147)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeC
Confidence            4678888888 889999999999999999999999999999999865

>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=96.74  E-value=0.013  Score=42.27  Aligned_cols=48  Identities=10%  Similarity=0.165  Sum_probs=43.9

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        46 ~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   93 (162)
T 3k0l_A           46 LPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLANGWIEKA   93 (162)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEec
Confidence            336788888888899999999999999999999999999999999965

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=96.74  E-value=0.0072  Score=42.41  Aligned_cols=48  Identities=8%  Similarity=0.209  Sum_probs=43.5

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        37 ~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   84 (142)
T 2bv6_A           37 YPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRE   84 (142)
T ss_dssp             HHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            446778888888888999999999999999999999999999999865

>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=96.71  E-value=0.021  Score=39.97  Aligned_cols=47  Identities=9%  Similarity=0.062  Sum_probs=42.5

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|. ++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        37 ~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   83 (146)
T 2gxg_A           37 YLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRV   83 (146)
T ss_dssp             HHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEee
Confidence            33667888888 889999999999999999999999999999999865

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

Probab=96.68  E-value=0.069  Score=36.83  Aligned_cols=62  Identities=10%  Similarity=0.236  Sum_probs=49.7

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      ....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|....   ...|   ....++++.-
T Consensus        30 ~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~---~~~d---~R~~~~~lT~   91 (138)
T 3bpv_A           30 AQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQ---DPEN---RRRYILEVTR   91 (138)
T ss_dssp             HHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE---ETTE---EEEEEEEECH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeec---CCCC---ceeEEeeECH
Confidence            367788888888999999999999999999999999999999998652   2122   3345566664

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=96.66  E-value=0.0025  Score=42.05  Aligned_cols=41  Identities=15%  Similarity=0.217  Sum_probs=35.1

Q ss_pred             HHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          38 DMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        38 D~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.|..++..|.-+||.+||++.+.|+++|+.|.+.|.|...
T Consensus        22 ~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~   62 (75)
T 1sfu_A           22 LSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   62 (75)
T ss_dssp             HTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecC
Confidence            33333455999999999999999999999999999999865

>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=0.023  Score=39.40  Aligned_cols=46  Identities=9%  Similarity=0.149  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        36 ~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~   81 (138)
T 1jgs_A           36 QFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             HHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            5678888888888999999999999999999999999999999865

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=96.64  E-value=0.0035  Score=41.58  Aligned_cols=44  Identities=11%  Similarity=0.180  Sum_probs=39.4

Q ss_pred             HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .||++|-. .+.++--|||+.+|++.|+|.++|..|+.++.|.+-
T Consensus        23 kVLe~LkeaG~PlkageIae~~GvdKKeVdKaik~LKkEgkI~SP   67 (80)
T 2lnb_A           23 RILQVLTEAGSPVKLAQLVKECQAPKRELNQVLYRMKKELKVSLT   67 (80)
T ss_dssp             HHHHHHHHHTSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCccCC
Confidence            57888876 578999999999999999999999999999998764

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=96.64  E-value=0.0042  Score=44.32  Aligned_cols=64  Identities=8%  Similarity=0.102  Sum_probs=44.8

Q ss_pred             CchHHHHHHHHh-----CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          31 IEDSLIIDMLVR-----NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        31 ~e~ivIlD~L~~-----~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      +...+|+-.|.+     +...+-++||+.+|++...|.++|..|.+.|+|......+.  +|+  ...+|.++
T Consensus        32 ~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~~~~--~g~--~~~~Ydl~  100 (128)
T 2vn2_A           32 EGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEHTDE--QGI--RNEKYTLE  100 (128)
T ss_dssp             HHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC--------------CEECH
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEECC--CCc--EEEEEehH
Confidence            445667777775     24589999999999999999999999999999998644322  343  23456666

>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=96.64  E-value=0.0025  Score=45.29  Aligned_cols=47  Identities=15%  Similarity=0.305  Sum_probs=43.3

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++.++-.+||+.+|++...+.+++..|.+.|+|...
T Consensus        41 ~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~   87 (152)
T 3bj6_A           41 GQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERR   87 (152)
T ss_dssp             HHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence            36778888888889999999999999999999999999999999975

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

Probab=96.61  E-value=0.0026  Score=42.06  Aligned_cols=45  Identities=16%  Similarity=0.247  Sum_probs=39.9

Q ss_pred             HHHHHHHHhC------CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRN------PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~------~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      --|+++|-.+      +.+|=.|||+.+|++...||+-|..|++.|+|...
T Consensus         7 ~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            7 TKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             HHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence            4578887765      78999999999999999999999999999999854

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=96.58  E-value=0.013  Score=40.05  Aligned_cols=71  Identities=14%  Similarity=0.068  Sum_probs=53.3

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      .+...+-+.-.+.||..|. ++.++=.|||+.+ |+++..|.+.|..|+++|||...  ... .|   ....+|++.-.
T Consensus        17 ~~l~~l~~~~~~~IL~~L~-~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~--~~~-~d---~r~~~y~LT~~   88 (107)
T 2fsw_A           17 KSMQIFAGKWTLLIIFQIN-RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKK--QYP-EV---PPRVEYSLTPL   88 (107)
T ss_dssp             HHHHHHTSSSHHHHHHHHT-TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEE--EEC-SS---SCEEEEEECHH
T ss_pred             HHHHHHcCccHHHHHHHHH-hCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEe--ecC-CC---CCeeEEEECcc
Confidence            3344555666677888876 7889999999999 59999999999999999999864  211 23   33567777754

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

Probab=96.54  E-value=0.019  Score=39.87  Aligned_cols=48  Identities=15%  Similarity=0.289  Sum_probs=43.6

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        31 ~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~   78 (142)
T 3bdd_A           31 LTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEESGYIIRK   78 (142)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            346778888888889999999999999999999999999999999865

>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=96.53  E-value=0.029  Score=39.15  Aligned_cols=48  Identities=10%  Similarity=0.137  Sum_probs=43.5

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        33 ~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~   80 (145)
T 2a61_A           33 PAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   80 (145)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            336778888888889999999999999999999999999999999865

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

Probab=96.51  E-value=0.0097  Score=41.82  Aligned_cols=45  Identities=13%  Similarity=0.333  Sum_probs=41.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++ ++-.+||+.+|+++.-|.+++..|.+.|+|...
T Consensus        40 ~~~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~   84 (146)
T 3tgn_A           40 QEHILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETS   84 (146)
T ss_dssp             HHHHHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEec
Confidence            577898988888 999999999999999999999999999999865

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=96.44  E-value=0.0043  Score=45.15  Aligned_cols=46  Identities=17%  Similarity=0.294  Sum_probs=38.3

Q ss_pred             hHHHHHHHHhC---CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN---PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~---~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-+|-.|..+   +.++-++||+.+|++++.|++++..|.+.|||.+.
T Consensus        13 Al~~L~~La~~~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~   61 (143)
T 3t8r_A           13 GLTLMISLAKKEGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSV   61 (143)
T ss_dssp             HHHHHHHHHTTTTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEec
Confidence            34455555543   36999999999999999999999999999999876

>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=96.43  E-value=0.0064  Score=43.27  Aligned_cols=48  Identities=21%  Similarity=0.339  Sum_probs=43.1

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+....||..| .++.++-.+||+.+|+++..|.+++..|.+.|+|..+
T Consensus        37 t~~q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~   84 (151)
T 3kp7_A           37 SAEQSHVLNML-SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLE   84 (151)
T ss_dssp             CHHHHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC-
T ss_pred             CHHHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            34467788898 8899999999999999999999999999999999975

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=96.43  E-value=0.014  Score=41.58  Aligned_cols=36  Identities=8%  Similarity=0.134  Sum_probs=32.7

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ ++.+||+.+|++..-||+++..|..+|||..+
T Consensus        35 G~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~~   71 (134)
T 4ham_A           35 GEKILSIREFASRIGVNPNTVSKAYQELERQEVIITV   71 (134)
T ss_dssp             TCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            3456 79999999999999999999999999999876

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

Probab=96.42  E-value=0.014  Score=40.53  Aligned_cols=35  Identities=14%  Similarity=0.235  Sum_probs=31.9

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+ ++.+||+.+|++..-||+++..|.++|+|...
T Consensus        31 ~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           31 EMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             CEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            345 89999999999999999999999999999754

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

Probab=96.42  E-value=0.022  Score=41.05  Aligned_cols=72  Identities=8%  Similarity=0.122  Sum_probs=55.3

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      +..+...+-+.-.+.||-.|. ++.++=.||++.+ |++++.+.+.|..|+++|||....   ...+   ....+|.+--
T Consensus        16 i~~~l~~lg~kW~l~IL~~L~-~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~---~~~d---~r~v~y~LT~   88 (131)
T 4a5n_A           16 VEFTLDVIGGKWKGILFYHMI-DGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREV---YHQV---PPKVEYSLTE   88 (131)
T ss_dssp             HHHHHHHHCSSSHHHHHHHHT-TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEE---ECSS---SCEEEEEECT
T ss_pred             HHHHHHHHcCcCHHHHHHHHh-cCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEe---cCCC---CCeEEEEECH
Confidence            455555666666788888876 7899999999999 999999999999999999998652   2112   2355667664

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=96.40  E-value=0.0071  Score=45.00  Aligned_cols=47  Identities=17%  Similarity=0.168  Sum_probs=38.4

Q ss_pred             hHHHHHHHHh---CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVR---NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~---~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-+|=.|..   .+.++-++||+.+|++++.|++++..|.+.|||.+.+
T Consensus        29 Alr~L~~LA~~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~r   78 (159)
T 3lwf_A           29 GLTITLELAKRIGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIR   78 (159)
T ss_dssp             HHHHHHHHHHTTTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEec
Confidence            3444444443   2469999999999999999999999999999999863

>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=96.40  E-value=0.006  Score=47.01  Aligned_cols=55  Identities=13%  Similarity=0.167  Sum_probs=46.6

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +.+++-++-...|+..|. ++.++=.+||+.+|+++..|...|..|.+.|||..+.
T Consensus         8 ilkaL~~~~rl~IL~~L~-~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~   62 (202)
T 2p4w_A            8 LLDVLGNETRRRILFLLT-KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRV   62 (202)
T ss_dssp             HHHHHHSHHHHHHHHHHH-HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEe
Confidence            445555666677888874 6789999999999999999999999999999999864

>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=96.40  E-value=0.02  Score=39.42  Aligned_cols=72  Identities=11%  Similarity=0.172  Sum_probs=54.3

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ..+...+-+.-.+.||..|. ++.++-.+||+.+ |++...|.+.|..|+++|||..+.   ...|   ....+|++.-.
T Consensus        13 ~~~l~~l~~~~~~~IL~~L~-~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~---~~~d---~r~~~~~LT~~   85 (112)
T 1z7u_A           13 NLALSTINGKWKLSLMDELF-QGTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRES---FNEL---PPRVEYTLTPE   85 (112)
T ss_dssp             HHHHHTTCSTTHHHHHHHHH-HSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEE---ECCS---SCEEEEEECHH
T ss_pred             HHHHHHHcCccHHHHHHHHH-hCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEee---cCCC---CCeEEEEECHh
Confidence            34455555665677888877 4789999999999 999999999999999999998652   1123   23456677653

>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=96.40  E-value=0.0074  Score=43.37  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...|+++|..++.++-.+||+.+|++...+++.+.+|.+.|+|....
T Consensus         7 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~   53 (144)
T 2cfx_A            7 DLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQYT   53 (144)
T ss_dssp             HHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEe
Confidence            35688888888999999999999999999999999999999998653

>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=96.38  E-value=0.058  Score=37.36  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=42.7

Q ss_pred             chHHHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++  .++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        35 ~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   83 (141)
T 3bro_A           35 TQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   83 (141)
T ss_dssp             HHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEee
Confidence            3577888888876  8999999999999999999999999999999865

>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=96.37  E-value=0.0077  Score=43.46  Aligned_cols=47  Identities=11%  Similarity=0.224  Sum_probs=42.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...|+.+|..++.++-.+||+.+|++...+++.+.+|.+.|+|....
T Consensus         9 ~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~   55 (150)
T 2w25_A            9 DRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESRGVVQGYS   55 (150)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEE
Confidence            45688888888999999999999999999999999999999997653

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=96.35  E-value=0.063  Score=37.39  Aligned_cols=48  Identities=23%  Similarity=0.353  Sum_probs=44.0

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        29 ~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~   76 (144)
T 1lj9_A           29 RGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             TTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            446788888888889999999999999999999999999999999875

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

Probab=96.34  E-value=0.035  Score=39.75  Aligned_cols=48  Identities=13%  Similarity=0.225  Sum_probs=43.9

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        50 ~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   97 (159)
T 3s2w_A           50 SGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQ   97 (159)
T ss_dssp             TTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            446778888888899999999999999999999999999999999865

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=96.33  E-value=0.026  Score=40.63  Aligned_cols=47  Identities=17%  Similarity=0.278  Sum_probs=42.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ..-|+.+|..++.++-.+||+.+|++...+++.+..|.+.|+|....
T Consensus        10 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~   56 (152)
T 2cg4_A           10 DRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGAR   56 (152)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceEE
Confidence            45688888888999999999999999999999999999999998653

>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=96.29  E-value=0.021  Score=40.47  Aligned_cols=76  Identities=4%  Similarity=0.183  Sum_probs=53.5

Q ss_pred             CCCCCcccccchHHHHHHHHHHHHHc--------CCCchHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744           3 TSDEGYVHTEVPTSLKQLSRLVVRGF--------YSIEDSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus         3 ~~~~~~~~~~ip~~~~~Lv~~v~R~F--------y~~e~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      |++.......+.-.+..+.+.+.+.+        .+.....||..|..+ +.++-.+||+.+++++..+.+++..|.+.|
T Consensus         3 M~~~~~l~~~l~~~l~~~~~~~~~~~~~~l~~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~G   82 (150)
T 3fm5_A            3 MAESQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERG   82 (150)
T ss_dssp             CCSCCCGGGCHHHHHHHHHHHHHHHHHHHHGGGTCCHHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHTTT
T ss_pred             CccccCcchhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHHCC
Confidence            33444444455555554444444333        123367788888765 478999999999999999999999999999


Q ss_pred             ceeee
Q psy5744          74 IIQTR   78 (157)
Q Consensus        74 Lv~~~   78 (157)
                      +|...
T Consensus        83 lv~r~   87 (150)
T 3fm5_A           83 LVVRT   87 (150)
T ss_dssp             SEEC-
T ss_pred             CEEee
Confidence            99865

>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=96.28  E-value=0.013  Score=41.61  Aligned_cols=46  Identities=13%  Similarity=0.279  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        39 ~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   84 (155)
T 1s3j_A           39 QLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   84 (155)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            5778888888888999999999999999999999999999999865

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=96.22  E-value=0.027  Score=41.91  Aligned_cols=47  Identities=21%  Similarity=0.343  Sum_probs=42.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...|++.|-+++.++-.+||+.+|++...+++.+.+|.+.|+|....
T Consensus        19 d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~~~   65 (171)
T 2ia0_A           19 DRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQERGVIERYT   65 (171)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            34688888888999999999999999999999999999999997553

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

Probab=96.22  E-value=0.0048  Score=43.44  Aligned_cols=46  Identities=11%  Similarity=0.264  Sum_probs=41.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL--KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-||..|.+++.++-.+||+.+  |+++..|++.|..|.++|||...
T Consensus        15 d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           15 DDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             HHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            35578888888999999999999  99999999999999999999863

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=96.21  E-value=0.0076  Score=43.88  Aligned_cols=47  Identities=17%  Similarity=0.212  Sum_probs=38.4

Q ss_pred             hHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-+|-.|..  .+.++-++||+.+|++++.|++++..|.+.|||.+.+
T Consensus        16 Al~~L~~La~~~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~r   64 (149)
T 1ylf_A           16 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNR   64 (149)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEcc
Confidence            3445555554  3469999999999999999999999999999998763

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=96.20  E-value=0.0067  Score=43.06  Aligned_cols=46  Identities=22%  Similarity=0.412  Sum_probs=41.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...|+..|..++.++-.+||+.+|++...+++.+..|.+.|+|...
T Consensus         6 ~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            6 DKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            4567888877888999999999999999999999999999999754

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=96.19  E-value=0.011  Score=43.32  Aligned_cols=47  Identities=17%  Similarity=0.258  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...|+++|..++.++-.|||+.+|++...+++.+..|.+.|+|....
T Consensus        12 ~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~   58 (162)
T 2p5v_A           12 DIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQYA   58 (162)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEeeec
Confidence            45688888888899999999999999999999999999999998653

>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=96.19  E-value=0.0039  Score=43.04  Aligned_cols=36  Identities=17%  Similarity=0.360  Sum_probs=32.8

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+.+ ++.+||+.+|++..-||+.|..|.++|+|...
T Consensus        40 g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~   76 (102)
T 2b0l_A           40 NEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR   76 (102)
T ss_dssp             TEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4456 99999999999999999999999999999865

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

Probab=96.18  E-value=0.02  Score=40.95  Aligned_cols=48  Identities=13%  Similarity=0.261  Sum_probs=43.2

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        49 ~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~   96 (162)
T 2fa5_A           49 IPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRE   96 (162)
T ss_dssp             HHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeee
Confidence            336778989888899999999999999999999999999999999865

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=96.18  E-value=0.0084  Score=43.22  Aligned_cols=47  Identities=23%  Similarity=0.379  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...|+..|-.++.++-.+||+.+|++...+++.+..|.+.|+|....
T Consensus        11 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~   57 (151)
T 2dbb_A           11 DMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFT   57 (151)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEE
Confidence            45688888888999999999999999999999999999999998553

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

Probab=96.18  E-value=0.015  Score=40.98  Aligned_cols=68  Identities=13%  Similarity=0.247  Sum_probs=51.3

Q ss_pred             ccchHHHHHHHHHHHHHcCC---------CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          11 TEVPTSLKQLSRLVVRGFYS---------IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        11 ~~ip~~~~~Lv~~v~R~Fy~---------~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+.-.+..+.+.+.+.|-.         .....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        11 ~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           11 RHATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             GCHHHHHHHHHHHHHHC----CCGGGTCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            34445555555555544422         225678888888899999999999999999999999999999999865

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

Probab=96.17  E-value=0.012  Score=42.11  Aligned_cols=68  Identities=15%  Similarity=0.106  Sum_probs=51.3

Q ss_pred             HHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          26 RGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        26 R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ..+-+.-.+.||..|. ++.++=.+|++.+ |+++..|-+.|..|+++|||..+.  .. .|   ....+|++.-.
T Consensus        30 ~~l~~~w~l~IL~~L~-~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~--~~-~d---~r~~~y~LT~~   98 (131)
T 1yyv_A           30 KHVTSRWGVLILVALR-DGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVS--YP-VV---PPHVEYSLTPL   98 (131)
T ss_dssp             HHHHSHHHHHHHHHGG-GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEE--EC-SS---SCEEEEEECHH
T ss_pred             HHHcCCcHHHHHHHHH-cCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEe--cC-CC---CCeEEEEECcc
Confidence            3333444567787776 7889999999999 799999999999999999999652  11 23   33567777753

>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=96.13  E-value=0.078  Score=36.76  Aligned_cols=48  Identities=17%  Similarity=0.239  Sum_probs=43.2

Q ss_pred             CchHHHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++  .++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        31 ~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   80 (139)
T 3eco_A           31 NEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRY   80 (139)
T ss_dssp             HHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            34677888888875  8999999999999999999999999999999865

>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=96.13  E-value=0.036  Score=41.26  Aligned_cols=50  Identities=6%  Similarity=0.143  Sum_probs=45.0

Q ss_pred             CCCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          29 YSIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        29 y~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+.....||..|.+  ++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   90 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVI   90 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            45667889999887  568999999999999999999999999999999975

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=96.05  E-value=0.0066  Score=45.14  Aligned_cols=47  Identities=15%  Similarity=0.201  Sum_probs=38.6

Q ss_pred             hHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-+|-.|..  .+.++-++||+.+|++++.|+|++..|.+.|||.+.+
T Consensus        14 Alr~l~~La~~~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~r   62 (162)
T 3k69_A           14 AVHSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTV   62 (162)
T ss_dssp             HHHHHHHHHTTTTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEEC
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            3445545553  3569999999999999999999999999999998763

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

Probab=96.05  E-value=0.03  Score=39.66  Aligned_cols=46  Identities=15%  Similarity=0.199  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        49 ~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   94 (153)
T 2pex_A           49 QYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRT   94 (153)
T ss_dssp             HHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            5678888888889999999999999999999999999999999865

>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=96.05  E-value=0.0084  Score=43.10  Aligned_cols=46  Identities=26%  Similarity=0.380  Sum_probs=41.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-|+..|..++.++-.+||+.+|+++..+++.+.+|.+.|+|...
T Consensus         5 ~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            5 DLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            3467888877889999999999999999999999999999999864

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=96.00  E-value=0.01  Score=38.44  Aligned_cols=47  Identities=6%  Similarity=0.264  Sum_probs=42.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||++|..++.++-.|||+.++    +++..|.++|..|.+.|+|...
T Consensus        10 ~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~   60 (82)
T 1p6r_A           10 AELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHH   60 (82)
T ss_dssp             HHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEE
Confidence            3567899988888999999999996    7899999999999999999865

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

Probab=96.00  E-value=0.23  Score=34.58  Aligned_cols=63  Identities=13%  Similarity=0.110  Sum_probs=49.9

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      ++....||..|..++. +-.+||+.+|+++..+-+++..|.+.|+|....   ...|   ....++++.-
T Consensus        36 t~~~~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~---~~~D---~R~~~~~LT~   98 (144)
T 3f3x_A           36 SYLDFSILKATSEEPR-SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIR---DSKD---RRIVIVEITP   98 (144)
T ss_dssp             CHHHHHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE---ETTE---EEEEEEEECH
T ss_pred             CHHHHHHHHHHHHCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc---CCCC---CceEEEEECH
Confidence            4456789989888877 999999999999999999999999999999652   2122   3455666664

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

Probab=95.99  E-value=0.038  Score=38.68  Aligned_cols=48  Identities=13%  Similarity=0.159  Sum_probs=43.6

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        37 ~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   84 (143)
T 3oop_A           37 PEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVRE   84 (143)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeecc
Confidence            336778888888899999999999999999999999999999999865

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

Probab=95.99  E-value=0.011  Score=42.10  Aligned_cols=47  Identities=15%  Similarity=0.241  Sum_probs=43.1

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|..
T Consensus        41 ~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           41 IQQLAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             HHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            33577888888888999999999999999999999999999999986

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

Probab=95.98  E-value=0.012  Score=38.20  Aligned_cols=47  Identities=11%  Similarity=0.216  Sum_probs=42.1

Q ss_pred             chHHHHHHHHhC--CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRN--PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~--~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....|+++|..+  +.++-+||++.+     +++...|++.|..|.+.|+|...
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~   71 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH   71 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEE
Confidence            357799998864  689999999999     99999999999999999999854

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

Probab=95.98  E-value=0.031  Score=38.63  Aligned_cols=47  Identities=15%  Similarity=0.168  Sum_probs=43.2

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        34 ~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   80 (139)
T 3bja_A           34 VQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTE   80 (139)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeec
Confidence            36778888888889999999999999999999999999999999865

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

Probab=95.98  E-value=0.033  Score=39.35  Aligned_cols=36  Identities=8%  Similarity=0.095  Sum_probs=32.3

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ ++.+||+.+|++..-||+++..|.++|+|..+
T Consensus        34 g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   70 (125)
T 3neu_A           34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK   70 (125)
T ss_dssp             TCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEe
Confidence            3345 69999999999999999999999999999865

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=95.94  E-value=0.018  Score=40.47  Aligned_cols=46  Identities=13%  Similarity=0.247  Sum_probs=42.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        42 ~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~   87 (147)
T 1z91_A           42 QYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   87 (147)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEec
Confidence            5678888888889999999999999999999999999999999865

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=95.92  E-value=0.01  Score=43.64  Aligned_cols=45  Identities=18%  Similarity=0.344  Sum_probs=41.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|+++|-+++.++-.+||+.+|++...+++-+.+|.+.|+|...
T Consensus         6 ~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            6 RKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeec
Confidence            468888888999999999999999999999999999999999854

>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=95.87  E-value=0.17  Score=35.10  Aligned_cols=62  Identities=13%  Similarity=0.111  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHcCC-CchHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          17 LKQLSRLVVRGFYS-IEDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        17 ~~~Lv~~v~R~Fy~-~e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.+......+.+-- +...-++..|. .++.++-.|||+.+|+++..+.+++..|.+.|+|...
T Consensus        11 ~~~~~~~~~~~~gl~~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           11 IIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCChhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            33444444444432 22445676765 4678999999999999999999999999999999864

>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=95.86  E-value=0.017  Score=38.57  Aligned_cols=48  Identities=10%  Similarity=0.198  Sum_probs=42.5

Q ss_pred             CchHHHHHHHHhCCCcCHHHH----HHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDI----CELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedL----a~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|.+++.++-.+|    |+.+|+++..|.+++..|.+.|+|...
T Consensus         8 ~~q~~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~   59 (99)
T 1tbx_A            8 YPEAIVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKER   59 (99)
T ss_dssp             CHHHHHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEE
Confidence            345678888888888999999    899999999999999999999999864

>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=95.83  E-value=0.0098  Score=42.98  Aligned_cols=46  Identities=20%  Similarity=0.325  Sum_probs=42.0

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-|+++|..++.++-.+||+.+|++...+++.+..|.+.|+|...
T Consensus         9 ~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            9 DKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4568888888899999999999999999999999999999999764

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

Probab=95.79  E-value=0.034  Score=39.67  Aligned_cols=35  Identities=9%  Similarity=0.241  Sum_probs=32.0

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+ ++.+||+.+|++..-||++|..|..+|+|...
T Consensus        26 ~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~   61 (129)
T 2ek5_A           26 QRVPSTNELAAFHRINPATARNGLTLLVEAGILYKK   61 (129)
T ss_dssp             SCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            356 89999999999999999999999999999754

>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=95.78  E-value=0.016  Score=41.97  Aligned_cols=45  Identities=20%  Similarity=0.298  Sum_probs=36.8

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +-+|=.|.. .+. +-++||+.++++++.|+|+|.+|.+.|||.+.+
T Consensus        12 l~~L~~La~~~~~-s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~r   57 (145)
T 1xd7_A           12 IHILSLISMDEKT-SSEIIADSVNTNPVVVRRMISLLKKADILTSRA   57 (145)
T ss_dssp             HHHHHHHHTCSCC-CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHHHHHHHhCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeec
Confidence            444444553 235 999999999999999999999999999998763

>2e72_A POGO transposable element with ZNF domain; zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.76  E-value=0.0037  Score=37.67  Aligned_cols=23  Identities=26%  Similarity=0.429  Sum_probs=19.7

Q ss_pred             cCCCCeeecCCCCCccchhhhhh
Q psy5744         124 ATSRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       124 ~~~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      ..+...|.||+|++.|+..++++
T Consensus         7 ~~~~~~~~CPrCn~~f~~~~sLr   29 (49)
T 2e72_A            7 GQDGGRKICPRCNAQFRVTEALR   29 (49)
T ss_dssp             SCCSSCCCCTTTCCCCSSHHHHH
T ss_pred             cccCCceeCCcccccccchHHHH
Confidence            34557899999999999999986

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=95.75  E-value=0.14  Score=36.83  Aligned_cols=47  Identities=13%  Similarity=0.100  Sum_probs=39.2

Q ss_pred             chHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..+  +.++-.+||+.+|++...|.+++..|.+.|+|...
T Consensus        47 ~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   95 (168)
T 3u2r_A           47 QQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRT   95 (168)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeec
Confidence            367788888874  58999999999999999999999999999999965

>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=95.74  E-value=0.022  Score=39.43  Aligned_cols=52  Identities=23%  Similarity=0.278  Sum_probs=43.1

Q ss_pred             HHcCCCchHHHHHHHHhCCCcC--HHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          26 RGFYSIEDSLIIDMLVRNPCMK--EDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        26 R~Fy~~e~ivIlD~L~~~~~i~--dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+-++-.+.|+..|. ++..+  =.||++.+ |++++.+.+.|..|+++|||..+
T Consensus        22 ~~l~~~wrl~IL~~L~-~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~   76 (111)
T 3df8_A           22 HLLGKKYTMLIISVLG-NGSTRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERR   76 (111)
T ss_dssp             HHHHSTTHHHHHHHHT-SSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHcCccHHHHHHHHh-cCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3444555677887776 66766  99999999 99999999999999999999854

>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=95.72  E-value=0.018  Score=40.67  Aligned_cols=38  Identities=16%  Similarity=0.213  Sum_probs=34.9

Q ss_pred             HhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          41 VRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        41 ~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -.++.++-.+||+.+|+++.-|++++..|.+.|+|...
T Consensus        18 ~~~~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~   55 (142)
T 1on2_A           18 EEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_dssp             HHHSSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34678999999999999999999999999999999864

>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=95.70  E-value=0.016  Score=40.83  Aligned_cols=47  Identities=6%  Similarity=0.151  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++.++-.|||+.+|+++..+.+++..|.+.|+|...
T Consensus        37 ~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   83 (140)
T 3hsr_A           37 TGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRT   83 (140)
T ss_dssp             HHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEec
Confidence            36778888888899999999999999999999999999999999965

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=95.68  E-value=0.018  Score=41.47  Aligned_cols=44  Identities=16%  Similarity=0.193  Sum_probs=37.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+..|..++.++..+||+.+|++..-|+++|..|.+.|+|..+
T Consensus        44 ~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~   87 (155)
T 2h09_A           44 LISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMI   87 (155)
T ss_dssp             HHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34555556678999999999999999999999999999998754

>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=95.67  E-value=0.13  Score=37.37  Aligned_cols=46  Identities=11%  Similarity=0.231  Sum_probs=42.0

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|.. ++.++-.|||+.+|++...|.+++..|.+.|+|...
T Consensus        55 q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~  101 (166)
T 3deu_A           55 HWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ  101 (166)
T ss_dssp             HHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEee
Confidence            5678888887 678999999999999999999999999999999865

>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=95.65  E-value=0.022  Score=43.41  Aligned_cols=51  Identities=18%  Similarity=0.252  Sum_probs=44.2

Q ss_pred             HcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          27 GFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        27 ~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++...-|+..|. ++.++-.+||+.+|+++..|++.+..|++.|+|...
T Consensus        16 ~l~d~~~~~IL~~L~-~~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           16 VMLEDTRRKILKLLR-NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHSHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCCHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            334455567888887 788999999999999999999999999999999876

>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=95.61  E-value=0.019  Score=40.11  Aligned_cols=46  Identities=11%  Similarity=0.242  Sum_probs=42.3

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..+  +.++-.|||+.+|+++..+-+++..|.+.|+|...
T Consensus        39 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   86 (127)
T 2frh_A           39 EFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKK   86 (127)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCB
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            56788888877  88999999999999999999999999999999865

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

Probab=95.54  E-value=0.053  Score=39.15  Aligned_cols=80  Identities=14%  Similarity=0.190  Sum_probs=59.7

Q ss_pred             CchHHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHH
Q psy5744          31 IEDSLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVN  104 (157)
Q Consensus        31 ~e~ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~  104 (157)
                      +.-..|+++|.. ++.+|-+||.+.+     +++...|=+.|..|.+.|||...   +. ++|..+    |-++-     
T Consensus        22 ~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~---~~-~~~~~~----Y~~~~-----   88 (145)
T 2fe3_A           22 PQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKEL---TY-GDASSR----FDFVT-----   88 (145)
T ss_dssp             HHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEE---CC-TTSCCE----EEECC-----
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEE---ee-CCCceE----EECCC-----
Confidence            335679999986 4689999999999     89999999999999999999864   22 343221    22220     


Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         105 IVKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       105 vik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                          ..-..++|..||+.+.+.+
T Consensus        89 --------------------~~H~HliC~~Cg~v~~~~~  107 (145)
T 2fe3_A           89 --------------------SDHYHAICENCGKIVDFHY  107 (145)
T ss_dssp             --------------------CCEEEEEETTTCCEEECCC
T ss_pred             --------------------CCcceEEECCCCCEEEecC
Confidence                                1234799999999988753

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=95.54  E-value=0.11  Score=37.69  Aligned_cols=79  Identities=15%  Similarity=0.241  Sum_probs=59.8

