Citrus Sinensis ID: 033931

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHcccEEEcHHHHHHHHHcccccEEEcHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccHHcccccccccccccccHHHHHccEEEEcHHHHHHHHHHccccEEEcHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEcccc
Coil and Loop (DISEMBL)
mapkkdkapppaskpaksgggkqkkkkwskgkqkekvnnmvlfDQATYDKLLseapkfklitpsilsdRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
Flexible Loop (DISEMBL)
mapkkdkapppaskpaksgggkqkkkkwskgkqkekvnnmVLFDQATYDKLLSeapkfklitpsilsdrlriNGSLARRAIKDLMARGSirmisahasqqiytratnt
Low Complexity Region (SEG)
MapkkdkapppaskpaksgggkqkkkkwskgkqkekVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
Disordered region (IsUnstruct)
**************************************NMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS**************
Disordered Region (DISOPRED)
***********************************KVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT**
Disordered Region (DISEMBL)
*********************************KEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
Disordered Region (DISPRO)
******************************GKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
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	108	2.2.26 [Sep-21-2011]
Q9T029	108	40S ribosomal protein S25	yes	no	1.0	1.0	0.898	5e-41
Q8GYL5	108	40S ribosomal protein S25	yes	no	0.990	0.990	0.915	7e-41
Q9SIK2	108	40S ribosomal protein S25	yes	no	1.0	1.0	0.898	1e-40
P46301	108	40S ribosomal protein S25	N/A	no	1.0	1.0	0.898	2e-40
Q9SIW5	109	40S ribosomal protein S25	no	no	0.981	0.972	0.886	9e-39
Q94G66	114	40S ribosomal protein S25	N/A	no	0.981	0.929	0.757	2e-30
Q03409	110	40S ribosomal protein S25	yes	no	0.916	0.9	0.470	9e-21
Q8ISN9	123	40S ribosomal protein S25	N/A	no	0.981	0.861	0.587	5e-20
Q9N9V4	120	40S ribosomal protein S25	yes	no	0.824	0.741	0.505	8e-20
Q6PBI5	124	40S ribosomal protein S25	yes	no	0.981	0.854	0.535	2e-19

>sp|Q9T029|RS254_ARATH 40S ribosomal protein S25-4 OS=Arabidopsis thaliana GN=RPS25E PE=2 SV=1

 Score =  166 bits (419), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 97/108 (89%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDK PPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLL+EAPKFKL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLTEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDR+RINGSLARRAI++LMA+G IRM++AH+SQQIYTRATNT
Sbjct: 61  ITPSILSDRMRINGSLARRAIRELMAKGVIRMVAAHSSQQIYTRATNT 108

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GYL5|RS253_ARATH 40S ribosomal protein S25-3 OS=Arabidopsis thaliana GN=RPS25D PE=3 SV=2

 Score =  165 bits (418), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 98/107 (91%), Positives = 106/107 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDK PPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATN 107
           ITPSILSDRLRINGSLARRAI++LMA+G+IRM+SAH+SQQIYTRAT+
Sbjct: 61  ITPSILSDRLRINGSLARRAIRELMAKGTIRMVSAHSSQQIYTRATH 107

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIK2|RS252_ARATH 40S ribosomal protein S25-2 OS=Arabidopsis thaliana GN=RPS25B PE=2 SV=1

 Score =  164 bits (415), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 97/108 (89%), Positives = 105/108 (97%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDK PPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLL+EAPKFKL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLTEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDR+RINGSLARRAI++LMA+G IRM+SAH+SQQIYTRATNT
Sbjct: 61  ITPSILSDRMRINGSLARRAIRELMAKGLIRMVSAHSSQQIYTRATNT 108

Arabidopsis thaliana (taxid: 3702)

>sp|P46301|RS25_SOLLC 40S ribosomal protein S25 OS=Solanum lycopersicum GN=RPS25 PE=3 SV=1

 Score =  163 bits (413), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 97/108 (89%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKK +APPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFD++TYDKLLSEAPK+KL
Sbjct: 1   MAPKKAQAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDKSTYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPS+LSDRLRI+GSLAR+AI+DLMARGSIRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSVLSDRLRISGSLARKAIRDLMARGSIRMVSAHASQQIYTRATNT 108

Solanum lycopersicum (taxid: 4081)

>sp|Q9SIW5|RS251_ARATH 40S ribosomal protein S25-1 OS=Arabidopsis thaliana GN=RPS25A PE=3 SV=3

 Score =  158 bits (400), Expect = 9e-39,   Method: Compositional matrix adjust.
 Identities = 94/106 (88%), Positives = 102/106 (96%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDK PPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKL+SEAPKFKL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLMSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT 106
           ITPSILSDRLRINGSLAR+AI+DLM +G+IRM+S H+SQQI TRAT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRDLMVKGTIRMVSTHSSQQINTRAT 106

Arabidopsis thaliana (taxid: 3702)

>sp|Q94G66|RS25_AMACR 40S ribosomal protein S25 OS=Amaranthus cruentus GN=RPS25 PE=3 SV=1

 Score =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/107 (75%), Positives = 97/107 (90%), Gaps = 1/107 (0%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKS GGKQKKKKWSKGKQKEKVNN+VLFD AT+DKLLSEA K K+
Sbjct: 1   MAPKKDKAPPPSSKPAKS-GGKQKKKKWSKGKQKEKVNNLVLFDNATFDKLLSEAGKQKV 59

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATN 107
           +T + LS+R RINGSLARRAI++L++RG+I+M+  H+S QIYTR+TN
Sbjct: 60  VTAATLSERFRINGSLARRAIRELVSRGAIKMVCHHSSLQIYTRSTN 106

Amaranthus cruentus (taxid: 117272)

>sp|Q03409|RS25_DICDI 40S ribosomal protein S25 OS=Dictyostelium discoideum GN=rps25 PE=3 SV=1

 Score = 98.6 bits (244), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 48/102 (47%), Positives = 72/102 (70%), Gaps = 3/102 (2%)

Query: 4   KKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITP 63
           K+ +A   A+K +  G G+   KKWSKG+ +EK+NN +LFD+ TY KLL E P  K+IT 
Sbjct: 11  KQIQASKAAAKGSSGGAGR---KKWSKGRSREKLNNAILFDKETYAKLLKEMPTAKVITT 67

Query: 64  SILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA 105
           +++S+R++ NGSLARRAIK+L+++G I+ I       +YT+A
Sbjct: 68  AVVSERMKCNGSLARRAIKELLSKGLIKQIIKGHGNGVYTKA 109

Dictyostelium discoideum (taxid: 44689)

>sp|Q8ISN9|RS25_BRABE 40S ribosomal protein S25 OS=Branchiostoma belcheri GN=RPS25 PE=2 SV=1

 Score = 96.3 bits (238), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 64/109 (58%), Positives = 84/109 (77%), Gaps = 3/109 (2%)

Query: 1   MAPKKD---KAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPK 57
           M PKKD    +       A SGGGK KKKKWSKGK ++K+NN+VLFD+ATYDKL  E P 
Sbjct: 1   MPPKKDTKGDSKKGQKAKAGSGGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLYKEVPS 60

Query: 58  FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT 106
           +KLITPS++S+RL+I GSLAR A+K+L ++G I+++S H++Q IYTRAT
Sbjct: 61  YKLITPSVVSERLKIRGSLARAALKELHSKGMIKLVSKHSAQVIYTRAT 109

Branchiostoma belcheri (taxid: 7741)

>sp|Q9N9V4|RS25_LEIIN 40S ribosomal protein S25 OS=Leishmania infantum GN=RPS25 PE=2 SV=1

 Score = 95.5 bits (236), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 62/89 (69%)

Query: 16  AKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGS 75
           A + G K+  KKWSKG+ +E + N V+FD+ TYDKL SE PK+KLITPSI+SDRL+I  S
Sbjct: 15  AANKGAKKTTKKWSKGQSREALQNAVMFDKETYDKLRSEVPKYKLITPSIISDRLKIAVS 74

Query: 76  LARRAIKDLMARGSIRMISAHASQQIYTR 104
           +A   +K L     IR++S  +  ++YTR
Sbjct: 75  IAAAGLKQLCREKLIRLVSCSSKTRVYTR 103

Leishmania infantum (taxid: 5671)

>sp|Q6PBI5|RS25_DANRE 40S ribosomal protein S25 OS=Danio rerio GN=rps25 PE=2 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 60/112 (53%), Positives = 80/112 (71%), Gaps = 6/112 (5%)

Query: 1   MAPKKDKAPPPASK------PAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSE 54
           M PK  K    A K      P    GGK KKKKWSKGK ++K+NN+VLFD+ATYDKL  E
Sbjct: 1   MPPKDSKQKKDAGKSKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLYKE 60

Query: 55  APKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT 106
            P +KLITP+++S+RL+I GSLAR A+++L+ +G I+++S H +Q IYTR T
Sbjct: 61  VPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKLVSKHRAQVIYTRNT 112

Danio rerio (taxid: 7955)

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	108
255565659	108	40S ribosomal protein S25, putative [Ric	1.0	1.0	0.972	4e-42
116779097	108	unknown [Picea sitchensis] gi|116779909|	1.0	1.0	0.962	8e-42
388504588	108	unknown [Lotus japonicus] gi|388522993|g	1.0	1.0	0.944	2e-41
255549396	108	40S ribosomal protein S25, putative [Ric	1.0	1.0	0.944	4e-41
356538747	108	PREDICTED: 40S ribosomal protein S25-2-l	1.0	1.0	0.944	5e-41
255543727	108	40S ribosomal protein S25-1, putative [R	1.0	1.0	0.935	7e-41
313586507	108	40S ribosomal protein S25A [Hevea brasil	1.0	1.0	0.935	9e-41
449446287	108	PREDICTED: 40S ribosomal protein S25-2-l	1.0	1.0	0.925	1e-40
164564736	108	CM0216.350.nc [Lotus japonicus]	0.990	0.990	0.943	1e-40
351725913	108	uncharacterized protein LOC100499810 [Gl	1.0	1.0	0.935	1e-40

>gi|255565659|ref|XP_002523819.1| 40S ribosomal protein S25, putative [Ricinus communis] gi|223536907|gb|EEF38545.1| 40S ribosomal protein S25, putative [Ricinus communis]