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHH
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIV  106 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vi  106 (157)
                      -..|+++|.. ++.+|-+||.+.+     +++...|=+.|..|.+.|||...   +. ++|.    .+|-.+        
T Consensus        29 R~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~---~~-~~~~----~~Y~~~--------   92 (150)
T 2xig_A           29 REEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVL---ET-SKSG----RRYEIA--------   92 (150)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEE---EE-TTTE----EEEEES--------
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEE---Ee-CCCc----eEEEec--------
Confidence            4679999986 4689999999999     89999999999999999999864   33 3442    222222        


Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         107 KYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       107 k~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                      .......++|..||+.+.+.+
T Consensus        93 ----------------~~~~H~HliC~~Cg~v~~~~~  113 (150)
T 2xig_A           93 ----------------AKEHHDHIICLHCGKIIEFAD  113 (150)
T ss_dssp             ----------------CSCCCEEEEETTTCCEEEECC
T ss_pred             ----------------CCCCceEEEECCCCCEEEecC
Confidence                            011346899999999988753

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

Probab=95.54  E-value=0.066  Score=37.95  Aligned_cols=45  Identities=9%  Similarity=0.200  Sum_probs=40.7

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..|+++|.. ++.+|-+||.+.+     +++...|=+.|..|.+.|||...
T Consensus        14 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~   64 (131)
T 2o03_A           14 AAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTL   64 (131)
T ss_dssp             HHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEE
Confidence            568999986 4689999999999     99999999999999999999865

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=95.53  E-value=0.046  Score=41.08  Aligned_cols=72  Identities=15%  Similarity=0.207  Sum_probs=55.1

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhC-CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLK-FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~-i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      +.++.-.|--+-|+..|. ++..+=-+||+.+| +++..|-+.|..|++.|||........    ++....||.+.-.
T Consensus        16 ~~~~La~P~Rl~il~~L~-~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv~~~~e~~~----~g~~er~y~~~~~   88 (182)
T 4g6q_A           16 LVDLLHHPLRWRITQLLI-GRSLTTRELAELLPDVATTTLYRQVGILVKAGVLMVTAEHQV----RGAVERTYTLNTQ   88 (182)
T ss_dssp             HHHHTTSHHHHHHHHHTT-TSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSEEEEEEEEE----TTEEEEEEEECTT
T ss_pred             HHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCeEEEEeecc----cCcceeEEEeccc
Confidence            445555666677888875 67889999999996 999999999999999999997743322    2355668877643

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

Probab=95.51  E-value=0.036  Score=39.29  Aligned_cols=48  Identities=13%  Similarity=0.153  Sum_probs=43.4

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||..|..++.++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        41 ~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           41 YSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeC
Confidence            346788989888999999999999999999999999999999999865

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

Probab=95.51  E-value=0.043  Score=39.39  Aligned_cols=48  Identities=8%  Similarity=0.102  Sum_probs=43.6

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+..||..|..++.++-.+||+.+|+++..+.+++.+|.+.|+|...
T Consensus        53 ~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~  100 (161)
T 3e6m_A           53 TPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARS  100 (161)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            336778888888889999999999999999999999999999999865

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

Probab=95.48  E-value=0.026  Score=40.27  Aligned_cols=48  Identities=10%  Similarity=0.126  Sum_probs=42.4

Q ss_pred             CchHHHHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+..||..|. .++.++-.+||+.+|++...+.+++..|.+.|+|...
T Consensus        47 ~~~~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~   95 (160)
T 3boq_A           47 LAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKA   95 (160)
T ss_dssp             HHHHHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            33677888884 5788999999999999999999999999999999865

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

Probab=95.45  E-value=0.052  Score=38.44  Aligned_cols=35  Identities=14%  Similarity=0.141  Sum_probs=32.1

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+ ++.+||+.+|++..-||++|..|..+|+|...
T Consensus        33 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   68 (126)
T 3by6_A           33 DQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTI   68 (126)
T ss_dssp             CEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            456 89999999999999999999999999999754

>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=95.44  E-value=0.028  Score=42.82  Aligned_cols=46  Identities=7%  Similarity=-0.031  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.++-.+||+.+|++...+-+++..|.+.|+|...
T Consensus        50 q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~   95 (207)
T 2fxa_A           50 EHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFS   95 (207)
T ss_dssp             HHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            5678888888889999999999999999999999999999999865

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

Probab=95.43  E-value=0.024  Score=39.86  Aligned_cols=47  Identities=13%  Similarity=0.141  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..++.++-.+||+.+|++...+.+++..|.+.|+|...
T Consensus        32 ~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   78 (145)
T 3g3z_A           32 NLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQ   78 (145)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            36788888888888999999999999999999999999999999864

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=95.43  E-value=0.045  Score=39.07  Aligned_cols=78  Identities=12%  Similarity=0.173  Sum_probs=58.5

Q ss_pred             hHHHHHHHHh-C-CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744          33 DSLIIDMLVR-N-PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI  105 (157)
Q Consensus        33 ~ivIlD~L~~-~-~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v  105 (157)
                      -..|+++|.. + +.+|-+||.+.+     +++...|=+.|..|.+.|||...   +. ++|..    +|-++..     
T Consensus        20 R~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~---~~-~~~~~----~Y~~~~~-----   86 (136)
T 1mzb_A           20 RVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRH---NF-DGGHA----VFELADS-----   86 (136)
T ss_dssp             HHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEE---CS-SSSSC----EEEESSS-----
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEE---Ee-CCCce----EEEeCCC-----
Confidence            4679999986 3 679999999999     89999999999999999999864   22 33322    2222211     


Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchh
Q psy5744         106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDL  142 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~l  142 (157)
                                         .....++|..||+.+.+.
T Consensus        87 -------------------~~H~HliC~~Cg~v~~~~  104 (136)
T 1mzb_A           87 -------------------GHHDHMVCVDTGEVIEFM  104 (136)
T ss_dssp             -------------------CCCEEEEETTTCCEEEEC
T ss_pred             -------------------CcceEEEECCCCCEEEec
Confidence                               234679999999999874

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

Probab=95.41  E-value=0.034  Score=39.03  Aligned_cols=36  Identities=17%  Similarity=0.252  Sum_probs=33.8

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.++-.+||+.+|++...|++++..|.+.|+|...
T Consensus        29 ~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~   64 (139)
T 2x4h_A           29 GEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKK   64 (139)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEec
Confidence            578999999999999999999999999999999864

>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=95.39  E-value=0.05  Score=42.34  Aligned_cols=36  Identities=11%  Similarity=0.399  Sum_probs=33.6

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||+.|..|..+|||...
T Consensus        47 G~~L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~   82 (237)
T 3c7j_A           47 GTALRQQELATLFGVSRMPVREALRQLEAQSLLRVE   82 (237)
T ss_dssp             TCBCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCeeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            557899999999999999999999999999999865

>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=95.36  E-value=0.18  Score=36.52  Aligned_cols=63  Identities=17%  Similarity=0.324  Sum_probs=47.3

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ...||-+|. .+.++-.+|++.+        +++...|-.+|.+|+++|||..+... . +++  ..+.+|.|.-.
T Consensus        43 ~~~IL~~L~-~~~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~-~-~~~--~~rk~Y~LT~~  113 (145)
T 1xma_A           43 DTIILSLLI-EGDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGE-E-TQG--KRRTYYRITPE  113 (145)
T ss_dssp             HHHHHHHHH-HCCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEE-E-C----CEEEEEEECHH
T ss_pred             HHHHHHHHH-hCCCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEec-c-CCC--CCeEEEEECHH
Confidence            466777775 4678888998888        69999999999999999999976332 1 122  34667788853

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=95.31  E-value=0.017  Score=45.52  Aligned_cols=53  Identities=4%  Similarity=-0.025  Sum_probs=44.0

Q ss_pred             HHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          25 VRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        25 ~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+++-++--.-|+..|. ++.++=.+||+.+|+++..|.+.|..|.+.|||...
T Consensus         6 lkaL~~~~R~~IL~~L~-~g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~~   58 (232)
T 2qlz_A            6 FYILGNKVRRDLLSHLT-CMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSY   58 (232)
T ss_dssp             HHHHTSHHHHHHHHHHT-TTTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34444555566888776 578899999999999999999999999999999974

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

Probab=95.30  E-value=0.039  Score=42.14  Aligned_cols=36  Identities=17%  Similarity=0.320  Sum_probs=33.6

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||.+|..|..+|||..+
T Consensus        37 G~~L~E~~La~~lgVSRtpVREAl~~L~~eGlv~~~   72 (222)
T 3ihu_A           37 GQRLVETDLVAHFGVGRNSVREALQRLAAEGIVDLQ   72 (222)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            457889999999999999999999999999999875

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=95.30  E-value=0.026  Score=38.12  Aligned_cols=36  Identities=17%  Similarity=0.317  Sum_probs=32.6

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +..+||+.+|++..-||+.|..|.++|+|..+
T Consensus        32 g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           32 GDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             TSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            3456 89999999999999999999999999999754

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=95.23  E-value=0.069  Score=38.37  Aligned_cols=79  Identities=11%  Similarity=0.192  Sum_probs=58.6

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK  107 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik  107 (157)
                      ..|+++|.. ++.+|-+||.+.+     +++...|=+.|..|.+.|||...   +. ++|..    +|-++..       
T Consensus        17 ~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~---~~-~~g~~----~Y~~~~~-------   81 (139)
T 3mwm_A           17 AAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVL---RT-AEGES----VYRRCST-------   81 (139)
T ss_dssp             HHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEE---EC-TTSCE----EEECCSC-------
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEE---Ec-CCCce----EEEECCC-------
Confidence            568999886 4689999999998     79999999999999999999754   22 34422    2323311       


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         108 YKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       108 ~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                      ......++|..||+.+.+.+
T Consensus        82 ----------------~~~H~HliC~~Cg~v~~~~~  101 (139)
T 3mwm_A           82 ----------------GDHHHHLVCRACGKAVEVEG  101 (139)
T ss_dssp             ----------------SSCCEEEEETTTCCEEEECC
T ss_pred             ----------------CCCccEEEECCCCCEeeccc
Confidence                            02355799999999987753

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=95.20  E-value=0.029  Score=44.33  Aligned_cols=49  Identities=20%  Similarity=0.302  Sum_probs=44.5

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++...-||.+|..++.++-.|||+.+|++...+.++|..|.+.|+|...
T Consensus       151 ~~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          151 SREEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             CHHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4556789999888888999999999999999999999999999999875

>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=95.17  E-value=0.02  Score=46.60  Aligned_cols=75  Identities=13%  Similarity=0.098  Sum_probs=49.6

Q ss_pred             CCCCCCCcccccchHHHHHHHHHHHHHcCCC------chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcc
Q psy5744           1 MSTSDEGYVHTEVPTSLKQLSRLVVRGFYSI------EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKI   74 (157)
Q Consensus         1 ~~~~~~~~~~~~ip~~~~~Lv~~v~R~Fy~~------e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~L   74 (157)
                      ||.+..+..+...++.+..|.+.+. +|...      -..-|+|.| ..+.++-+|||+.+|+++.-++++|..|...|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~l~~~~~l~i~~~l-~~~~~t~~eLA~~~g~~~~~l~r~Lr~L~~~Gl   78 (374)
T 1qzz_A            1 MSSSSPGEPLEPTDQDLDVLLKNLG-NLVTPMALRVAATLRLVDHL-LAGADTLAGLADRTDTHPQALSRLVRHLTVVGV   78 (374)
T ss_dssp             ---------CCCCHHHHHHHHHTTT-CCHHHHHHHHHHHTTHHHHH-HTTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCCCchHHHHHHHHHH-hhHHHHHHHHHHHcChHHHH-hCCCCCHHHHHHHhCcCHHHHHHHHHHHhhCCC
Confidence            5666666666666676666655432 11111      123488888 467899999999999999999999999999999


Q ss_pred             eee
Q psy5744          75 IQT   77 (157)
Q Consensus        75 v~~   77 (157)
                      +..
T Consensus        79 l~~   81 (374)
T 1qzz_A           79 LEG   81 (374)
T ss_dssp             EEC
T ss_pred             EEE
Confidence            986

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=95.15  E-value=0.049  Score=41.81  Aligned_cols=36  Identities=22%  Similarity=0.400  Sum_probs=33.2

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..+
T Consensus        28 G~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~   64 (239)
T 1hw1_A           28 GTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   64 (239)
T ss_dssp             TSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            4467 79999999999999999999999999999875

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=95.12  E-value=0.026  Score=38.66  Aligned_cols=49  Identities=10%  Similarity=0.229  Sum_probs=42.8

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++....||.+|-.++.++-.||++.++    ++...|.++|..|.+.|+|...
T Consensus        34 T~~e~~VL~~L~~~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~   86 (99)
T 2k4b_A           34 SNAELIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTE   86 (99)
T ss_dssp             CCSCSHHHHHHHHHSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEE
T ss_pred             CHHHHHHHHHHHhCCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEE
Confidence            345678899998888899999999997    5689999999999999999864

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=95.03  E-value=0.058  Score=42.33  Aligned_cols=36  Identities=19%  Similarity=0.278  Sum_probs=33.4

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+ ++.+||+.+|++..-||++|..|.++|+|.. +
T Consensus        33 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~-~   69 (248)
T 3f8m_A           33 GDPFPAEREIAEQFEVARETVRQALRELLIDGRVER-R   69 (248)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE-E
T ss_pred             CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe-C
Confidence            5567 8999999999999999999999999999987 5

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=94.95  E-value=0.0027  Score=52.67  Aligned_cols=79  Identities=16%  Similarity=0.092  Sum_probs=66.6

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHHHHH
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRK  115 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~m~~  115 (157)
                      +.-+|++++..+-.|||+.+|++...|..+|..|.+.|||...    .   |  +...|+-++.+.+++.++.++....+
T Consensus        23 vY~~Ll~~g~~t~~eia~~~gv~~~~Vy~~L~~L~~~GlV~~~----~---g--~p~~y~av~p~~~l~~l~~~~~~~~~   93 (342)
T 3qph_A           23 TYWTLLVYGPSTAKEISTKSGIPYNRVYDTISSLKLRGFVTEI----E---G--TPKVYAAYSPRIAFFRFKKELEDIMK   93 (342)
T ss_dssp             CSHHHHHHHHHHHSCCSSSTTSSSCSCCHHHHHHHHHTSEEEE----C---C--TTCEEEECCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE----c---C--ceeEEEEcCHHHHHHHHHHHHHHHHH
Confidence            3445677889999999999999999999999999999999864    1   1  22457789999999999999999999


Q ss_pred             HHHHHHhh
Q psy5744         116 RMEMEERD  123 (157)
Q Consensus       116 ~L~~~~~~  123 (157)
                      .|++.++.
T Consensus        94 ~L~~~~~~  101 (342)
T 3qph_A           94 KLEIELNN  101 (342)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhh
Confidence            99887654

>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=94.91  E-value=0.015  Score=41.09  Aligned_cols=46  Identities=13%  Similarity=0.278  Sum_probs=36.3

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..+  +.++-.+||+.+|+++..+.+++..|.+.|+|...
T Consensus        43 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           43 QGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEee
Confidence            57788888876  78999999999999999999999999999999865

>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=94.82  E-value=0.039  Score=37.80  Aligned_cols=50  Identities=12%  Similarity=0.188  Sum_probs=43.7

Q ss_pred             CCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          30 SIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        30 ~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      +++..+|+..+-.  +..|.-.||+..+|+++..|.++|-.|+..+||+...
T Consensus        36 t~~E~lVy~~I~~aGn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vk   87 (95)
T 2yu3_A           36 DNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVK   87 (95)
T ss_dssp             SHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEec
Confidence            4556788888776  5569999999999999999999999999999999873

>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=94.79  E-value=0.058  Score=41.07  Aligned_cols=36  Identities=11%  Similarity=0.202  Sum_probs=33.4

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||.+|..|..+|||..+
T Consensus        33 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~   68 (218)
T 3sxy_A           33 GEKLNVRELSEKLGISFTPVRDALLQLATEGLVKVV   68 (218)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            446899999999999999999999999999999865

>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=94.78  E-value=0.042  Score=37.87  Aligned_cols=48  Identities=15%  Similarity=0.309  Sum_probs=43.0

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||.+|-.++.++-.|||+.++    ++...|..+|..|.+.|+|...
T Consensus        10 ~~q~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~   61 (126)
T 1sd4_A           10 MAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRY   61 (126)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEE
Confidence            34577889999888999999999997    5899999999999999999975

>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=94.75  E-value=0.096  Score=37.85  Aligned_cols=46  Identities=11%  Similarity=0.145  Sum_probs=40.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -..|+++|..++.++-+||.+.+     +++...|=+.|..|.+.|||...
T Consensus        21 R~~Il~~l~~~~h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i   71 (145)
T 3eyy_A           21 RQLVLEAVDTLEHATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHA   71 (145)
T ss_dssp             HHHHHHHHHHHSSBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEE
Confidence            46789999875589999999988     79999999999999999999864

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

Probab=94.72  E-value=0.31  Score=34.89  Aligned_cols=47  Identities=13%  Similarity=0.194  Sum_probs=41.0

Q ss_pred             chHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||-.|.++ +.++-.+||+.+|+++..+-+++..|.+.|+|...
T Consensus        32 ~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~   79 (151)
T 4aik_A           32 THWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRH   79 (151)
T ss_dssp             HHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEee
Confidence            356788888764 56888999999999999999999999999999875

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=94.70  E-value=0.59  Score=32.49  Aligned_cols=85  Identities=11%  Similarity=0.182  Sum_probs=56.5

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HHHH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FVNI  105 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~~v  105 (157)
                      .+||-.|. ++..+=-+|++.+      +++...|-.+|.+|+++|+|...... . ++|  ..+.||.|.-..  ....
T Consensus        14 ~~IL~lL~-~~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~-~-~~g--~~rk~Y~LT~~G~~~l~~   88 (117)
T 4esf_A           14 GCVLEIIS-RRETYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKP-S-DMG--PPRKFYSLNEAGRQELEL   88 (117)
T ss_dssp             HHHHHHHH-HSCBCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC---------CEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeec-C-CCC--CCceEEEECHHHHHHHHH
Confidence            45665554 5778899999998      89999999999999999999987332 1 222  346788888532  2333


Q ss_pred             HHHHHHHHHHHHHHHHhh
Q psy5744         106 VKYKLDVMRKRMEMEERD  123 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~  123 (157)
                      .......+.+.++.-+..
T Consensus        89 ~~~~~~~~~~~i~~il~~  106 (117)
T 4esf_A           89 FWKKWDFVSSKINVLKSS  106 (117)
T ss_dssp             HHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHcc
Confidence            334555555556555433

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=94.68  E-value=0.053  Score=35.90  Aligned_cols=42  Identities=7%  Similarity=-0.003  Sum_probs=37.7

Q ss_pred             HHHHHHHhCC-CcCHHHHHHHhCCChHH-HHHHHHHHhhCccee
Q psy5744          35 LIIDMLVRNP-CMKEDDICELLKFERKM-LRARISTLKNDKIIQ   76 (157)
Q Consensus        35 vIlD~L~~~~-~i~dedLa~~l~i~~k~-vRkiL~~L~~d~Lv~   76 (157)
                      .+|..|..++ .++-.+||+.+|+++.. +.+++..|.+.|+|.
T Consensus        19 ~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           19 PTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCee
Confidence            3565666676 89999999999999999 999999999999999

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=94.60  E-value=0.089  Score=41.91  Aligned_cols=37  Identities=11%  Similarity=0.119  Sum_probs=33.3

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+ ++.+||+.+|++..-||++|..|.++|+|..++
T Consensus        50 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   87 (272)
T 3eet_A           50 HTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGRS   87 (272)
T ss_dssp             TSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            3456 899999999999999999999999999998754

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A

Probab=94.54  E-value=0.026  Score=36.60  Aligned_cols=58  Identities=17%  Similarity=0.182  Sum_probs=44.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChH-HHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEe
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERK-MLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFI   97 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k-~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I   97 (157)
                      -.|+++|-.+|.-+-=.||+.||+... +|+..|+.|+..+++..-   |   ..+.|..|=|.|
T Consensus        13 e~I~~fL~~~Gp~~AL~IAK~LGlktAK~VNp~LY~m~~~~lL~~D---e---k~~~W~iy~~~~   71 (72)
T 3eyi_A           13 EDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSRHLLDMD---E---QSKAWTIYRWTI   71 (72)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHTTCCSGGGTHHHHHHHHHTTSEEEC---T---TTCEEEEC----
T ss_pred             HHHHHHHHHcCCchHHHHHHHhCcchhhhcCHHHHHHHHccCcCCC---C---CCCceeEEEeee
Confidence            458899988999999999999999875 599999999999999642   2   224677777765

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=94.53  E-value=0.12  Score=37.62  Aligned_cols=79  Identities=11%  Similarity=0.251  Sum_probs=58.8

Q ss_pred             hHHHHHHHHh-C-CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744          33 DSLIIDMLVR-N-PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI  105 (157)
Q Consensus        33 ~ivIlD~L~~-~-~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v  105 (157)
                      -..|+++|.. + +.+|-+||.+.+     +++...|=+.|..|.+.|||...   +. ++|.    .+|-++..     
T Consensus        19 R~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~---~~-~~~~----~~Y~~~~~-----   85 (150)
T 2w57_A           19 RLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRH---HF-EGGK----SVFELSTQ-----   85 (150)
T ss_dssp             HHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEE---EC-GGGC----EEEEECCS-----
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEE---Ee-CCCc----eEEEecCC-----
Confidence            4678999885 3 679999999999     89999999999999999999865   22 2332    22222210     


Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                         .....++|..||+.+.+.+
T Consensus        86 -------------------~~H~HliC~~Cg~v~~~~~  104 (150)
T 2w57_A           86 -------------------HHHDHLVCLDCGEVIEFSD  104 (150)
T ss_dssp             -------------------SCCEEEEETTTCCEEEECC
T ss_pred             -------------------CceeEEEECCCCCEEEecc
Confidence                               2345799999999998743

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=94.51  E-value=0.11  Score=40.66  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=32.8

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..+ ++.+||+.+|++..-||++|..|.++|+|..+
T Consensus        31 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   67 (243)
T 2wv0_A           31 DMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRL   67 (243)
T ss_dssp             TCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            4456 89999999999999999999999999999864

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=94.47  E-value=0.092  Score=40.86  Aligned_cols=36  Identities=6%  Similarity=0.109  Sum_probs=32.9

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..+ ++.+||+.+|++..-||++|..|.++|+|..+
T Consensus        26 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~   62 (239)
T 3bwg_A           26 GDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQV   62 (239)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            3457 89999999999999999999999999999865

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=94.46  E-value=0.078  Score=41.30  Aligned_cols=36  Identities=17%  Similarity=0.314  Sum_probs=31.6

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ ++.+||+.+|++..-||++|..|.++|+|..+
T Consensus        30 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   66 (236)
T 3edp_A           30 GMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRK   66 (236)
T ss_dssp             CC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3456 89999999999999999999999999999875

>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=94.46  E-value=0.1  Score=35.20  Aligned_cols=35  Identities=14%  Similarity=0.072  Sum_probs=32.9

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++ ++-.+||..+|++...+++.+..|++.|||...
T Consensus        19 ~~-~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~   53 (95)
T 1r7j_A           19 SG-SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE   53 (95)
T ss_dssp             TC-BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEE
Confidence            56 999999999999999999999999999999864

>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=94.42  E-value=0.11  Score=40.29  Aligned_cols=36  Identities=25%  Similarity=0.515  Sum_probs=33.3

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||.+|..|..+|||..+
T Consensus        49 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~   84 (239)
T 2hs5_A           49 GARLSEPDICAALDVSRNTVREAFQILIEDRLVAHE   84 (239)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            346899999999999999999999999999999875

>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=94.21  E-value=0.039  Score=37.91  Aligned_cols=47  Identities=15%  Similarity=0.314  Sum_probs=41.9

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||.+|..++.++-.|||+.++    ++...|.++|..|.+.|+|...
T Consensus        11 ~~~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~   61 (123)
T 1okr_A           11 AEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK   61 (123)
T ss_dssp             HHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEE
Confidence            3566888888788899999999999    7899999999999999999865

>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=94.19  E-value=0.043  Score=36.50  Aligned_cols=48  Identities=8%  Similarity=0.078  Sum_probs=39.6

Q ss_pred             cCCCchHHHHHHHHh-CCC---cCHHHHHHHhCCChHHHHHHHHHHhhCcce
Q psy5744          28 FYSIEDSLIIDMLVR-NPC---MKEDDICELLKFERKMLRARISTLKNDKII   75 (157)
Q Consensus        28 Fy~~e~ivIlD~L~~-~~~---i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      +.......||..|.. .+.   ++-.+||+.+|++...+.+++..|.+.|+|
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc
Confidence            334445667777764 344   999999999999999999999999999999

>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=94.19  E-value=0.84  Score=31.51  Aligned_cols=84  Identities=15%  Similarity=0.153  Sum_probs=55.1

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FV  103 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~  103 (157)
                      ..||-+|. .+..+--+|++.+        +++...|-.+|.+|+++|+|...... . ++|  ..+.||.|--..  ..
T Consensus        15 ~~IL~~L~-~~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~-~-~~~--~~rk~Y~LT~~G~~~l   89 (116)
T 3f8b_A           15 VILLNVLK-QGDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGD-E-SQG--GRRKYYRLTEIGHENM   89 (116)
T ss_dssp             HHHHHHHH-HCCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC--------CCEEEEEECHHHHHHH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeec-c-CCC--CCceEEEECHHHHHHH
Confidence            45666655 5678888888887        79999999999999999999976321 1 232  346788887533  23


Q ss_pred             HHHHHHHHHHHHHHHHHHh
Q psy5744         104 NIVKYKLDVMRKRMEMEER  122 (157)
Q Consensus       104 ~vik~rl~~m~~~L~~~~~  122 (157)
                      .........+.+.++.-+.
T Consensus        90 ~~~~~~~~~~~~~i~~il~  108 (116)
T 3f8b_A           90 RLAFESWSRVDKIIENLEA  108 (116)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHc
Confidence            3333444555555555443

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=93.97  E-value=0.62  Score=32.24  Aligned_cols=83  Identities=13%  Similarity=0.195  Sum_probs=56.9

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhC------CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HHHH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLK------FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FVNI  105 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~------i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~~v  105 (157)
                      .+||-+|. .+..+--+|++.+.      ++...|-.+|.+|+++|+|...... . ++|  ..+.||.|.-..  ....
T Consensus        12 ~~IL~~L~-~~~~~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~~-~-~~g--~~rk~Y~LT~~G~~~l~~   86 (115)
T 4esb_A           12 GCILYIIS-QEEVYGYELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLKA-S-SLG--PKRKYYHITDKGLEQLEE   86 (115)
T ss_dssp             HHHHHHHH-HSCEEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEEE-C-TTS--CEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEeee-c-CCC--CCcEEEEECHHHHHHHHH
Confidence            45666665 56788899999984      9999999999999999999986322 1 233  456788888533  2333


Q ss_pred             HHHHHHHHHHHHHHHH
Q psy5744         106 VKYKLDVMRKRMEMEE  121 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~  121 (157)
                      .......+.+.++.-+
T Consensus        87 ~~~~~~~~~~~i~~il  102 (115)
T 4esb_A           87 FKQSWGMVSTTVNNLL  102 (115)
T ss_dssp             HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3335555555555544

>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=93.94  E-value=0.17  Score=42.50  Aligned_cols=46  Identities=17%  Similarity=0.380  Sum_probs=43.0

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||-.|-++  +.++-.+||+.+++++..+-+++.+|++.|||.++
T Consensus       406 q~~vl~~l~~~~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~  453 (487)
T 1hsj_A          406 EIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKK  453 (487)
T ss_dssp             HHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCE
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            57788888888  88999999999999999999999999999999976

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

Probab=93.82  E-value=0.12  Score=40.19  Aligned_cols=46  Identities=17%  Similarity=0.296  Sum_probs=40.9

Q ss_pred             hHHHHHHHHhCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-||++|..++ .++=.|||+.+|++...+.++|..|.+.|+|...
T Consensus        10 ~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           10 AFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            456888888764 7999999999999999999999999999999853

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

Probab=93.82  E-value=0.1  Score=36.94  Aligned_cols=48  Identities=13%  Similarity=0.131  Sum_probs=42.8

Q ss_pred             CchHHHHHHHHh-CCCcCHHHHHHHhC----CChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVR-NPCMKEDDICELLK----FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~-~~~i~dedLa~~l~----i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +....||.+|-. ++.++-.||++.++    ++...|.++|..|.+.|+|...
T Consensus         9 ~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~   61 (138)
T 2g9w_A            9 DLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI   61 (138)
T ss_dssp             HHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEE
Confidence            345678999987 58999999999998    8999999999999999999865

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=93.79  E-value=0.007  Score=44.48  Aligned_cols=50  Identities=14%  Similarity=0.177  Sum_probs=42.2

Q ss_pred             CCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          29 YSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        29 y~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.-.-.|++.|..++.+++.+||+.+|++..-||+.+..|.++|+|...
T Consensus        11 ~d~l~~~Il~~l~~~~~ls~~eLa~~lgvSr~~vr~al~~L~~~Gli~~~   60 (163)
T 2gqq_A           11 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGY   60 (163)
T ss_dssp             CCSHHHHHHHHHHHCSSCCTTGGGTSSSCCTTTSSSTHHHHHHHTSEEEE
T ss_pred             hhHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            44444567776666888999999999999999999999999999999854

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

Probab=93.76  E-value=0.28  Score=34.88  Aligned_cols=46  Identities=13%  Similarity=0.122  Sum_probs=39.4

Q ss_pred             hHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-||-.|..  ++.++-.+||+.+++++..+-+++.+|.+.|+|...
T Consensus        37 q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~   84 (147)
T 4b8x_A           37 RYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKR   84 (147)
T ss_dssp             HHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEe
Confidence            4556666653  467999999999999999999999999999999976

>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=93.71  E-value=0.0067  Score=37.16  Aligned_cols=32  Identities=50%  Similarity=0.760  Sum_probs=22.3

Q ss_pred             CCCCeeecCCCCCccchhhhhhccCC--CCcccC
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPCLLVLW--CACPCK  156 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~~L~d~--~~F~C~  156 (157)
                      .+...|.|+.|++.|+...++.....  ..|.|+
T Consensus        10 ~~~k~~~C~~C~k~F~~~~~l~~~H~~~k~~~C~   43 (62)
T 1vd4_A           10 TNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCT   43 (62)
T ss_dssp             CSSSEEECSSSCCEEEHHHHHHHEETTTTEEBCS
T ss_pred             CCCCCccCCCCCchhccHHHhHhhcCCCCCEECC
Confidence            34567899999999988877764432  357775

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=93.69  E-value=0.18  Score=39.50  Aligned_cols=42  Identities=12%  Similarity=0.252  Sum_probs=36.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .|+-. +.++..+-++||+.+|+++..|+..|..|.+.|+|..
T Consensus       169 ~l~~~-l~~~~~t~~~la~~~~l~~~~V~~~l~~L~~~~~v~~  210 (232)
T 2qlz_A          169 ILHYL-LLNGRATVEELSDRLNLKEREVREKISEMARFVPVKI  210 (232)
T ss_dssp             HHHHH-HHSSEEEHHHHHHHHTCCHHHHHHHHHHHTTTSCEEE
T ss_pred             HHHHH-HhcCCCCHHHHHHHhCcCHHHHHHHHHHHHhcCCeEE
Confidence            34434 5589999999999999999999999999999999983

>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=93.66  E-value=0.1  Score=40.56  Aligned_cols=46  Identities=15%  Similarity=0.264  Sum_probs=40.9

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-||++|..+ +.++=.|||+.+|++...+.++|..|.+.|+|...
T Consensus         8 ~l~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   54 (241)
T 2xrn_A            8 AASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEAL   54 (241)
T ss_dssp             HHHHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            45788988875 47999999999999999999999999999999853

>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=93.65  E-value=1.2  Score=30.89  Aligned_cols=83  Identities=8%  Similarity=0.153  Sum_probs=55.8

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HHHH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FVNI  105 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~~v  105 (157)
                      .+||-.|. .+..+=-+|++.+      +++...|-.+|.+|+++|+|...... . ++|  ..+.||.|.-..  ....
T Consensus        16 ~~IL~lL~-~~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~-~-~~g--~~rk~Y~lT~~G~~~l~~   90 (116)
T 3hhh_A           16 GLVLAIIQ-RKETYGYEITKILNDQGFTEIVEGTVYTILLRLEKNQWVIAEKKP-S-EKG--PMRKFYRLTSSGEAELAD   90 (116)
T ss_dssp             HHHHHHHH-HSCBCHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHTTSEEEEEEE-C-C----CEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHh-cCCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeee-c-CCC--CCceEEEECHHHHHHHHH
Confidence            45666665 5678889999998      79999999999999999999987332 1 232  446788888532  2223


Q ss_pred             HHHHHHHHHHHHHHHH
Q psy5744         106 VKYKLDVMRKRMEMEE  121 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~  121 (157)
                      .......+.+.++.-+
T Consensus        91 ~~~~~~~~~~~i~~il  106 (116)
T 3hhh_A           91 FWQRWTLLSKQVNKMK  106 (116)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3344445555555444

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

Probab=93.59  E-value=0.035  Score=39.29  Aligned_cols=35  Identities=6%  Similarity=0.189  Sum_probs=30.9

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+ ++.+||+.+|++..-||+++..|..+|+|...
T Consensus        33 ~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   68 (126)
T 3ic7_A           33 GRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNK   68 (126)
T ss_dssp             SEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEE
T ss_pred             CcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            345 89999999999999999999999999999865

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=93.58  E-value=1.1  Score=30.86  Aligned_cols=62  Identities=15%  Similarity=0.126  Sum_probs=46.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh------C--CCh-HHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL------K--FER-KMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l------~--i~~-k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ...||.+|. ++.++-.+|++.+      +  +++ ..|-.+|.+|+++|+|......   .+|  ..+.+|.|.-.
T Consensus        15 ~~~IL~~L~-~~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~---~~~--~~r~~Y~LT~~   85 (118)
T 2esh_A           15 ASTILLLVA-EKPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDT---TVS--PPRKIYRITPQ   85 (118)
T ss_dssp             HHHHHHHHH-HSCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEEC---SSS--SCEEEEEECHH
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeec---CCC--CCceEEEEChH
Confidence            356777765 4678999999999      3  899 9999999999999999976321   132  33566788753

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=93.55  E-value=0.17  Score=37.28  Aligned_cols=34  Identities=9%  Similarity=0.239  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+++..|.++|.+|+++|+|...
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~  202 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVKLS  202 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeC
Confidence            6899999999999999999999999999999864

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=93.52  E-value=0.16  Score=39.12  Aligned_cols=35  Identities=26%  Similarity=0.313  Sum_probs=32.2

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ...+ +|.+||+.+|++..-||.+|..|..+|||..
T Consensus        25 G~~LpsE~~La~~lgVSRtpVREAL~~L~~~GlV~~   60 (239)
T 2di3_A           25 GDHLPSERALSETLGVSRSSLREALRVLEALGTIST   60 (239)
T ss_dssp             TCBCCCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC
T ss_pred             CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEe
Confidence            3467 6889999999999999999999999999997

>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=93.48  E-value=0.31  Score=38.38  Aligned_cols=47  Identities=11%  Similarity=0.159  Sum_probs=42.1

Q ss_pred             chHHHHHHHHhCC--CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNP--CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~--~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|.+++  .++-.|||+.+++++..+-+++.+|++.|+|...
T Consensus       159 ~q~~vL~~L~~~~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~  207 (250)
T 1p4x_A          159 VEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE  207 (250)
T ss_dssp             HHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             HHHHHHHHHHhCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            3577888888764  5999999999999999999999999999999976

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

Probab=93.34  E-value=0.12  Score=39.62  Aligned_cols=37  Identities=11%  Similarity=0.300  Sum_probs=34.6

Q ss_pred             hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          42 RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        42 ~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++.++-.|||+.+|+++..|.+++.+|.++|||.+.
T Consensus        17 ~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~   53 (214)
T 3hrs_A           17 RHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKD   53 (214)
T ss_dssp             SCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEe
Confidence            3678999999999999999999999999999999875

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=93.30  E-value=0.27  Score=35.12  Aligned_cols=44  Identities=9%  Similarity=0.246  Sum_probs=36.0

Q ss_pred             hHHHHHHHHhC-----CCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          33 DSLIIDMLVRN-----PCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        33 ~ivIlD~L~~~-----~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      ..-||-.|..+     +.++--+||+.+++++..+-+++..|++.|||.
T Consensus        35 q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr   83 (148)
T 4fx0_A           35 QFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLVR   83 (148)
T ss_dssp             HHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC
T ss_pred             HHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEE
Confidence            56677777754     348999999999999999999999999999993

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=93.29  E-value=0.14  Score=41.25  Aligned_cols=44  Identities=16%  Similarity=0.173  Sum_probs=37.7

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+-.|..++.++-.|||+.||++.-.||+.|..|++.|+|+.+
T Consensus        11 ~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~ir   54 (315)
T 2w48_A           11 VKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIA   54 (315)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            33445556778999999999999999999999999999999843

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

Probab=93.21  E-value=1.3  Score=30.01  Aligned_cols=84  Identities=13%  Similarity=0.214  Sum_probs=56.1

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh--HHHHHH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT--FVNIVK  107 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~--~~~vik  107 (157)
                      ..||-.|.. +..+-.+|++.+    +++...|-.+|.+|+++|+|.....  . .+|  ..+.||.|.-..  ......
T Consensus        12 ~~IL~~L~~-~~~~gyel~~~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~--~-~~~--r~r~~y~LT~~G~~~l~~~~   85 (108)
T 3l7w_A           12 YLILAIVSK-HDSYGYDISQTIKLIASIKESTLYPILKKLEKAGYLSTYTQ--E-HQG--RRRKYYHLTDSGEKHLVYLT   85 (108)
T ss_dssp             HHHHHHHHH-SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEEE--E-ETT--EEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCcHHHHHHHHHHHhCCCcChHHHHHHHHHHCCCeEEEee--c-CCC--CcceEEEECHHHHHHHHHHH
Confidence            346666654 566777777774    8999999999999999999997632  2 143  456788887532  333444


Q ss_pred             HHHHHHHHHHHHHHhh
Q psy5744         108 YKLDVMRKRMEMEERD  123 (157)
Q Consensus       108 ~rl~~m~~~L~~~~~~  123 (157)
                      .....+.+.+++-+..
T Consensus        86 ~~~~~~~~~i~~~l~~  101 (108)
T 3l7w_A           86 KEWSVYKMTIDGIVEG  101 (108)
T ss_dssp             HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHCc
Confidence            4556666666655533

>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=93.05  E-value=0.097  Score=38.31  Aligned_cols=33  Identities=12%  Similarity=0.409  Sum_probs=31.4

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       165 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  197 (207)
T 2oz6_A          165 ITRQEIGRIVGCSREMVGRVLKSLEEQGLVHVK  197 (207)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            789999999999999999999999999999865

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B

Probab=93.01  E-value=0.46  Score=36.95  Aligned_cols=46  Identities=4%  Similarity=0.126  Sum_probs=40.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.|++.+-.++.+|..+||..+|++....+..|..+..+|++-..
T Consensus       156 ~~~il~~~~~~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D  201 (218)
T 3cuq_B          156 VASALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRD  201 (218)
T ss_dssp             HHHHHHHHHHTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEE
Confidence            4456776666899999999999999999999999999999999864

>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=92.97  E-value=0.1  Score=38.27  Aligned_cols=34  Identities=12%  Similarity=0.326  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~~  200 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRILKMLEDQNLISAH  200 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEeC
Confidence            4788999999999999999999999999999875

>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=92.96  E-value=0.15  Score=42.23  Aligned_cols=45  Identities=7%  Similarity=0.139  Sum_probs=41.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..|++.|.+++.+|=.|||+.+|++...|.+++..|.++|+|...
T Consensus        19 ~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~~   63 (406)
T 1z6r_A           19 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   63 (406)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEee
Confidence            458888888999999999999999999999999999999999774

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=92.92  E-value=0.18  Score=31.35  Aligned_cols=43  Identities=19%  Similarity=0.355  Sum_probs=38.2

Q ss_pred             HHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .++|.+-.+ |.+.=++.|+..|++..+|=.+|.+|.+.||++-
T Consensus        14 ~lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           14 ELLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCeec
Confidence            477887764 6788899999999999999999999999999974

>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=92.90  E-value=0.13  Score=42.49  Aligned_cols=43  Identities=9%  Similarity=0.173  Sum_probs=40.5

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|++.|. ++.+|=.|||+.+|+++..|.+++..|.++|+|...
T Consensus        24 ~il~~l~-~~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~~   66 (380)
T 2hoe_A           24 RILKRIM-KSPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEE   66 (380)
T ss_dssp             CSHHHHH-HSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            4788888 999999999999999999999999999999999875

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=92.81  E-value=0.11  Score=38.30  Aligned_cols=34  Identities=9%  Similarity=0.279  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       163 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  196 (216)
T 4ev0_A          163 QIRHHELAALAGTSRETVSRVLHALAEEGVVRLG  196 (216)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            4789999999999999999999999999999864

>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=92.75  E-value=0.11  Score=38.60  Aligned_cols=33  Identities=18%  Similarity=0.433  Sum_probs=31.5

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~  220 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLHAR  220 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEEC
Confidence            789999999999999999999999999999875

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

Probab=92.65  E-value=0.25  Score=40.29  Aligned_cols=60  Identities=10%  Similarity=0.115  Sum_probs=47.2

Q ss_pred             HHHHHHHHHcCCCc------hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          19 QLSRLVVRGFYSIE------DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        19 ~Lv~~v~R~Fy~~e------~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +++..++.+|....      ..-|.|.|... +.++-++||+.+|+++.-++++|..|...|++...
T Consensus        10 ~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~~p~t~~eLA~~~g~~~~~l~rlLr~L~~~gll~~~   76 (353)
T 4a6d_A           10 RLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASAHGTELLLDICVSLKLLKVE   76 (353)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSSSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCCCCCCHHHHHHhhCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34444555554444      23489998864 67999999999999999999999999999999754

>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=92.58  E-value=0.15  Score=41.56  Aligned_cols=45  Identities=18%  Similarity=0.221  Sum_probs=39.8

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|++.|-.++.++-++||+.+|++...||+-|..|++.|++...
T Consensus         8 ~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~   52 (321)
T 1bia_A            8 LKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFT   52 (321)
T ss_dssp             HHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEE
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEE
Confidence            457777766788999999999999999999999999999998643

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=92.58  E-value=0.18  Score=38.95  Aligned_cols=37  Identities=19%  Similarity=0.290  Sum_probs=33.9

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++.++=.+||+.||++...||..+.+|++.|||.+..
T Consensus        28 ~~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~   64 (200)
T 2p8t_A           28 KEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ   64 (200)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             cCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            4679999999999999999999999999999998864

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=92.53  E-value=0.42  Score=34.78  Aligned_cols=33  Identities=15%  Similarity=0.315  Sum_probs=31.4

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+++..|.++|.+|+++|+|...
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~  172 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRREGLIATA  172 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            789999999999999999999999999999864

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=92.51  E-value=0.16  Score=38.13  Aligned_cols=44  Identities=9%  Similarity=0.149  Sum_probs=36.6

Q ss_pred             HHHHHHH----hCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLV----RNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~----~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|+++|.    .++ ..|-.|||+.+|+++.-+++.|..|+++|+|...
T Consensus         9 ~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A            9 KVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEec
Confidence            3455543    344 5899999999999999999999999999999764

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=92.51  E-value=0.1  Score=38.19  Aligned_cols=46  Identities=17%  Similarity=0.231  Sum_probs=41.4

Q ss_pred             hHHHHHHHHhCCC---cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPC---MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~---i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..++.   ++-.+||+.+|+++..|.+++..|.+.|+|...
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~  119 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERR  119 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEec
Confidence            5678888887654   999999999999999999999999999999865

>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=92.50  E-value=0.17  Score=41.39  Aligned_cols=43  Identities=19%  Similarity=0.277  Sum_probs=37.5

Q ss_pred             HHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -|+++|..  ...+|-++||+.+|++..-|+|.+..|++.|++-.
T Consensus         7 ~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~   51 (323)
T 3rkx_A            7 DVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLEGCKID   51 (323)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEE
T ss_pred             HHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEE
Confidence            47888764  35899999999999999999999999999999554

>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=92.40  E-value=0.13  Score=38.43  Aligned_cols=34  Identities=9%  Similarity=0.244  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+++..|.++|.+|+++|+|...
T Consensus       180 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  213 (232)
T 2gau_A          180 YLSREELATLSNMTVSNAIRTLSTFVSERMLALD  213 (232)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeC
Confidence            4789999999999999999999999999999864

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=92.35  E-value=0.14  Score=37.60  Aligned_cols=33  Identities=15%  Similarity=0.253  Sum_probs=31.3

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+.+..|.++|..|+++|+|...
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~  179 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRSG  179 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeC
Confidence            789999999999999999999999999999864

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=92.10  E-value=2  Score=29.55  Aligned_cols=64  Identities=14%  Similarity=0.201  Sum_probs=46.1

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh-------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL-------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l-------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      .+||-.|. .+..+--+|++.+       +++...|-.+|.+|+++|+|........ .+|  ..+.||.|.-..
T Consensus        25 ~~IL~lL~-~~~~~Gyei~~~l~~~~~~~~is~gtLY~~L~rLe~~GlI~~~~~~~~-~~~--~~rk~Y~LT~~G   95 (115)
T 2dql_A           25 CYILYVLL-QGESYGTELIQQLETEHPTYRLSDTVLYSAIKFLEDNRAITGYWKKLE-GRG--RPRRMYQVSPEW   95 (115)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHHHHHCTTEECCHHHHHHHHHHHHHTTSEEEEEECCT-TCS--SCEEEEEECGGG
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHHHHcCCCCCCcchHHHHHHHHHHCCCEEEEeeecC-CCC--CCcEEEEECHHH
Confidence            34666655 5678888887776       5999999999999999999998632210 122  447888988543

>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=92.04  E-value=0.15  Score=38.15  Aligned_cols=34  Identities=15%  Similarity=0.223  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|..|+++|+|...
T Consensus       175 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~~  208 (231)
T 3e97_A          175 PLGTQDIMARTSSSRETVSRVLKRLEAHNILEVS  208 (231)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEec
Confidence            4789999999999999999999999999999865

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=92.02  E-value=0.36  Score=33.61  Aligned_cols=83  Identities=16%  Similarity=0.173  Sum_probs=54.5

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhC------CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHH
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLK------FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVK  107 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~------i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik  107 (157)
                      ..||-.|. .+..+--+|++.++      ++...|-.+|.+|+++|+|...... . ++|  ..+.||.|.-..--..-.
T Consensus        17 ~~IL~lL~-~~p~~gyel~~~l~~~~~~~i~~gtly~~L~~Le~~GlI~~~~~~-~-~~~--~~rk~Y~lT~~G~~~l~~   91 (117)
T 3elk_A           17 LYILKELV-KRPMHGYELQKSMFETTGQALPQGSIYILLKTMKERGFVISESSV-N-EKG--QQLTVYHITDAGKKFLCD   91 (117)
T ss_dssp             HHHHHHHH-HSCEEHHHHHHHHHHHHSCCCCTTHHHHHHHHHHHHTSEEEEEEE-C--CC--CEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHHHHhCCCCCcchHHHHHHHHHHCCCEEEEeee-c-CCC--CCceEEEECHHHHHHHHH
Confidence            45676665 56788889998886      8999999999999999999987322 1 232  446788888543322222


Q ss_pred             --HHHHHHHHHHHHHH
Q psy5744         108 --YKLDVMRKRMEMEE  121 (157)
Q Consensus       108 --~rl~~m~~~L~~~~  121 (157)
                        .....+.+.++.-+
T Consensus        92 ~~~~~~~~~~~i~~~l  107 (117)
T 3elk_A           92 HSQALQLARKIIDDLL  107 (117)
T ss_dssp             TSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence              13444444444443

>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=91.99  E-value=0.16  Score=38.68  Aligned_cols=34  Identities=18%  Similarity=0.288  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       193 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~~  226 (243)
T 3la7_A          193 KLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIH  226 (243)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEEc
Confidence            5789999999999999999999999999999875

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=91.97  E-value=0.36  Score=35.78  Aligned_cols=44  Identities=11%  Similarity=0.194  Sum_probs=38.2

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..||-.|. .+.++-.||++.+        +++...|-.+|.+|+++|+|...
T Consensus         5 ~~iL~lL~-~~~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~   56 (179)
T 1yg2_A            5 HVILTVLS-TRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCV   56 (179)
T ss_dssp             HHHHHHHH-HCCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHh-cCCCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEE
Confidence            35666665 4789999999999        79999999999999999999875

>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=91.82  E-value=0.17  Score=37.71  Aligned_cols=34  Identities=12%  Similarity=0.297  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|..|+++|+|...
T Consensus       177 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  210 (227)
T 3d0s_A          177 DLTQEEIAQLVGASRETVNKALADFAHRGWIRLE  210 (227)
T ss_dssp             CCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            3799999999999999999999999999999864

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=91.75  E-value=0.23  Score=37.06  Aligned_cols=44  Identities=20%  Similarity=0.286  Sum_probs=38.3

Q ss_pred             HHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcc-eee
Q psy5744          34 SLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKI-IQT   77 (157)
Q Consensus        34 ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~L-v~~   77 (157)
                      .-|++.|..+ +.++-.+||+.+|++...|++-+..|++.|+ |..
T Consensus        24 ~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           24 KSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4578887764 5699999999999999999999999999998 653

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=91.75  E-value=0.24  Score=37.65  Aligned_cols=46  Identities=13%  Similarity=0.281  Sum_probs=41.9

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+-.|++.|-.++.++++|||+.+|++...+|+=|..|...+|...
T Consensus        13 R~~~i~~~l~~~~~~~~~~la~~~~vs~~TiRrDl~eL~~~~l~~r   58 (190)
T 4a0z_A           13 RREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKR   58 (190)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHTCCCHHHH
T ss_pred             HHHHHHHHHHHCCCEeHHHHHHHHCCCHHHHHHHHHHhcCcchhhH
Confidence            4567899988999999999999999999999999999999988754

>2k9l_A RNA polymerase sigma factor RPON; protein, transcription; NMR {Aquifex aeolicus}

Probab=91.67  E-value=1.4  Score=28.33  Aligned_cols=63  Identities=13%  Similarity=0.187  Sum_probs=46.9

Q ss_pred             CcccccchHHHHHHHHHHHHHcCCCchH----HHHHHHHhCCCcC--HHHHHHHhCCChHHHHHHHHHHh
Q psy5744           7 GYVHTEVPTSLKQLSRLVVRGFYSIEDS----LIIDMLVRNPCMK--EDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus         7 ~~~~~~ip~~~~~Lv~~v~R~Fy~~e~i----vIlD~L~~~~~i~--dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      |..+...++.-.+|...+. ...++...    .|++.|=.+|+++  -++||..+|++..+|.++|..+.
T Consensus         5 ~~~~~~~~~e~ehL~~Ql~-~~~~~~~~~Ia~~iI~~LD~~GYL~~~l~eia~~l~~~~~eve~vL~~lQ   73 (76)
T 2k9l_A            5 PYQIPYTPSELEELQQNIK-LELEGKEQELALELLNYLNEKGFLSKSVEEISDVLRCSVEELEKVRQKVL   73 (76)
T ss_dssp             CSSSSCCHHHHHHHHHHHH-HHCCTTSHHHHHHHHHHCTTSSTTCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             hhhhccCCchHHHHHHHHc-ccCCHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHcCCCHHHHHHHHHHHh
Confidence            3334444544788888888 77777644    3556655678855  78999999999999999998775

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=91.67  E-value=0.22  Score=39.26  Aligned_cols=82  Identities=15%  Similarity=0.199  Sum_probs=56.8

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc--hhHHHHHHH
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY--QTFVNIVKY  108 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y--~~~~~vik~  108 (157)
                      ...||..|-.+  +.++-.|||+.+++++..+-++|.+|++.|+|...+ .+  .|.|..   +=++.-  ..++..+..
T Consensus        36 q~~vL~~L~~~~~~~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~-~~--~DrR~~---~i~LT~~G~~~~~~~~~  109 (250)
T 1p4x_A           36 EFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVR-SK--IDERNT---YISISEEQREKIAERVT  109 (250)
T ss_dssp             HHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEE-CS--SSTTSE---EEECCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecC-CC--CCCCeE---EEEECHHHHHHHHHHHH
Confidence            57888898874  479999999999999999999999999999999762 21  243332   223332  234455555


Q ss_pred             HHHHHHHHHHHH
Q psy5744         109 KLDVMRKRMEME  120 (157)
Q Consensus       109 rl~~m~~~L~~~  120 (157)
                      .+..+.+.+..+
T Consensus       110 ~~~~~~eq~s~E  121 (250)
T 1p4x_A          110 LFDQIIKQFNLA  121 (250)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc
Confidence            555555555554

>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=91.58  E-value=0.85  Score=34.48  Aligned_cols=34  Identities=15%  Similarity=0.327  Sum_probs=32.1

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|..|+++|+|...
T Consensus       177 ~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~~  210 (250)
T 3e6c_C          177 PLSQKSIGEITGVHHVTVSRVLASLKRENILDKK  210 (250)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEeC
Confidence            5799999999999999999999999999999865

>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=91.47  E-value=0.16  Score=37.83  Aligned_cols=33  Identities=15%  Similarity=0.326  Sum_probs=31.5

Q ss_pred             cCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          46 MKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        46 i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++-++||..+|+.+..|.++|..|+++|+|...
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~~  196 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ  196 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEEc
Confidence            789999999999999999999999999999864

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=91.41  E-value=0.26  Score=38.56  Aligned_cols=45  Identities=11%  Similarity=0.090  Sum_probs=39.8

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+-||++|.. ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus        16 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~   61 (257)
T 2g7u_A           16 GFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAG   61 (257)
T ss_dssp             HHHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            3568888875 46799999999999999999999999999999975

>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=91.40  E-value=0.036  Score=45.53  Aligned_cols=48  Identities=17%  Similarity=0.232  Sum_probs=0.0

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.+..||..|..++.++-.|||+.+|++...||+.|..|++.|+|..+
T Consensus        20 ~r~~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~~   67 (345)
T 2o0m_A           20 QERFQILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQLNLIEPS   67 (345)
T ss_dssp             ------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            345678888888899999999999999999999999999999999743

>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=91.32  E-value=0.3  Score=40.88  Aligned_cols=45  Identities=7%  Similarity=0.121  Sum_probs=41.9

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..|++.|.+++.+|=.|||+.+|+++..|.+++..|.++|+|...
T Consensus        42 ~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~~   86 (429)
T 1z05_A           42 GRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHET   86 (429)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            458888888999999999999999999999999999999999875

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=91.25  E-value=0.25  Score=38.82  Aligned_cols=44  Identities=9%  Similarity=0.222  Sum_probs=39.7

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +-||++|.. ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~   70 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTS   70 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            578888864 56899999999999999999999999999999974

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

Probab=91.24  E-value=0.63  Score=33.49  Aligned_cols=63  Identities=11%  Similarity=0.218  Sum_probs=45.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh-------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL-------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l-------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      .+||.+|. .+..+--+|++.+       +++...|-.+|.+|+++|+|.......  ++ ....+.||.|.-.
T Consensus        37 ~~IL~lL~-~~~~~Gyei~k~l~~~~~~~~is~gtLYp~L~rLe~~GlI~~~~~~~--~~-~g~~rk~Y~LT~~  106 (138)
T 2e1n_A           37 CYVLAVLR-HEDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKKV--EG-RGRPRRMYQLAQA  106 (138)
T ss_dssp             HHHHHHHT-TSCEEHHHHHHHHHHHSTTEECCHHHHHHHHHHHHHTTSEEEEEECC--TT-CSSCEEEEEESCS
T ss_pred             HHHHHHHH-hCCCcHHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecc--cC-CCCCcEEEEECHH
Confidence            44676665 5677777877776       599999999999999999999863221  11 1244788898864

>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=91.22  E-value=0.21  Score=38.50  Aligned_cols=34  Identities=12%  Similarity=0.326  Sum_probs=31.8

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~~  250 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRILKMLEDQNLISAH  250 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEc
Confidence            4688999999999999999999999999999875

>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=91.17  E-value=0.24  Score=36.68  Aligned_cols=34  Identities=15%  Similarity=0.286  Sum_probs=31.9

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+++..|.++|.+|+++|+|...
T Consensus       167 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  200 (220)
T 2fmy_A          167 GLNTEEIALMLGTTRQTVSVLLNDFKKMGILERV  200 (220)
T ss_dssp             SSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEES
T ss_pred             cCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEEc
Confidence            5899999999999999999999999999999863

>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=91.13  E-value=0.47  Score=32.31  Aligned_cols=42  Identities=17%  Similarity=0.270  Sum_probs=36.1

Q ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCce
Q psy5744          44 PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKA   89 (157)
Q Consensus        44 ~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~   89 (157)
                      +.++--+||+.++++.--+++.+..|++.|||...  ..  .|||.
T Consensus        35 ~~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~--~~--~D~R~   76 (96)
T 2obp_A           35 TPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVS--VE--ADGRG   76 (96)
T ss_dssp             CCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--EC--TTSCE
T ss_pred             CCcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEee--cC--CCCce
Confidence            56899999999999999999999999999999963  22  46665

>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=91.10  E-value=0.21  Score=37.64  Aligned_cols=69  Identities=16%  Similarity=0.146  Sum_probs=47.8

Q ss_pred             cccchHHHHHHHHHHHHHcCC-----------CchHHHHHHHHhC----C-----CcCHHHHHHHhCCChHHHHHHHHHH
Q psy5744          10 HTEVPTSLKQLSRLVVRGFYS-----------IEDSLIIDMLVRN----P-----CMKEDDICELLKFERKMLRARISTL   69 (157)
Q Consensus        10 ~~~ip~~~~~Lv~~v~R~Fy~-----------~e~ivIlD~L~~~----~-----~i~dedLa~~l~i~~k~vRkiL~~L   69 (157)
                      ....|+....+++.+++.+..           +-.--+..+|+..    +     .++-++||..+|+.+..|.++|..|
T Consensus       131 ~~~~p~~~~~l~~~l~~~l~~~~~~~~~l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~l  210 (232)
T 1zyb_A          131 LFRYDIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNEL  210 (232)
T ss_dssp             GGGSHHHHHHHHHHHHHHHHHHHHHTTSCCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHhCCChhHHHHHHHHH
Confidence            345566666666665554322           1122244455531    1     3789999999999999999999999


Q ss_pred             hhCcceeee
Q psy5744          70 KNDKIIQTR   78 (157)
Q Consensus        70 ~~d~Lv~~~   78 (157)
                      +++|+|...
T Consensus       211 ~~~glI~~~  219 (232)
T 1zyb_A          211 QDNGLIELH  219 (232)
T ss_dssp             HHTTSCEEE
T ss_pred             HHCCCEEec
Confidence            999999865

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

Probab=90.96  E-value=0.24  Score=39.39  Aligned_cols=44  Identities=7%  Similarity=0.254  Sum_probs=38.4

Q ss_pred             HHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +-||++|..+ +.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus        33 l~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~   77 (275)
T 3mq0_A           33 VRILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLAR   77 (275)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5799999875 5799999999999999999999999999999974

>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=90.85  E-value=0.23  Score=37.57  Aligned_cols=34  Identities=18%  Similarity=0.214  Sum_probs=31.7

Q ss_pred             CcCHHHHHHHhCCCh-HHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFER-KMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~-k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+ ..|.++|.+|+++|+|...
T Consensus       169 ~~t~~~lA~~lG~sr~etvsR~l~~l~~~glI~~~  203 (238)
T 2bgc_A          169 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYK  203 (238)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhCCChHHHHHHHHHHHHHCCCEEec
Confidence            588999999999999 6999999999999999864

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=90.84  E-value=0.15  Score=37.90  Aligned_cols=34  Identities=12%  Similarity=0.186  Sum_probs=31.7

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       178 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~  211 (227)
T 3dkw_A          178 PVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHLD  211 (227)
T ss_dssp             CSCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEES
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEec
Confidence            4678999999999999999999999999999865

>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=90.62  E-value=0.2  Score=39.39  Aligned_cols=45  Identities=9%  Similarity=0.159  Sum_probs=40.6

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+-||++|.. ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus         8 al~IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~   53 (260)
T 3r4k_A            8 ALTLLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQ   53 (260)
T ss_dssp             HHHHHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3568888886 57899999999999999999999999999999974

>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=90.57  E-value=0.48  Score=38.32  Aligned_cols=66  Identities=11%  Similarity=0.137  Sum_probs=48.7

Q ss_pred             cchHHHHHHHHHHHHHcCCCc------hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          12 EVPTSLKQLSRLVVRGFYSIE------DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        12 ~ip~~~~~Lv~~v~R~Fy~~e------~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++.+...++.+.+.-+|....      ..-|.|.|.. +.+|-+|||+.+|+++.-++++|..|...|++...
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~-~~~t~~eLA~~~g~~~~~l~rlLr~L~~~gll~~~   97 (359)
T 1x19_A           26 DLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE-GPKDLATLAADTGSVPPRLEMLLETLRQMRVINLE   97 (359)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC-CCCCHHHHHHHhCcChHHHHHHHHHHHhCCCeEee
Confidence            344445555555443333332      2347888764 78999999999999999999999999999999853

>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=90.55  E-value=0.48  Score=32.31  Aligned_cols=43  Identities=9%  Similarity=0.259  Sum_probs=39.4

Q ss_pred             HHHHHHHHhCCCcCHHHHHH-HhCCChHHHHHHHHHHhhCccee
Q psy5744          34 SLIIDMLVRNPCMKEDDICE-LLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~-~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      .-||=+|.+++..|-.|||+ .++|+...|-+-+..|.++|+|.
T Consensus        19 fsiL~~L~~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           19 ATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             HHHHHHHHHSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee
Confidence            45666777889999999999 99999999999999999999998

>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=90.37  E-value=0.44  Score=38.36  Aligned_cols=45  Identities=9%  Similarity=0.073  Sum_probs=40.0

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..-|+|.|. .+.++-+|||+.+|+++.-++++|..|...|++...
T Consensus        41 ~l~i~~~l~-~~~~t~~ela~~~~~~~~~l~r~L~~L~~~g~~~~~   85 (360)
T 1tw3_A           41 TLRLVDHIL-AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEED   85 (360)
T ss_dssp             HTTHHHHHH-TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HhCHHHHHh-CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEec
Confidence            345888884 678999999999999999999999999999999874

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=90.19  E-value=0.41  Score=42.29  Aligned_cols=45  Identities=13%  Similarity=0.284  Sum_probs=40.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh-----Ccceee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN-----DKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~-----d~Lv~~   77 (157)
                      ...||+.|..++.+|-.+||+.+|++...++++|.+|.+     .|||..
T Consensus       432 ~~~iL~~l~~~~~it~~~la~~l~~s~~~~~~~L~~L~~~~~~~~glie~  481 (583)
T 3lmm_A          432 IAIVLYLLFQRPFITIDVVARGLQSGKEAARNALEAARQTTVAGAPLIIA  481 (583)
T ss_dssp             HHHHHHHHHHSSSBCHHHHHHHHTSCHHHHHHHHHHHHTCEETTEESEEE
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHhCcCHHHHHHHHHHHHhhhccccceEEE
Confidence            357899989999999999999999999999999999999     667764

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=90.10  E-value=0.091  Score=31.42  Aligned_cols=22  Identities=36%  Similarity=0.676  Sum_probs=16.5

Q ss_pred             CeeecCCCCCccchhhhhhccC
Q psy5744         128 SSFKCPRCLKTFTDLEPCLLVL  149 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda~~L~d  149 (157)
                      .-|.|-+||++||..|...|..
T Consensus         2 ~iY~C~rCg~~fs~~el~~lP~   23 (48)
T 4ayb_P            2 AVYRCGKCWKTFTDEQLKVLPG   23 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCSS
T ss_pred             cEEEeeccCCCccHHHHhhCCC
Confidence            3699999999999999877643

>3mjh_B Early endosome antigen 1; protein-zinc finger complex, beta BETA alpha fold, beta HAIR RAB5A GTPase, EEA1, protein transport; HET: GTP; 2.03A {Homo sapiens}

Probab=90.08  E-value=0.15  Score=28.45  Aligned_cols=20  Identities=30%  Similarity=0.800  Sum_probs=16.2

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +..+|+||.|.+.+..-+.+
T Consensus         2 ~~EGFiCP~C~~~l~s~~~L   21 (34)
T 3mjh_B            2 SSEGFICPQCMKSLGSADEL   21 (34)
T ss_dssp             CSEEEECTTTCCEESSHHHH
T ss_pred             CCcccCCcHHHHHcCCHHHH
Confidence            45689999999999877654

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

Probab=90.00  E-value=0.31  Score=35.81  Aligned_cols=35  Identities=6%  Similarity=0.100  Sum_probs=31.5