 Score =  175 bits (443), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 105/108 (97%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSE PK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEVPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116779097|gb|ABK21138.1| unknown [Picea sitchensis] gi|116779909|gb|ABK21473.1| unknown [Picea sitchensis] gi|116788763|gb|ABK24990.1| unknown [Picea sitchensis] gi|116790134|gb|ABK25512.1| unknown [Picea sitchensis] gi|116793648|gb|ABK26827.1| unknown [Picea sitchensis] gi|148906644|gb|ABR16473.1| unknown [Picea sitchensis] gi|148906786|gb|ABR16539.1| unknown [Picea sitchensis] gi|224284082|gb|ACN39778.1| unknown [Picea sitchensis] gi|224286580|gb|ACN40995.1| unknown [Picea sitchensis] gi|224286704|gb|ACN41055.1| unknown [Picea sitchensis]

 Score =  174 bits (440), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 104/108 (96%), Positives = 108/108 (100%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLAR+AIKDLMARGSIRMISAH+SQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIKDLMARGSIRMISAHSSQQIYTRATNT 108

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388504588|gb|AFK40360.1| unknown [Lotus japonicus] gi|388522993|gb|AFK49558.1| unknown [Lotus japonicus]

 Score =  172 bits (436), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 102/108 (94%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPKFKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLR+NGSLARRAI++LMARGSIRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRVNGSLARRAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549396|ref|XP_002515751.1| 40S ribosomal protein S25, putative [Ricinus communis] gi|223545079|gb|EEF46590.1| 40S ribosomal protein S25, putative [Ricinus communis]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 102/108 (94%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNM+LFDQATYDKLLSE PKFKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMILFDQATYDKLLSEVPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           +TPSILSDRLRINGSLARRAIKDLMA GSIRM+SAHASQQIYTRATNT
Sbjct: 61  VTPSILSDRLRINGSLARRAIKDLMAGGSIRMVSAHASQQIYTRATNT 108

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538747|ref|XP_003537862.1| PREDICTED: 40S ribosomal protein S25-2-like [Glycine max]

 Score =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 102/108 (94%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPKFKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLAR+AI++LMARGSIRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543727|ref|XP_002512926.1| 40S ribosomal protein S25-1, putative [Ricinus communis] gi|223547937|gb|EEF49429.1| 40S ribosomal protein S25-1, putative [Ricinus communis]

 Score =  171 bits (432), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 101/108 (93%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLR+NGSLARRAI++LMARG IRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRVNGSLARRAIRELMARGLIRMVSAHASQQIYTRATNT 108

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586507|gb|ADR71264.1| 40S ribosomal protein S25A [Hevea brasiliensis]

 Score =  170 bits (431), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 101/108 (93%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNM+LFDQATYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMILFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARRAI++LMARG IRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARRAIRELMARGLIRMVSAHASQQIYTRATNT 108

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446287|ref|XP_004140903.1| PREDICTED: 40S ribosomal protein S25-2-like [Cucumis sativus] gi|449494149|ref|XP_004159463.1| PREDICTED: 40S ribosomal protein S25-2-like [Cucumis sativus]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/108 (92%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSE PK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEVPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           +TPSILSDR+R+NGSLARRAIKDLMARGSIRMISAH+SQQIYTRATNT
Sbjct: 61  VTPSILSDRMRVNGSLARRAIKDLMARGSIRMISAHSSQQIYTRATNT 108

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|164564736|dbj|BAF98218.1| CM0216.350.nc [Lotus japonicus]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 101/107 (94%), Positives = 106/107 (99%)

Query: 2   APKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLI 61
           APKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPKFKLI
Sbjct: 2   APKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKLI 61

Query: 62  TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           TPSILSDRLR+NGSLARRAI++LMARGSIRM+SAHASQQIYTRATNT
Sbjct: 62  TPSILSDRLRVNGSLARRAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725913|ref|NP_001236341.1| uncharacterized protein LOC100499810 [Glycine max] gi|356508325|ref|XP_003522908.1| PREDICTED: 40S ribosomal protein S25-2-like [Glycine max] gi|255626799|gb|ACU13744.1| unknown [Glycine max]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 101/108 (93%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLAR+AI++LMARGSIRM+SAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	108
TAIR|locus:505006559	108	AT4G34555 "AT4G34555" [Arabido	0.657	0.657	0.901	3.4e-29
TAIR|locus:2136348	108	AT4G39200 "AT4G39200" [Arabido	0.666	0.666	0.875	4.4e-29
TAIR|locus:2049369	108	AT2G21580 "AT2G21580" [Arabido	0.666	0.666	0.875	5.6e-29
UNIPROTKB|Q56JX5	125	RPS25 "40S ribosomal protein S	0.648	0.56	0.571	1.1e-18
UNIPROTKB|P62851	125	RPS25 "40S ribosomal protein S	0.648	0.56	0.571	1.1e-18
UNIPROTKB|F2Z5G8	125	RPS25 "Uncharacterized protein	0.648	0.56	0.571	1.1e-18
MGI|MGI:1922867	125	Rps25 "ribosomal protein S25"	0.648	0.56	0.571	1.1e-18
RGD|621043	125	Rps25 "ribosomal protein s25"	0.648	0.56	0.571	1.1e-18
UNIPROTKB|F1NU56	139	RPS25 "Uncharacterized protein	0.648	0.503	0.571	1.4e-18
ZFIN|ZDB-GENE-040426-1788	132	rps25 "ribosomal protein S25"	0.648	0.530	0.571	1.4e-18

TAIR|locus:505006559 AT4G34555 "AT4G34555" [Arabidopsis thaliana (taxid:3702)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 64/71 (90%), Positives = 71/71 (100%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAI++LMA+G+IRM+SAH
Sbjct:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIRELMAKGTIRMVSAH 96

Query:    97 ASQQIYTRATN 107
             +SQQIYTRAT+
Sbjct:    97 SSQQIYTRATH 107

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2136348 AT4G39200 "AT4G39200" [Arabidopsis thaliana (taxid:3702)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 63/72 (87%), Positives = 71/72 (98%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             VNNMVLFDQATYDKLL+EAPKFKLITPSILSDR+RINGSLARRAI++LMA+G IRM++AH
Sbjct:    37 VNNMVLFDQATYDKLLTEAPKFKLITPSILSDRMRINGSLARRAIRELMAKGVIRMVAAH 96

Query:    97 ASQQIYTRATNT 108
             +SQQIYTRATNT
Sbjct:    97 SSQQIYTRATNT 108

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

TAIR|locus:2049369 AT2G21580 "AT2G21580" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 63/72 (87%), Positives = 70/72 (97%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             VNNMVLFDQ TYDKLL+EAPKFKLITPSILSDR+RINGSLARRAI++LMA+G IRM+SAH
Sbjct:    37 VNNMVLFDQGTYDKLLTEAPKFKLITPSILSDRMRINGSLARRAIRELMAKGLIRMVSAH 96

Query:    97 ASQQIYTRATNT 108
             +SQQIYTRATNT
Sbjct:    97 SSQQIYTRATNT 108

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0022626 "cytosolic ribosome" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0001510 "RNA methylation" evidence=RCA

UNIPROTKB|Q56JX5 RPS25 "40S ribosomal protein S25" [Bos taurus (taxid:9913)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 40/70 (57%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+++G I+++S H
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   104 RAQVIYTRNT 113

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|P62851 RPS25 "40S ribosomal protein S25" [Homo sapiens (taxid:9606)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 40/70 (57%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+++G I+++S H
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   104 RAQVIYTRNT 113

GO:0000028 "ribosomal small subunit assembly" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0006412 "translation" evidence=IC;NAS;TAS

GO:0015935 "small ribosomal subunit" evidence=IDA

GO:0005840 "ribosome" evidence=NAS;IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0003723 "RNA binding" evidence=NAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F2Z5G8 RPS25 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 40/70 (57%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+++G I+++S H
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   104 RAQVIYTRNT 113

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

MGI|MGI:1922867 Rps25 "ribosomal protein S25" [Mus musculus (taxid:10090)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 40/70 (57%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+++G I+++S H
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   104 RAQVIYTRNT 113

GO:0000028 "ribosomal small subunit assembly" evidence=ISO

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

RGD|621043 Rps25 "ribosomal protein s25" [Rattus norvegicus (taxid:10116)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 40/70 (57%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+++G I+++S H
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   104 RAQVIYTRNT 113

GO:0000028 "ribosomal small subunit assembly" evidence=IMP

GO:0003735 "structural constituent of ribosome" evidence=IMP

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO;IDA

UNIPROTKB|F1NU56 RPS25 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 40/70 (57%), Positives = 58/70 (82%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+ +G I+++S H
Sbjct:    58 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKLVSKH 117

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   118 RAQVIYTRNT 127

GO:0005730 "nucleolus" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

ZFIN|ZDB-GENE-040426-1788 rps25 "ribosomal protein S25" [Danio rerio (taxid:7955)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 40/70 (57%), Positives = 58/70 (82%)

Query:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
             +NN+VLFD+ATYDKL  E P +KLITP+++S+RL+I GSLAR A+++L+ +G I+++S H
Sbjct:    51 LNNLVLFDKATYDKLYKEVPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKLVSKH 110

Query:    97 ASQQIYTRAT 106
              +Q IYTR T
Sbjct:   111 RAQVIYTRNT 120

GO:0005840 "ribosome" evidence=IEA

GO:0030529 "ribonucleoprotein complex" 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)
P62851	RS25_HUMAN	No assigned EC number	0.5398	0.9814	0.848	yes	no
P62852	RS25_MOUSE	No assigned EC number	0.5398	0.9814	0.848	yes	no
Q03409	RS25_DICDI	No assigned EC number	0.4705	0.9166	0.9	yes	no
Q7SC06	RS25_NEUCR	No assigned EC number	0.5054	0.8333	0.9278	N/A	no
Q6PBI5	RS25_DANRE	No assigned EC number	0.5357	0.9814	0.8548	yes	no
Q9N9V4	RS25_LEIIN	No assigned EC number	0.5056	0.8240	0.7416	yes	no
Q9SIW5	RS251_ARATH	No assigned EC number	0.8867	0.9814	0.9724	no	no
P52821	RS25_CAEEL	No assigned EC number	0.5342	0.6759	0.6239	yes	no
P48588	RS25_DROME	No assigned EC number	0.4375	0.9814	0.9059	yes	no
P46301	RS25_SOLLC	No assigned EC number	0.8981	1.0	1.0	N/A	no
Q90YP9	RS25_ICTPU	No assigned EC number	0.5357	0.9814	0.8548	N/A	no
Q56JX5	RS25_BOVIN	No assigned EC number	0.5398	0.9814	0.848	yes	no
Q8ISN9	RS25_BRABE	No assigned EC number	0.5871	0.9814	0.8617	N/A	no
Q8GYL5	RS253_ARATH	No assigned EC number	0.9158	0.9907	0.9907	yes	no
Q9T029	RS254_ARATH	No assigned EC number	0.8981	1.0	1.0	yes	no
Q94G66	RS25_AMACR	No assigned EC number	0.7570	0.9814	0.9298	N/A	no
Q6Q311	RS25_SHEEP	No assigned EC number	0.5398	0.9814	0.848	N/A	no
Q9SIK2	RS252_ARATH	No assigned EC number	0.8981	1.0	1.0	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00007016001	SubName- Full=Chromosome chr13 scaffold_181, whole genome shotgun sequence; (110 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00023139001	SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (136 aa)				•	•	•	•		0.878
	GSVIVG00034206001	SubName- Full=Putative uncharacterized protein (Chromosome chr9 scaffold_7, whole genome shotgu [...] (129 aa)				•	•	•	•		0.832
	GSVIVG00017233001	RecName- Full=40S ribosomal protein S12; (140 aa)				•	•	•			0.831
	GSVIVG00018552001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (155 aa)				•	•	•			0.829
	GSVIVG00016616001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (107 aa)				•	•	•	•		0.828
	GSVIVG00016417001	SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (83 aa)				•	•	•	•		0.823
	GSVIVG00031140001	SubName- Full=Chromosome chr14 scaffold_54, whole genome shotgun sequence; (234 aa)				•	•	•	•		0.823
	GSVIVG00025575001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (307 aa)				•	•	•	•		0.818
	GSVIVG00026857001	RecName- Full=60S ribosomal protein L36; (110 aa)				•		•	•		0.818
	GSVIVG00029522001	SubName- Full=Chromosome chr13 scaffold_48, whole genome shotgun sequence; (129 aa)				•		•	•		0.810

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	108
pfam03297	105	pfam03297, Ribosomal_S25, S25 ribosomal protein	4e-47
COG4901	107	COG4901, COG4901, Ribosomal protein S25 [Translati	7e-19
PRK09334	86	PRK09334, PRK09334, 30S ribosomal protein S25e; Pr	1e-05

>gnl|CDD|217479 pfam03297, Ribosomal_S25, S25 ribosomal protein

 Score =  145 bits (369), Expect = 4e-47
 Identities = 67/106 (63%), Positives = 82/106 (77%), Gaps = 1/106 (0%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           M PKK +    A   A S GGK KKKKWSKGK K+K+NN VLFD+ATYDKLL E P +KL
Sbjct: 1   MPPKKQQKKA-AKAAAASAGGKAKKKKWSKGKVKDKLNNAVLFDKATYDKLLKEVPTYKL 59

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT 106
           ITPS+LSDRL+INGSLARRA+++L  +G I+ +  H++Q IYTRAT
Sbjct: 60  ITPSVLSDRLKINGSLARRALRELEEKGLIKPVVKHSAQLIYTRAT 105

Length = 105

>gnl|CDD|227238 COG4901, COG4901, Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

 Score = 74.6 bits (183), Expect = 7e-19
 Identities = 36/104 (34%), Positives = 56/104 (53%)

Query: 3   PKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLIT 62
             K +            G  + KKKWSK K+KE+    V  D+   DK+  E P+ +++T
Sbjct: 2   APKSQLSKEKKAEKAKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVT 61

Query: 63  PSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT 106
           P +L+ R  INGS+AR  ++ L   G ++++S +  Q IYTRA 
Sbjct: 62  PYVLASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYTRAK 105

Length = 107

>gnl|CDD|181784 PRK09334, PRK09334, 30S ribosomal protein S25e; Provisional

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 24/84 (28%), Positives = 45/84 (53%)

Query: 22  KQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAI 81
           K+KKKK     +KE  + ++  D+    ++  E  K K++TP  L+ +  I  S+A++ +
Sbjct: 3   KKKKKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVL 62

Query: 82  KDLMARGSIRMISAHASQQIYTRA 105
           ++L  RG + + S +    IY  A
Sbjct: 63  RELEKRGVLVLYSKNRRTPIYVPA 86

Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	108
KOG1767	110	consensus 40S ribosomal protein S25 [Translation,	100.0
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	100.0
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	100.0
PRK09334	86	30S ribosomal protein S25e; Provisional	100.0
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.19
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	97.18
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.98
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	96.96
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.95
PF14502	48	HTH_41: Helix-turn-helix domain	96.78
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.77
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.62
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.59
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.53
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	96.39
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.24
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.17
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	96.04
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	96.04
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.02
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.0
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	95.97
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	95.97
PRK13509	251	transcriptional repressor UlaR; Provisional	95.97
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	95.88
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	95.8
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.8
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.79
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	95.78
PRK03837	241	transcriptional regulator NanR; Provisional	95.77
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.76
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	95.76
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.73
PRK14165	217	winged helix-turn-helix domain-containing protein/	95.61
PHA02943	165	hypothetical protein; Provisional	95.41
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	95.4
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.36
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	95.33
TIGR03338	212	phnR_burk phosphonate utilization associated trans	95.32
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	95.31
COG2188	236	PhnF Transcriptional regulators [Transcription]	95.27
PRK11014	141	transcriptional repressor NsrR; Provisional	95.23
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	95.21
smart00843	63	Ftsk_gamma This domain directs oriented DNA transl	95.19
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	95.17
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.14
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	95.13
PRK04984	239	fatty acid metabolism regulator; Provisional	95.11
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	95.1
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.09
PRK14999	241	histidine utilization repressor; Provisional	95.07
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.06
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	94.98
TIGR03337	231	phnR transcriptional regulator protein. This famil	94.92
PF13730	55	HTH_36: Helix-turn-helix domain	94.92
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	94.88
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	94.86
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.78
COG3355	126	Predicted transcriptional regulator [Transcription	94.72
PRK10079	241	phosphonate metabolism transcriptional regulator P	94.67
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	94.67
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	94.57
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	94.42
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	94.4
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	94.23
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	94.09
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	94.08
PF04157	223	EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP	94.05
PRK10870	176	transcriptional repressor MprA; Provisional	93.89
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.89
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	93.75
PRK03573	144	transcriptional regulator SlyA; Provisional	93.71
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.67
COG4465	261	CodY Pleiotropic transcriptional repressor [Transc	93.46
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	93.45
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.36
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.28
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	93.27
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.27
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	93.22
COG1959	150	Predicted transcriptional regulator [Transcription	93.21
PRK04158	256	transcriptional repressor CodY; Validated	93.02
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	92.86
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	92.75
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.75
PRK03902	142	manganese transport transcriptional regulator; Pro	92.7
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	92.64
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	92.53
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	92.23
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	92.01
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	92.01
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	91.96
COG1846	126	MarR Transcriptional regulators [Transcription]	91.92
PRK11050	152	manganese transport regulator MntR; Provisional	91.8
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	91.77
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	91.54
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	91.54
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.49
COG1802	230	GntR Transcriptional regulators [Transcription]	91.43
COG2512	258	Predicted membrane-associated trancriptional regul	91.32
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	91.17
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	91.07
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	90.92
COG1725	125	Predicted transcriptional regulators [Transcriptio	90.89
PRK06266	178	transcription initiation factor E subunit alpha; V	90.84
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	90.82
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	90.79
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	90.7
PRK09954	362	putative kinase; Provisional	90.66
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	90.61
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	90.46
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	90.42
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	90.32
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	90.23
PRK13777	185	transcriptional regulator Hpr; Provisional	90.22
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	90.13
PRK11169	164	leucine-responsive transcriptional regulator; Prov	90.05
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	88.97
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	88.84
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	88.74
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	88.74
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	88.66
PRK09462	148	fur ferric uptake regulator; Provisional	88.52
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	88.04
COG2186	241	FadR Transcriptional regulators [Transcription]	87.88
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	87.75
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	87.62
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	87.61
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	87.41
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	87.39
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	87.32
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	87.25
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	86.92
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	86.89
PF12728	51	HTH_17: Helix-turn-helix domain	86.86
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	86.52
PRK12423	202	LexA repressor; Provisional	86.36
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	86.36
PRK09333	150	30S ribosomal protein S19e; Provisional	86.13
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	86.01
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	85.84
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	85.71
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	85.53
TIGR01764	49	excise DNA binding domain, excisionase family. An	85.48
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	85.4
TIGR02054	120	MerD mercuric resistence transcriptional repressor	85.31
COG1733	120	Predicted transcriptional regulators [Transcriptio	85.17
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	84.87
PRK05472	213	redox-sensing transcriptional repressor Rex; Provi	84.82
PRK00215	205	LexA repressor; Validated	84.72
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	84.45
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	84.36
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	84.32
PRK11569	274	transcriptional repressor IclR; Provisional	84.31
PF01090	139	Ribosomal_S19e: Ribosomal protein S19e; InterPro:	84.27
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	84.13
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	84.01
PF13814	191	Replic_Relax: Replication-relaxation	83.68
PRK13749	121	transcriptional regulator MerD; Provisional	83.38
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	83.08
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	83.05
COG1414	246	IclR Transcriptional regulator [Transcription]	82.73
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	82.59
PRK13752	144	putative transcriptional regulator MerR; Provision	82.5
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	82.45
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	82.43
PRK06474	178	hypothetical protein; Provisional	82.33
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	82.31
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	82.19
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	82.14
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	82.02
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	82.0
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	81.93
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	81.77
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	81.54
KOG2760	432	consensus Vacuolar sorting protein VPS36 [Intracel	81.4
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	81.06
PRK05638	442	threonine synthase; Validated	80.99
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	80.95
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	80.82
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	80.37
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	80.32
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	80.2
COG3177	348	Fic family protein [Function unknown]	80.03

>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=2.3e-50  Score=285.08  Aligned_cols=106  Identities=63%  Similarity=0.936  Sum_probs=102.0

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033931            1 MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRA   80 (108)
Q Consensus         1 M~~k~~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~   80 (108)
                      ||+++|.++++++. ++.+||+++|||||||+++||+||+|+||++|||||++|||+|+|||||+|+|||+|||||||++
T Consensus         2 ~~~k~q~sK~~k~~-~~~~ggk~~KKKWskGk~kdkvnn~Vlfdqatydkl~kevp~~k~it~svl~dRlkIngsLAr~a   80 (110)
T KOG1767|consen    2 MPKKQQLSKEKKAP-AASSGGKAKKKKWSKGKVKDKVNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAA   80 (110)
T ss_pred             CccccccCchhccc-cccCCCcccccccccchHHHHhhhheeecHHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHH
Confidence            78888888887777 48899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEecccceeEEEecccC
Q 033931           81 IKDLMARGSIRMISAHASQQIYTRATN  107 (108)
Q Consensus        81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~  107 (108)
                      ||||.++|+|++|++||+|.||||+++
T Consensus        81 lr~L~~kG~Ik~Vs~h~~q~IYTrat~  107 (110)
T KOG1767|consen   81 LRELSNKGVIKQVSKHSKQVIYTRATA  107 (110)
T ss_pred             HHHHHhcchHHHHhhcchheeeccccc
Confidence            999999999999999999999999986