Q ss_pred             CCcCHHHHHHHhC--------------CChHHHHHHHHHHhhCcceeee
Q psy5744          44 PCMKEDDICELLK--------------FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        44 ~~i~dedLa~~l~--------------i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..-+.+||+.+|              ++..-||++|..|+.+|||...
T Consensus        66 g~~G~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~  114 (150)
T 2v7f_A           66 GPVGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKV  114 (150)
T ss_dssp             CSBCHHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEe
Confidence            3555799999999              9999999999999999999864

>2ra5_A Putative transcriptional regulator; beta structure, UTRA domain, structural genomics, PSI-2, protein structure initiative; HET: SRT; 2.40A {Streptomyces coelicolor A3} SCOP: d.190.1.2

Probab=89.95  E-value=0.078  Score=41.53  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=4.9

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+ ++.+||+.+|++..-||++|..|.++|+|..+
T Consensus        37 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   73 (247)
T 2ra5_A           37 GSLLGNEIELAARLGLSRPTVRQAIQSLVDKGLLVRR   73 (247)
T ss_dssp             -------------------------------CEEEEE
T ss_pred             CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3456 89999999999999999999999999999765

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=89.72  E-value=0.53  Score=34.36  Aligned_cols=62  Identities=13%  Similarity=0.306  Sum_probs=44.4

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh-------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL-------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l-------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      .+||-+|. .+..+-.+|++.+       +++...|-.+|.+|+++|+|..+...   .++....+.||.|--
T Consensus        47 ~~IL~lL~-~~p~~GYeI~k~l~~~~~~~~is~gtLYp~L~rLE~~GlI~~~~~~---~~~~g~~rk~Y~LT~  115 (148)
T 2zfw_A           47 CYVLAVLR-HEDSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDEQIISGYWKK---VEGRGRPRRMYQLAQ  115 (148)
T ss_dssp             HHHHHHHT-TCCEEHHHHHHHHHHHCTTEECCSHHHHHHHHHHHHTSSEEEECCC---CTTSSCCCCEEEESS
T ss_pred             HHHHHHHH-hCCCcHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHCCCEEEEeec---cCCCCCCcEEEEECH
Confidence            34666655 5678888888777       59999999999999999999976321   111123467888874

>2kvh_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=89.57  E-value=0.14  Score=24.85  Aligned_cols=17  Identities=24%  Similarity=0.608  Sum_probs=13.8

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         3 ~~~C~~C~k~f~~~~~l   19 (27)
T 2kvh_A            3 PFSCSLCPQRSRDFSAM   19 (27)
T ss_dssp             CEECSSSSCEESSHHHH
T ss_pred             CccCCCcChhhCCHHHH
Confidence            58999999999876543

>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=89.56  E-value=0.61  Score=25.87  Aligned_cols=29  Identities=7%  Similarity=0.084  Sum_probs=25.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCc
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDK   73 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~   73 (157)
                      .++-.+||+.+|++...|++.+....+.|
T Consensus        21 g~s~~~IA~~lgis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C           21 NVSLHEMSRKISRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHCSTTTT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHhhHHhcC
Confidence            47899999999999999999998766554

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=89.46  E-value=0.17  Score=37.58  Aligned_cols=34  Identities=15%  Similarity=0.267  Sum_probs=0.0

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+|...
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~G~I~~~  197 (213)
T 1o5l_A          164 PVTLEELSRLFGCARPALSRVFQELEREGYIEKH  197 (213)
T ss_dssp             ----------------------------------
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEc
Confidence            5789999999999999999999999999999865

>2i5o_A DNA polymerase ETA; zinc finger, DNA polymerase,POL ETA, UBZ, ubiquitin-binding zinc finger, translesion synthesis, ubiquitin-binding domain; HET: DNA; NMR {Homo sapiens}

Probab=89.37  E-value=0.24  Score=28.43  Aligned_cols=22  Identities=9%  Similarity=0.197  Sum_probs=17.0

Q ss_pred             CCCCeeecCCCCCccchhhhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      .....|.||+||..+...+.+.
T Consensus         5 ~~~~~~~C~~C~~~i~~~~~~E   26 (39)
T 2i5o_A            5 AAEDQVPCEKCGSLVPVWDMPE   26 (39)
T ss_dssp             -CCCEEECTTTCCEEEGGGHHH
T ss_pred             CcCCCcccccccCcCCcccccc
Confidence            3567899999999998876554

>1znf_A 31ST zinc finger from XFIN; zinc finger DNA binding domain; NMR {Xenopus laevis} SCOP: g.37.1.1

Probab=89.12  E-value=0.14  Score=24.66  Aligned_cols=16  Identities=25%  Similarity=0.739  Sum_probs=13.3

Q ss_pred             eecCCCCCccchhhhh
Q psy5744         130 FKCPRCLKTFTDLEPC  145 (157)
Q Consensus       130 Y~Cp~C~~~Ys~lda~  145 (157)
                      |.|+.|++.|+....+
T Consensus         2 ~~C~~C~k~f~~~~~l   17 (27)
T 1znf_A            2 YKCGLCERSFVEKSAL   17 (27)
T ss_dssp             CBCSSSCCBCSSHHHH
T ss_pred             ccCCCCCCcCCCHHHH
Confidence            8899999999876554

>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=89.11  E-value=0.41  Score=38.69  Aligned_cols=77  Identities=13%  Similarity=0.177  Sum_probs=49.4

Q ss_pred             CCCCCCCcccccchHHHHHHHHHHHHHcCCCc------hHHHHHHHHhC-CCcCHHHHHHHhCCC---hHHHHHHHHHHh
Q psy5744           1 MSTSDEGYVHTEVPTSLKQLSRLVVRGFYSIE------DSLIIDMLVRN-PCMKEDDICELLKFE---RKMLRARISTLK   70 (157)
Q Consensus         1 ~~~~~~~~~~~~ip~~~~~Lv~~v~R~Fy~~e------~ivIlD~L~~~-~~i~dedLa~~l~i~---~k~vRkiL~~L~   70 (157)
                      |+.+-+.....++.+.-.+|.+.+. +|....      ..-|.|.|..+ +.++-+|||+.+|++   ..-++++|..|.
T Consensus         1 ~~~~~~~~~~~~~~~a~~~l~~~~~-~~~~~~~l~~a~~lgif~~L~~~~~~~t~~ela~~~~~~~~~~~~l~rlLr~L~   79 (352)
T 1fp2_A            1 MASSINGRKPSEIFKAQALLYKHIY-AFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLA   79 (352)
T ss_dssp             -------CCSTHHHHHHHHHHHHHT-THHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHH
T ss_pred             CCccccCCChHHHhhHHHHHHHHHH-HHHHHHHHHHHHHCChhhhhhhcCCCccHHHHHHHhCcCCCChHHHHHHHHHHH
Confidence            3333344334455555555554433 333322      23478888764 489999999999995   778999999999


Q ss_pred             hCcceeee
Q psy5744          71 NDKIIQTR   78 (157)
Q Consensus        71 ~d~Lv~~~   78 (157)
                      ..|++...
T Consensus        80 ~~gll~~~   87 (352)
T 1fp2_A           80 HNGFFEII   87 (352)
T ss_dssp             HTTSEEEE
T ss_pred             hCCeEEEe
Confidence            99999865

>2kvf_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=89.11  E-value=0.16  Score=24.72  Aligned_cols=17  Identities=24%  Similarity=0.536  Sum_probs=13.9

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         3 ~~~C~~C~k~f~~~~~l   19 (28)
T 2kvf_A            3 PYSCSVCGKRFSLKHQM   19 (28)
T ss_dssp             SEECSSSCCEESCHHHH
T ss_pred             CccCCCCCcccCCHHHH
Confidence            48999999999876544

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

Probab=89.07  E-value=0.7  Score=36.73  Aligned_cols=44  Identities=9%  Similarity=0.099  Sum_probs=39.3

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|.|.|. .+.+|-+|||+.+|+++.-++++|..|...|++...
T Consensus        31 lgi~~~l~-~~~~t~~ela~~~~~~~~~l~r~Lr~L~~~g~l~~~   74 (334)
T 2ip2_A           31 LGLADLIE-SGIDSDETLAAAVGSDAERIHRLMRLLVAFEIFQGD   74 (334)
T ss_dssp             TTHHHHHH-TTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCcHHHHh-CCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCceEec
Confidence            44788885 478999999999999999999999999999999864

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=88.82  E-value=0.33  Score=38.20  Aligned_cols=45  Identities=18%  Similarity=0.135  Sum_probs=39.9

Q ss_pred             hHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .+-||++|.. ++.++=.|||+.+|++...+.++|..|.+.|+|..
T Consensus        23 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~   68 (265)
T 2ia2_A           23 GLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT   68 (265)
T ss_dssp             HHHHHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            3568888875 46799999999999999999999999999999975

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

Probab=88.60  E-value=0.62  Score=37.91  Aligned_cols=43  Identities=12%  Similarity=0.010  Sum_probs=39.1

Q ss_pred             HHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -|.|.|.. .+.+|-+|||+.+|+++.-++++|..|...|++..
T Consensus        39 gifd~L~~~~~~~t~~eLA~~~g~~~~~l~rlLr~l~~~g~l~~   82 (363)
T 3dp7_A           39 GIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTIGTILL   82 (363)
T ss_dssp             THHHHHHTCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHhhCCCeEe
Confidence            38899886 47899999999999999999999999999999964

>2kvg_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=88.47  E-value=0.15  Score=24.95  Aligned_cols=17  Identities=24%  Similarity=0.710  Sum_probs=13.6

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         3 ~~~C~~C~k~f~~~~~l   19 (27)
T 2kvg_A            3 PYRCPLCRAGCPSLASM   19 (27)
T ss_dssp             TEEETTTTEEESCHHHH
T ss_pred             CcCCCCCCcccCCHHHH
Confidence            48999999999875543

>1p7a_A BF3, BKLF, kruppel-like factor 3; classical zinc finger, transcription factor, DNA binding protein; NMR {Mus musculus} SCOP: g.37.1.1 PDB: 1u85_A 1u86_A

Probab=88.42  E-value=0.21  Score=26.14  Aligned_cols=20  Identities=25%  Similarity=0.728  Sum_probs=15.7

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|.|+.|++.|+....+
T Consensus         8 ~~k~~~C~~C~k~f~~~~~l   27 (37)
T 1p7a_A            8 GIKPFQCPDCDRSFSRSDHL   27 (37)
T ss_dssp             CSSSBCCTTTCCCBSSHHHH
T ss_pred             CCCCccCCCCCcccCcHHHH
Confidence            44579999999999876544

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

Probab=88.35  E-value=0.6  Score=36.97  Aligned_cols=43  Identities=5%  Similarity=-0.002  Sum_probs=38.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .-|.|.|.. +.+|-+|||+.+|+++.-++++|..|...|++..
T Consensus        29 l~i~~~l~~-~~~t~~ela~~~~~~~~~l~r~L~~L~~~g~l~~   71 (335)
T 2r3s_A           29 LNVFTAISQ-GIESSQSLAQKCQTSERGMRMLCDYLVIIGFMTK   71 (335)
T ss_dssp             TTHHHHHTT-SEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cChHHHHhc-CCCCHHHHHHHhCCCchHHHHHHHHHHhcCCeEe
Confidence            457888774 7899999999999999999999999999999974

>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=88.09  E-value=0.22  Score=24.30  Aligned_cols=17  Identities=24%  Similarity=0.700  Sum_probs=13.8

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         3 ~~~C~~C~~~f~~~~~l   19 (30)
T 2m0d_A            3 PYQCDYCGRSFSDPTSK   19 (30)
T ss_dssp             CEECTTTCCEESCHHHH
T ss_pred             CccCCCCCcccCCHHHH
Confidence            58999999999876544

>1ard_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 PDB: 1arf_A 1are_A

Probab=88.03  E-value=0.19  Score=24.45  Aligned_cols=17  Identities=35%  Similarity=0.720  Sum_probs=13.7

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         2 ~~~C~~C~~~f~~~~~l   18 (29)
T 1ard_A            2 SFVCEVCTRAFARQEHL   18 (29)
T ss_dssp             CCBCTTTCCBCSSHHHH
T ss_pred             CeECCCCCcccCCHHHH
Confidence            48999999999876544

>1rik_A E6APC1 peptide; E6-binding domain, zinc finger, human papillomavirus, HPV E6 protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1 PDB: 1sp1_A 1va3_A

Probab=88.00  E-value=0.19  Score=24.53  Aligned_cols=17  Identities=35%  Similarity=0.833  Sum_probs=13.7

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+....+
T Consensus         2 ~~~C~~C~k~f~~~~~l   18 (29)
T 1rik_A            2 KFACPECPKRFMRSDHL   18 (29)
T ss_dssp             CEECSSSSCEESCSHHH
T ss_pred             CccCCCCCchhCCHHHH
Confidence            48999999999876544

>2el5_A Zinc finger protein 268; alternative splicing, DNA-binding, metal-binding, nuclear protein, repeat, transcription, transcription regulation; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2eol_A 2emv_A 2eqw_A 2en0_A 2epy_A

Probab=87.93  E-value=0.36  Score=26.02  Aligned_cols=31  Identities=13%  Similarity=0.266  Sum_probs=21.4

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         7 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   42 (42)
T 2el5_A            7 GENPYECSECGKAFNRKDQLISHQRTHAGESGPSSG   42 (42)
T ss_dssp             SCCSEECSSSCCEESSHHHHHHHHGGGCCCCSCCCC
T ss_pred             CCCCccCCCcChhhCCHHHHHHHHHhcCCCCCCCCC
Confidence            34569999999999987665422     23467774

>2eof_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=87.73  E-value=0.37  Score=26.19  Aligned_cols=31  Identities=13%  Similarity=0.284  Sum_probs=21.5

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (44)
T 2eof_A            9 GEKPYECNECQKAFNTKSNLMVHQRTHTGESGPSSG   44 (44)
T ss_dssp             CCCSEECTTTCCEESCHHHHHHHHHHTTTSSCSCCC
T ss_pred             CCCCeECCCCCcccCCHhHHHHHHHHhCCCCCCCCC
Confidence            44569999999999987765422     23367775

>2elx_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=87.68  E-value=0.29  Score=25.08  Aligned_cols=19  Identities=32%  Similarity=0.606  Sum_probs=15.1

Q ss_pred             CCeeecCCCCCccchhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...|.|+.|++.|+....+
T Consensus         5 ~k~~~C~~C~k~f~~~~~L   23 (35)
T 2elx_A            5 SSGYVCALCLKKFVSSIRL   23 (35)
T ss_dssp             CCSEECSSSCCEESSHHHH
T ss_pred             CCCeECCCCcchhCCHHHH
Confidence            4569999999999876544

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

Probab=87.60  E-value=0.85  Score=36.33  Aligned_cols=44  Identities=9%  Similarity=0.034  Sum_probs=39.3

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|.|.|. .+.+|-+|||+.+|+++..++++|..|...|++...
T Consensus        28 lglf~~l~-~g~~t~~elA~~~~~~~~~l~rlLr~l~~~gl~~~~   71 (332)
T 3i53_A           28 LRVADHIA-AGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRD   71 (332)
T ss_dssp             HTHHHHHH-TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cChHHHHh-cCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEec
Confidence            34888886 578999999999999999999999999999999863

>2m0f_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=87.58  E-value=0.24  Score=24.00  Aligned_cols=17  Identities=35%  Similarity=0.610  Sum_probs=13.5

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         2 ~~~C~~C~k~f~~~~~l   18 (29)
T 2m0f_A            2 PLKCRECGKQFTTSGNL   18 (29)
T ss_dssp             CEECTTTSCEESCHHHH
T ss_pred             CccCCCCCCccCChhHH
Confidence            48999999999865543

>2lvu_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}

Probab=87.41  E-value=0.11  Score=25.10  Aligned_cols=17  Identities=29%  Similarity=0.665  Sum_probs=13.4

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+....+
T Consensus         2 p~~C~~C~k~f~~~~~l   18 (26)
T 2lvu_A            2 PYVCERCGKRFVQSSQL   18 (26)
Confidence            48999999999875443

>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=87.37  E-value=1.3  Score=26.54  Aligned_cols=38  Identities=18%  Similarity=0.421  Sum_probs=30.8

Q ss_pred             HHHHHHHhCCCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcce
Q psy5744          35 LIIDMLVRNPCMKEDDICELL-----KFERKMLRARISTLKNDKII   75 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv   75 (157)
                      +|+..|-.++.++-+||++.+     +++...|++.|..|   |++
T Consensus         9 ~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~l---g~v   51 (64)
T 2p5k_A            9 KIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKEL---HLV   51 (64)
T ss_dssp             HHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHHHH---TCE
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHHHc---CCE
Confidence            344444457899999999999     99999999999944   677

>2emb_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.36  E-value=0.42  Score=26.10  Aligned_cols=31  Identities=16%  Similarity=0.327  Sum_probs=21.3

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (44)
T 2emb_A            9 TRKRYECSKCQATFNLRKHLIQHQKTHAAKSGPSSG   44 (44)
T ss_dssp             CCSSEECTTTCCEESCHHHHHHHGGGGCCCCCTTCC
T ss_pred             CCCCeECCCCCCccCCHHHHHHHHHHcCCCCCcCCC
Confidence            44579999999999987655422     12357774

>2eoj_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=87.31  E-value=0.29  Score=26.74  Aligned_cols=31  Identities=13%  Similarity=0.239  Sum_probs=21.6

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (44)
T 2eoj_A            9 GENPYECCECGKVFSRKDQLVSHQKTHSGQSGPSSG   44 (44)
T ss_dssp             SCCSCEETTTTEECSSHHHHHHHHTTSSSSCSCCCC
T ss_pred             CCcCeeCCCCCCccCCHHHHHHHHHHcCCCCCCCCC
Confidence            34569999999999987765422     12367775

>2en3_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=87.29  E-value=0.3  Score=27.01  Aligned_cols=32  Identities=13%  Similarity=0.096  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccCC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCKR  157 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~~  157 (157)
                      +...|.|+.|++.|+....+.--     +...|.|++
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~C~~   45 (46)
T 2en3_A            9 GEKPFQCKECGMNFSWSCSLFKHLRSHERTDPSGPSS   45 (46)
T ss_dssp             CCCSEECSSSCCEESSSHHHHHHHHHHHHSCCSSCSC
T ss_pred             CCCCeeCcccChhhCCHHHHHHHHHHhCCCCCCCCCC
Confidence            34569999999999887655322     234677764

>2els_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.97  E-value=0.37  Score=25.02  Aligned_cols=20  Identities=30%  Similarity=0.456  Sum_probs=15.7

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~l   25 (36)
T 2els_A            6 SGKIFTCEYCNKVFKFKHSL   25 (36)
T ss_dssp             CCCCEECTTTCCEESSHHHH
T ss_pred             CCCCEECCCCCceeCCHHHH
Confidence            44579999999999876544

>2ytp_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=86.86  E-value=0.47  Score=26.23  Aligned_cols=31  Identities=13%  Similarity=0.236  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ytp_A            9 GERHYECSECGKAFARKSTLIMHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CCCCEECSSSCCEESSHHHHHHHHTTTSCCCCCSSC
T ss_pred             CCCCeECCcCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            45579999999999987765432     12367776

>1srk_A Zinc finger protein ZFPM1; classical zinc finger, transcription; NMR {Mus musculus} SCOP: g.37.1.1

Probab=86.65  E-value=0.38  Score=24.70  Aligned_cols=19  Identities=37%  Similarity=0.887  Sum_probs=15.2

Q ss_pred             CCeeecCCCCCccchhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...|.|+.|++.|+....+
T Consensus         5 ~k~~~C~~C~k~f~~~~~l   23 (35)
T 1srk_A            5 KRPFVCRICLSAFTTKANC   23 (35)
T ss_dssp             CSCEECSSSCCEESSHHHH
T ss_pred             CcCeeCCCCCcccCCHHHH
Confidence            4569999999999876544

>2eor_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=86.64  E-value=0.5  Score=25.96  Aligned_cols=31  Identities=13%  Similarity=0.096  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      ....|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~kp~~C~   44 (46)
T 2eor_A            9 GEKPYNCEECGKAFIHDSQLQEHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECTTTCCEESSHHHHHHHHHHHHSCCCSSST
T ss_pred             CCcCccCCCCCCCcCCHHHHHHHHHhcCCCCCCCCC
Confidence            34569999999999987765422     23467776

>2elm_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.53  E-value=0.36  Score=25.49  Aligned_cols=20  Identities=15%  Similarity=0.253  Sum_probs=15.5

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~L   25 (37)
T 2elm_A            6 SGHLYYCSQCHYSSITKNCL   25 (37)
T ss_dssp             SSCEEECSSSSCEEECHHHH
T ss_pred             CCcCeECCCCCcccCCHHHH
Confidence            34579999999999876543

>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=86.51  E-value=0.89  Score=34.84  Aligned_cols=32  Identities=16%  Similarity=0.254  Sum_probs=29.7

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          47 KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.+||+.+|+++..+.+++.+|.+.|+|...
T Consensus        26 ~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~   57 (230)
T 1fx7_A           26 LRARIAERLDQSGPTVSQTVSRMERDGLLRVA   57 (230)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34999999999999999999999999999864

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=86.46  E-value=0.31  Score=36.49  Aligned_cols=14  Identities=29%  Similarity=0.636  Sum_probs=12.5

Q ss_pred             CCeeecCCCCCccc
Q psy5744         127 RSSFKCPRCLKTFT  140 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys  140 (157)
                      ...|+||.||-.|.
T Consensus       136 ~~~~~C~~CG~i~~  149 (170)
T 3pwf_A          136 KKVYICPICGYTAV  149 (170)
T ss_dssp             SCEEECTTTCCEEE
T ss_pred             CCeeEeCCCCCeeC
Confidence            35899999999998

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=86.27  E-value=0.57  Score=31.12  Aligned_cols=31  Identities=19%  Similarity=0.274  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHhhcCCCCeeecCCCCCccchhhhh
Q psy5744         110 LDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       110 l~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +.++.++|+....     ..|.||.||+..-+.-+.
T Consensus        13 lRk~vk~ie~~q~-----~~y~Cp~CG~~~v~r~at   43 (83)
T 1vq8_Z           13 SRRRVAEIESEMN-----EDHACPNCGEDRVDRQGT   43 (83)
T ss_dssp             HHHHHHHHHHHHH-----SCEECSSSCCEEEEEEET
T ss_pred             HHHHHHHHHHhcc-----ccCcCCCCCCcceeccCC
Confidence            5566666666554     379999999865554444

>2elo_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.22  E-value=0.28  Score=25.60  Aligned_cols=20  Identities=35%  Similarity=0.718  Sum_probs=15.9

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~l   25 (37)
T 2elo_A            6 SGRSYSCPVCEKSFSEDRLI   25 (37)
T ss_dssp             CCCCCEETTTTEECSSHHHH
T ss_pred             CCCCcCCCCCCCccCCHHHH
Confidence            34569999999999876654

>2eon_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=86.19  E-value=0.44  Score=26.39  Aligned_cols=31  Identities=16%  Similarity=0.134  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      ....|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eon_A            9 GEKPYKCQVCGKAFRVSSHLVQHHSVHSGERPSGPS   44 (46)
T ss_dssp             SCCSCBCSSSCCBCSSHHHHHHHTTTTTSCCSCTTS
T ss_pred             CCcccCCCCCCcccCcHHHHHHHHHhcCCCCCCCCC
Confidence            34579999999999987765432     12368886

>2en7_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=86.12  E-value=0.38  Score=26.13  Aligned_cols=31  Identities=13%  Similarity=0.186  Sum_probs=21.6

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (44)
T 2en7_A            9 GMKPYVCNECGKAFRSKSYLIIHTRTHTGESGPSSG   44 (44)
T ss_dssp             SSSSSCCTTTCCCCSSHHHHHHHHTTTCCSSSSCCC
T ss_pred             CCcCeECCCCCCccCCHHHHHHHhhhcCCCCCCCCC
Confidence            34569999999999987765432     12367775

>2elt_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.12  E-value=0.38  Score=24.82  Aligned_cols=20  Identities=25%  Similarity=0.468  Sum_probs=15.4

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~l   25 (36)
T 2elt_A            6 SGKPYKCPQCSYASAIKANL   25 (36)
T ss_dssp             CCCSEECSSSSCEESSHHHH
T ss_pred             CCCCCCCCCCCcccCCHHHH
Confidence            34569999999999876543

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

Probab=86.10  E-value=0.85  Score=36.77  Aligned_cols=42  Identities=14%  Similarity=0.180  Sum_probs=37.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -|.|.|. .+.+|-+|||+.+|+++.-++++|..|...|++..
T Consensus        46 glf~~l~-~g~~t~~elA~~~g~~~~~l~rlLr~l~~~g~l~~   87 (348)
T 3lst_A           46 GVADHLV-DGPRTPAELAAATGTDADALRRVLRLLAVRDVVRE   87 (348)
T ss_dssp             TGGGGGT-TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CchhHhh-CCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEe
Confidence            3777775 46899999999999999999999999999999986

>2m0e_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=85.96  E-value=0.26  Score=23.78  Aligned_cols=16  Identities=38%  Similarity=0.881  Sum_probs=12.8

Q ss_pred             eeecCCCCCccchhhh
Q psy5744         129 SFKCPRCLKTFTDLEP  144 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda  144 (157)
                      .|.|+.|++.|+....
T Consensus         2 ~~~C~~C~~~f~~~~~   17 (29)
T 2m0e_A            2 EHKCPHCDKKFNQVGN   17 (29)
T ss_dssp             CCCCSSCCCCCCTTTH
T ss_pred             CCcCCCCCcccCCHHH
Confidence            4889999999986544

>1paa_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1

Probab=85.95  E-value=0.26  Score=24.20  Aligned_cols=17  Identities=24%  Similarity=0.612  Sum_probs=13.5

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         2 ~~~C~~C~k~f~~~~~l   18 (30)
T 1paa_A            2 AYACGLCNRAFTRRDLL   18 (30)
T ss_dssp             CSBCTTTCCBCSSSHHH
T ss_pred             CcCCcccCcccCChHHH
Confidence            48999999999865543

>2elv_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.90  E-value=0.43  Score=24.74  Aligned_cols=20  Identities=20%  Similarity=0.383  Sum_probs=15.7

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~l   25 (36)
T 2elv_A            6 SGLLYDCHICERKFKNELDR   25 (36)
T ss_dssp             CCCCEECSSSCCEESSHHHH
T ss_pred             CCCCeECCCCCCccCCHHHH
Confidence            34579999999999876554

>2emg_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=85.86  E-value=0.47  Score=26.13  Aligned_cols=31  Identities=19%  Similarity=0.253  Sum_probs=21.8

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2emg_A            9 GENPFICSECGKVFTHKTNLIIHQKIHTGERPSGPS   44 (46)
T ss_dssp             SCCSCBCTTTCCBCSSHHHHHHHHTTTSCCCCSCSC
T ss_pred             CCCCEECCccCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987766432     12367775

>2eoz_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=85.84  E-value=0.44  Score=26.33  Aligned_cols=31  Identities=13%  Similarity=0.063  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2eoz_A            9 GEKPYSCNVCGKAFVLSAHLNQHLRVHTQETLSGPS   44 (46)
T ss_dssp             SCCSEEETTTTEEESSHHHHHHHHHHHSSCCSSSCC
T ss_pred             CCCCeECcccChhhCCHHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987765422     23467776

>2elq_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.83  E-value=0.4  Score=24.89  Aligned_cols=20  Identities=25%  Similarity=0.378  Sum_probs=15.8

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|.|+.|++.|+....+
T Consensus         6 ~~k~~~C~~C~k~f~~~~~l   25 (36)
T 2elq_A            6 SGKPFKCSLCEYATRSKSNL   25 (36)
T ss_dssp             CCCSEECSSSSCEESCHHHH
T ss_pred             CCCCccCCCCCchhCCHHHH
Confidence            44579999999999876554

>2elr_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.81  E-value=0.38  Score=24.84  Aligned_cols=20  Identities=25%  Similarity=0.391  Sum_probs=15.6

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|.|+.|++.|+....+
T Consensus         6 ~~~~~~C~~C~k~f~~~~~l   25 (36)
T 2elr_A            6 SGKTHLCDMCGKKFKSKGTL   25 (36)
T ss_dssp             CCSSCBCTTTCCBCSSHHHH
T ss_pred             CCCCeecCcCCCCcCchHHH
Confidence            34569999999999876544

>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=85.80  E-value=1.3  Score=39.13  Aligned_cols=46  Identities=11%  Similarity=0.198  Sum_probs=40.2

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhC-------CChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLK-------FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~-------i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.|++.+-.++.++..+||..+|       +.....+..|..+.++|++-..
T Consensus       496 ~~~il~l~~~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~~~e~eG~l~rD  548 (566)
T 1w7p_D          496 KEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLID  548 (566)
T ss_dssp             HHHHHHHHTTSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCccccCcccHHHHHHHHHHHHHcCCEEEE
Confidence            445666655579999999999999       9999999999999999999854

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=85.78  E-value=0.6  Score=27.61  Aligned_cols=29  Identities=14%  Similarity=0.186  Sum_probs=18.3

Q ss_pred             CeeecCCCCCccchhhhh-hcc-C-CCCcccC
Q psy5744         128 SSFKCPRCLKTFTDLEPC-LLV-L-WCACPCK  156 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda~-~L~-d-~~~F~C~  156 (157)
                      ..|+|+.||-.|....-. .-+ | +..+.||
T Consensus         3 ~~y~C~vCGyvyd~~~Gd~t~f~~lP~dw~CP   34 (46)
T 6rxn_A            3 QKYVCNVCGYEYDPAEHDNVPFDQLPDDWCCP   34 (46)
T ss_dssp             CCEEETTTCCEECGGGGTTCCGGGSCTTCBCT
T ss_pred             CEEECCCCCeEEeCCcCCCcchhhCCCCCcCc
Confidence            469999999888764333 111 1 2457777

>2en9_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=85.50  E-value=0.51  Score=26.08  Aligned_cols=31  Identities=26%  Similarity=0.298  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2en9_A            9 GKKLFKCNECKKTFTQSSSLTVHQRIHTGEKPSGPS   44 (46)
T ss_dssp             SSCCCBCTTTCCBCSSHHHHHHHHHHHTSSCCCSCC
T ss_pred             CCCCEECCccCcccCCHHHHHHHHHHcCCCCCCCCC
Confidence            34579999999999987765432     23467776

>2ytf_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=85.44  E-value=0.57  Score=25.73  Aligned_cols=31  Identities=16%  Similarity=0.277  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ytf_A            9 GEKPFECSECQKAFNTKSNLIVHQRTHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSHHHHHHHHHTSCSSSSSCCC
T ss_pred             CCCCcCCCCCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987766432     22367776

>2epc_A Zinc finger protein 32; zinc finger domain, C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2yta_A

Probab=85.32  E-value=0.44  Score=25.60  Aligned_cols=21  Identities=24%  Similarity=0.540  Sum_probs=16.5

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         8 ~~~~~~C~~C~k~f~~~~~l~   28 (42)
T 2epc_A            8 GETPYLCGQCGKSFTQRGSLA   28 (42)
T ss_dssp             SSCCEECSSSCCEESSHHHHH
T ss_pred             CCCCeECCCCCcccCCHHHHH
Confidence            345699999999998876554

>2ema_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2emc_A

Probab=85.24  E-value=0.61  Score=25.65  Aligned_cols=31  Identities=16%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ema_A            9 GEKRYKCNECGKVFSRNSQLSQHQKIHTGEKPSGPS   44 (46)
T ss_dssp             TSCCEECSSSCCEESSHHHHHHHHTGGGCCCCCSSS
T ss_pred             CCcCcCCCCCcchhCCHHHHHHHHHhcCCCCCCCCC
Confidence            44579999999999987765432     23467776

>1rim_A E6APC2 peptide; E6-binding domain, zinc finger, human papillomavirus, HPV E6 protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1

Probab=85.22  E-value=0.29  Score=25.32  Aligned_cols=17  Identities=35%  Similarity=0.833  Sum_probs=13.8

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+....+
T Consensus         2 p~~C~~C~k~F~~~~~L   18 (33)
T 1rim_A            2 KFACPECPKRFMRSDHL   18 (33)
T ss_dssp             CCCCSSSCCCCSSHHHH
T ss_pred             cccCCCCCchhCCHHHH
Confidence            48999999999876554

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

Probab=85.19  E-value=1.2  Score=35.53  Aligned_cols=42  Identities=5%  Similarity=0.065  Sum_probs=37.3

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|.|.|- . .+|-+|||+.+|+++..++++|..|...|++...
T Consensus        48 gif~~l~-~-~~t~~elA~~~~~~~~~l~rlLr~L~~~gll~~~   89 (352)
T 3mcz_A           48 KLFDLTQ-T-GRTPAEVAASFGMVEGKAAILLHALAALGLLTKE   89 (352)
T ss_dssp             THHHHTT-S-CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ChHHHhC-C-CCCHHHHHHHhCcChHHHHHHHHHHHHCCCeEec
Confidence            3777774 3 8999999999999999999999999999999853

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=85.18  E-value=1  Score=29.14  Aligned_cols=42  Identities=12%  Similarity=0.180  Sum_probs=37.8

Q ss_pred             HHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          37 IDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        37 lD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++++-.+.++.=+|||..+|++..++..-+..|.++|.++=.
T Consensus        13 i~yIk~~Kvv~LedLA~~F~l~t~~~i~RI~~Le~~g~ltGV   54 (72)
T 1wi9_A           13 INYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGV   54 (72)
T ss_dssp             HHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEE
T ss_pred             HHHHHHcCeeeHHHHHHHhCCChHHHHHHHHHHHHCCCeEEE
Confidence            566667899999999999999999999999999999998754

>2lvt_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}

Probab=85.35  E-value=0.17  Score=24.87  Aligned_cols=17  Identities=29%  Similarity=0.555  Sum_probs=13.6

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         2 ~~~C~~C~k~f~~~~~l   18 (29)
T 2lvt_A            2 PCQCVMCGKAFTQASSL   18 (29)
Confidence            48999999999876543

>2ytg_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=85.02  E-value=0.75  Score=25.25  Aligned_cols=31  Identities=16%  Similarity=0.140  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ytg_A            9 GEKPFKCGECGKSYNQRVHLTQHQRVHTGEKPSGPS   44 (46)
T ss_dssp             SCCSEECTTTCCEESSSHHHHTTGGGGSSCCSSCSC
T ss_pred             CCCCeECCCCCcccCCHHHHHHHHHHcCCCCCCCCC
Confidence            44579999999999987766432     22367775

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=85.01  E-value=0.52  Score=30.36  Aligned_cols=18  Identities=11%  Similarity=0.399  Sum_probs=15.4

Q ss_pred             CCCeeecCCCCCccchhh
Q psy5744         126 SRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~ld  143 (157)
                      ....|+|+.||..|+..+
T Consensus        25 ~~v~Y~C~~CG~~~e~~~   42 (70)
T 1twf_L           25 ATLKYICAECSSKLSLSR   42 (70)
T ss_dssp             CCCCEECSSSCCEECCCT
T ss_pred             ceEEEECCCCCCcceeCC
Confidence            567899999999998763

>2ytn_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.98  E-value=0.58  Score=25.74  Aligned_cols=31  Identities=19%  Similarity=0.186  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ytn_A            9 GKKPYKCNECGKVFTQNSHLARHRGIHTGEKPSGPS   44 (46)
T ss_dssp             CCSSCBCTTTCCBCSSHHHHHHHGGGTSCCCCCSCC
T ss_pred             CCcCeECCCCCCeeCCHHHHHHHhhhcCCCCCCCCC
Confidence            45579999999999987765432     23367776

>2yti_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.93  E-value=0.41  Score=26.39  Aligned_cols=31  Identities=19%  Similarity=0.161  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2yti_A            9 GEKPYKCNECGKVFTQNSHLARHRGIHTGEKPSGPS   44 (46)
T ss_dssp             CCCTTCCSSSCCCCSSHHHHHHHHTTTSCSCCSSTT
T ss_pred             CCcCeECCCCCcccCChhHHHHHhHhcCCCCCCCCC
Confidence            44569999999999987765432     12367886

>2eq1_A Zinc finger protein 347; C2H2, zinc finger domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.92  E-value=0.51  Score=25.98  Aligned_cols=31  Identities=16%  Similarity=0.148  Sum_probs=21.8

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eq1_A            9 GEKPYKCNECGKAFRAHSNLTTHQVIHTGEKPSGPS   44 (46)
T ss_dssp             CSCCCCCTTTTCCCSSHHHHHHHHTTTCCSCCSSCC
T ss_pred             CCCCeECCcCChhhCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999887665432     12367776

>2elp_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.90  E-value=0.46  Score=24.78  Aligned_cols=17  Identities=35%  Similarity=0.596  Sum_probs=13.9

Q ss_pred             CCCeeecCCCCCccchh
Q psy5744         126 SRSSFKCPRCLKTFTDL  142 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~l  142 (157)
                      ....|.|+.|++.|+..
T Consensus         6 ~~k~~~C~~C~k~f~~~   22 (37)
T 2elp_A            6 SGRAMKCPYCDFYFMKN   22 (37)
T ss_dssp             CCCCEECSSSSCEECSS
T ss_pred             CCCCeECCCCChhhccC
Confidence            34569999999999875

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

Probab=84.88  E-value=0.73  Score=37.59  Aligned_cols=42  Identities=12%  Similarity=0.108  Sum_probs=37.9

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -|.|.|. .+.+|-+|||+.+|+++..++++|..|...|++..
T Consensus        62 glf~~l~-~g~~t~~eLA~~~g~~~~~l~rlLr~L~~~g~l~~  103 (369)
T 3gwz_A           62 GVPELLQ-EGPRTATALAEATGAHEQTLRRLLRLLATVGVFDD  103 (369)
T ss_dssp             TTGGGGT-TSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEE
T ss_pred             Chhhhhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCCEEE
Confidence            3777776 56899999999999999999999999999999986

>2kfq_A FP1; protein, de novo protein; NMR {Synthetic}

Probab=84.77  E-value=0.22  Score=25.51  Aligned_cols=17  Identities=35%  Similarity=0.860  Sum_probs=13.9

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+....+
T Consensus         2 p~~C~~C~k~f~~~~~L   18 (32)
T 2kfq_A            2 AFACPACPKRFMRSDAL   18 (32)
T ss_dssp             CSSSSSSCTTHHHHHTT
T ss_pred             CCCCCCCCcccCCHHHH
Confidence            48999999999876554

>2eou_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.62  E-value=0.54  Score=25.68  Aligned_cols=31  Identities=13%  Similarity=0.156  Sum_probs=21.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      ....|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (44)
T 2eou_A            9 AKTTSECQECGKIFRHSSLLIEHQALHAGESGPSSG   44 (44)
T ss_dssp             SSCCCCCTTTCCCCSSHHHHHHHHHHHTTSCCCCCC
T ss_pred             CCcCeECCCCCcccCCHHHHHHHHHHHCCCCCCCCC
Confidence            34569999999999987655422     23357774

>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=84.58  E-value=0.86  Score=37.08  Aligned_cols=45  Identities=11%  Similarity=0.180  Sum_probs=39.3

Q ss_pred             HHHHHHHHhCC-C---cCHHHHHHHhCC------ChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNP-C---MKEDDICELLKF------ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~-~---i~dedLa~~l~i------~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|+|.|..++ .   +|-+|||+.+|+      ++.-++++|..|...|++...
T Consensus        47 lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L~~~gll~~~  101 (372)
T 1fp1_D           47 LNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLTST  101 (372)
T ss_dssp             TTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEEEE
T ss_pred             CChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHHhhCCceEec
Confidence            45889988654 4   999999999999      678999999999999999865

>2yte_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.54  E-value=0.44  Score=25.58  Aligned_cols=21  Identities=24%  Similarity=0.672  Sum_probs=16.6

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         7 ~~k~~~C~~C~k~f~~~~~L~   27 (42)
T 2yte_A            7 GEKPYSCAECKETFSDNNRLV   27 (42)
T ss_dssp             SCCSCBCTTTCCBCSSHHHHH
T ss_pred             CCCCeECCCCCCccCCHHHHH
Confidence            345699999999999876654

>2eq3_A Zinc finger protein 347; C2H2, zinc finger domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.53  E-value=0.47  Score=26.08  Aligned_cols=31  Identities=13%  Similarity=0.148  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eq3_A            9 GEKPYECNQCGKAFSVRSSLTTHQAIHTGKKPSGPS   44 (46)
T ss_dssp             CCCSSEETTTTEECSSHHHHHHHHTTSCCCCCCCSC
T ss_pred             CCCCeECCCCChhhCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987765432     23368886

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=84.44  E-value=0.29  Score=37.09  Aligned_cols=17  Identities=12%  Similarity=0.430  Sum_probs=13.7

Q ss_pred             CeeecCCCCCccchhhh
Q psy5744         128 SSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda  144 (157)
                      ..|+|+.||-.|+-.++
T Consensus       154 ~~~~C~~CG~~~~g~~~  170 (191)
T 1lko_A          154 TKWRCRNCGYVHEGTGA  170 (191)
T ss_dssp             EEEEETTTCCEEEEEEC
T ss_pred             ceEEECCCCCEeeCCCC
Confidence            38999999999985443

>1klr_A Zinc finger Y-chromosomal protein; transcription; NMR {Synthetic} SCOP: g.37.1.1 PDB: 5znf_A 1kls_A 1xrz_A* 7znf_A

Probab=84.41  E-value=0.29  Score=23.79  Aligned_cols=16  Identities=19%  Similarity=0.470  Sum_probs=12.9

Q ss_pred             eeecCCCCCccchhhh
Q psy5744         129 SFKCPRCLKTFTDLEP  144 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda  144 (157)
                      .|.|+.|++.|+....
T Consensus         2 ~~~C~~C~k~f~~~~~   17 (30)
T 1klr_A            2 TYQCQYCEFRSADSSN   17 (30)
T ss_dssp             CCCCSSSSCCCSCSHH
T ss_pred             CccCCCCCCccCCHHH
Confidence            4899999999986544

>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=84.41  E-value=1.1  Score=36.06  Aligned_cols=45  Identities=16%  Similarity=0.205  Sum_probs=39.4

Q ss_pred             HHHHHHHHhC-CCcCHHHHHHHhCC---ChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRN-PCMKEDDICELLKF---ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~-~~i~dedLa~~l~i---~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|+|.|..+ +.+|-+|||+.+|+   +..-++++|..|...|++...
T Consensus        33 lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~gll~~~   81 (358)
T 1zg3_A           33 LGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHNGFFAKT   81 (358)
T ss_dssp             HTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHHHHTTSEEEE
T ss_pred             CChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHHhhCCcEEEe
Confidence            4488888865 48999999999999   588999999999999999865

>2ytb_A Zinc finger protein 32; zinc-finger domain, C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.32  E-value=0.45  Score=25.54  Aligned_cols=21  Identities=19%  Similarity=0.643  Sum_probs=16.7

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         8 ~~k~~~C~~C~k~f~~~~~L~   28 (42)
T 2ytb_A            8 GEKPYRCDQCGKAFSQKGSLI   28 (42)
T ss_dssp             SCCSBCCTTTTCCBSSHHHHH
T ss_pred             CCCCeeCCCccchhCCHHHHH
Confidence            345799999999999876654

>2lvr_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, classical zinc finger, transcription; NMR {Homo sapiens}

Probab=84.58  E-value=0.2  Score=24.61  Aligned_cols=17  Identities=24%  Similarity=0.665  Sum_probs=13.7

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|.|+.|++.|+....+
T Consensus         3 ~~~C~~C~k~f~~~~~l   19 (30)
T 2lvr_A            3 PYVCIHCQRQFADPGAL   19 (30)
Confidence            48999999999876543

>2en2_A B-cell lymphoma 6 protein; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.07  E-value=0.54  Score=25.28  Aligned_cols=21  Identities=19%  Similarity=0.506  Sum_probs=16.6

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         8 ~~k~~~C~~C~k~f~~~~~L~   28 (42)
T 2en2_A            8 GEKPYKCETCGARFVQVAHLR   28 (42)
T ss_dssp             SSCSEECTTTCCEESSHHHHH
T ss_pred             CCCCEeCCCcChhhCCHHHHH
Confidence            345799999999999876654

>2ysp_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.84  E-value=0.62  Score=25.63  Aligned_cols=31  Identities=13%  Similarity=0.130  Sum_probs=21.8

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2ysp_A            9 GEKPYKCEKCGKGYNSKFNLDMHQKVHTGERPSGPS   44 (46)
T ss_dssp             SCCSEEETTTTEEESCHHHHHHHHTTSCSCCSSCCS
T ss_pred             CCCCeECCCCCCccCCHHHHHHHHHhhCCCCCCCCC
Confidence            44579999999999987765432     12357776

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=83.82  E-value=0.21  Score=44.15  Aligned_cols=43  Identities=12%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      +|++.|-.++.++-.|+++.+|++..+++++|.+|.++|++..
T Consensus       520 ~I~~~l~~~g~it~~di~~l~~ls~~qa~~~L~~Lv~~G~l~~  562 (583)
T 3lmm_A          520 AAMLWLSEVGDLATSDLMAMCGVSRGTAKACVDGLVDEERVVA  562 (583)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEE
Confidence            6888888899999999999999999999999999999999864

>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=83.81  E-value=1.6  Score=35.79  Aligned_cols=49  Identities=10%  Similarity=0.144  Sum_probs=41.4

Q ss_pred             CCchHHHHH-----HHHhCCCcCHHHHHHHh--CCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIID-----MLVRNPCMKEDDICELL--KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD-----~L~~~~~i~dedLa~~l--~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+.+-.|++     .+-.++.++=.+||+.+  |+++..||+-|..|++.|++..-
T Consensus        16 ~eR~~~IL~~i~~~yl~~~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~   71 (338)
T 1stz_A           16 NDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQP   71 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHHHHHHHHHHHHcCCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEc
Confidence            455666777     44457899999999999  99999999999999999999853

>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 g.37.1.1

Probab=83.78  E-value=1.1  Score=25.97  Aligned_cols=21  Identities=24%  Similarity=0.543  Sum_probs=15.8

Q ss_pred             CCCCeeecCCCCCccchhhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      .+...|.|+.|++.|+....+
T Consensus        26 ~~~~~~~C~~C~~~f~~~~~l   46 (60)
T 2adr_A           26 TNEKPYPCGLCNRAFTRRDLL   46 (60)
T ss_dssp             TSSCSEECTTTCCEESSHHHH
T ss_pred             CCCCCccCCCCCCccCCHHHH
Confidence            345579999999999876654

>1fv5_A First zinc finger of U-shaped; CCHC, protein interaction, transcription; NMR {Drosophila melanogaster} SCOP: g.37.1.2 PDB: 1y0j_B 2l6z_B

Probab=83.77  E-value=0.36  Score=26.66  Aligned_cols=20  Identities=20%  Similarity=0.419  Sum_probs=15.8

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...-|.|+.|++.|+....+
T Consensus         5 gekp~~C~~CgK~F~~~s~L   24 (36)
T 1fv5_A            5 KPARFMCLPCGIAFSSPSTL   24 (36)
T ss_dssp             SCCCCEETTTTEECSCHHHH
T ss_pred             CccCeECCCCCCccCCHhHc
Confidence            34579999999999876544

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

Probab=83.76  E-value=1.5  Score=35.79  Aligned_cols=44  Identities=11%  Similarity=0.236  Sum_probs=39.0

Q ss_pred             HHHHHHHhC--CCcCHHHHHHHhCC--ChH---HHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRN--PCMKEDDICELLKF--ERK---MLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~--~~i~dedLa~~l~i--~~k---~vRkiL~~L~~d~Lv~~~   78 (157)
                      -|.|+|..+  +.+|-+|||+.+|+  ++.   -++++|..|...|++...
T Consensus        44 gifd~L~~~g~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g~l~~~   94 (364)
T 3p9c_A           44 GLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASYNVVTCL   94 (364)
T ss_dssp             THHHHHHHTTTCCBCHHHHHHTTTCTTCTTHHHHHHHHHHHHHHTTSEEEE
T ss_pred             ChHHHHhhcCCCCCCHHHHHHhcCCCCCccchhhHHHHHHHHHhCCCEEEe
Confidence            388998875  58999999999998  776   899999999999999875

>1bbo_A Human enhancer-binding protein MBP-1; DNA-binding protein; HET: ABA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 PDB: 3znf_A 4znf_A

Probab=83.49  E-value=1.1  Score=25.49  Aligned_cols=21  Identities=19%  Similarity=0.401  Sum_probs=16.0

Q ss_pred             CCCCeeecCCCCCccchhhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      .+...|.|+.|++.|+....+
T Consensus        25 ~~~~~~~C~~C~~~f~~~~~l   45 (57)
T 1bbo_A           25 TDVRPYHCTYCNFSFKTKGNL   45 (57)
T ss_dssp             SSCCCEECSSSSCEESSHHHH
T ss_pred             CCCCCccCCCCCchhcCHHHH
Confidence            345679999999999876554

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.42  E-value=0.86  Score=30.33  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744         109 KLDVMRKRMEMEERDATSRSSFKCPRCLKT  138 (157)
Q Consensus       109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~  138 (157)
                      .+.++.++++.....     -|.||.||+.
T Consensus        20 slRK~vkkie~~q~~-----ky~CpfCGk~   44 (83)
T 3j21_i           20 KIRRRVAAVEAKMRQ-----KHTCPVCGRK   44 (83)
T ss_dssp             HHHHHHHHHHHHHHS-----CBCCSSSCSS
T ss_pred             hHHHHHHHHHHHhhc-----ccCCCCCCCc
Confidence            456666777776544     6889999876

>2epu_A Zinc finger protein 32; C2H2, zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.41  E-value=0.65  Score=25.47  Aligned_cols=31  Identities=19%  Similarity=0.321  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      ....|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (45)
T 2epu_A            9 GQKPFECTHCGKSFRAKGNLVTHQRIHTGEKSGPSS   44 (45)
T ss_dssp             SCCSEEETTTTEEESSHHHHHHHHTTTSSCCCCCSC
T ss_pred             CCcCccCCCCCCccCChHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987665422     23367776

>1njq_A Superman protein; zinc-finger, peptide-zinc complex, beta-BETA-ALFA motif, metal binding protein; NMR {Synthetic} SCOP: g.37.1.3 PDB: 2l1o_A

Probab=83.34  E-value=0.63  Score=24.65  Aligned_cols=19  Identities=21%  Similarity=0.590  Sum_probs=15.2

Q ss_pred             CCeeecCCCCCccchhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...|.|+.|++.|+....+
T Consensus         4 ~k~~~C~~C~k~f~~~~~L   22 (39)
T 1njq_A            4 PRSYTCSFCKREFRSAQAL   22 (39)
T ss_dssp             SSSEECTTTCCEESSHHHH
T ss_pred             CCceECCCCCcccCCHHHH
Confidence            3469999999999876554

>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB: 1w7p_A

Probab=83.31  E-value=1.5  Score=34.48  Aligned_cols=60  Identities=7%  Similarity=0.031  Sum_probs=47.6

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      ++..|+.+.-..|.+|.++|+..+|++.-..+..|..|..+|++=.-   +. ..| .  ..|||-+
T Consensus       168 D~~~vLe~a~~~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD---~q-~~~-e--~~Yw~P~  227 (233)
T 1u5t_A          168 DQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWID---YQ-GGA-E--ALYWDPS  227 (233)
T ss_dssp             THHHHHHTTTTTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEE---CS-SSS-S--CEEECGG
T ss_pred             HHHHHHHHHHhcCcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---CC-CCC-c--cceechh
Confidence            36778877666899999999999999999999999999999999854   22 211 1  4788765

>2emi_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.29  E-value=0.62  Score=25.63  Aligned_cols=31  Identities=13%  Similarity=0.184  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2emi_A            9 GERHYECSECGKAFIQKSTLSMHQRIHRGEKPSGPS   44 (46)
T ss_dssp             SCCCEECSSSCCEESSHHHHHHHHGGGCSCCCCSCC
T ss_pred             CCCCCCCCCCCcccCCHHHHHHHHhHhCCCCCCCCC
Confidence            44579999999999987665432     23367775

>2en6_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.15  E-value=0.68  Score=25.43  Aligned_cols=31  Identities=16%  Similarity=0.126  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2en6_A            9 GEKPYGCNECGKTFSQKSILSAHQRTHTGEKPSGPS   44 (46)
T ss_dssp             SSCCEEETTTTEEESSHHHHHHHHHHHSSCCCSSSC
T ss_pred             CCcCeECCCCCcccCchHHHHHHHHHcCCCCCCCCC
Confidence            44579999999999987765432     23467775

>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=83.14  E-value=1.1  Score=34.33  Aligned_cols=32  Identities=13%  Similarity=0.222  Sum_probs=29.8

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          47 KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        47 ~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-.+||+.+|+++..|.+++.+|.+.|||.+.
T Consensus        26 ~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~   57 (226)
T 2qq9_A           26 LRARIAERLEQSGPTVSQTVARMERDGLVVVA   57 (226)
T ss_dssp             BHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            44899999999999999999999999999875

>2enf_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.02  E-value=0.54  Score=25.89  Aligned_cols=31  Identities=19%  Similarity=0.193  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2enf_A            9 GEKPYKCNECGKVFTQNSHLVRHRGIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSCBCSSSCCBCSSHHHHHHHHTTTTTSSCCCCS
T ss_pred             CCcCeECCCCCcccCCHHHHHHHHHhhCCCCCCCCC
Confidence            45579999999999987765432     12367776

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=82.94  E-value=0.3  Score=29.82  Aligned_cols=19  Identities=32%  Similarity=0.683  Sum_probs=15.4

Q ss_pred             hcCCCCeeecCCCCCccch
Q psy5744         123 DATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       123 ~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      ++....+|+|+.||.++..
T Consensus        37 dep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           37 DEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             SCSSEEEEEESSSCCEEEC
T ss_pred             CCCCcEEEEcCCCCCEecc
Confidence            4556789999999998865

>2eos_A B-cell lymphoma 6 protein; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.87  E-value=0.56  Score=25.27  Aligned_cols=21  Identities=19%  Similarity=0.490  Sum_probs=16.8

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         8 ~~k~~~C~~C~k~f~~~~~L~   28 (42)
T 2eos_A            8 GEKPYPCEICGTRFRHLQTLK   28 (42)
T ss_dssp             SSCCBCCSSSCCCBSSHHHHH
T ss_pred             CCCCEECCCCCCccCCHHHHH
Confidence            345799999999999876654

>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=82.74  E-value=1  Score=33.57  Aligned_cols=30  Identities=20%  Similarity=0.132  Sum_probs=28.0

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcc
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKI   74 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~L   74 (157)
                      .++-++||..+|+.+..|.++|.+|+++|+
T Consensus       178 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          178 PYDKMLIAGRLGMKPESLSRAFSRLKAAGV  207 (237)
T ss_dssp             CSCTHHHHHHTTCCHHHHHHHHHHHGGGTE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCe
Confidence            366899999999999999999999999996

>2ept_A Zinc finger protein 32; C2H2, zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.73  E-value=0.69  Score=24.71  Aligned_cols=21  Identities=19%  Similarity=0.523  Sum_probs=16.5

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         7 ~~k~~~C~~C~k~f~~~~~L~   27 (41)
T 2ept_A            7 GQRVYECQECGKSFRQKGSLT   27 (41)
T ss_dssp             CCCCEECSSSCCEESSHHHHH
T ss_pred             CCCCeECCCCCCCcCCHHHHH
Confidence            345799999999998876653

>2em0_A Zinc finger protein 224; DNA-binding, metal-binding, nuclear protein, phosphorylation, polymorphism, repeat, repressor, transcription; NMR {Homo sapiens}

Probab=82.71  E-value=0.72  Score=25.34  Aligned_cols=31  Identities=16%  Similarity=0.187  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2em0_A            9 GEKTWKCRECDMCFSQASSLRLHQNVHVGEKPSGPS   44 (46)
T ss_dssp             CCCCCCCSSSCCCCSSHHHHHHHGGGGSSSSCSCSS
T ss_pred             CCcCeECCCCCcccCCHHHHHHHHHHcCCCCCcCCC
Confidence            44569999999999987765432     23367776

>1x4s_A Protein FON, zinc finger HIT domain containing protein 2; structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.85.1.2

Probab=82.69  E-value=0.44  Score=29.78  Aligned_cols=21  Identities=24%  Similarity=0.652  Sum_probs=16.5

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      ....|.||+|+.+|=.+.-..
T Consensus        23 ~~akY~CPrC~~rYCSl~C~k   43 (59)
T 1x4s_A           23 QPARYTCPRCNAPYCSLRCYR   43 (59)
T ss_dssp             EEECEECTTTCCEESSHHHHH
T ss_pred             CCccccCcCCCCCccChHHHH
Confidence            356899999999997776544

>2eow_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=82.59  E-value=0.71  Score=25.28  Aligned_cols=31  Identities=16%  Similarity=0.204  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eow_A            9 GEKPYKCNECGKAFRARSSLAIHQATHSGEKPSGPS   44 (46)
T ss_dssp             CCCCEECTTSCCEESSHHHHHHHHHHHCCCSCSCTT
T ss_pred             CCCCeeccccCChhcCHHHHHHHHHHcCCCCCCCCC
Confidence            44569999999999987765432     23367775

>3uk3_C Zinc finger protein 217; transcription factor, DNA binding, DNA-metal BI protein complex; 2.10A {Homo sapiens}

Probab=82.46  E-value=1  Score=25.73  Aligned_cols=19  Identities=16%  Similarity=0.354  Sum_probs=13.7

Q ss_pred             CCeeecCCCCCccchhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...|.|+.|++.|+....+
T Consensus        30 ~~~~~C~~C~~~f~~~~~l   48 (57)
T 3uk3_C           30 EKPYKCEFCEYAAAQKTSL   48 (57)
T ss_dssp             CCCEECSSSSCEESSHHHH
T ss_pred             CCCcCCCCCcchhCCHHHH
Confidence            4458888888888766544

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A

Probab=82.44  E-value=1.2  Score=35.12  Aligned_cols=60  Identities=15%  Similarity=0.289  Sum_probs=47.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      |..|+.+.-..|.+|.++|+..+|++....+..|..|..+|++=.-   +. ..|   -..|||-+.
T Consensus       156 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD---~q-~~g---e~~Yw~P~l  215 (234)
T 3cuq_A          156 HTVVLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLD---LQ-APG---EAHYWLPAL  215 (234)
T ss_dssp             HHHHHHHHTTTSEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEE---SS-SSS---SCEEECTTS
T ss_pred             HHHHHHHHHhcCcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEe---CC-CCC---cceeecchh
Confidence            6677777666899999999999999999999999999999999854   11 122   236887653

>1bm9_A RTP, TER, replication terminator protein; DNA-binding protein, contrahelicase; 2.00A {Bacillus subtilis} SCOP: a.4.5.7 PDB: 1f4k_A 1j0r_A 2dpd_A 2dpu_A 2efw_A* 2dqr_A

Probab=82.42  E-value=11  Score=26.65  Aligned_cols=64  Identities=20%  Similarity=0.194  Sum_probs=40.3

Q ss_pred             hCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHH----HHHHHHHHHHHHHHHHH
Q psy5744          55 LKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFV----NIVKYKLDVMRKRMEME  120 (157)
Q Consensus        55 l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~----~vik~rl~~m~~~L~~~  120 (157)
                      ..++.-.|=.+|..|+++|+|+.+.+.+.++++  ..+.||.+.-..--    ...+.........|+.-
T Consensus        50 ~~is~gtlYp~L~rLe~~Gll~~~~~~~~g~~r--~~rkyY~lT~~G~~~~~~~~~~~~~~~~~~~i~~~  117 (122)
T 1bm9_A           50 FKPNHTEVYRSLHELLDDGILKQIKVKKEGAKL--QEVVLYQFKDYEAAKLYKKQLKVELDRCKKLIEKA  117 (122)
T ss_dssp             CCCCHHHHHHHHHHHHHTTSEEEEEEECTTSTT--CEEEEEEESCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCcccHHHHHHHHHHCCCeEEEEeecCCCCC--CceeEEEEChhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            356777899999999999999988554223332  36789998864333    23333344444444433

>2epv_A Zinc finger protein 268; C2H2, zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=82.40  E-value=0.68  Score=25.29  Aligned_cols=21  Identities=19%  Similarity=0.442  Sum_probs=16.4

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      ....|.|+.|++.|+....+.
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~   29 (44)
T 2epv_A            9 GEKPYECNECGKAFIWKSLLI   29 (44)
T ss_dssp             CCCSEECSSSCCEESSHHHHH
T ss_pred             CCcCeECCCCCcccCchHHHH
Confidence            345799999999998766543

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=82.36  E-value=3.5  Score=34.21  Aligned_cols=45  Identities=9%  Similarity=0.204  Sum_probs=41.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ...+++.|..++.++-.++++.+|++...+++.|..|.+.|++..
T Consensus       299 ~~~ll~~l~~~p~~t~~~~~~~~~~S~~TA~r~L~~L~e~GiL~~  343 (373)
T 3eqx_A          299 SHELVQVIFEQPYCRIQNLVESGLAKRQTASVYLKQLCDIGVLEE  343 (373)
T ss_dssp             CHHHHHHHHHCSEEEHHHHHHTSSSCHHHHHHHHHHHHHTTSCEE
T ss_pred             HHHHHHHHHHCCCccHHHHHHHhCcCHHHHHHHHHHHHHCCcEEE
Confidence            456899999999999999999999999999999999999999974

>2eoy_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.26  E-value=0.66  Score=25.57  Aligned_cols=31  Identities=26%  Similarity=0.354  Sum_probs=21.4

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----C-CCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----L-WCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d-~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     + ...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~~C~   45 (46)
T 2eoy_A            9 KEKCFKCNKCEKTFSCSKYLTQHERIHTRGVKSGPSS   45 (46)
T ss_dssp             CSCCEECSSSCCEESSSHHHHHHHTTCCSCCTTSSSC
T ss_pred             CCCCEECcCCCCcCCCHHHHHHHHHHcCCCCCCCCCC
Confidence            34569999999999987665422     2 2357775

>2ep3_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=82.21  E-value=0.71  Score=25.37  Aligned_cols=31  Identities=19%  Similarity=0.270  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2ep3_A            9 GEKPYRCAECGKAFTDRSNLFTHQKIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSHHHHHHHHTTTTTSCCCCTT
T ss_pred             CCCCeECCCCCchhCCHHHHHHHHHHcCCCCCCCCC
Confidence            44579999999999987765432     12357775

>2yu5_A Zinc finger protein 473; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.15  E-value=0.65  Score=25.25  Aligned_cols=21  Identities=29%  Similarity=0.689  Sum_probs=16.6

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~   29 (44)
T 2yu5_A            9 GENPFKCSKCDRVFTQRNYLV   29 (44)
T ss_dssp             CCCSEECSSSSCEESSSHHHH
T ss_pred             CCCCeECCCCCchhCCHHHHH
Confidence            345699999999999876654

>2yto_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.97  E-value=0.73  Score=25.36  Aligned_cols=31  Identities=19%  Similarity=0.206  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      ....|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2yto_A            9 GEKPYKCSDCGKAFTRKSGLHIHQQSHTGERHSGPS   44 (46)
T ss_dssp             SCCCEECSSSCCEESSHHHHHHHHHHHTCCCBTTTB
T ss_pred             CCCCEECcccCCccCCHhHHHHHHHHcCCCCCCCCC
Confidence            34579999999999987665432     23467775

>2yts_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.97  E-value=0.7  Score=25.31  Aligned_cols=31  Identities=13%  Similarity=0.078  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~C~   44 (46)
T 2yts_A            9 GEKPYICNECGKSFIQKSHLNRHRRIHTGEKPSGPS   44 (46)
T ss_dssp             SCCSEECSSSCCEESSHHHHHHHGGGTSSCCSSCCC
T ss_pred             CCcCEECCCCChhhCChHHHHHHHHhcCCCCCcCCC
Confidence            44579999999999987765432     23367776

>2emj_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2eoi_A

Probab=81.94  E-value=0.7  Score=25.44  Aligned_cols=31  Identities=16%  Similarity=0.157  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2emj_A            9 GEKPFECAECGKSFSISSQLATHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSSCEESSHHHHHHHHHHHTTSCSSSSC
T ss_pred             CCCCEECCCCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987765432     23367775

>2yrj_A Zinc finger protein 473; C2H2-type zinc finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.75  E-value=0.78  Score=25.12  Aligned_cols=31  Identities=13%  Similarity=0.149  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2yrj_A            9 GEKPYRCGECGKAFAQKANLTQHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CCCCEECSSSCCEESSHHHHHHHHTTTSSCCSSCSC
T ss_pred             CCCCeECCCCCCccCCHHHHHHHHHHcCCCCCCCCC
Confidence            44579999999999987665422     23367776