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

Probab=100.00  E-value=1.2e-49  Score=280.80  Aligned_cols=105  Identities=63%  Similarity=0.968  Sum_probs=79.4

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033931            1 MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRA   80 (108)
Q Consensus         1 M~~k~~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~   80 (108)
                      ||||.++++++.++ ++++||++++||||||+++|++||+|+||+++||+|++|||+|++||||+|||||+|++||||++
T Consensus         1 M~pK~~~~k~~k~~-~~~~~~k~~KKKwsKgk~kek~~~~v~~d~~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~   79 (105)
T PF03297_consen    1 MPPKKQKSKKQKAK-KAKSGGKAKKKKWSKGKVKEKLNNAVLFDKETYDKLLKEVPKMKLITPSVLSERLKINGSLARKA   79 (105)
T ss_dssp             ----------------TT------SSS--SS-SCHHHCCCSCCTCHHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHH
T ss_pred             CCCCcccchhhHHH-HHhccCccccccccccchHHHHhcceEecHHHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHH
Confidence            99999888777777 48899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEecccceeEEEeccc
Q 033931           81 IKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        81 Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      ||||+++|+|++|++||+|.||||+|
T Consensus        80 Lr~L~~kG~Ik~V~k~~~~~IYtr~~  105 (105)
T PF03297_consen   80 LRELESKGLIKPVSKHHRQRIYTRAT  105 (105)
T ss_dssp             HHHHHHCCSSEEEECCTTCEEEEES-
T ss_pred             HHHHHHCCCEEEEeccCCeEEEecCC
Confidence            99999999999999999999999986

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

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

Probab=100.00  E-value=2.2e-38  Score=223.50  Aligned_cols=106  Identities=37%  Similarity=0.607  Sum_probs=102.1

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033931            1 MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRA   80 (108)
Q Consensus         1 M~~k~~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~   80 (108)
                      |||+.|.+++.++.+ +.+|+.+.+|||++++.+|...++|+||+++||++++|||++++||||+|++||+|++||||.+
T Consensus         1 m~pk~qlsK~~Ka~~-~~a~~~k~kKK~~~k~~k~~~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~v   79 (107)
T COG4901           1 MAPKSQLSKEKKAEK-AKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIV   79 (107)
T ss_pred             CcchhHHHHHHHHHH-HHhhhhhhhhccccccccchhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHH
Confidence            999999999888885 7789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEecccceeEEEecccC
Q 033931           81 IKDLMARGSIRMISAHASQQIYTRATN  107 (108)
Q Consensus        81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~  107 (108)
                      ||+|+++|+|++|++||+|.||+++.+
T Consensus        80 LR~LeeeGvv~lvsknrR~~IY~~a~a  106 (107)
T COG4901          80 LRHLEEEGVVQLVSKNRRQAIYTRAKA  106 (107)
T ss_pred             HHHHHhCCceeeeccCccceeeecccC
Confidence            999999999999999999999999864

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=100.00  E-value=2.7e-36  Score=206.74  Aligned_cols=81  Identities=27%  Similarity=0.425  Sum_probs=76.7

Q ss_pred             ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        25 KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+-.++..++.+||+|+||++|||||++|||+|++||||+|||||+|++||||++||||+++|+|++|++||+|.|||+
T Consensus         6 ~k~~~~~~~~~~~~n~v~~dk~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~   85 (86)
T PRK09334          6 KKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP   85 (86)
T ss_pred             cccccccchhhhhhceeecCHHHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence            44556667999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 033931          105 A  105 (108)
Q Consensus       105 ~  105 (108)
                      +
T Consensus        86 ~   86 (86)
T PRK09334         86 A   86 (86)
T ss_pred             C
Confidence            4

>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=97.19  E-value=0.0004  Score=41.09  Aligned_cols=42  Identities=31%  Similarity=0.370  Sum_probs=32.6

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      +|+..+-...-+|...||++++++.+-+...|++|+++|+|+
T Consensus         7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence            333333334449999999999999999999999999999985

...

>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=97.18  E-value=0.0014  Score=40.93  Aligned_cols=50  Identities=22%  Similarity=0.296  Sum_probs=37.3

Q ss_pred             HHHHHHHhhCCC-----Ceee-chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           46 ATYDKLLSEAPK-----FKLI-TPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        46 ~t~dKl~KEVpk-----~k~I-Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..|+.|..+|-.     -..+ |...||++|+|+-+.+|.+|+.|++.|+|....+
T Consensus         4 ~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen    4 QIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             HHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence            344555544433     3455 9999999999999999999999999999988654

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 ....

>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=96.98  E-value=0.0014  Score=40.84  Aligned_cols=46  Identities=15%  Similarity=0.245  Sum_probs=39.0

Q ss_pred             HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           49 DKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++|+.-+.....+|...||+.|+|+-+-+|+=|.+|+++|+|..+.
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            3455555556789999999999999999999999999999987653

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

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

Probab=96.96  E-value=0.0037  Score=37.63  Aligned_cols=50  Identities=20%  Similarity=0.266  Sum_probs=39.2

Q ss_pred             HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEAP------KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +++++.|...+.      .-.+.|...||+.|+|+-+-++++|..|++.|+|....
T Consensus         4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~   59 (66)
T cd07377           4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRP   59 (66)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            456666666632      23445699999999999999999999999999987543

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

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.95  E-value=0.0019  Score=38.20  Aligned_cols=38  Identities=24%  Similarity=0.265  Sum_probs=32.9

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..+-|...||++|+++-+-.+++|+.|++.|+|..+.
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            33444999999999999999999999999999987653

>PF14502 HTH_41: Helix-turn-helix domain

Probab=96.78  E-value=0.0028  Score=39.57  Aligned_cols=41  Identities=22%  Similarity=0.233  Sum_probs=37.6

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      .-++=|.+.+|++|++....-..+|+.|++.|-|.+.++.|
T Consensus         3 GdRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh   43 (48)
T PF14502_consen    3 GDRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGH   43 (48)
T ss_pred             CcccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCc
Confidence            45677999999999999999999999999999999998766

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=96.77  E-value=0.0047  Score=38.82  Aligned_cols=45  Identities=22%  Similarity=0.303  Sum_probs=38.3

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ..=.|+..||+.++|.-+-+..+|+.|+++|+|......  ..+|..
T Consensus        20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~a   64 (68)
T PF01978_consen   20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYRA   64 (68)
T ss_dssp             HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEEE
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEEE
Confidence            344899999999999999999999999999999988743  456653

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.

>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=96.62  E-value=0.0089  Score=39.15  Aligned_cols=52  Identities=21%  Similarity=0.293  Sum_probs=39.8

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           54 EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      ..+....+|...||++++++-+..+++|+.|.+.|+|.-....+......|.
T Consensus        19 ~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~   70 (83)
T PF02082_consen   19 RHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARP   70 (83)
T ss_dssp             CTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-
T ss_pred             hCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCC
Confidence            4455556999999999999999999999999999999887655554444443

(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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.59  E-value=0.0078  Score=35.20  Aligned_cols=44  Identities=16%  Similarity=0.189  Sum_probs=36.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|++.++++-+-++.+|+.|.++|+|.....++ ...|.
T Consensus         9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~-~~~~~   52 (66)
T smart00418        9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGK-RVYYS   52 (66)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCC-EEEEE
Confidence            447999999999999999999999999999999776544 44454

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

Probab=96.53  E-value=0.0054  Score=39.66  Aligned_cols=42  Identities=17%  Similarity=0.263  Sum_probs=33.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      +|...|||.++|+.+-||..|..|+..|.|+.+-..+....|
T Consensus        16 ~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~   57 (62)
T PF04703_consen   16 LKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTY   57 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-E
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCccee
Confidence            788999999999999999999999999999986433333334

>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=96.39  E-value=0.012  Score=38.40  Aligned_cols=34  Identities=26%  Similarity=0.366  Sum_probs=29.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ++|.|.|||+++|+-|+--.+||-|++-|+|.--
T Consensus         4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesr   37 (61)
T PF08222_consen    4 RLVASKIADRVGITRSVIVNALRKLESAGVIESR   37 (61)
T ss_dssp             EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             eehHHHHHHHhCccHHHHHHHHHHHHhcCceeec
Confidence            6899999999999999999999999999999843

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.

>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=96.24  E-value=0.011  Score=35.83  Aligned_cols=34  Identities=32%  Similarity=0.416  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.|++.+++.-+-.-++++.|+++|+|....
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            6999999999999999999999999999998873

...

>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=96.17  E-value=0.016  Score=35.50  Aligned_cols=47  Identities=28%  Similarity=0.295  Sum_probs=35.1

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEEEe
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQIYT  103 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IYt  103 (108)
                      ...-+|+..|++.+++.-+-+.++|+.|+++|+|....  .++|...|.
T Consensus        15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~   63 (68)
T PF13463_consen   15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYR   63 (68)
T ss_dssp             -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEE
Confidence            44668999999999999999999999999999997773  334544443

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=96.04  E-value=0.02  Score=43.18  Aligned_cols=40  Identities=23%  Similarity=0.193  Sum_probs=36.6

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.+|=|-..||++|+|+-...|+||++|+++|+|..+.+
T Consensus        20 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G   59 (233)
T TIGR02404        20 EGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQG   59 (233)
T ss_pred             CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            5678889999999999999999999999999999988654

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.

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=96.04  E-value=0.02  Score=42.92  Aligned_cols=40  Identities=30%  Similarity=0.364  Sum_probs=36.8

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.+|=|-..||++|+|+-...|+||.+|+.+|+|....+
T Consensus        28 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G   67 (238)
T TIGR02325        28 AGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG   67 (238)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            5678999999999999999999999999999999988644

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.

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

Probab=96.02  E-value=0.022  Score=33.94  Aligned_cols=42  Identities=26%  Similarity=0.357  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ++...+++.+++..+-++++|+.|++.|+|...... +...|.
T Consensus        21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~   62 (78)
T cd00090          21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG-RRVYYS   62 (78)
T ss_pred             cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEE
Confidence            999999999999999999999999999999987544 344454

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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.00  E-value=0.013  Score=33.46  Aligned_cols=33  Identities=21%  Similarity=0.277  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|...||+.++++-+-+.++|+.|++.|+|...
T Consensus         9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            688999999999999999999999999999753

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=95.97  E-value=0.023  Score=42.97  Aligned_cols=40  Identities=15%  Similarity=0.245  Sum_probs=36.2

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.+|=|-..||++|+|+-...|+||.+|+++|+|..+-+
T Consensus        21 ~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G   60 (230)
T TIGR02018        21 PGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQG   60 (230)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            5678889999999999999999999999999999987543

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.

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=95.97  E-value=0.023  Score=43.40  Aligned_cols=40  Identities=23%  Similarity=0.323  Sum_probs=36.3

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.++=|-..||++|+|+-.-.|+||.+|+.+|+|..+-+
T Consensus        25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G   64 (240)
T PRK09764         25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQG   64 (240)
T ss_pred             CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            4568889999999999999999999999999999988654

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=95.97  E-value=0.012  Score=45.92  Aligned_cols=50  Identities=24%  Similarity=0.345  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .+-.++|+..+-....+|...|+++|+|+.+-+|+=|++|+++|+|..+-
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~   53 (251)
T PRK13509          4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVR   53 (251)
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            45567788888888999999999999999999999999999999998753

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=95.88  E-value=0.021  Score=42.83  Aligned_cols=53  Identities=19%  Similarity=0.255  Sum_probs=43.4

Q ss_pred             eCHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           43 FDQATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +-...|+.|...|-.      .+ |+...||++|+|+-+--|-||+.|+..|+|..+-+.
T Consensus         8 ~~~~vy~~i~~~I~~g~l~pG~~-L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~   66 (224)
T PRK11534          8 TALDGYRWLKNDIIRGNFQPDEK-LRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK   66 (224)
T ss_pred             hhHHHHHHHHHHHHhCCCCCCCc-CCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence            345678888877644      44 477899999999999999999999999999876543

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=95.80  E-value=0.029  Score=42.96  Aligned_cols=51  Identities=14%  Similarity=0.126  Sum_probs=42.1

Q ss_pred             HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEAP------KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|-      +.++-|-..||++|+|+-+-.|.||+.|+..|+|...-+
T Consensus        12 ~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~   68 (257)
T PRK10225         12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG   68 (257)
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            456777776664      445557889999999999999999999999999997654

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.80  E-value=0.048  Score=31.27  Aligned_cols=46  Identities=15%  Similarity=0.258  Sum_probs=37.6

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..++-|..+    ..+|...|++.|++.-+-+++.|..|++.|+|....+
T Consensus         4 ~il~~l~~~----~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        4 QILELLAQQ----GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            455555543    2489999999999999999999999999999986543

>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=95.79  E-value=0.016  Score=36.63  Aligned_cols=37  Identities=14%  Similarity=0.219  Sum_probs=33.1

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-..|++..||++|+|+-+-+-..|+.|+++|+|...
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            4567999999999999999999999999999999764

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 ....

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=95.78  E-value=0.027  Score=45.50  Aligned_cols=58  Identities=22%  Similarity=0.331  Sum_probs=50.2

Q ss_pred             hhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           37 VNNMVLFDQATYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        37 ~nn~V~~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++..-+-.-+..++|+.+.... -.++-+.||++++|+-|..|.+|+.|++.|+|..-.
T Consensus       174 i~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       174 INTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            4444445667889999999994 899999999999999999999999999999998654

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.

>PRK03837 transcriptional regulator NanR; Provisional

Probab=95.77  E-value=0.021  Score=42.93  Aligned_cols=52  Identities=13%  Similarity=0.177  Sum_probs=42.0

Q ss_pred             HHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           45 QATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        45 k~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +..|+.|...|-.      .++-+-..||++|+|+-+..|.||+.|+..|+|...-+.
T Consensus        16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~   73 (241)
T PRK03837         16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGE   73 (241)
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            4566666666543      445589999999999999999999999999999886443

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

Probab=95.76  E-value=0.0071  Score=38.57  Aligned_cols=47  Identities=13%  Similarity=0.205  Sum_probs=36.4

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      |..-+-.-..+|...||.+|++.-+..+..|..|+.+|.|..+..+.
T Consensus         5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~   51 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS   51 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            33334445789999999999999999999999999999999986543

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

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=95.76  E-value=0.018  Score=45.17  Aligned_cols=49  Identities=14%  Similarity=0.228  Sum_probs=43.4

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +-.++|+..+.....+|...|+++|+|+-+-+|+=|.+|+++|+|..+-
T Consensus         5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~   53 (252)
T PRK10906          5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHH   53 (252)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4567777777778899999999999999999999999999999998753

>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=95.73  E-value=0.028  Score=34.18  Aligned_cols=37  Identities=22%  Similarity=0.243  Sum_probs=33.7

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .--+|...||+.+++.-+-+.++|+.|++.|+|....
T Consensus        23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            3458999999999999999999999999999998765

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

Probab=95.61  E-value=0.025  Score=44.26  Aligned_cols=50  Identities=20%  Similarity=0.155  Sum_probs=42.3

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           54 EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .+.+.--||.+.||++++++-+-+-++|+.|+++|+|......+.+.||.
T Consensus        15 ~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L   64 (217)
T PRK14165         15 AVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITI   64 (217)
T ss_pred             ccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence            44445569999999999999999999999999999999886556676664

>PHA02943 hypothetical protein; Provisional

Probab=95.41  E-value=0.049  Score=41.60  Aligned_cols=54  Identities=20%  Similarity=0.159  Sum_probs=44.7

Q ss_pred             HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           49 DKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +.|+.-+ +.-.-|.+.||++++++-|-|+-+|.-||++|.|+.|..+.....+.
T Consensus        14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l   67 (165)
T PHA02943         14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCL   67 (165)
T ss_pred             HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEE
Confidence            3445444 77788999999999999999999999999999999998766554443

>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=95.40  E-value=0.03  Score=33.78  Aligned_cols=33  Identities=39%  Similarity=0.441  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||+.+++.-|-.-++++.|+.+|+|..-
T Consensus        18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~   50 (59)
T PF01047_consen   18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERE   50 (59)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            899999999999999999999999999999876

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 ....

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

Probab=95.36  E-value=0.036  Score=33.39  Aligned_cols=32  Identities=22%  Similarity=0.326  Sum_probs=29.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|.+.||+++++.-|-+.++|+.|++.|++..
T Consensus        19 ~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen   19 LTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            69999999999999999999999999999964

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.

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=95.33  E-value=0.025  Score=44.26  Aligned_cols=49  Identities=14%  Similarity=0.108  Sum_probs=43.4

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +=.++|+..+.....||+..||+.|+|+.+-.|+=|++|+++|+|..+-
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            3456778888888889999999999999999999999999999998763

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=95.32  E-value=0.045  Score=40.45  Aligned_cols=49  Identities=24%  Similarity=0.302  Sum_probs=40.0

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...|+.|...|      |+.++ +-..||++|+|+-+--|.||+.|+..|+|...-
T Consensus        14 ~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~   68 (212)
T TIGR03338        14 TLVQDEIERAILSGELPPGAKL-NESDIAARLGVSRGPVREAFRALEEAGLVRNEK   68 (212)
T ss_pred             HHHHHHHHHHHHcCCCCCCCEe-cHHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence            45666666654      44566 889999999999999999999999999998644

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.

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=95.31  E-value=0.036  Score=42.15  Aligned_cols=39  Identities=23%  Similarity=0.279  Sum_probs=36.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.++=|=..||++|+|+-...|+||.+|+++|+|....
T Consensus        29 ~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   67 (241)
T PRK11402         29 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQ   67 (241)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            357999999999999999999999999999999998764

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=95.27  E-value=0.036  Score=42.70  Aligned_cols=42  Identities=21%  Similarity=0.330  Sum_probs=37.7

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      |+.++=|=..||++|+|+-...|+||++|++.|+|....+.+
T Consensus        27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~G   68 (236)
T COG2188          27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKG   68 (236)
T ss_pred             CCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCe
Confidence            457899999999999999999999999999999999876543

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=95.23  E-value=0.052  Score=38.72  Aligned_cols=46  Identities=11%  Similarity=0.184  Sum_probs=38.8

Q ss_pred             CCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeE
Q 033931           55 APKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQ  100 (108)
Q Consensus        55 Vpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~  100 (108)
                      .+.-.+++...||++++|+-.-.|++|+.|...|+|..+.+.+...
T Consensus        20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~   65 (141)
T PRK11014         20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGI   65 (141)
T ss_pred             CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCe
Confidence            3334688999999999999999999999999999999887654443

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

Probab=95.21  E-value=0.026  Score=44.26  Aligned_cols=48  Identities=15%  Similarity=0.214  Sum_probs=44.1

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      =.++|+..+.....|++..||++|+|+-.-.|+=|++|+++|++..+.
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            457888888889999999999999999999999999999999998764

>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure

Probab=95.19  E-value=0.024  Score=36.92  Aligned_cols=54  Identities=24%  Similarity=0.308  Sum_probs=48.4

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      +.++|+....=|....-+++|.|=-+|+|-..-|-+++.+||+.|+|-+...+.
T Consensus         3 ~D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~~g~~   56 (63)
T smart00843        3 EDELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPANGSK   56 (63)
T ss_pred             ccHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCCCCCC
Confidence            467889888888888999999999999999999999999999999999975544

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.

>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []

Probab=95.17  E-value=0.016  Score=37.79  Aligned_cols=58  Identities=17%  Similarity=0.238  Sum_probs=43.1

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      .++|++...=|-...-++.|.|--+|+|...-|-+++..||+.|+|-+-..+..-.|+
T Consensus         5 D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl   62 (65)
T PF09397_consen    5 DPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL   62 (65)
T ss_dssp             STTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred             cHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence            4567777766666788999999999999999999999999999999998655443343

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_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=95.14  E-value=0.028  Score=34.79  Aligned_cols=50  Identities=24%  Similarity=0.187  Sum_probs=41.0

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ++--+|+..+....=.|.+.||+.+++.-+-+..=|+.|++-|+|..+..
T Consensus        10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence            55556666665556689999999999999999999999999999988753

...