>2ene_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.71  E-value=0.74  Score=25.29  Aligned_cols=31  Identities=16%  Similarity=0.096  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ene_A            9 GEKPYKCNECGKVFRHNSYLSRHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CSSSEECSSSCCEESSHHHHHHHHTTTCCCCCCSCC
T ss_pred             CCCCeECCCCCchhCChHHHHHHHhhcCCCCCCCCC
Confidence            44579999999999987765432     12357775

>2ytj_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.70  E-value=0.74  Score=25.29  Aligned_cols=31  Identities=16%  Similarity=0.170  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ytj_A            9 GEKPYICAECGKAFTIRSNLIKHQKIHTKQKPSGPS   44 (46)
T ss_dssp             SCCSEECSSSCCEESSHHHHHHHHHHTSCCCCSSCS
T ss_pred             CCcCeECCCCChhhCCHHHHHHHHHHcCCCCCCCCC
Confidence            34569999999999987776432     23367776

>2eml_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.69  E-value=0.74  Score=25.29  Aligned_cols=31  Identities=13%  Similarity=0.201  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2eml_A            9 GEKPYECSVCGKAFSHRQSLSVHQRIHSGKKPSGPS   44 (46)
T ss_dssp             SCCSEECSSSCCEESSHHHHHHHHGGGSSCCCSCSS
T ss_pred             CCCCeeCCCcCCccCCHHHHHHHHHHhcCCCCCCCC
Confidence            44579999999999987765432     23367776

>2emh_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.69  E-value=0.79  Score=25.15  Aligned_cols=31  Identities=19%  Similarity=0.188  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2emh_A            9 GERPYICTVCGKAFTDRSNLIKHQKIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECTTTCCEESSHHHHHHHHHHHHCSSCSSSC
T ss_pred             CCCCcCCCCCCchhCCHHHHHHHHHhcCCCCCCCCC
Confidence            44579999999999987766432     23467775

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=81.56  E-value=1.8  Score=33.11  Aligned_cols=28  Identities=11%  Similarity=0.075  Sum_probs=20.0

Q ss_pred             HHHHHHHHhhcCCCCeeecCCCCCccch
Q psy5744         114 RKRMEMEERDATSRSSFKCPRCLKTFTD  141 (157)
Q Consensus       114 ~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~  141 (157)
                      -+++-++++...+...|+|+.||-.|..
T Consensus       156 ~~~ll~~l~~~~~~~~~~C~~CG~i~~g  183 (202)
T 1yuz_A          156 YLAAYNDIDAPDDDKFHLCPICGYIHKG  183 (202)
T ss_dssp             HHHHHHTTTCCCSCCEEECSSSCCEEES
T ss_pred             HHHHHHHHhcCCCCcEEEECCCCCEEcC
Confidence            3344445555566789999999999974

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=81.53  E-value=2.9  Score=25.46  Aligned_cols=35  Identities=20%  Similarity=0.235  Sum_probs=26.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      ..|+..+  ....+..+||+.+|++.+.|+..+..+.
T Consensus        17 ~~il~~~--~~g~s~~eIA~~l~is~~tV~~~~~~~~   51 (74)
T 1fse_A           17 REVFELL--VQDKTTKEIASELFISEKTVRNHISNAM   51 (74)
T ss_dssp             HHHHHHH--TTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3445443  2346999999999999999998888755

>2em4_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.47  E-value=0.76  Score=25.30  Aligned_cols=31  Identities=13%  Similarity=0.177  Sum_probs=21.5

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2em4_A            9 GQRPYECIECGKAFKTKSSLICHRRSHTGEKPSGPS   44 (46)
T ss_dssp             CSSSEECSSSCCEESSHHHHHHHHHHHSSSSCCCCC
T ss_pred             CCcCcCCCCCCCccCCHHHHHHHHHhcCCCCCCCCC
Confidence            34569999999999987665422     23357775

>2eme_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.45  E-value=0.77  Score=25.13  Aligned_cols=31  Identities=13%  Similarity=0.049  Sum_probs=21.6

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2eme_A            9 GEKPYVCDYCGKAFGLSAELVRHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSHHHHHHHHGGGCCCSCCSSC
T ss_pred             CCCCeECCCCChhhCCHHHHHHHHHhcCCCCCCCCC
Confidence            44579999999999987665422     12357775

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=81.37  E-value=2.9  Score=27.48  Aligned_cols=39  Identities=13%  Similarity=0.348  Sum_probs=30.7

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN   71 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~   71 (157)
                      +...-|+.++.  ..++..+||..||++.+.|+..+..+.+
T Consensus        32 ~rE~~Vl~l~~--~G~s~~eIA~~L~iS~~TV~~~~~~i~~   70 (90)
T 3ulq_B           32 PRECLILQEVE--KGFTNQEIADALHLSKRSIEYSLTSIFN   70 (90)
T ss_dssp             HHHHHHHHHHH--TTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            33556666655  4689999999999999999998887653

>2emx_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.31  E-value=0.79  Score=24.88  Aligned_cols=31  Identities=19%  Similarity=0.234  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         7 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   42 (44)
T 2emx_A            7 GEKPFGCSCCEKAFSSKSYLLVHQQTHAEEKPSGPS   42 (44)
T ss_dssp             SCCCEECSSSSCEESSHHHHHHHHHHHTSSCSCSCC
T ss_pred             CCcCccCCCCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987766432     23467775

>2eoo_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.31  E-value=0.83  Score=25.12  Aligned_cols=31  Identities=13%  Similarity=0.146  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eoo_A            9 GERPYGCNECGKNFGRHSHLIEHLKRHFREKSSGPS   44 (46)
T ss_dssp             CCCCEECSSSCCEESSHHHHHHHHHHHHSTTSSCCS
T ss_pred             CCCCEEccccCcccCCHHHHHHHHHHHcCCCCCCCC
Confidence            44579999999999987765432     23457775

>2ep2_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.27  E-value=0.8  Score=25.13  Aligned_cols=31  Identities=16%  Similarity=0.190  Sum_probs=22.5

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2ep2_A            9 GEKPYECSICGKSFTKKSQLHVHQQIHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSHHHHHHHHHTTSSCCSCCSC
T ss_pred             CCcCcCCCCCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            45579999999999987766432     23367776

>1f2i_G Fusion of N-terminal 17-MER peptide extension to ZIF12; zinc finger, dimer, protein-DNA complex, cooperativity, transcription/DNA complex; 2.35A {Mus musculus} SCOP: g.37.1.1 g.37.1.1

Probab=81.24  E-value=1.2  Score=26.92  Aligned_cols=19  Identities=21%  Similarity=0.744  Sum_probs=14.3

Q ss_pred             CCeeecCCCCCccchhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ...|.|+.|++.|+....+
T Consensus        47 ~~~~~C~~C~~~f~~~~~l   65 (73)
T 1f2i_G           47 QKPFQCRICMRNFSRSDHL   65 (73)
T ss_dssp             CCCEECTTTCCEESCHHHH
T ss_pred             CCCeECCCCCchhCCHHHH
Confidence            4468999999998876554

>2em7_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.24  E-value=0.79  Score=25.16  Aligned_cols=31  Identities=16%  Similarity=0.114  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2em7_A            9 GEKPYKCEECGKGFICRRDLYTHHMVHTGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESCHHHHHHHGGGGTTCCCSSTT
T ss_pred             CCcCccCCCccchhCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987765432     22367775

>1x6e_A Zinc finger protein 24; ZNF24, KOX17, ZNF191, zscan3, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=81.21  E-value=1.5  Score=26.49  Aligned_cols=20  Identities=25%  Similarity=0.561  Sum_probs=13.4

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|.|+.|++.|.....+
T Consensus        39 ~~~~~~C~~C~~~f~~~~~L   58 (72)
T 1x6e_A           39 GEKPYKCLECGKAFSQNSGL   58 (72)
T ss_dssp             CSCCEECSSSCCEESSHHHH
T ss_pred             CCCCeECCCCCcccCCHHHH
Confidence            34568888888887765543

>2emf_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.01  E-value=0.8  Score=25.18  Aligned_cols=31  Identities=19%  Similarity=0.209  Sum_probs=21.8

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2emf_A            9 GGKHFECTECGKAFTRKSTLSMHQKIHTGEKPSGPS   44 (46)
T ss_dssp             SSCCEECSSSCCEESCHHHHHHHGGGTSCSSCSCCC
T ss_pred             CCCCeECCCCCchhCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987765432     12367775

>2eq0_A Zinc finger protein 347; C2H2, zinc finger domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.91  E-value=0.9  Score=24.91  Aligned_cols=31  Identities=16%  Similarity=0.117  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eq0_A            9 GEKPYKCHECGKVFRRNSHLARHQLIHTGEKPSGPS   44 (46)
T ss_dssp             CCCCEECTTTCCEESSHHHHHHHHTTTCCCCCSCCS
T ss_pred             CCCCeECCCCCchhCCHHHHHHHHHHcCCCCCCCCC
Confidence            45579999999999987765432     12367775

>2eov_A Zinc finger protein 484; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.87  E-value=0.71  Score=25.30  Aligned_cols=31  Identities=19%  Similarity=0.168  Sum_probs=21.5

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2eov_A            9 GEKPYKCSDCGKSFTWKSRLRIHQKCHTGERHSGPS   44 (46)
T ss_dssp             SCCSCBCSSSCCBCSSHHHHHHHHHHHSCCSSCCSC
T ss_pred             CCCCccCCccChhhCCHHHHHHHHHhcCCCCCCCCC
Confidence            34569999999999987665422     23357775

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=80.85  E-value=2.4  Score=34.61  Aligned_cols=59  Identities=10%  Similarity=0.061  Sum_probs=46.2

Q ss_pred             chHHHHHHHHHHHHHcCCCchH--------HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          13 VPTSLKQLSRLVVRGFYSIEDS--------LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        13 ip~~~~~Lv~~v~R~Fy~~e~i--------vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .++.++.+++.+.    ++-.+        -++..| + +..+-++||..+|++..-++..|..|...|++..
T Consensus        21 ~~~~~~~~~~~~~----~~~~l~~~~~~~~~ll~~L-~-~~~t~~eLa~~~g~~~~~v~~~L~~l~~~gll~~   87 (373)
T 2qm3_A           21 QSNAMKEIVERVK----TKTKIPVYERSVENVLSAV-L-ASDDIWRIVDLSEEPLPLVVAILESLNELGYVTF   87 (373)
T ss_dssp             SCCHHHHHHHHHH----TTCSSCCCHHHHHHHHHHH-H-HCSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEC
T ss_pred             hhhHHHHHHHHHH----HhcCccHhHHHHHHHHHHh-c-CCCCHHHHHHHhCCChHHHHHHHHHHhhCCcEEE
Confidence            3455666666665    33334        577777 4 5689999999999999999999999999999974

>2em3_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.83  E-value=0.82  Score=25.08  Aligned_cols=31  Identities=16%  Similarity=0.162  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2em3_A            9 GEKPYECKVCSKAFTQKAHLAQHQKTHTGEKPSGPS   44 (46)
T ss_dssp             SCCSEECSSSCCEESSHHHHHHHHHHHCCCCCCCSC
T ss_pred             CCcCeECCCCCcccCCHHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987765432     23467776

>2epw_A Zinc finger protein 268; C2H2, zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.73  E-value=0.79  Score=25.08  Aligned_cols=31  Identities=16%  Similarity=0.116  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2epw_A            9 GEKPCKCTECGKAFCWKSQLIMHQRTHVDDKHSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSSHHHHHHHHHCCSCCCSCCC
T ss_pred             CCCCeeCCCCCCccCCHHHHHHHHHHhCCCCCCCCC
Confidence            34569999999999987765432     23367775

>2em9_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2yrh_A

Probab=80.73  E-value=0.85  Score=24.95  Aligned_cols=31  Identities=16%  Similarity=0.115  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2em9_A            9 GEKPYNCKECGKSFRWASCLLKHQRVHSGEKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSCCEESSHHHHHHHGGGGTSCCCCSTT
T ss_pred             CCcCeECCccccccCChHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987665422     12357775

>2el4_A Zinc finger protein 268; alternative splicing, DNA-binding, metal-binding, nuclear protein, repeat, transcription, transcription regulation; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2eog_A 2em1_A 2emw_A 2eok_A

Probab=80.64  E-value=0.83  Score=24.99  Aligned_cols=31  Identities=16%  Similarity=0.236  Sum_probs=22.2

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2el4_A            9 GVKPYGCSQCAKTFSLKSQLIVHQRSHTGVKPSGPS   44 (46)
T ss_dssp             CCCSEECSSSSCEESSHHHHHHHGGGSSSCCCSCCT
T ss_pred             CCCceECCCCCchhCCHHHHHHHHHHhCCCCCCCCC
Confidence            44569999999999987766432     23367776

>2em6_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.58  E-value=0.78  Score=25.25  Aligned_cols=31  Identities=16%  Similarity=0.138  Sum_probs=21.9

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2em6_A            9 GEKCYKCDVCGKEFSQSSHLQTHQRVHTGEKPSGPS   44 (46)
T ss_dssp             CCCCCBCSSSCCBCSSHHHHHHHHTTTSSSCCCCTT
T ss_pred             CCCCeECCCCCcccCCHHHHHHHHHHcCCCCCCCCC
Confidence            45579999999999987765432     12367786

>2eox_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.52  E-value=0.69  Score=25.14  Aligned_cols=21  Identities=29%  Similarity=0.550  Sum_probs=16.9

Q ss_pred             CCCeeecCCCCCccchhhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +...|.|+.|++.|+....+.
T Consensus         9 ~~~~~~C~~C~k~F~~~~~L~   29 (44)
T 2eox_A            9 DSKSYNCNECGKAFTRIFHLT   29 (44)
T ss_dssp             CCCCEEETTTTEEESSSHHHH
T ss_pred             CCCCeECcccCcccCCHHHHH
Confidence            445799999999999877654

>2em5_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.46  E-value=0.85  Score=25.08  Aligned_cols=31  Identities=19%  Similarity=0.044  Sum_probs=21.8

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2em5_A            9 STKSHQCHECGRGFTLKSHLNQHQRIHTGEKPSGPS   44 (46)
T ss_dssp             CSCSEECSSSCCEESSHHHHHHHHTTTSCSCCSSCC
T ss_pred             CCCCeECCcCCCccCCHHHHHHHHHHhCCCCCCCCC
Confidence            44579999999999987765422     12357776

>2yu8_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.39  E-value=0.84  Score=25.05  Aligned_cols=31  Identities=19%  Similarity=0.164  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2yu8_A            9 GEKPYKCNECGKVFTQNSHLARHRRVHTGGKPSGPS   44 (46)
T ss_dssp             CCSSEECSSSCCEESSSHHHHHHTHHHHSCCCSCSC
T ss_pred             CCCCeECCcCCchhCCHHHHHHHHHhcCCCCCCCCC
Confidence            45679999999999987765432     23467775

>2ytk_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.32  E-value=0.85  Score=25.01  Aligned_cols=31  Identities=19%  Similarity=0.151  Sum_probs=22.0

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~   44 (46)
T 2ytk_A            9 GEKPYKCNECGKVFTQNSHLTNHWRIHTGEKPSGPS   44 (46)
T ss_dssp             SSCSEECSSSCCEESSHHHHHHHHHHHSSSSCSSCC
T ss_pred             CCCCEeCCcCCCccCCHHHHHHHHHHHCCCCCCCCC
Confidence            44579999999999987765432     23467775

>1x5w_A Zinc finger protein 64, isoforms 1; ZNF338, nuclear protein, DNA binding, transcription, C2H2 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=80.16  E-value=1.8  Score=25.91  Aligned_cols=20  Identities=20%  Similarity=0.348  Sum_probs=13.1

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ....|.|+.|++.|+....+
T Consensus        34 ~~~~~~C~~C~~~f~~~~~L   53 (70)
T 1x5w_A           34 TDRPFKCNYCSFDTKQPSNL   53 (70)
T ss_dssp             CSCSEECSSSSCEESSHHHH
T ss_pred             CCCCEeCCCCCCccCCHHHH
Confidence            34457788888777765544

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=80.15  E-value=0.67  Score=30.06  Aligned_cols=25  Identities=24%  Similarity=0.558  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744         109 KLDVMRKRMEMEERDATSRSSFKCPRCLKT  138 (157)
Q Consensus       109 rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~  138 (157)
                      .+.++.++||.....     -|.||.||+.
T Consensus        11 slRK~vkkie~~q~~-----ky~C~fCgk~   35 (72)
T 3jyw_9           11 SLRRQVKKLEIQQHA-----RYDCSFCGKK   35 (72)
T ss_dssp             HHHTTTHHHHHHHHS-----CBCCSSCCSS
T ss_pred             hHHHHHHHHHHHhcc-----CccCCCCCCc
Confidence            355666677766544     6899999976

>2eop_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.15  E-value=0.82  Score=25.02  Aligned_cols=31  Identities=13%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+..-     +...|.|+
T Consensus         9 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2eop_A            9 GEKPHECRECGKSFSFNSQLIVHQRIHTGENPSGPS   44 (46)
T ss_dssp             CCCSCBCTTTCCBCSSHHHHHHHHTTTTTSCCSCCC
T ss_pred             CCCCeeCCCCCchhCCHHHHHHHHHHcCCCCCCCCC
Confidence            44579999999999987766432     12367776

>2yth_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.07  E-value=0.78  Score=25.25  Aligned_cols=31  Identities=19%  Similarity=0.159  Sum_probs=21.7

Q ss_pred             CCCeeecCCCCCccchhhhhhcc-----CCCCcccC
Q psy5744         126 SRSSFKCPRCLKTFTDLEPCLLV-----LWCACPCK  156 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~~L~-----d~~~F~C~  156 (157)
                      +...|.|+.|++.|+....+.--     +...|.|+
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~   44 (46)
T 2yth_A            9 GEKPFQCEECGKRFTQNSHLHSHQRVHTGEKPSGPS   44 (46)
T ss_dssp             CSSSBCCSSSCCCBSSHHHHHHHGGGGTTCCCSSCC
T ss_pred             CCcCCCCCCCCcccCCHHHHHHHHHhcCCCCCCCCC
Confidence            34569999999999987665422     23367775

---

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	157
d1vd4a_	62	g.41.3.1 (A:) Transcription initiation factor TFII	2e-07

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIE-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (103), Expect = 2e-07
 Identities = 19/28 (67%), Positives = 24/28 (85%)

Query: 116 RMEMEERDATSRSSFKCPRCLKTFTDLE 143
           R+E +ERD+T+R+SFKCP C  TFTDLE
Sbjct: 1   RIETDERDSTNRASFKCPVCSSTFTDLE 28

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	157
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	99.71
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	99.21
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	98.51
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.99
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	97.97
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	97.69
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	97.66
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	97.55
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.54
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	97.52
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.38
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	97.21
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	97.2
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	97.01
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.99
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	96.91
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.91
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	96.82
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	96.78
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.72
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	96.71
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	96.68
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.66
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.64
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.64
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.63
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.62
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.6
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	96.27
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	96.27
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.16
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	96.12
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	96.02
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	95.93
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	95.92
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	95.84
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	95.81
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.79
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.72
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	95.64
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.55
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.54
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.54
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	95.44
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	95.4
d1zyba1	73	Probable transcription regulator BT4300, C-termina	95.29
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	95.24
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	95.04
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.03
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	94.93
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.42
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	94.4
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	94.34
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	94.31
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	94.31
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	94.06
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	94.01
d2htja1	73	P fimbrial regulatory protein PapI {Escherichia co	94.01
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	93.94
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.69
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.64
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	93.28
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	93.27
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.11
d1ldja3	276	Cullin homolog 1, cul-1 {Human (Homo sapiens) [Tax	92.51
d1x6ea2	26	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	92.09
d1a1ia2	28	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	91.91
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	91.73
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	91.68
d2adra1	29	ADR1 {Synthetic, based on Saccharomyces cerevisiae	91.29
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	91.04
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	90.92
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	90.65
d1x6ha1	37	Transcriptional repressor CTCF {Human (Homo sapien	90.55
d1sp1a_	29	Transcription factor sp1 {Human (Homo sapiens) [Ta	90.45
d1y0jb1	36	U-shaped transcription factor, different fingers {	90.38
d1okra_	120	Methicillin resistance regulatory protein MecI {St	90.36
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	90.14
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	89.8
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	89.55
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	89.19
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	89.0
d2dlqa2	28	GLI-Krueppel family member HKR3 {Mouse (Mus muscul	88.97
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	88.76
d2cota2	38	Zinc finger and SCAN domain-containing protein 16,	88.51
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	88.25
d2ct1a2	36	Transcriptional repressor CTCF {Human (Homo sapien	88.17
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	88.13
d1p7aa_	37	Kruppel-like factor 3, Bklf {Mouse (Mus musculus)	88.03
d1x6ea1	33	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	88.01
d1srka_	35	Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musc	87.88
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	87.7
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	87.62
d1njqa_	37	SUPERMAN zinc finger domain {Thale cress (Arabidop	87.61
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	87.17
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	87.05
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	86.86
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	86.16
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	85.76
d1x6ha2	36	Transcriptional repressor CTCF {Human (Homo sapien	85.5
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	84.98
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	84.18
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	83.99
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	83.29
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	82.37
d2epsa1	39	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	82.18
d2drpa2	26	Tramtrack protein (two zinc-finger peptide) {Droso	81.7
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	81.53
d1sp2a_	31	Transcription factor sp1 {Human (Homo sapiens) [Ta	81.52
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	81.22
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	81.03
d2dt5a1	74	Transcriptional repressor Rex, N-terminal domain {	80.93
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	80.61
d1ubdc4	28	Ying-yang 1 (yy1, zinc finger domain) {Human (Homo	80.32
d1hlva1	66	DNA-binding domain of centromere binding protein B	80.21

>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=99.71  E-value=1e-17  Score=113.12  Aligned_cols=82  Identities=13%  Similarity=0.240  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHcCCCchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEE
Q psy5744          18 KQLSRLVVRGFYSIEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYF   96 (157)
Q Consensus        18 ~~Lv~~v~R~Fy~~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~   96 (157)
                      .+++..+++...|++++-|+++|+. ++.+|||+||+.+|++.|+||++|+.|++.|||++++.+.  ++ ++|..|||+
T Consensus         5 e~ll~~~~~~i~Ge~~~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd--~~-~gw~~Y~W~   81 (88)
T d1q1ha_           5 EDLFINLAKSLLGDDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRD--KD-SGWFIYYWK   81 (88)
T ss_dssp             TTHHHHHHHTTSCSTTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC------CCCCEEEEE
T ss_pred             HHHHHHHHHHHccHHHHHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeec--CC-CCcEEEEEE
Confidence            4577788999999999999999995 6799999999999999999999999999999999985543  23 579999999


Q ss_pred             ecchhH
Q psy5744          97 INYQTF  102 (157)
Q Consensus        97 I~y~~~  102 (157)
                      ++++.+
T Consensus        82 ~~~e~i   87 (88)
T d1q1ha_          82 PNIDQI   87 (88)
T ss_dssp             CTHHHH
T ss_pred             echhcC
Confidence            998765

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIE-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.21  E-value=3.4e-13  Score=85.27  Aligned_cols=40  Identities=50%  Similarity=0.794  Sum_probs=36.5

Q ss_pred             HHHHHhhcCCCCeeecCCCCCccchhhhhhccCC--CCcccC
Q psy5744         117 MEMEERDATSRSSFKCPRCLKTFTDLEPCLLVLW--CACPCK  156 (157)
Q Consensus       117 L~~~~~~~~~~~~Y~Cp~C~~~Ys~lda~~L~d~--~~F~C~  156 (157)
                      |+.++++..++++|+||.|+++||.|||.+|+|+  +.|+|.
T Consensus         2 ie~~~rd~~~~~~y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~   43 (62)
T d1vd4a_           2 IETDERDSTNRASFKCPVCSSTFTDLEANQLFDPMTGTFRCT   43 (62)
T ss_dssp             CCCCSSSCCSSSEEECSSSCCEEEHHHHHHHEETTTTEEBCS
T ss_pred             cchhhhccccCCceECCCCCCCcchhhHHHhcCcCCCeEEec
Confidence            5677889999999999999999999999999985  699995

>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=98.51  E-value=1e-06  Score=60.09  Aligned_cols=101  Identities=15%  Similarity=0.168  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEE
Q psy5744          16 SLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYY   95 (157)
Q Consensus        16 ~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw   95 (157)
                      .+.+|++.+...-..+....|+-+|..++.++-.+||+.+|++...|..+|..|.+.|||.... . . .+  .+...|.
T Consensus         5 ~~~~l~~~L~~lGlt~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~-~-~-~~--~r~~~~~   79 (109)
T d1sfxa_           5 PLGELVKALEKLSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREI-V-E-KG--WVGYIYS   79 (109)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE-E-E-SS--SEEEEEE
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEe-c-c-CC--Ccccccc
Confidence            4678888887766677789999999999999999999999999999999999999999997542 2 1 22  2444566


Q ss_pred             EecchhHHHHHHHHHHHHHHHHHHHH
Q psy5744          96 FINYQTFVNIVKYKLDVMRKRMEMEE  121 (157)
Q Consensus        96 ~I~y~~~~~vik~rl~~m~~~L~~~~  121 (157)
                      -.+...++.-++..+.+..+.|++.+
T Consensus        80 a~~~~e~l~~~~~~~~~~l~eLe~~l  105 (109)
T d1sfxa_          80 AEKPEKVLKEFKSSILGEIERIEKMF  105 (109)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            67766666666666655555555544

>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=97.99  E-value=2.2e-05  Score=52.95  Aligned_cols=84  Identities=14%  Similarity=0.235  Sum_probs=58.6

Q ss_pred             CchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHH
Q psy5744          31 IEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYK  109 (157)
Q Consensus        31 ~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~r  109 (157)
                      +...-|+..|.+ ++.++-.|||+.+|+++..|+++|..|.+.|+|.....   ..|++++..++|.+.. .+...+..-
T Consensus        21 ~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~---~~d~rg~~~~~~~~~~-~~~~~i~~~   96 (109)
T d2d1ha1          21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKT---EGKKIGRPKYYYSISS-NILEKIRND   96 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC----------CCEEEEECT-THHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEeec---CCCCCceeEEEeeCCH-HHHHHHHHH
Confidence            445678888875 67899999999999999999999999999999986522   2344566677777774 455555555


Q ss_pred             HHHHHHHHH
Q psy5744         110 LDVMRKRME  118 (157)
Q Consensus       110 l~~m~~~L~  118 (157)
                      +....++++
T Consensus        97 ~~~~~~k~~  105 (109)
T d2d1ha1          97 LLNCAKRME  105 (109)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555544443

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=97.97  E-value=2.8e-05  Score=52.11  Aligned_cols=84  Identities=13%  Similarity=0.275  Sum_probs=64.3

Q ss_pred             chHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEE
Q psy5744          13 VPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKV   92 (157)
Q Consensus        13 ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~   92 (157)
                      .|+.+.++. .+.+++-++--.-|+..|. ++.++=.|||+.+|+++..+-+.|..|++.|||..+  + .   |+   .
T Consensus         6 ~pe~~~~la-~~~kaL~~p~Rl~Il~~L~-~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~--r-~---G~---~   74 (98)
T d1r1ta_           6 APEVAQSLA-EFFAVLADPNRLRLLSLLA-RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYR--K-Q---GR---H   74 (98)
T ss_dssp             CHHHHHHHH-HHHHHHCCHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--E-E---TT---E
T ss_pred             CHHHHHHHH-HHHHHhCCHHHHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE--E-E---CC---E
Confidence            455566655 4446776777778888775 677999999999999999999999999999999976  1 2   32   3


Q ss_pred             EEEEecchhHHHHHH
Q psy5744          93 NYYFINYQTFVNIVK  107 (157)
Q Consensus        93 ~yw~I~y~~~~~vik  107 (157)
                      .||+++-+.+...+.
T Consensus        75 ~~Y~l~~~~i~~l~~   89 (98)
T d1r1ta_          75 VYYQLQDHHIVALYQ   89 (98)
T ss_dssp             EEEEESSHHHHHHHH
T ss_pred             EEEEEChHHHHHHHH
Confidence            488899876665544

>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=97.69  E-value=9.1e-05  Score=54.24  Aligned_cols=70  Identities=19%  Similarity=0.243  Sum_probs=54.7

Q ss_pred             HHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          24 VVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        24 v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      +.+++-++--.-|++.| .++.+|=.+||+.+|+++.-+++.|..|.++|||..++....    ++....||.++
T Consensus        12 ~~~~l~~p~R~~Il~~L-~~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~~~~~----~g~~~k~y~~~   81 (190)
T d1ulya_          12 VIKVMLEDTRRKILKLL-RNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMK----GNLVEKYYGRT   81 (190)
T ss_dssp             HHHHHHSHHHHHHHHHH-TTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEEE----TTEEEEEEEES
T ss_pred             HHHHhCCHHHHHHHHHH-HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeecc----CCcceEEEEEc
Confidence            34455555566788877 478899999999999999999999999999999988743222    34667788776

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.66  E-value=6.9e-05  Score=50.98  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=60.5

Q ss_pred             HHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhH
Q psy5744          23 LVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTF  102 (157)
Q Consensus        23 ~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~  102 (157)
                      .+.+++-++--+-|+..|.+++.++=.+||+.+|+++..+-+-|..|++.|||..+  +    +|+   ..||+++.+.+
T Consensus        23 ~~~kaLadp~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~--r----~G~---~~~Y~l~~~~i   93 (108)
T d1u2wa1          23 QILKAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR--K----EGK---LALYSLGDEHI   93 (108)
T ss_dssp             HHHHHHHSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-------------CCEEEESCHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEE--E----ECC---EEEEEECHHHH
Confidence            45566656666889999988889999999999999999999999999999999976  1    232   35889998776


Q ss_pred             HHHHH
Q psy5744         103 VNIVK  107 (157)
Q Consensus       103 ~~vik  107 (157)
                      ...+.
T Consensus        94 ~~ll~   98 (108)
T d1u2wa1          94 RQIMM   98 (108)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65544

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=97.55  E-value=0.00065  Score=44.80  Aligned_cols=84  Identities=12%  Similarity=0.246  Sum_probs=63.5

Q ss_pred             hHHHHHHHHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEE
Q psy5744          14 PTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVN   93 (157)
Q Consensus        14 p~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~   93 (157)
                      |+.+.++. .+.+++-++--+-|+..|. ++.++=.|||+.+|+++..+-+-|..|++.|||..+  + +   |+   ..
T Consensus         2 ~d~~e~~a-~~fkaL~d~~Rl~Il~~L~-~~~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~--r-~---G~---~~   70 (94)
T d1r1ua_           2 TDTLERVT-EIFKALGDYNRIRIMELLS-VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAK--R-Q---GQ---SM   70 (94)
T ss_dssp             HHHHHHHH-HHHHHTCSHHHHHHHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--E-E---TT---EE
T ss_pred             hHHHHHHH-HHHHHhCCHHHHHHHHHHH-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEE--E-E---CC---EE
Confidence            44455543 3456776666677888776 567889999999999999999999999999999976  1 2   32   44


Q ss_pred             EEEecchhHHHHHHH
Q psy5744          94 YYFINYQTFVNIVKY  108 (157)
Q Consensus        94 yw~I~y~~~~~vik~  108 (157)
                      ||+|+-+.+...++.
T Consensus        71 ~Y~l~~~~v~~ll~~   85 (94)
T d1r1ua_          71 IYSLDDIHVATMLKQ   85 (94)
T ss_dssp             EEEESSHHHHHHHHH
T ss_pred             EEEECcHHHHHHHHH
Confidence            899998877665554

>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=97.54  E-value=0.0002  Score=47.18  Aligned_cols=65  Identities=15%  Similarity=0.090  Sum_probs=53.5

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      ++-..-||.+|..++.++=.|||+.+|+++.-+.+.|.+|.+.|+|..+. . . .|   ....||.|...
T Consensus        15 ~p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~-~-~-~d---~r~~~~~LT~~   79 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYK-V-I-AD---RPRTVVEITDF   79 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE-E-C-SS---SCEEEEEECHH
T ss_pred             CHHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEE-c-C-cC---CccccccCCHH
Confidence            44467899999888999999999999999999999999999999999762 1 1 23   34677888854

>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=97.52  E-value=6.9e-05  Score=55.43  Aligned_cols=72  Identities=14%  Similarity=0.191  Sum_probs=54.6

Q ss_pred             HHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          22 RLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        22 ~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      ..+.+++-++--.-||..|. ++.++=.+||+.+|+++.-|++.|..|+++|||..+..  ..+.  +....||++.
T Consensus         6 ~~~~~~l~~~~R~~Il~~L~-~~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~~~--~~~~--G~~~~~y~l~   77 (194)
T d2p4wa1           6 NRLLDVLGNETRRRILFLLT-KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE--KIPR--GRPRKYYMIK   77 (194)
T ss_dssp             HHHHHHHHSHHHHHHHHHHH-HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CBTT--BCCCEEEEEC
T ss_pred             HHHHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe--ecCC--CCceEEEEec
Confidence            34555555555677888775 57899999999999999999999999999999997632  2233  4556667754

>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=97.38  E-value=5.8e-05  Score=47.31  Aligned_cols=44  Identities=7%  Similarity=0.120  Sum_probs=41.0

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .|+.+|..++.+|=-|||+.+|++..-|++++..|.++|+|...
T Consensus        10 ~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1          10 RVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            58888888999999999999999999999999999999999754

>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=97.21  E-value=0.00022  Score=44.89  Aligned_cols=43  Identities=14%  Similarity=0.210  Sum_probs=39.1

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++|.|-..+.++--+||..||++.++|.+.|++|.+.|.|...
T Consensus        15 ~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~   57 (70)
T d1sfua_          15 EVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMV   57 (70)
T ss_dssp             HHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecC
Confidence            5677777788999999999999999999999999999999865

>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=97.20  E-value=0.00026  Score=48.87  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=40.3

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++-+|=.|..++.++=++||+.+|+++..|||++.+|...|||.+.+
T Consensus         6 Av~~L~~la~~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~r   52 (127)
T d1xd7a_           6 AIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRA   52 (127)
T ss_dssp             HHHHHHHHHTCSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccC
Confidence            34455555667789999999999999999999999999999999763

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=97.01  E-value=0.00096  Score=40.74  Aligned_cols=46  Identities=20%  Similarity=0.283  Sum_probs=42.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...|+.+|..++-++-.+||+.+|++...|++-+.+|++.|++...
T Consensus         7 D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           7 DLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence            3568999999999999999999999999999999999999999754

>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=96.99  E-value=0.0053  Score=42.05  Aligned_cols=47  Identities=11%  Similarity=0.158  Sum_probs=43.1

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||-.|-.++.++-.|||+.+|++...|-+++..|.+.|+|...
T Consensus        31 ~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~   77 (139)
T d2a61a1          31 AQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   77 (139)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeee
Confidence            36778888888889999999999999999999999999999999876

>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=96.91  E-value=0.0076  Score=41.49  Aligned_cols=66  Identities=12%  Similarity=0.076  Sum_probs=50.3

Q ss_pred             chHHHHHHHHHHHHHcCCCc-hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          13 VPTSLKQLSRLVVRGFYSIE-DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        13 ip~~~~~Lv~~v~R~Fy~~e-~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +-..+......+.+.+.=+. +.-|+-.|..+ +.+|-.|||+.+|++...+..+|..|.+.|+|.+.
T Consensus         7 ~~~~~~~~~~~~~~~~Gl~~~~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~   74 (151)
T d1ku9a_           7 AKKLIIELFSELAKIHGLNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (151)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEE
Confidence            33445555666666654333 45566666544 56999999999999999999999999999999975

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=96.91  E-value=0.00096  Score=40.68  Aligned_cols=59  Identities=10%  Similarity=0.167  Sum_probs=43.3

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      |+..|.+ +.++-.|||+.+|++..-|.+++..|.++|+|......+   .++++....|.||
T Consensus         4 Il~~i~~-~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~~~~---~~~GRp~~~l~ln   62 (62)
T d2hoea1           4 ILKRIMK-SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEKDSP---KGVGRPTKSLKIS   62 (62)
T ss_dssp             SHHHHHH-SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEECCC-------CCCEEEEEC
T ss_pred             HHHHHHH-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCC---CCCCCCCceeecC
Confidence            5667754 469999999999999999999999999999998763222   2233445555554

>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=96.82  E-value=0.00097  Score=46.39  Aligned_cols=47  Identities=19%  Similarity=0.232  Sum_probs=39.8

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++.+|-+|..+  ..++=++||+.+|++++.+||++..|.+.|||.+.+
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~r   57 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNR   57 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            45666677643  468999999999999999999999999999999863

>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=96.78  E-value=0.0018  Score=40.67  Aligned_cols=45  Identities=16%  Similarity=0.214  Sum_probs=41.1

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ++-|||++.++ +.++-.|||+.+|++...+.++|..|.+.|+|.+
T Consensus         7 ~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~   52 (75)
T d1mkma1           7 AFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            45789999875 6799999999999999999999999999999984

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.72  E-value=0.0016  Score=39.61  Aligned_cols=45  Identities=16%  Similarity=0.271  Sum_probs=41.9

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|+..|-.++-++-.+||+.+|++...|+.-+.+|.++|++...
T Consensus         8 ~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           8 RGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            468889899999999999999999999999999999999999854

>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=96.71  E-value=0.0038  Score=39.28  Aligned_cols=37  Identities=5%  Similarity=0.086  Sum_probs=33.5

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ...+ ++.+||+.+|++..-||+++..|..+|+|..+.
T Consensus        19 G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            3456 899999999999999999999999999999763

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.0012  Score=41.81  Aligned_cols=46  Identities=9%  Similarity=0.128  Sum_probs=41.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCCh-HHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFER-KMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~-k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-.|+++|-.++.-+--+||+.+|++. ++|.++|+.|...|.|...
T Consensus         7 eekI~~~L~~~g~~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~   53 (73)
T d1xmka1           7 KEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   53 (73)
T ss_dssp             HHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCchHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecC
Confidence            346899998888899999999999999 7999999999999999865

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.66  E-value=0.0015  Score=39.88  Aligned_cols=43  Identities=19%  Similarity=0.250  Sum_probs=38.6

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      .-|+.+|-.++.+|=+|||+.+|++..-|++-+..|++.|+.-
T Consensus         8 ~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I   50 (63)
T d1biaa1           8 LKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDV   50 (63)
T ss_dssp             HHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcE
Confidence            4578877778899999999999999999999999999999854

>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=96.64  E-value=0.007  Score=41.62  Aligned_cols=46  Identities=9%  Similarity=0.304  Sum_probs=42.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.-||..|-.++.++-.|||+.++++...|.+++..|.+.|+|...
T Consensus        38 q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~   83 (141)
T d1lnwa_          38 DVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   83 (141)
T ss_dssp             HHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeee
Confidence            6778888877888999999999999999999999999999999976

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.64  E-value=0.0016  Score=40.41  Aligned_cols=45  Identities=7%  Similarity=0.139  Sum_probs=41.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      -.|+.+|..++.+|-.|||+.+|++.--|.+++..|.++|+|...
T Consensus         8 ~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           8 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            358888889999999999999999999999999999999999754

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.63  E-value=0.0013  Score=39.80  Aligned_cols=45  Identities=20%  Similarity=0.386  Sum_probs=41.3

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|+..|..++-++-.+||+.+|++...|+.-+.+|.++|++...
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   50 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            458888888999999999999999999999999999999999743

>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=96.62  E-value=0.007  Score=41.42  Aligned_cols=46  Identities=11%  Similarity=0.130  Sum_probs=42.9

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|-.++.++--+||+.+|++...+-+++..|.+.|+|...
T Consensus        34 q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~   79 (140)
T d2etha1          34 ELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   79 (140)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            5678888888899999999999999999999999999999999976

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.60  E-value=0.0014  Score=39.47  Aligned_cols=45  Identities=18%  Similarity=0.298  Sum_probs=41.5

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..|+..|..++-++-.+||+.+|++...|..-+.+|.++|++...
T Consensus         6 ~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           6 KKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            468889899999999999999999999999999999999999844

>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=96.27  E-value=0.0035  Score=38.01  Aligned_cols=42  Identities=14%  Similarity=0.208  Sum_probs=36.4

Q ss_pred             HHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          37 IDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        37 lD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+..+++.++--|||+.||+++--|.+.+.+|.++|||.+.
T Consensus        13 ~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1          13 YMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             HHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEc
Confidence            333335789999999999999999999999999999999986

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=96.27  E-value=0.0089  Score=36.70  Aligned_cols=36  Identities=25%  Similarity=0.515  Sum_probs=33.2

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+++.+||+.+|++..-||+++..|.++|+|..+
T Consensus        23 G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   58 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVREAFQILIEDRLVAHE   58 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            345789999999999999999999999999999976

>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=96.16  E-value=0.0076  Score=41.14  Aligned_cols=78  Identities=9%  Similarity=0.232  Sum_probs=56.3

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHHHHHHHHH
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDV  112 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~vik~rl~~  112 (157)
                      +..||..|-.++.++-.+||+.+|++...+.+++.+|.+.|+|... +  ...|+|   ..+.++.-...  .+..++..
T Consensus        36 q~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~-~--~~~D~R---~~~l~lT~~G~--~~~~~~~~  107 (136)
T d2bv6a1          36 QFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRE-R--SEVDQR---EVFIHLTDKSE--TIRPELSN  107 (136)
T ss_dssp             HHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEE-E--CSSSTT---CEEEEECHHHH--HHHHHHTT
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEe-e--cCCccc---chhhccCHHHH--HHHHHHHH
Confidence            5678888888999999999999999999999999999999999965 2  223433   34556664432  23334444


Q ss_pred             HHHHHH
Q psy5744         113 MRKRME  118 (157)
Q Consensus       113 m~~~L~  118 (157)
                      ....+.
T Consensus       108 ~~~~~~  113 (136)
T d2bv6a1         108 ASDKVA  113 (136)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=96.12  E-value=0.02  Score=39.32  Aligned_cols=48  Identities=23%  Similarity=0.353  Sum_probs=43.6

Q ss_pred             CchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .....||..|..++.++-.+||+.+++++.-+.+++.+|.+.|+|...
T Consensus        29 ~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~   76 (144)
T d1lj9a_          29 RGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             TTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHHHHHhhhccccc
Confidence            336778888888888999999999999999999999999999999976

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.02  E-value=0.011  Score=36.95  Aligned_cols=36  Identities=22%  Similarity=0.400  Sum_probs=33.1

Q ss_pred             CCCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCM-KEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..+ ++.+||+.+|++..-||+++..|.++|+|..+
T Consensus        24 G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~   60 (74)
T d1hw1a1          24 GTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   60 (74)
T ss_dssp             TSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            3467 79999999999999999999999999999976

>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=95.93  E-value=0.027  Score=38.33  Aligned_cols=62  Identities=8%  Similarity=0.065  Sum_probs=49.6

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      .+..+|-.|-.++.++-.|||..++++...+.+++.+|.++|+|...  . ...|+   ...++++.-
T Consensus        35 ~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~--~-~~~D~---R~~~i~lT~   96 (138)
T d1jgsa_          35 AQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL--P-NPNDK---RGVLVKLTT   96 (138)
T ss_dssp             HHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--E-CTTCS---SCEEEEECH
T ss_pred             HHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEe--e-ccCCC---CeeEEEECH
Confidence            36788888888889999999999999999999999999999999754  1 22343   344566664

>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=95.92  E-value=0.01  Score=35.68  Aligned_cols=36  Identities=14%  Similarity=0.183  Sum_probs=33.3

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...++-.+||..+|++.|+|+++|+.|...|.+..+
T Consensus        14 ~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~k~   49 (59)
T d2gxba1          14 GKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKE   49 (59)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccchhHHHHHHHhCCcHHHHHHHHHHHHHccchhhc
Confidence            467999999999999999999999999999999865

>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=95.84  E-value=0.0051  Score=37.68  Aligned_cols=34  Identities=12%  Similarity=0.326  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+....|.++|..|+++|+|...
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L~~l~~~glI~~~   62 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRILKMLEDQNLISAH   62 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence            4899999999999999999999999999999865

>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=95.81  E-value=0.011  Score=35.89  Aligned_cols=43  Identities=16%  Similarity=0.157  Sum_probs=37.3

Q ss_pred             HHHHHH-hCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLV-RNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~-~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-.|. .++.++--|||+.||+++--|-+.+.+|.++|||.+.
T Consensus        13 ~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~~   56 (63)
T d2isya1          13 TIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA   56 (63)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEEc
Confidence            333444 3688999999999999999999999999999999976

>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=95.79  E-value=0.033  Score=37.47  Aligned_cols=61  Identities=13%  Similarity=0.189  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHcC-CCchHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          18 KQLSRLVVRGFY-SIEDSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        18 ~~Lv~~v~R~Fy-~~e~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .......++.|- ...+..|+..|.++  +.+|-.|||+.++++...+.+++.+|.+.|+|...
T Consensus        15 ~~~~~~~l~~~glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~   78 (135)
T d3broa1          15 STRFDIFAKKYDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   78 (135)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHH
Confidence            333334444431 24466788888876  45999999999999999999999999999999976

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.72  E-value=0.036  Score=37.40  Aligned_cols=48  Identities=13%  Similarity=0.202  Sum_probs=42.5

Q ss_pred             CchHHHHHHHHhCC-CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVRNP-CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~~~-~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+..||-.|.+++ .++-.+||+.++++...+.+++..|.+.|+|...
T Consensus        28 ~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~   76 (137)
T d2fbha1          28 QARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRL   76 (137)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCcccc
Confidence            45677888887765 5899999999999999999999999999999976

>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=95.64  E-value=0.055  Score=36.48  Aligned_cols=61  Identities=16%  Similarity=0.183  Sum_probs=49.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecc
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINY   99 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y   99 (157)
                      ...||..|-+++.++--+||+.++++..-+-+++..|.+.|+|....   ...|   ....+.++.-
T Consensus        32 q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~---~~~D---~R~~~l~lT~   92 (136)
T d2fbia1          32 QWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWK---APKD---QRRVYVNLTE   92 (136)
T ss_dssp             HHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE---ETTE---EEEEEEEECH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee---cCcc---CchhhhccCH
Confidence            67788888888999999999999999999999999999999998652   1123   4455666663

>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=95.55  E-value=0.012  Score=35.68  Aligned_cols=42  Identities=19%  Similarity=0.244  Sum_probs=37.4

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcc
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKI   74 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~L   74 (157)
                      ..-|+..|..+ +.++-++||+.+|++...||+-+..|++.|+
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            34678888765 6799999999999999999999999999997

>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=95.54  E-value=0.023  Score=38.76  Aligned_cols=49  Identities=12%  Similarity=0.255  Sum_probs=44.5

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...+..||-.|..++.++-.+||..+++++..+.+++..|.+.|+|...
T Consensus        34 t~~q~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~   82 (143)
T d1s3ja_          34 TPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   82 (143)
T ss_dssp             CHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheee
Confidence            3456778888888888999999999999999999999999999999976

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.54  E-value=0.03  Score=37.96  Aligned_cols=48  Identities=10%  Similarity=0.208  Sum_probs=42.3

Q ss_pred             CchHHHHHHHHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDMLVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+..+|-.|.. ++.++-.|||..++++...+-+++..|.+.|+|...
T Consensus        31 ~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~   79 (140)
T d3deua1          31 QTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ   79 (140)
T ss_dssp             HHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEec
Confidence            346678888876 567999999999999999999999999999999865

>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=95.44  E-value=0.011  Score=37.00  Aligned_cols=34  Identities=9%  Similarity=0.244  Sum_probs=32.2

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+....|.++|..|+++|+|...
T Consensus        29 ~lt~~eLA~~~G~sretvsr~L~~l~~~glI~~~   62 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAIRTLSTFVSERMLALD   62 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            5899999999999999999999999999999864

>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=95.40  E-value=0.0088  Score=37.46  Aligned_cols=34  Identities=15%  Similarity=0.327  Sum_probs=31.6

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+....|.++|.+|+++|+|...
T Consensus        30 ~lt~~elA~~~g~sretvsr~l~~l~~~glI~~~   63 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVSRVLASLKRENILDKK   63 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence            6899999999999999999999999999999864

>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=95.29  E-value=0.0095  Score=37.06  Aligned_cols=34  Identities=21%  Similarity=0.336  Sum_probs=31.8

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++-+|||..+|+....|.++|.+|.++|+|...
T Consensus        27 ~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~~~   60 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNISKTLNELQDNGLIELH   60 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEEE
T ss_pred             ecCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            4689999999999999999999999999999865

>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=95.04  E-value=0.016  Score=39.46  Aligned_cols=46  Identities=11%  Similarity=0.177  Sum_probs=41.0

Q ss_pred             hHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..  ++.++-.+||+.+|++...+.+++..|.+.|+|..+
T Consensus        35 q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~   82 (125)
T d1p4xa2          35 EFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE   82 (125)
T ss_dssp             HHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             HHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeee
Confidence            5778888864  457999999999999999999999999999999865

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=95.03  E-value=0.021  Score=36.34  Aligned_cols=35  Identities=11%  Similarity=0.256  Sum_probs=32.8

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ++.+|--|||+.+|+++..+.++|..|+++|||..
T Consensus        19 ~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r   53 (85)
T d3ctaa1          19 RAYLTSSKLADMLGISQQSASRIIIDLEKNGYITR   53 (85)
T ss_dssp             EEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence            35799999999999999999999999999999985

>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=94.93  E-value=0.012  Score=40.03  Aligned_cols=46  Identities=13%  Similarity=0.247  Sum_probs=42.8

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +..||..|-.++.++--+||+.+++++..+-+++.+|.+.|+|...
T Consensus        35 q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~   80 (137)
T d1z91a1          35 QYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   80 (137)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEe
Confidence            5778888888899999999999999999999999999999999976

>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=94.42  E-value=0.38  Score=32.36  Aligned_cols=46  Identities=11%  Similarity=0.184  Sum_probs=41.1

Q ss_pred             hHHHHHHHHhC-CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN-PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~-~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||-+|.++ +.++-.+||+.+|++..-+-+++..|...|+|..+
T Consensus        36 q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~   82 (145)
T d2hr3a1          36 QLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH   82 (145)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEee
Confidence            45688888765 57999999999999999999999999999999765

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=94.40  E-value=0.027  Score=39.90  Aligned_cols=46  Identities=7%  Similarity=-0.031  Sum_probs=42.5

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|-+++.++-.|||+.++++...+-+++.+|.+.|+|...
T Consensus        43 q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~   88 (162)
T d2fxaa1          43 EHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFS   88 (162)
T ss_dssp             HHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceee
Confidence            5678888888889999999999999999999999999999999865

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=94.34  E-value=0.024  Score=37.42  Aligned_cols=34  Identities=18%  Similarity=0.206  Sum_probs=31.0

Q ss_pred             CcCHHHHHHHhCCC-hHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFE-RKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~-~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+. ...|.++|..|+++|+|+..
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~~   65 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYK   65 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEEc
Confidence            58999999999997 56799999999999999975

>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=94.31  E-value=0.03  Score=37.26  Aligned_cols=46  Identities=17%  Similarity=0.380  Sum_probs=40.7

Q ss_pred             hHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||..|..  ++.++-.+||+.++++...+-+++..|.+.|+|...
T Consensus        34 q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~   81 (115)
T d1hsja1          34 EIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKK   81 (115)
T ss_dssp             HHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCE
T ss_pred             HHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEE
Confidence            5667877774  457999999999999999999999999999999876

>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=94.31  E-value=0.047  Score=34.58  Aligned_cols=42  Identities=10%  Similarity=0.097  Sum_probs=38.5

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      -|.|.|. .+.+|=++||+.+|+++.-++++|..|..-|++..
T Consensus        25 ~ifd~l~-~gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e   66 (85)
T d1tw3a1          25 RLVDHIL-AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEE   66 (85)
T ss_dssp             THHHHHH-TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CcHHHhc-cCCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEe
Confidence            4888874 77899999999999999999999999999999974

>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=94.06  E-value=0.031  Score=34.81  Aligned_cols=34  Identities=15%  Similarity=0.285  Sum_probs=32.1

Q ss_pred             CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          45 CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        45 ~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+|-+|||..+|+....|-++|..|+++|+|...
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Confidence            5889999999999999999999999999999864

>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=94.01  E-value=0.014  Score=38.37  Aligned_cols=36  Identities=17%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             CCc-CHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          44 PCM-KEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        44 ~~i-~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ..+ ++.+||+.+|++...||+++..|.++|+|..+.
T Consensus        31 ~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   67 (100)
T d1v4ra1          31 DTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRG   67 (100)
T ss_dssp             SBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEec
Confidence            356 899999999999999999999999999999763

>d2htja1 a.4.5.73 (A:1-73) P fimbrial regulatory protein PapI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FaeA-like
domain: P fimbrial regulatory protein PapI
species: Escherichia coli [TaxId: 562]

Probab=94.01  E-value=0.058  Score=32.97  Aligned_cols=57  Identities=21%  Similarity=0.294  Sum_probs=45.5

Q ss_pred             HHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEec
Q psy5744          35 LIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFIN   98 (157)
Q Consensus        35 vIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~   98 (157)
                      -||.+|-+++.=+-.+||+-+|++.=+.|-.|.-|+.+|.|+..      |= |..-.+||++-
T Consensus         4 ~Il~fl~~~~~~~T~EIAea~gvsaYQARyYL~~Lekegki~Rs------Pl-RrGa~TlW~~~   60 (73)
T d2htja1           4 EILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRS------PL-RRGMATYWFLK   60 (73)
T ss_dssp             HHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE------CC-SSSSSCEEEES
T ss_pred             HHHHHHHhcCCccHHHHHHHhhhHHHHHHHHHHHHHHhcCcccC------hh-hhhhHHHHHHh
Confidence            37888888766699999999999999999999999999999853      11 22235678764

>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=93.94  E-value=0.15  Score=33.95  Aligned_cols=53  Identities=19%  Similarity=0.244  Sum_probs=42.4

Q ss_pred             HHHHHHHhCC---CcCHHHHHHHhCCC----hHHHHHHHHHHhhCcceeeeEeeeecCCCce
Q psy5744          35 LIIDMLVRNP---CMKEDDICELLKFE----RKMLRARISTLKNDKIIQTRLRMETGLDGKA   89 (157)
Q Consensus        35 vIlD~L~~~~---~i~dedLa~~l~i~----~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~   89 (157)
                      -|.|+|-++|   .++..|||..++.+    +.-++++|..|-..|+++...+.  .+||+.
T Consensus        31 gI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~~vf~~~~~~--~~dg~~   90 (107)
T d1kyza1          31 DLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRT--QQDGKV   90 (107)
T ss_dssp             THHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHTTSEEEEEEE--CTTSCE
T ss_pred             CCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhcCceEEeeec--CCCCCe
Confidence            4899998765   68999999999885    44699999999999999987432  356643

>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=93.69  E-value=0.068  Score=35.40  Aligned_cols=47  Identities=13%  Similarity=0.263  Sum_probs=40.8

Q ss_pred             chHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ....||..|..+  +.++--+||+.+++++..+-+++..|++.|+|...
T Consensus        34 ~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~   82 (115)
T d2frha1          34 EEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKK   82 (115)
T ss_dssp             HHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCB
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheee
Confidence            356777777764  45999999999999999999999999999999865

>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=93.64  E-value=0.047  Score=36.77  Aligned_cols=46  Identities=15%  Similarity=0.215  Sum_probs=41.3

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||-.|.++  +.++-.|||+.+++++..+-+++.+|.+.|+|...
T Consensus        36 q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~   83 (125)
T d1p4xa1          36 EFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKV   83 (125)
T ss_dssp             HHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEE
T ss_pred             HHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceee
Confidence            67788888764  46999999999999999999999999999999976

>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=93.28  E-value=0.12  Score=32.58  Aligned_cols=49  Identities=12%  Similarity=0.188  Sum_probs=41.9

Q ss_pred             CchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeeeE
Q psy5744          31 IEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL   79 (157)
Q Consensus        31 ~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~~   79 (157)
                      ++.-+|.+++-.  +..+--.||...+|++.++|.|+|-.|+..+||+...
T Consensus        13 ~~E~lVY~~I~~ag~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~Vk   63 (78)
T d2dk5a1          13 NQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVK   63 (78)
T ss_dssp             SSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHccccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceeec
Confidence            455667777664  4678899999999999999999999999999999874

>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=93.27  E-value=0.08  Score=34.11  Aligned_cols=44  Identities=9%  Similarity=0.090  Sum_probs=39.7

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|.|.|. .+.+|=++||+.+|+++.-++++|..|..-||+...
T Consensus        30 L~ifd~L~-~gp~t~~eLA~~~g~~~~~l~rLlr~L~a~gll~~~   73 (92)
T d1qzza1          30 LRLVDHLL-AGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGG   73 (92)
T ss_dssp             TTHHHHHH-TTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECC
T ss_pred             cCchHHHh-CCCCCHHHHHHHHCcCchHHHHHHHHHHHCCCeeee
Confidence            34888875 789999999999999999999999999999999854

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=93.11  E-value=0.092  Score=32.16  Aligned_cols=38  Identities=13%  Similarity=0.203  Sum_probs=32.8

Q ss_pred             HhCC-CcCHHHHHHHhCC-ChHHHHHHHHHHhhCcceeee
Q psy5744          41 VRNP-CMKEDDICELLKF-ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        41 ~~~~-~i~dedLa~~l~i-~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ..+| .-|-.|||+.+|+ +++.|+..|..|++.|++...
T Consensus        19 ~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~   58 (71)
T d1jhfa1          19 SQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIV   58 (71)
T ss_dssp             HHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecC
Confidence            3455 4789999999999 578899999999999999864

>d1ldja3 e.40.1.1 (A:411-686) Cullin homolog 1, cul-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Multi-domain proteins (alpha and beta)
fold: Cullin homology domain
superfamily: Cullin homology domain
family: Cullin homology domain
domain: Cullin homolog 1, cul-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.51  E-value=0.087  Score=39.94  Aligned_cols=68  Identities=12%  Similarity=0.216  Sum_probs=55.1

Q ss_pred             cccchHHHHHHHHHHHHHcCCCc---------------------------------hHHHHHHHHhCCCcCHHHHHHHhC
Q psy5744          10 HTEVPTSLKQLSRLVVRGFYSIE---------------------------------DSLIIDMLVRNPCMKEDDICELLK   56 (157)
Q Consensus        10 ~~~ip~~~~~Lv~~v~R~Fy~~e---------------------------------~ivIlD~L~~~~~i~dedLa~~l~   56 (157)
                      ...+|+.+...+.... .||...                                 +..||.++-.++.+|-++|++.+|
T Consensus       142 ~~~lP~~l~~~~~~f~-~~Y~~~~~~RkL~w~~~lg~~~l~~~~~~~~~~l~vs~~Qa~ILllFN~~~~~t~~ei~~~~~  220 (276)
T d1ldja3         142 TFALPSELERSYQRFT-AFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQ  220 (276)
T ss_dssp             CCCCCGGGHHHHHHHH-HHTTTTCTTCCEEECGGGCCCEEEESSSSSCCEEECCHHHHHHHHGGGSSSEEEHHHHHHHTC
T ss_pred             CccCCHHHHHHHHHHH-HHHHHhCCCCeEEEecCCCcEEEEEEECCCcEEEEECHHHHHHHHhhcCCCccCHHHHHHHHC
Confidence            4568888888888775 777755                                 455665545567899999999999


Q ss_pred             CChHHHHHHHHHHhhCcceeee
Q psy5744          57 FERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        57 i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++..++++.|..|...|++...
T Consensus       221 i~~~~l~~~L~~L~~~kll~~~  242 (276)
T d1ldja3         221 IKMDILAQVLQILLKSKLLVLE  242 (276)
T ss_dssp             CCHHHHHHHHHHHHHTTTEECS
T ss_pred             cCHHHHHHHHHHHHhCCEEEec
Confidence            9999999999999999998753

>d1x6ea2 g.37.1.1 (A:41-66) Zinc finger protein 24 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 24
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.09  E-value=0.025  Score=28.50  Aligned_cols=14  Identities=36%  Similarity=0.847  Sum_probs=12.0

Q ss_pred             eeecCCCCCccchh
Q psy5744         129 SFKCPRCLKTFTDL  142 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~l  142 (157)
                      -|.|+.||+.|+.-
T Consensus         2 Py~C~eCgK~F~~~   15 (26)
T d1x6ea2           2 PYKCLECGKAFSQN   15 (26)
T ss_dssp             CEECSSSCCEESSH
T ss_pred             CccCCCCcCeeccC
Confidence            49999999999854

>d1a1ia2 g.37.1.1 (A:132-159) ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ZIF268
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.91  E-value=0.028  Score=28.74  Aligned_cols=17  Identities=24%  Similarity=0.800  Sum_probs=14.0

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+..+-+
T Consensus         3 Py~C~~C~k~F~~~~~L   19 (28)
T d1a1ia2           3 PFQCRICMRNFSRSDHL   19 (28)
T ss_dssp             CEECTTTCCEESCHHHH
T ss_pred             CccCCCCcCEecccccc
Confidence            59999999999876543

>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=91.73  E-value=0.1  Score=31.35  Aligned_cols=43  Identities=7%  Similarity=0.069  Sum_probs=33.8

Q ss_pred             HHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRN--PCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |.+++...  ..-+=.|||..+|++.+++|.+|..|.+.|.+...
T Consensus        12 I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI   56 (64)
T d1lvaa3          12 LEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKI   56 (64)
T ss_dssp             HHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34444432  23456899999999999999999999999998754

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=91.68  E-value=0.97  Score=28.76  Aligned_cols=51  Identities=18%  Similarity=0.242  Sum_probs=42.7

Q ss_pred             HcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          27 GFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        27 ~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .+-+.=...|+..|. +|...=.||...+ |++++.+-+-|..|.++|||...
T Consensus         7 ilg~kW~l~Il~~L~-~g~~rF~el~~~l~gis~~~Ls~rLk~Le~~glv~r~   58 (95)
T d2hzta1           7 VIGGKWKCVILCHLT-HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRI   58 (95)
T ss_dssp             HHCSTTHHHHHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHcCCCHHHHHHHHH-cCCCCHHHHHHHhhcCChhHHHHHHHHHHHhHHHhhe
Confidence            333444567888874 7888999999998 99999999999999999999965

>d2adra1 g.37.1.1 (A:102-130) ADR1 {Synthetic, based on Saccharomyces cerevisiae sequence}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ADR1
species: Synthetic, based on Saccharomyces cerevisiae sequence

Probab=91.29  E-value=0.03  Score=28.78  Aligned_cols=17  Identities=35%  Similarity=0.720  Sum_probs=14.0

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      -|.|+.|++.|+..+-+
T Consensus         2 p~~C~~C~k~F~~~~~L   18 (29)
T d2adra1           2 SFVCEVCTRAFARQEHL   18 (29)
T ss_dssp             CBCCTTTCCCBSCHHHH
T ss_pred             cCCCCCCCCCCCCchHc
Confidence            48999999999976644

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.04  E-value=0.16  Score=32.72  Aligned_cols=48  Identities=15%  Similarity=0.133  Sum_probs=39.3

Q ss_pred             CchHHHHHH---HHh-CCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          31 IEDSLIIDM---LVR-NPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        31 ~e~ivIlD~---L~~-~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++..-||.+   -.+ |++|+-+.|+...|++...+.+.|..|...+||..+
T Consensus        11 ~~dfRvL~aiE~gmrnhE~VP~~lI~~~a~l~~~~~~~~L~~L~k~kLv~~~   62 (89)
T d1zara1          11 KHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQNR   62 (89)
T ss_dssp             HHHHHHHHHHHTTTTTCSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhccccCccccHHHHHHHHCCCHHHHHHHHHHHHHcCCeecc
Confidence            344444444   444 799999999999999999999999999999999753

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.92  E-value=0.51  Score=27.34  Aligned_cols=48  Identities=17%  Similarity=0.202  Sum_probs=38.8

Q ss_pred             cchHHHHHHHHHHHHHcCCCchHHHHHHHHh--CCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744          12 EVPTSLKQLSRLVVRGFYSIEDSLIIDMLVR--NPCMKEDDICELLKFERKMLRARIST   68 (157)
Q Consensus        12 ~ip~~~~~Lv~~v~R~Fy~~e~ivIlD~L~~--~~~i~dedLa~~l~i~~k~vRkiL~~   68 (157)
                      .||-.+++++..+-++.         ..|..  +..-|.+|||+.||++..+|..+|..
T Consensus         5 rvPr~~~e~~~ki~~~~---------~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_           5 KVSRSLKEMGNKIRKAK---------DELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             TTHHHHHHHHHHHHHHH---------HHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             eCcHHHHHHHHHHHHHH---------HHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            48899999998888764         33342  45789999999999999999998864

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=90.65  E-value=1.1  Score=28.93  Aligned_cols=57  Identities=18%  Similarity=0.184  Sum_probs=46.4