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=95.13  E-value=0.071  Score=40.57  Aligned_cols=52  Identities=17%  Similarity=0.187  Sum_probs=43.6

Q ss_pred             CHHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           44 DQATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        44 dk~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...+|+.|...|      |+.+|=|-..||++|+|+-+--|-||+.|+..|+|...-+
T Consensus         9 ~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~   66 (251)
T PRK09990          9 ADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG   66 (251)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            356777777776      4455558899999999999999999999999999987654

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=95.11  E-value=0.044  Score=41.31  Aligned_cols=50  Identities=14%  Similarity=0.193  Sum_probs=40.3

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..|+.|...|      |+.++-|-..||++|+|+-+..|.||+.|+..|+|...-
T Consensus        10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~   65 (239)
T PRK04984         10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH   65 (239)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            34556665555      445566899999999999999999999999999998754

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=95.10  E-value=0.047  Score=37.35  Aligned_cols=52  Identities=10%  Similarity=0.049  Sum_probs=39.8

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEEE
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQIY  102 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IY  102 (108)
                      ++-.+-...-+|++.||+.+++.-+..-++|+.|+++|+|....  .++|...|
T Consensus        33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v   86 (118)
T TIGR02337        33 ILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYI   86 (118)
T ss_pred             HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEE
Confidence            33334344458999999999999999999999999999999873  34444443

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.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.09  E-value=0.052  Score=38.11  Aligned_cols=47  Identities=28%  Similarity=0.350  Sum_probs=42.7

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|..+++-|+.+.+    ++...||++++++.+-.+.-++.|++.|+|+-+
T Consensus         9 ~D~~IL~~L~~d~r----~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~   55 (154)
T COG1522           9 IDRRILRLLQEDAR----ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY   55 (154)
T ss_pred             HHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence            56777888888887    999999999999999999999999999999876

>PRK14999 histidine utilization repressor; Provisional

Probab=95.07  E-value=0.045  Score=41.70  Aligned_cols=39  Identities=15%  Similarity=0.267  Sum_probs=35.5

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.+|=|-..||++|+|+-...|+||.+|+.+|+|...-
T Consensus        32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   70 (241)
T PRK14999         32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ   70 (241)
T ss_pred             CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            466888999999999999999999999999999997654

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

Probab=95.06  E-value=0.072  Score=34.12  Aligned_cols=35  Identities=17%  Similarity=0.191  Sum_probs=32.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +|...||+.++|.-+-++++|..|+++|+|.....
T Consensus        23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~   57 (68)
T smart00550       23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG   57 (68)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence            89999999999999999999999999999977543

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

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=94.98  E-value=0.052  Score=40.95  Aligned_cols=51  Identities=14%  Similarity=0.186  Sum_probs=41.7

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +..|+.|...|      |+.++-|-..||++|+|+-+-.|-||+.|+..|+|...-+
T Consensus         9 ~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~   65 (235)
T TIGR02812         9 GFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG   65 (235)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence            45666666665      3445558999999999999999999999999999987654

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.

>TIGR03337 phnR transcriptional regulator protein

Probab=94.92  E-value=0.083  Score=39.44  Aligned_cols=40  Identities=28%  Similarity=0.278  Sum_probs=36.8

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.++=|...||++|+|+-...|++|++|+.+|+|....+
T Consensus        21 ~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g   60 (231)
T TIGR03337        21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDR   60 (231)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence            6678889999999999999999999999999999988654

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.92  E-value=0.035  Score=33.22  Aligned_cols=31  Identities=29%  Similarity=0.452  Sum_probs=28.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSI   90 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlI   90 (108)
                      +-+...||+.+++.-+-.+++|++|++.|+|
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            3367899999999999999999999999987

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=94.88  E-value=0.051  Score=40.86  Aligned_cols=43  Identities=30%  Similarity=0.381  Sum_probs=36.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----ccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS----AHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYt  103 (108)
                      +|...||++++|+-+-.++.|+.|++.|+|....    .+++..+|.
T Consensus        16 ~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~   62 (203)
T TIGR02702        16 ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQ   62 (203)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEE
Confidence            8999999999999999999999999999998762    245555554

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.

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=94.86  E-value=0.055  Score=41.43  Aligned_cols=52  Identities=19%  Similarity=0.202  Sum_probs=42.0

Q ss_pred             CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           44 DQATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        44 dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      -...|+.|...|-.      .++-|-..||++|+|+-+-.|.||+.|+..|+|...-+
T Consensus        10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~   67 (253)
T PRK11523         10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG   67 (253)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            34566666666543      46667899999999999999999999999999987553

>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=94.78  E-value=0.061  Score=34.64  Aligned_cols=36  Identities=28%  Similarity=0.347  Sum_probs=31.2

Q ss_pred             chhhhhhhhccc-HHHHHHHHHHHHHcCCeeEecccc
Q 033931           62 TPSILSDRLRIN-GSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        62 Tps~vserlkI~-~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      |...|++.|+++ -|-+..-|+.|+++|+|....+-.
T Consensus        27 t~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~~~   63 (65)
T PF01726_consen   27 TVREIAEALGLKSTSTVQRHLKALERKGYIRRDPGKA   63 (65)
T ss_dssp             -HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCCSC
T ss_pred             CHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCCCC
Confidence            778999999998 999999999999999999875433

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.72  E-value=0.12  Score=37.73  Aligned_cols=59  Identities=22%  Similarity=0.360  Sum_probs=48.4

Q ss_pred             eCHHHHHHHHh-hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe----cccceeEEEecc
Q 033931           43 FDQATYDKLLS-EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI----SAHASQQIYTRA  105 (108)
Q Consensus        43 ~dk~t~dKl~K-EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V----~k~~~q~IYtr~  105 (108)
                      .|-+.|..|+. +-|    .|...|||++++.-|.|.++|+-|.+.|+|...    -+++.-.||-+.
T Consensus        28 ~Dv~v~~~LL~~~~~----~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i   91 (126)
T COG3355          28 LDVEVYKALLEENGP----LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPI   91 (126)
T ss_pred             HHHHHHHHHHhhcCC----cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecC
Confidence            57788999994 444    699999999999999999999999999999876    344555677543

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=94.67  E-value=0.057  Score=41.13  Aligned_cols=49  Identities=22%  Similarity=0.209  Sum_probs=39.7

Q ss_pred             HHHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           47 TYDKLLSEA-PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        47 t~dKl~KEV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +.++|..+. |+.+|=|-..||++|+|+-...|+||.+|+.+|+|...-+
T Consensus        21 L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G   70 (241)
T PRK10079         21 LEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG   70 (241)
T ss_pred             HHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            444444333 4568889999999999999999999999999999987654

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=94.67  E-value=0.049  Score=43.06  Aligned_cols=49  Identities=10%  Similarity=0.045  Sum_probs=43.2

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +=+++|+..+.....+|...||+.|+|...-+|+=|.+|++.|++..+.
T Consensus        17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~   65 (269)
T PRK09802         17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY   65 (269)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence            4566777777777779999999999999999999999999999999765

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=94.57  E-value=0.077  Score=40.45  Aligned_cols=52  Identities=19%  Similarity=0.144  Sum_probs=42.9

Q ss_pred             CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           44 DQATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        44 dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .+..|+.|...|-.      .+|-|-..||++|+|+-+..|-||+.|+..|+|...-+
T Consensus        12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~   69 (254)
T PRK09464         12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG   69 (254)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            35677777776644      45558899999999999999999999999999997653

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=94.42  E-value=0.087  Score=37.35  Aligned_cols=42  Identities=17%  Similarity=0.182  Sum_probs=36.3

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccce
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHAS   98 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      .-..+|...||++++|.....+++|+.|.+.|+|.-+...+.
T Consensus        22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~G   63 (135)
T TIGR02010        22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGG   63 (135)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCC
Confidence            346799999999999999999999999999999987644443

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

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=94.40  E-value=0.084  Score=40.41  Aligned_cols=50  Identities=18%  Similarity=0.225  Sum_probs=41.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..|+.|...|      |+.++-|-..||++|+|+-+-.|-||+.|+..|+|...-
T Consensus         5 ~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~   60 (253)
T PRK10421          5 DEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR   60 (253)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            45677777775      344555889999999999999999999999999998754

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=94.23  E-value=0.11  Score=33.45  Aligned_cols=34  Identities=26%  Similarity=0.299  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.++++-+-+++.|+.|++.|+|...
T Consensus        20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346       20 GLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence            4999999999999999999999999999999874

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=94.09  E-value=0.084  Score=36.50  Aligned_cols=39  Identities=15%  Similarity=0.284  Sum_probs=34.9

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +.-..+|...||+.++|+.+..+++|+.|.+.|+|....
T Consensus        21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~   59 (132)
T TIGR00738        21 PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVR   59 (132)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecc
Confidence            445688999999999999999999999999999997653

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.

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=94.08  E-value=0.079  Score=39.67  Aligned_cols=49  Identities=16%  Similarity=0.250  Sum_probs=40.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..|+.|...|      |+.++ +...||++|+|+-+-.|-||+.|+..|||....
T Consensus        14 e~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~   68 (221)
T PRK11414         14 LQVENDLKHQLSIGALKPGARL-ITKNLAEQLGMSITPVREALLRLVSVNALSVAP   68 (221)
T ss_pred             HHHHHHHHHHHHhCCCCCCCcc-CHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence            55777777766      44566 568899999999999999999999999998654

>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex

Probab=94.05  E-value=0.1  Score=40.01  Aligned_cols=46  Identities=22%  Similarity=0.234  Sum_probs=40.3

Q ss_pred             HHHHHHHhhC--CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           46 ATYDKLLSEA--PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        46 ~t~dKl~KEV--pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      ....+|+.=+  .....+|+..|++.+++...+|+..|.+|+..|++-
T Consensus       174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~  221 (223)
T PF04157_consen  174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW  221 (223)
T ss_dssp             HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence            5567777777  778999999999999999999999999999999984

The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.

>PRK10870 transcriptional repressor MprA; Provisional

Probab=93.89  E-value=0.13  Score=38.15  Aligned_cols=35  Identities=34%  Similarity=0.287  Sum_probs=33.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+.+++..+-.-++|..|+++|+|...
T Consensus        70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~  104 (176)
T PRK10870         70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERR  104 (176)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            56899999999999999999999999999999998

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.89  E-value=0.082  Score=36.86  Aligned_cols=36  Identities=11%  Similarity=0.226  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..+|...||++++|+-+..+++|+.|++.|+|.-+.
T Consensus        24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~   59 (130)
T TIGR02944        24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR   59 (130)
T ss_pred             CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence            468999999999999999999999999999997653

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.