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |..++..+-+.=...|+..|. +|..+=.||...+ |++++.+-+-|..|.++|||...
T Consensus        10 v~~~l~ilg~kW~l~Il~~L~-~g~~rF~el~~~l~gIs~~~Ls~rLkeL~~~glv~r~   67 (102)
T d2fswa1          10 VRKSMQIFAGKWTLLIIFQIN-RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKK   67 (102)
T ss_dssp             HHHHHHHHTSSSHHHHHHHHT-TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCCHHHHHHHHc-cCCCCHHHHHhhCcccchhHHHHHHHHHHHCCceeec
Confidence            444555555555677887765 6788999999998 99999999999999999999865

>d1x6ha1 g.37.1.1 (A:44-80) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.55  E-value=0.05  Score=28.85  Aligned_cols=17  Identities=41%  Similarity=0.841  Sum_probs=13.8

Q ss_pred             CeeecCCCCCccchhhh
Q psy5744         128 SSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       128 ~~Y~Cp~C~~~Ys~lda  144 (157)
                      ..|+|.+|+++|+--..
T Consensus         3 ~afvcskcgktftrrnt   19 (37)
T d1x6ha1           3 AAFVCSKCGKTFTRRNT   19 (37)
T ss_dssp             CCEECSSSCCEESCHHH
T ss_pred             ceeeecccccchhcchH
Confidence            57999999999986543

>d1sp1a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcription factor sp1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.45  E-value=0.034  Score=28.58  Aligned_cols=16  Identities=38%  Similarity=0.916  Sum_probs=13.1

Q ss_pred             eeecCCCCCccchhhh
Q psy5744         129 SFKCPRCLKTFTDLEP  144 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda  144 (157)
                      -|.|+.||+.|+--.-
T Consensus         2 py~C~~C~k~F~~~s~   17 (29)
T d1sp1a_           2 KFACPECPKRFMRSDH   17 (29)
T ss_dssp             CSCCTTTTCCCSCSHH
T ss_pred             CEECCcCCCeecchHH
Confidence            4899999999986543

>d1y0jb1 g.37.1.2 (B:1-36) U-shaped transcription factor, different fingers {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: C2HC finger
domain: U-shaped transcription factor, different fingers
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=90.38  E-value=0.041  Score=28.97  Aligned_cols=16  Identities=25%  Similarity=0.546  Sum_probs=13.6

Q ss_pred             CCeeecCCCCCccchh
Q psy5744         127 RSSFKCPRCLKTFTDL  142 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~l  142 (157)
                      ..-|+|+.||.+||..
T Consensus         6 parf~c~pcgirfss~   21 (36)
T d1y0jb1           6 PARFMCLPCGIAFSSP   21 (36)
T ss_dssp             CCCCBCTTTCCBCSCH
T ss_pred             ccceeccccceeecCh
Confidence            4579999999999864

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.36  E-value=0.15  Score=33.71  Aligned_cols=46  Identities=15%  Similarity=0.314  Sum_probs=41.0

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||.+|=.++.++=.||++.+    ++..+-|..+|..|.+.|+|..+
T Consensus         9 E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~   58 (120)
T d1okra_           9 EWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK   58 (120)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEE
Confidence            46789999988889989888877    79999999999999999999864

>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=90.14  E-value=0.32  Score=30.95  Aligned_cols=42  Identities=10%  Similarity=0.150  Sum_probs=33.9

Q ss_pred             HHHHHh-CCCcCHHHHHHHhCC--ChHHHHHHHHHHhhCcceeee
Q psy5744          37 IDMLVR-NPCMKEDDICELLKF--ERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        37 lD~L~~-~~~i~dedLa~~l~i--~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ++..+. ...++=.+||+.+|+  ++.-||-.|..|++.|++..-
T Consensus        14 ve~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~   58 (87)
T d1stza1          14 VREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQP   58 (87)
T ss_dssp             HHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCC
Confidence            333343 457999999999665  699999999999999999753

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=89.80  E-value=0.43  Score=29.15  Aligned_cols=46  Identities=24%  Similarity=0.369  Sum_probs=37.6

Q ss_pred             chHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          32 EDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        32 e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +|++..=.++ ++.+-=.-||+.||+.-..||..+..|++.|||...
T Consensus         5 ~~vl~~l~ll-~qPiGRr~La~~L~l~Er~vRte~~~Lk~~gLI~~~   50 (69)
T d2p8ta1           5 EDVLAVIFLL-KEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSK   50 (69)
T ss_dssp             HHHHHHHHHT-TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHH-cCCccHHHHHHHcCCcHHHHHHHHHHHHHCCCeeee
Confidence            4444333334 457999999999999999999999999999999875

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=89.55  E-value=0.081  Score=32.61  Aligned_cols=34  Identities=9%  Similarity=0.168  Sum_probs=27.8

Q ss_pred             CCCcCHHHHHHHhCCChHHHHHHHHHHhhCccee
Q psy5744          43 NPCMKEDDICELLKFERKMLRARISTLKNDKIIQ   76 (157)
Q Consensus        43 ~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~   76 (157)
                      +..-++++||+.|||+..++++++.......+++
T Consensus        24 GR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~S   57 (77)
T d1rp3a1          24 GREPTDEEVAKELGISTEELFKTLDKINFSYILS   57 (77)
T ss_dssp             SSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCcee
Confidence            4578999999999999999999987665554444

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=89.19  E-value=0.56  Score=30.73  Aligned_cols=57  Identities=12%  Similarity=0.270  Sum_probs=46.3

Q ss_pred             HHHHHHHcCCCchHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          21 SRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        21 v~~v~R~Fy~~e~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      |......+.+.=...|+..|. +|...=.||...+ |++++.+-+-|..|.++|||...
T Consensus         9 i~~al~iig~kW~~~Il~~L~-~g~~RF~el~~~l~gIS~~~Ls~rLk~L~~~glv~R~   66 (108)
T d1z7ua1           9 INLALSTINGKWKLSLMDELF-QGTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRE   66 (108)
T ss_dssp             HHHHHHTTCSTTHHHHHHHHH-HSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcCCCHHHHHHHHH-cCCCCHHHHHHHCcCCChhHHHHHHHHHHHCCcceee
Confidence            344455555555678888886 5788899999998 89999999999999999999864

>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=89.00  E-value=0.37  Score=32.01  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=40.7

Q ss_pred             HHHHHHHhCC----CcCHHHHHHHhCCC------hHHHHHHHHHHhhCcceeeeEeeeecCCCce
Q psy5744          35 LIIDMLVRNP----CMKEDDICELLKFE------RKMLRARISTLKNDKIIQTRLRMETGLDGKA   89 (157)
Q Consensus        35 vIlD~L~~~~----~i~dedLa~~l~i~------~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~   89 (157)
                      -|.|++.++|    .+|-.|||..+..+      +.-+.++|.-|-..++++....  ..++|+.
T Consensus        30 gI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlLas~~vf~~~~~--~~~~g~~   92 (110)
T d1fp1d1          30 NLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLTSTTR--TIEDGGA   92 (110)
T ss_dssp             THHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEEEEEE--ECTTSCE
T ss_pred             CCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHHHHcCccccccc--cCCCCCe
Confidence            4899998764    38999999999863      2359999999999999997633  2345543

>d2dlqa2 g.37.1.1 (A:35-62) GLI-Krueppel family member HKR3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: GLI-Krueppel family member HKR3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.97  E-value=0.06  Score=26.79  Aligned_cols=14  Identities=43%  Similarity=1.044  Sum_probs=11.3

Q ss_pred             eecCCCCCccchhh
Q psy5744         130 FKCPRCLKTFTDLE  143 (157)
Q Consensus       130 Y~Cp~C~~~Ys~ld  143 (157)
                      |.|+.||+.|---|
T Consensus         2 f~c~kcgkcyfrke   15 (28)
T d2dlqa2           2 FECPKCGKCYFRKE   15 (28)
T ss_dssp             CBCTTTCCBCSSHH
T ss_pred             CccccchhhhhhHh
Confidence            78999999996543

>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=88.76  E-value=0.56  Score=31.36  Aligned_cols=79  Identities=11%  Similarity=0.201  Sum_probs=56.7

Q ss_pred             hHHHHHHHHhC--CCcCHHHHHHHh-----CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchhHHHH
Q psy5744          33 DSLIIDMLVRN--PCMKEDDICELL-----KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQTFVNI  105 (157)
Q Consensus        33 ~ivIlD~L~~~--~~i~dedLa~~l-----~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~~~~v  105 (157)
                      -..|+++|...  .-+|-+||-..+     .++...|=+.|..|.+.|+|...   +. ++|.    .||+..       
T Consensus        18 R~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~---~~-~~~~----~~y~~~-------   82 (134)
T d1mzba_          18 RVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRH---NF-DGGH----AVFELA-------   82 (134)
T ss_dssp             HHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEE---CS-SSSS----CEEEES-------
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEE---ee-cCCc----eEEEec-------
Confidence            45789999864  369999998887     58889999999999999999965   22 2321    233322       


Q ss_pred             HHHHHHHHHHHHHHHHhhcCCCCeeecCCCCCccchhh
Q psy5744         106 VKYKLDVMRKRMEMEERDATSRSSFKCPRCLKTFTDLE  143 (157)
Q Consensus       106 ik~rl~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~Ys~ld  143 (157)
                                       .......++|..||+...+.+
T Consensus        83 -----------------~~~~h~H~~C~~Cg~i~~~~~  103 (134)
T d1mzba_          83 -----------------DSGHHDHMVCVDTGEVIEFMD  103 (134)
T ss_dssp             -----------------SSCCCEEEEETTTCCEEEECC
T ss_pred             -----------------CCccccEEEECCCCCEEEecc
Confidence                             112345899999999987643

>d2cota2 g.37.1.1 (A:7-44) Zinc finger and SCAN domain-containing protein 16, ZSCAN16 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger and SCAN domain-containing protein 16, ZSCAN16
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.51  E-value=0.075  Score=28.73  Aligned_cols=21  Identities=29%  Similarity=0.642  Sum_probs=16.2

Q ss_pred             CCCCeeecCCCCCccchhhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ++...|.|+.||+.|+....+
T Consensus         8 t~ekpy~C~~CgK~F~~~s~L   28 (38)
T d2cota2           8 RERRRYKCDECGKSFSHSSDL   28 (38)
T ss_dssp             CCSCSSBCSSSCCBCSCHHHH
T ss_pred             CCCCCEecCCCCceeeCHHHH
Confidence            345679999999999876543

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.25  E-value=0.25  Score=30.24  Aligned_cols=43  Identities=12%  Similarity=0.244  Sum_probs=33.8

Q ss_pred             HHHHHHHh---CCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceee
Q psy5744          35 LIIDMLVR---NPCMKEDDICELL-KFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        35 vIlD~L~~---~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      .|+.++-.   ...++=++|+..| ||+.++|++++..|.++|+|=+
T Consensus        10 ~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_          10 QVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             HHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCceec
Confidence            44544432   2357778999998 8999999999999999999853

>d2ct1a2 g.37.1.1 (A:8-43) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.17  E-value=0.11  Score=27.82  Aligned_cols=20  Identities=20%  Similarity=0.489  Sum_probs=15.9

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +..-|.|+.|++.|+.-..+
T Consensus         5 gekP~~C~~C~k~F~~~~~L   24 (36)
T d2ct1a2           5 GEKPYECYICHARFTQSGTM   24 (36)
T ss_dssp             CCCSEECTTTCCEESCHHHH
T ss_pred             CCCCEeCCCCcccccchHHH
Confidence            45679999999999876544

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.13  E-value=0.075  Score=29.00  Aligned_cols=19  Identities=21%  Similarity=0.604  Sum_probs=10.2

Q ss_pred             CCCeeecCCCCCccchhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda  144 (157)
                      +...|+||.|+..++..++
T Consensus        17 dg~l~vCPeC~hEW~~~~~   35 (38)
T d2akla2          17 DGALLVCPECAHEWSPNEA   35 (38)
T ss_dssp             CSSSEEETTTTEEECTTTT
T ss_pred             CCCEEECCcccCcCCcccc
Confidence            3445556666655555444

>d1p7aa_ g.37.1.1 (A:) Kruppel-like factor 3, Bklf {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Kruppel-like factor 3, Bklf
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.03  E-value=0.11  Score=27.91  Aligned_cols=21  Identities=29%  Similarity=0.733  Sum_probs=16.7

Q ss_pred             CCCCeeecCCCCCccchhhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      ++..-|.|+.|+++|+.-..+
T Consensus         7 TgeKPy~C~~C~k~F~~~~~L   27 (37)
T d1p7aa_           7 TGIKPFQCPDCDRSFSRSDHL   27 (37)
T ss_dssp             CCSSSBCCTTTCCCBSSHHHH
T ss_pred             CCccCeEeCCCCCEecCHHHH
Confidence            455689999999999976544

>d1x6ea1 g.37.1.1 (A:8-40) Zinc finger protein 24 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 24
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.01  E-value=0.11  Score=27.32  Aligned_cols=19  Identities=21%  Similarity=0.527  Sum_probs=15.2

Q ss_pred             CCCeeecCCCCCccchhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda  144 (157)
                      +..-|.|+.||+.|+....
T Consensus         4 gekpy~C~~Cgk~F~~~~~   22 (33)
T d1x6ea1           4 GEKPYGCVECGKAFSRSSI   22 (33)
T ss_dssp             TCCCEECSSSCCEESSHHH
T ss_pred             CCCCeeCCCCCCEeCchHH
Confidence            4567999999999986543

>d1srka_ g.37.1.1 (A:) Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein ZFPM1 (FOG-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.88  E-value=0.12  Score=27.58  Aligned_cols=20  Identities=30%  Similarity=0.683  Sum_probs=15.9

Q ss_pred             CCCCeeecCCCCCccchhhh
Q psy5744         125 TSRSSFKCPRCLKTFTDLEP  144 (157)
Q Consensus       125 ~~~~~Y~Cp~C~~~Ys~lda  144 (157)
                      ++..-|.|+.|++.|+.-.-
T Consensus         3 TGekPy~C~~C~k~F~~~~~   22 (35)
T d1srka_           3 SGKRPFVCRICLSAFTTKAN   22 (35)
T ss_dssp             SCCSCEECSSSCCEESSHHH
T ss_pred             CCCccccCCCCCCcccChHH
Confidence            45668999999999987543

>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=87.70  E-value=0.36  Score=31.33  Aligned_cols=45  Identities=9%  Similarity=0.169  Sum_probs=38.1

Q ss_pred             HHHHHHHHh-CCCcCHHHHHHHhCCChHH---HHHHHHHHhhCcceeee
Q psy5744          34 SLIIDMLVR-NPCMKEDDICELLKFERKM---LRARISTLKNDKIIQTR   78 (157)
Q Consensus        34 ivIlD~L~~-~~~i~dedLa~~l~i~~k~---vRkiL~~L~~d~Lv~~~   78 (157)
                      .-|.|+|-. .+.+|-+|||+.+|+++..   ++++|..|-..|+++..
T Consensus        32 Lgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~gi~~~~   80 (101)
T d1fp2a1          32 MNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEII   80 (101)
T ss_dssp             TTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHHHhCCceeee
Confidence            348899876 4679999999999997644   89999999999999763

>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=87.62  E-value=0.69  Score=28.71  Aligned_cols=46  Identities=7%  Similarity=0.270  Sum_probs=38.6

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||++|=.++.++=.||.+.+    ++...-|+.+|..|.+.|+|+.+
T Consensus        11 E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~   60 (82)
T d1p6ra_          11 ELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHH   60 (82)
T ss_dssp             HHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEE
Confidence            46788998888888877765554    88999999999999999999965

>d1njqa_ g.37.1.3 (A:) SUPERMAN zinc finger domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Plant C2H2 finger (QALGGH zinc finger)
domain: SUPERMAN zinc finger domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.61  E-value=0.12  Score=27.99  Aligned_cols=20  Identities=20%  Similarity=0.487  Sum_probs=17.2

Q ss_pred             CCeeecCCCCCccchhhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      +..|.|+.|++.|+.-.|+-
T Consensus         3 ~r~~~C~~C~k~F~s~qALG   22 (37)
T d1njqa_           3 PRSYTCSFCKREFRSAQALG   22 (37)
T ss_dssp             SSSEECTTTCCEESSHHHHH
T ss_pred             CCccCCCCCCCccCCccccc
Confidence            45799999999999988864

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein TM0937
species: Thermotoga maritima [TaxId: 2336]

Probab=87.17  E-value=1.8  Score=28.10  Aligned_cols=61  Identities=16%  Similarity=0.128  Sum_probs=42.2

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHhC---------CChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecch
Q psy5744          34 SLIIDMLVRNPCMKEDDICELLK---------FERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQ  100 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l~---------i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~  100 (157)
                      .+||-.| ..+.++=-+|.+.+.         ++.-.|=.+|.+|.++|+|+.+.  +. .+|  ..+.||.|.-.
T Consensus        13 ~~iL~lL-~~~~~~GYei~~~i~~~~~~~~~~~~~gtiY~~L~rLe~~G~I~~~~--~~-~~g--~~rk~Y~IT~~   82 (114)
T d2esha1          13 STILLLV-AEKPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEW--DT-TVS--PPRKIYRITPQ   82 (114)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEE--EC-SSS--SCEEEEEECHH
T ss_pred             HHHHHHH-hcCCccHHHHHHHHHHhcCCCcccCCCCcHHHHHHHHHHCCCeEEEe--ec-CCC--CCcEEEEECHH
Confidence            3455444 456788888888772         23457999999999999999762  22 344  34678999853

>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=87.05  E-value=0.78  Score=31.49  Aligned_cols=44  Identities=16%  Similarity=0.259  Sum_probs=39.1

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQT   77 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~   77 (157)
                      ...||-.|. .|..+=.||.+.+|++++.+-.-|..|.++|||..
T Consensus        22 ~l~Il~~l~-~G~~rf~el~~~lgis~~vLs~rL~~L~~~gLv~r   65 (142)
T d2f2ea1          22 SMLIVRDAF-EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVA   65 (142)
T ss_dssp             HHHHHHHHH-TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHhhccHHHHHHHHHHHHHhcceee
Confidence            567777765 68899999999999999999999999999999963

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MerB N-terminal domain-like
domain: Alkylmercury lyase MerB
species: Escherichia coli [TaxId: 562]

Probab=86.86  E-value=0.37  Score=28.61  Aligned_cols=38  Identities=8%  Similarity=0.148  Sum_probs=33.4

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      ++.++..|.....+|-++||..+|.+..+|+..|.++-
T Consensus         4 ~v~LLr~LA~G~PVs~~~LA~alg~~~~eV~~aL~~~p   41 (60)
T d1s6la1           4 LVPLLRELAKGRPVSRTTLAGILDWPAERVAAVLEQAT   41 (60)
T ss_dssp             CCHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHhCC
Confidence            45678888888899999999999999999999998654

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=86.16  E-value=1.2  Score=28.60  Aligned_cols=63  Identities=16%  Similarity=0.290  Sum_probs=44.2

Q ss_pred             HHHHHHHHhCCCcCHHHHHHHh--------CCChHHHHHHHHHHhhCcceeeeEeeeecCCCceeEEEEEEecchh
Q psy5744          34 SLIIDMLVRNPCMKEDDICELL--------KFERKMLRARISTLKNDKIIQTRLRMETGLDGKAQKVNYYFINYQT  101 (157)
Q Consensus        34 ivIlD~L~~~~~i~dedLa~~l--------~i~~k~vRkiL~~L~~d~Lv~~~~~~e~~~~gk~~~~~yw~I~y~~  101 (157)
                      .+||-.|.. +.++=-+|.+.+        +++.-.|=.+|.+|.++|+|..+... . ++|  ..+.||.|.-..
T Consensus        10 ~~IL~lL~~-~~~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~GlI~~~~~~-~-~~g--~~rk~Y~iT~~G   80 (103)
T d1xmaa_          10 TIILSLLIE-GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGE-E-TQG--KRRTYYRITPEG   80 (103)
T ss_dssp             HHHHHHHHH-CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEE-E-C----CEEEEEEECHHH
T ss_pred             HHHHHHHhh-CCccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHCCCeEEEeec-c-CCC--CCceEEEECHHH
Confidence            456666554 456766777665        58889999999999999999986332 2 233  457899998644

>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=85.76  E-value=0.29  Score=34.29  Aligned_cols=46  Identities=17%  Similarity=0.239  Sum_probs=40.1

Q ss_pred             hHHHHHHHHhCC---CcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNP---CMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~---~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||-.|.+++   .++--+||+.++++...+-+++..|++.|+|...
T Consensus        64 q~~vL~~L~~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~  112 (172)
T d2fbka1          64 GWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERR  112 (172)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECC
T ss_pred             HHHHHHHHHhhCCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeee
Confidence            556777776543   4999999999999999999999999999999976

>d1x6ha2 g.37.1.1 (A:8-43) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.50  E-value=0.18  Score=26.84  Aligned_cols=20  Identities=25%  Similarity=0.587  Sum_probs=16.0

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +..-|.|+.||+.|+.-..+
T Consensus         5 gekPy~C~~C~k~F~~~~~L   24 (36)
T d1x6ha2           5 GEKPYACSHCDKTFRQKQLL   24 (36)
T ss_dssp             CCCCEECSSSSCEESSHHHH
T ss_pred             CCCCEECCCCCCCcCCHhHH
Confidence            45689999999999876544

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.98  E-value=0.82  Score=27.76  Aligned_cols=49  Identities=6%  Similarity=0.060  Sum_probs=42.4

Q ss_pred             CCchHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          30 SIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        30 ~~e~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      +.+|-.|+.+--..|.+|...|...+|.+....+.+|..|-.+||+=.-
T Consensus         2 s~Dqt~vLe~a~~~G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD   50 (68)
T d1u5ta2           2 TSDQTKILEICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWID   50 (68)
T ss_dssp             CTTHHHHHHTTTTTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEE
T ss_pred             CchHHHHHHHHHHcCceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEe
Confidence            3456777776555799999999999999999999999999999999754

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.18  E-value=0.59  Score=28.73  Aligned_cols=43  Identities=12%  Similarity=0.184  Sum_probs=37.8

Q ss_pred             HHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhhCcceeee
Q psy5744          36 IIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        36 IlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      .++++-.+.++.=||||...|+...++..-+..|.++|.+.=.
T Consensus        12 FI~~Ik~~Kvv~LedLAa~F~lktqd~i~RIq~Le~~g~ltGV   54 (72)
T d1wi9a_          12 FINYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGV   54 (72)
T ss_dssp             HHHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEE
T ss_pred             HHHHHHHCCEeeHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeE
Confidence            3556667899999999999999999999999999999998754

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.99  E-value=0.79  Score=30.26  Aligned_cols=45  Identities=20%  Similarity=0.285  Sum_probs=39.2

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh-CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL-KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l-~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...|+-.|. +|...=.||...+ |++.+.+-+-|..|.++|||...
T Consensus        26 ~l~Il~~L~-~g~~RF~el~~~l~gis~~~Ls~rL~~Le~~glv~R~   71 (114)
T d1yyva1          26 GVLILVALR-DGTHRFSDLRRKMGGVSEKMLAQSLQALEQDGFLNRV   71 (114)
T ss_dssp             HHHHHHHGG-GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEE
T ss_pred             HHHHHHHHh-cCCCCHHHHHHHccccchhHHHHHHHHHHHHHHHhhc
Confidence            566777764 6788889999999 89999999999999999999865

>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=83.29  E-value=1.3  Score=29.26  Aligned_cols=46  Identities=15%  Similarity=0.302  Sum_probs=40.1

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELL----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||++|=.++.++=.||.+.+    +++..-|+.+|..|.+.|+|+.+
T Consensus         8 E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~   57 (122)
T d1sd4a_           8 EWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRY   57 (122)
T ss_dssp             HHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeee
Confidence            45789998888889988888776    78899999999999999999854

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=82.37  E-value=0.29  Score=26.19  Aligned_cols=19  Identities=21%  Similarity=0.328  Sum_probs=14.9

Q ss_pred             CCCeeecCCCCCccchhhhh
Q psy5744         126 SRSSFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       126 ~~~~Y~Cp~C~~~Ys~lda~  145 (157)
                      +...|+|+.||-.+.- +|-
T Consensus         2 ~~~~~vC~vCGyi~~g-~~P   20 (36)
T d1yuza2           2 DDKFHLCPICGYIHKG-EDF   20 (36)
T ss_dssp             SCCEEECSSSCCEEES-SCC
T ss_pred             CCCEEECCCCCCEeeC-CCC
Confidence            4678999999998875 444

>d2epsa1 g.37.1.1 (A:408-446) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.18  E-value=0.23  Score=27.00  Aligned_cols=20  Identities=20%  Similarity=0.431  Sum_probs=16.2

Q ss_pred             CCeeecCCCCCccchhhhhh
Q psy5744         127 RSSFKCPRCLKTFTDLEPCL  146 (157)
Q Consensus       127 ~~~Y~Cp~C~~~Ys~lda~~  146 (157)
                      ..-|.|+.||+.|+.-..+.
T Consensus         3 ~Kpy~C~~Cgk~F~~~~~L~   22 (39)
T d2epsa1           3 GKPYICQSCGKGFSRPDHLN   22 (39)
T ss_dssp             SCCEECSSSCCEESSHHHHH
T ss_pred             CCCccCCCCCCCcCChHHhh
Confidence            35799999999999876654

>d2drpa2 g.37.1.1 (A:140-165) Tramtrack protein (two zinc-finger peptide) {Drosophila melanogaster [TaxId: 7227]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Tramtrack protein (two zinc-finger peptide)
species: Drosophila melanogaster [TaxId: 7227]

Probab=81.70  E-value=0.32  Score=23.55  Aligned_cols=17  Identities=35%  Similarity=0.862  Sum_probs=13.8

Q ss_pred             eeecCCCCCccchhhhh
Q psy5744         129 SFKCPRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~C~~~Ys~lda~  145 (157)
                      .|-||.|-+.|+--|-+
T Consensus         1 vypcp~cfkeftrkdnm   17 (26)
T d2drpa2           1 VYPCPFCFKEFTRKDNM   17 (26)
T ss_dssp             CEECTTTCCEESCHHHH
T ss_pred             CcCCchhhHHhccccCc
Confidence            38899999999976643

>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=81.53  E-value=1.3  Score=29.08  Aligned_cols=46  Identities=13%  Similarity=0.189  Sum_probs=39.5

Q ss_pred             hHHHHHHHHhCC-CcCHHHHHHHh----CCChHHHHHHHHHHhhCcceeee
Q psy5744          33 DSLIIDMLVRNP-CMKEDDICELL----KFERKMLRARISTLKNDKIIQTR   78 (157)
Q Consensus        33 ~ivIlD~L~~~~-~i~dedLa~~l----~i~~k~vRkiL~~L~~d~Lv~~~   78 (157)
                      ...||++|-..+ .++=.||.+.+    ++..+-|+.+|..|.+.|+|..+
T Consensus         9 E~~IM~~lW~~g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~   59 (122)
T d2g9wa1           9 ERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI   59 (122)
T ss_dssp             HHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEe
Confidence            457899988764 68989999888    57889999999999999999964

>d1sp2a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcription factor sp1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.52  E-value=0.27  Score=25.29  Aligned_cols=17  Identities=35%  Similarity=0.667  Sum_probs=13.3

Q ss_pred             eeec--CCCCCccchhhhh
Q psy5744         129 SFKC--PRCLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~C--p~C~~~Ys~lda~  145 (157)
                      -|+|  |.|+++|+-.+.+
T Consensus         2 pf~C~~~~C~k~F~~~~~L   20 (31)
T d1sp2a_           2 PFMCTWSYCGKRFTRSDEL   20 (31)
T ss_dssp             CCBCCSTTCCCBCSSHHHH
T ss_pred             cCCCcCCCCCcCcCChhHh
Confidence            4899  5799999976654

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=81.22  E-value=0.55  Score=28.98  Aligned_cols=24  Identities=21%  Similarity=0.403  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744         110 LDVMRKRMEMEERDATSRSSFKCPRCLKT  138 (157)
Q Consensus       110 l~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~  138 (157)
                      +.++.++++.....     -|.||.|++.
T Consensus        13 lRk~v~~ie~~q~~-----ky~Cp~Cgk~   36 (73)
T d1vqoz1          13 SRRRVAEIESEMNE-----DHACPNCGED   36 (73)
T ss_dssp             HHHHHHHHHHHHHS-----CBCCSSSSCS
T ss_pred             HHHHHHHHHHHHhC-----CccCCCCCCc
Confidence            45555666665543     7999999975

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=81.03  E-value=0.58  Score=28.88  Aligned_cols=24  Identities=25%  Similarity=0.526  Sum_probs=16.4

Q ss_pred             HHHHHHHHHHHHhhcCCCCeeecCCCCCc
Q psy5744         110 LDVMRKRMEMEERDATSRSSFKCPRCLKT  138 (157)
Q Consensus       110 l~~m~~~L~~~~~~~~~~~~Y~Cp~C~~~  138 (157)
                      +.++.++|+....     ..|.||.||+.
T Consensus        13 lRk~v~kie~~q~-----~ky~Cp~Cgk~   36 (73)
T d1jj2y_          13 IRVRVADVEIKHK-----KKHKCPVCGFK   36 (73)
T ss_dssp             HHHHHHHHHHHHH-----SCBCCSSSCCS
T ss_pred             HHHHHHHHHHHhc-----CCccCCCCCCC
Confidence            4556666666554     37999999964

>d2dt5a1 a.4.5.38 (A:4-77) Transcriptional repressor Rex, N-terminal domain {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional repressor Rex, N-terminal domain
domain: Transcriptional repressor Rex, N-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=80.93  E-value=1.2  Score=27.30  Aligned_cols=36  Identities=14%  Similarity=0.157  Sum_probs=30.0

Q ss_pred             HHHHHHHhC--CCcCHHHHHHHhCCChHHHHHHHHHHh
Q psy5744          35 LIIDMLVRN--PCMKEDDICELLKFERKMLRARISTLK   70 (157)
Q Consensus        35 vIlD~L~~~--~~i~dedLa~~l~i~~k~vRkiL~~L~   70 (157)
                      -++..|...  ..++-++||+.+|+++-+|||=|+.+-
T Consensus        13 r~L~~l~~~g~~~vSS~~La~~~gi~~~qVRKDls~fG   50 (74)
T d2dt5a1          13 RILEELEAQGVHRTSSEQLGGLAQVTAFQVRKDLSYFG   50 (74)
T ss_dssp             HHHHHHHHTTCCEECHHHHHHHHTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCeeEcHHHHHHHHCcCHHHHHHHHHHhc
Confidence            356666654  469999999999999999999998774

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=80.61  E-value=1.6  Score=25.65  Aligned_cols=37  Identities=8%  Similarity=0.258  Sum_probs=29.7

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHHHhh
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKN   71 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~L~~   71 (157)
                      ..-|+..+. . ..+..+||..||++.+.|+..+..+.+
T Consensus        11 E~~vl~ll~-~-G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1          11 ERDILKLIA-Q-GLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             HHHHHHHHH-T-TCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-h-CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            455676666 3 479999999999999999988887764

>d1ubdc4 g.37.1.1 (C:381-408) Ying-yang 1 (yy1, zinc finger domain) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Ying-yang 1 (yy1, zinc finger domain)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.32  E-value=0.27  Score=24.86  Aligned_cols=17  Identities=29%  Similarity=0.694  Sum_probs=13.3

Q ss_pred             eeecCC--CCCccchhhhh
Q psy5744         129 SFKCPR--CLKTFTDLEPC  145 (157)
Q Consensus       129 ~Y~Cp~--C~~~Ys~lda~  145 (157)
                      -|+|+.  ||++|+-.+-+
T Consensus         2 Pf~C~~~gC~K~F~~~~~L   20 (28)
T d1ubdc4           2 PYVCPFDGCNKKFAQSTNL   20 (28)
T ss_dssp             CCCCCSTTCCCCCSSTTTT
T ss_pred             CcCCCCCCcCCcCCCHHHH
Confidence            489965  99999987654

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.21  E-value=1.6  Score=26.20  Aligned_cols=36  Identities=19%  Similarity=0.329  Sum_probs=30.2

Q ss_pred             hHHHHHHHHhCCCcCHHHHHHHhCCChHHHHHHHHH
Q psy5744          33 DSLIIDMLVRNPCMKEDDICELLKFERKMLRARIST   68 (157)
Q Consensus        33 ~ivIlD~L~~~~~i~dedLa~~l~i~~k~vRkiL~~   68 (157)
                      -+-|+..+-.++-++-.|||..+|++...|+.||..
T Consensus        13 K~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1          13 KSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            355777766677799999999999999999999863