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

Probab=93.75  E-value=0.14  Score=34.70  Aligned_cols=38  Identities=21%  Similarity=0.227  Sum_probs=34.5

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...-+|++.||+.+++.=+-..++|.+|+++|+|..-.
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence            45789999999999999999999999999999998643

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=93.71  E-value=0.15  Score=35.84  Aligned_cols=41  Identities=15%  Similarity=0.174  Sum_probs=35.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQ  100 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~  100 (108)
                      -+|++.||+++++.-|-.-+++..|+++|+|..+.  .++|..
T Consensus        46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~   88 (144)
T PRK03573         46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAK   88 (144)
T ss_pred             CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCee
Confidence            46899999999999999999999999999999983  344443

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.67  E-value=0.13  Score=36.30  Aligned_cols=36  Identities=22%  Similarity=0.325  Sum_probs=33.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..-+|++.||+++++.-|-.=++|..|+++|+|...
T Consensus        52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~   87 (144)
T PRK11512         52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   87 (144)
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            445999999999999999999999999999999988

>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]

Probab=93.46  E-value=0.15  Score=41.18  Aligned_cols=53  Identities=21%  Similarity=0.279  Sum_probs=45.4

Q ss_pred             ceeCHHHHHHHHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           41 VLFDQATYDKLLSEAPK-FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        41 V~~dk~t~dKl~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+-.-+.++-|..|.-. .=+++.|.||||.+|+-||-=.|||.||+-|+|.-=
T Consensus       184 SYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSR  237 (261)
T COG4465         184 SYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR  237 (261)
T ss_pred             cHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeec
Confidence            33455677888888876 479999999999999999999999999999999753

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues

Probab=93.45  E-value=0.11  Score=40.12  Aligned_cols=58  Identities=14%  Similarity=0.218  Sum_probs=45.1

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++..+..-|...+++....||..|+++-.-+-.-|++|+..|.|.-|.-.++..||+-
T Consensus       100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs  157 (188)
T PF09756_consen  100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS  157 (188)
T ss_dssp             HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred             HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence            6777888888889999999999999999999999999999999999988899999974

They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.36  E-value=0.15  Score=39.70  Aligned_cols=46  Identities=17%  Similarity=0.293  Sum_probs=40.4

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           48 YDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .++|+..+.....+|...|++.|+|+-+-+|+-|.+|++.|+|..+
T Consensus         6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~   51 (240)
T PRK10411          6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRN   51 (240)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4556666667789999999999999999999999999999999763

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.28  E-value=0.22  Score=31.65  Aligned_cols=34  Identities=29%  Similarity=0.419  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|+..|++.++++-+-..++|+.|++.|+|...
T Consensus        24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~   57 (101)
T smart00347       24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL   57 (101)
T ss_pred             CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence            4899999999999999999999999999999877

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=93.27  E-value=0.054  Score=40.76  Aligned_cols=48  Identities=15%  Similarity=0.043  Sum_probs=42.2

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +=.+.|+..+.....+|...||+.|+++.+-+|+=|.+|++.|++..+
T Consensus         7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424          7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence            345667777777889999999999999999999999999999998764

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=93.27  E-value=0.23  Score=31.04  Aligned_cols=33  Identities=24%  Similarity=0.319  Sum_probs=31.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      --+|...||+-++++-.-.-++|++|+++|+|.
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            347899999999999999999999999999998

...

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=93.22  E-value=0.2  Score=33.39  Aligned_cols=45  Identities=20%  Similarity=0.320  Sum_probs=37.4

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      |...+.-|..+    .-+|.+.||+.++++-+-+++.|+.|++.|+|..
T Consensus         5 D~~il~~L~~~----~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~   49 (108)
T smart00344        5 DRKILEELQKD----ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence            45555555544    2489999999999999999999999999999983

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

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=93.21  E-value=0.12  Score=37.77  Aligned_cols=48  Identities=13%  Similarity=0.194  Sum_probs=40.6

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ....+|...||++++|+-+.-+++|..|.+.|+|+-+-+...-..-.|
T Consensus        22 ~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar   69 (150)
T COG1959          22 GGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLAR   69 (150)
T ss_pred             CCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCC
Confidence            334899999999999999999999999999999999977665544443

>PRK04158 transcriptional repressor CodY; Validated

Probab=93.02  E-value=0.12  Score=41.77  Aligned_cols=60  Identities=20%  Similarity=0.308  Sum_probs=51.6

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           33 QKEKVNNMVLFDQATYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        33 ~keK~nn~V~~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +++-++..-+-.-+..+-|..|.... =+++.|-||||.+|+-||-=.|||-||+-|+|.-
T Consensus       173 V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIES  233 (256)
T PRK04158        173 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIES  233 (256)
T ss_pred             HHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceee
Confidence            45555656666678888999999885 7899999999999999999999999999999974

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=92.86  E-value=0.19  Score=37.82  Aligned_cols=46  Identities=15%  Similarity=0.130  Sum_probs=38.1

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .++.-+-...-+|...||+.+++.-|.+++.|+.|++.|+|.....
T Consensus       147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~  192 (203)
T TIGR01884       147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR  192 (203)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            4444443334589999999999999999999999999999998863

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.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=92.75  E-value=0.18  Score=36.98  Aligned_cols=42  Identities=10%  Similarity=0.165  Sum_probs=36.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeE
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQ  100 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~  100 (108)
                      ..+|...||++++|+-+.-+++|+.|.+.|+|.-+.+.+...
T Consensus        23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy   64 (153)
T PRK11920         23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGV   64 (153)
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCe
Confidence            467999999999999999999999999999999887655443

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

Probab=92.75  E-value=0.18  Score=32.86  Aligned_cols=32  Identities=19%  Similarity=0.321  Sum_probs=29.5

Q ss_pred             hhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           63 PSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        63 ps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..+|+.++|+-|-..++|+.|+++|+|....
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~   33 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP   33 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence            56899999999999999999999999998854

iron dependent repressor

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.70  E-value=0.26  Score=34.96  Aligned_cols=36  Identities=11%  Similarity=0.057  Sum_probs=32.7

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...+|.+.||+.++|.-+-+..+|+.|+++|+|...
T Consensus        20 ~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         20 KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            456799999999999999999999999999999754

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=92.64  E-value=0.28  Score=33.48  Aligned_cols=35  Identities=20%  Similarity=0.183  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+.+++.-|-.-++++.|+++|+|..+
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~   76 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE   76 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEecc
Confidence            56999999999999999999999999999999987

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.

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

Probab=92.53  E-value=0.26  Score=32.11  Aligned_cols=43  Identities=16%  Similarity=0.135  Sum_probs=30.9

Q ss_pred             HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           49 DKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -.|++.+. ..-.+++.|+...+++.+.+.+.|++|+++|+|..
T Consensus         9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~   51 (77)
T PF14947_consen    9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK   51 (77)
T ss_dssp             HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence            34444443 34567899999999999999999999999999943

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

Probab=92.23  E-value=0.27  Score=28.08  Aligned_cols=30  Identities=27%  Similarity=0.370  Sum_probs=25.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSI   90 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlI   90 (108)
                      +|-..||+-++......-++|..|+++|+|
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            577899999999999999999999999997

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 ....

>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=92.01  E-value=0.33  Score=28.60  Aligned_cols=33  Identities=24%  Similarity=0.308  Sum_probs=29.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      .-.|+..|++.+++.-|....=|+.|++.|+|.
T Consensus        14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen   14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence            347899999999999999999999999999985

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 ....

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

Probab=92.01  E-value=0.21  Score=34.57  Aligned_cols=47  Identities=21%  Similarity=0.237  Sum_probs=37.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +|+.-.-.+-.=+|-.+|-++++...-.+.+|++|++.|||..|...
T Consensus        11 ~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~   57 (92)
T PF10007_consen   11 KILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK   57 (92)
T ss_pred             HHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence            34444444444568899999999999999999999999999999743

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

Probab=91.96  E-value=0.21  Score=28.70  Aligned_cols=40  Identities=13%  Similarity=0.153  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+..+|+.++|+-+    -|+.++++|+|.+....++...|+.
T Consensus         1 ~~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~y~~   40 (49)
T cd04761           1 YTIGELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRLYSD   40 (49)
T ss_pred             CcHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEeCH
Confidence            377889999888766    5788899999986544457778875

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

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=91.92  E-value=0.38  Score=31.26  Aligned_cols=30  Identities=30%  Similarity=0.460  Sum_probs=29.4

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           64 SILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +.|++++++..|-.-++|+.|+++|+|...
T Consensus        40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~   69 (126)
T COG1846          40 KELAERLGLDRSTVTRLLKRLEDKGLIERL   69 (126)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence            999999999999999999999999999988

>PRK11050 manganese transport regulator MntR; Provisional

Probab=91.80  E-value=0.36  Score=35.13  Aligned_cols=35  Identities=17%  Similarity=0.221  Sum_probs=31.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|+..||++|+|+-|-..++|+.|++.|+|...
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34799999999999999999999999999998653

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=91.77  E-value=0.42  Score=35.39  Aligned_cols=50  Identities=10%  Similarity=0.160  Sum_probs=39.9

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++.+.-|+.-.-+--.++...||++|+|.-+-+..+|+.|++.|+|..+-
T Consensus         9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~   58 (154)
T COG1321           9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP   58 (154)
T ss_pred             HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence            33444444333356789999999999999999999999999999998764

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=91.54  E-value=0.29  Score=36.42  Aligned_cols=43  Identities=14%  Similarity=0.144  Sum_probs=36.9

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccce
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHAS   98 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      +.-..+|...||++++|.....+++|+.|.+.|+|.-....+.
T Consensus        21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~G   63 (164)
T PRK10857         21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGG   63 (164)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCC
Confidence            3446799999999999999999999999999999997644443

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

Probab=91.54  E-value=0.47  Score=31.98  Aligned_cols=45  Identities=22%  Similarity=0.269  Sum_probs=36.5

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|.+.|.+++     +|+.+-.-+.|+.|++.|+|..+.-..+...|-
T Consensus        15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~   64 (116)
T cd07153          15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE   64 (116)
T ss_pred             CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence            457899999988     688888999999999999999996544445553

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.

>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=91.49  E-value=0.7  Score=27.46  Aligned_cols=28  Identities=36%  Similarity=0.506  Sum_probs=26.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcC
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARG   88 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kG   88 (108)
                      ||...||+.|+|+-...++-|.+|.+.|
T Consensus        16 it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   16 ITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            9999999999999999999999999999

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 ....

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.43  E-value=0.33  Score=36.64  Aligned_cols=55  Identities=16%  Similarity=0.249  Sum_probs=45.8

Q ss_pred             cceeCHHHHHHHHhhCCCCe-----eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           40 MVLFDQATYDKLLSEAPKFK-----LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        40 ~V~~dk~t~dKl~KEVpk~k-----~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ........|+.|...|-.-.     -|+...||++|+|+-.--|.||..|+..|+|...-
T Consensus        14 ~~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p   73 (230)
T COG1802          14 PDTLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEP   73 (230)
T ss_pred             cccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecC
Confidence            34455667888877776654     48899999999999999999999999999999874

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=91.32  E-value=0.61  Score=37.38  Aligned_cols=80  Identities=18%  Similarity=0.135  Sum_probs=60.2

Q ss_pred             ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        25 KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .-.|+.+=..+-..+-.-|+++..+=|.=..-+-=-||.+.|...+++.=+-.-++|++||++|+|+..-+++...|-.+
T Consensus       175 ~~~~~~~~~~~~~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~  254 (258)
T COG2512         175 EPLLSRGDELRVLVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELR  254 (258)
T ss_pred             hhccccccccccccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEe
Confidence            34577754455555545565555554444444556799999999999999999999999999999999988888877554

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=91.17  E-value=1.1  Score=27.93  Aligned_cols=34  Identities=15%  Similarity=0.205  Sum_probs=30.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|...||++++|+-+..++.|+.|++.|+.....
T Consensus        14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~   47 (69)
T TIGR00122        14 FSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV   47 (69)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            6789999999999999999999999999965544

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.

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=91.07  E-value=0.23  Score=30.54  Aligned_cols=40  Identities=8%  Similarity=0.081  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-cccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI-SAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr  104 (108)
                      .|+..+|+.++|+-+    .|+.++++|+|.+. ...++...|+.
T Consensus         1 ~s~~eva~~~gvs~~----tlr~~~~~gli~~~~~~~~g~r~y~~   41 (70)
T smart00422        1 YTIGEVAKLAGVSVR----TLRYYERIGLLPPPIRTEGGYRLYSD   41 (70)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCEecCH
Confidence            478899999998765    46788899999987 44556677874

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

Probab=90.92  E-value=0.97  Score=30.91  Aligned_cols=54  Identities=31%  Similarity=0.405  Sum_probs=39.7

Q ss_pred             HHhhCCCCeeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           51 LLSEAPKFKLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      ++.+-+.  -+|+..|-+++     .|+.|-.-+.|+.|++.|+|..+...++...|-.+.
T Consensus        16 ~l~~~~~--~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~   74 (120)
T PF01475_consen   16 LLKESPE--HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST   74 (120)
T ss_dssp             HHHHHSS--SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred             HHHcCCC--CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence            3444454  57888888877     455666789999999999999998777777776543

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 ....

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=90.89  E-value=0.53  Score=34.30  Aligned_cols=46  Identities=22%  Similarity=0.297  Sum_probs=39.6

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |..+|=|.-.+|..++||.-...++.++|++.|+|.-.   ++...|..
T Consensus        31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~---rg~G~fV~   76 (125)
T COG1725          31 PGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK---RGKGTFVT   76 (125)
T ss_pred             CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---cCeeEEEc
Confidence            66899999999999999999999999999999999653   44556654

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=90.84  E-value=0.26  Score=37.29  Aligned_cols=50  Identities=12%  Similarity=0.030  Sum_probs=43.2

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +.++...|+.-++....+|-..||+.++|+..-.|++|..|.+.|||...
T Consensus        20 ~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~   69 (178)
T PRK06266         20 GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYK   69 (178)
T ss_pred             CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            45666777777777778999999999999999999999999999999843

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

Probab=90.82  E-value=0.49  Score=38.98  Aligned_cols=66  Identities=14%  Similarity=0.214  Sum_probs=43.0

Q ss_pred             hhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--cccceeEEEec
Q 033931           37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI--SAHASQQIYTR  104 (108)
Q Consensus        37 ~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr  104 (108)
                      ++..---+.-.|+-|. |- .-+=|....|-.+.++.-+.-.++|+.|+.++||+.|  .+|+...||.-
T Consensus        79 ~~~l~~~e~lvy~~I~-~a-g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml  146 (327)
T PF05158_consen   79 LKGLSDEERLVYQLIE-EA-GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYML  146 (327)
T ss_dssp             --SSSCCHHHHHHHHH-HH-TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEE
T ss_pred             hcCCCHHHHHHHHHHH-Hh-CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEE
Confidence            4444333444555543 32 3456777889999999999999999999999999999  55667778863

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

>TIGR00498 lexA SOS regulatory protein LexA

Probab=90.79  E-value=0.36  Score=35.77  Aligned_cols=53  Identities=15%  Similarity=0.112  Sum_probs=39.6

Q ss_pred             CHHHHHHHHhhCCCC-eeechhhhhhhhccc-HHHHHHHHHHHHHcCCeeEeccc
Q 033931           44 DQATYDKLLSEAPKF-KLITPSILSDRLRIN-GSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        44 dk~t~dKl~KEVpk~-k~ITps~vserlkI~-~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +.+.++-|....-.. --.|...||+++++. -|.....|+.|+++|+|......
T Consensus         8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~   62 (199)
T TIGR00498         8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK   62 (199)
T ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence            455666666432211 126677999999999 89999999999999999987544

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.

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

Probab=90.70  E-value=0.25  Score=32.89  Aligned_cols=41  Identities=17%  Similarity=0.232  Sum_probs=32.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc-eeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA-SQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~-~q~IYtr  104 (108)
                      +.|+..+|+.++|+.+-    ||..+++|+|.+..... +...|+.
T Consensus         1 ~~ti~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~   42 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSL   42 (88)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCH
Confidence            36899999999988764    78889999999875443 7778874

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

>PRK09954 putative kinase; Provisional

Probab=90.66  E-value=0.29  Score=39.19  Aligned_cols=42  Identities=31%  Similarity=0.428  Sum_probs=36.1

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      +|+..+.....||.+.||++|+|+-+-++..|+.|+++|+|.
T Consensus         7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          7 EILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence            355555555689999999999999999999999999999984

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=90.61  E-value=0.37  Score=27.98  Aligned_cols=37  Identities=14%  Similarity=0.166  Sum_probs=25.1

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCe-eEecccceeEEE
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSI-RMISAHASQQIY  102 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlI-k~V~k~~~q~IY  102 (108)
                      |+..+|+.++|+.    ..||..+++||| .+....+....|
T Consensus         1 ti~e~A~~~gvs~----~tlR~ye~~Gll~~~~r~~~g~R~Y   38 (38)
T PF00376_consen    1 TIGEVAKLLGVSP----RTLRYYEREGLLPPPERTEGGYRRY   38 (38)
T ss_dssp             EHHHHHHHHTS-H----HHHHHHHHTTSS-SSEETTTS-EEE
T ss_pred             CHHHHHHHHCCCH----HHHHHHHHCCCCCCCccCCCCeecC
Confidence            5678899888765    469999999999 555433444443

One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....

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

Probab=90.46  E-value=0.29  Score=33.25  Aligned_cols=41  Identities=15%  Similarity=0.190  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.|.+.+|+.++|+.+.    ||..++.|+|.+....++...|+.
T Consensus         1 ~~~i~eva~~~gVs~~t----LR~ye~~Gli~p~r~~~g~R~Ys~   41 (98)
T cd01279           1 LYPISVAAELLGIHPQT----LRVYDRLGLVSPARTNGGGRRYSN   41 (98)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeECH
Confidence            46889999999988765    678899999998644567788875

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

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

Probab=90.42  E-value=0.32  Score=32.26  Aligned_cols=41  Identities=7%  Similarity=0.101  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.|+..+|+.++|+.+.    |+..++.|+|.+....+....|+.
T Consensus         1 ~~~i~e~A~~~gvs~~t----Lr~ye~~Gli~p~r~~~g~R~y~~   41 (91)
T cd04766           1 VYVISVAAELSGMHPQT----LRLYERLGLLSPSRTDGGTRRYSE   41 (91)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCCeeECH
Confidence            36889999999988765    788899999998754456677874

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

>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=90.32  E-value=0.43  Score=32.10  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=29.5

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSI   90 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlI   90 (108)
                      -.=|....|+++|+++..=-|.+|++|.+.|.|
T Consensus        63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I   95 (102)
T PF08784_consen   63 EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI   95 (102)
T ss_dssp             TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence            355899999999999999999999999999987

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.

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=90.23  E-value=0.72  Score=32.93  Aligned_cols=44  Identities=16%  Similarity=0.168  Sum_probs=35.0

Q ss_pred             echhhhhhh----hcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           61 ITPSILSDR----LRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        61 ITps~vser----lkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      +|+..|.+.    +++.-+.....|+.|+++|+|... +.++..+|++.
T Consensus        19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~-k~gr~~~Y~p~   66 (130)
T TIGR02698        19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE-KEGRKFIYTAL   66 (130)
T ss_pred             CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee-cCCCcEEEEec
Confidence            488885554    478999999999999999999775 44567789864

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.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=90.22  E-value=0.5  Score=36.05  Aligned_cols=36  Identities=22%  Similarity=0.071  Sum_probs=32.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..-+|++.||+.+.+..|-.-++|..|+++|+|...
T Consensus        57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~   92 (185)
T PRK13777         57 LKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS   92 (185)
T ss_pred             CCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence            345899999999999988888999999999999987

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=90.13  E-value=0.61  Score=38.06  Aligned_cols=50  Identities=20%  Similarity=0.215  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..|+.|..+|      |..++=+.-.||+.|+|+-+-.++|+++|+++|+|....
T Consensus         8 ~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~   63 (431)
T PRK15481          8 NEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQG   63 (431)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            34555555554      345666788999999999999999999999999997543

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=90.05  E-value=0.64  Score=33.94  Aligned_cols=43  Identities=23%  Similarity=0.256  Sum_probs=35.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|+.....--=+|.+.||+++++.-+-.++=++.|++.|+|.-
T Consensus        18 ~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         18 NILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            4444444545577899999999999999999999999999974

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=88.97  E-value=0.93  Score=32.82  Aligned_cols=41  Identities=20%  Similarity=0.220  Sum_probs=34.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      -+|...||+.++++-.-.-++|++|+++|+|..-  ++...||
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~--~~~i~i~  208 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH--GKTIVVY  208 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec--CCEEEEe
Confidence            4888999999999999999999999999999742  3345554

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

Probab=88.84  E-value=0.38  Score=32.83  Aligned_cols=40  Identities=20%  Similarity=0.154  Sum_probs=32.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|...||++++|+.+.    ||.-++.|+|.+........+|+.
T Consensus         2 ~~i~eva~~~gvs~~t----lR~ye~~Gll~~~r~~~g~R~Y~~   41 (102)
T cd04789           2 YTISELAEKAGISRST----LLYYEKLGLITGTRNANGYRLYPD   41 (102)
T ss_pred             CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeCCH
Confidence            5889999999998765    779999999998655567778874

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

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

Probab=88.74  E-value=0.45  Score=32.39  Aligned_cols=40  Identities=18%  Similarity=0.242  Sum_probs=31.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|...||++++|+.+    .||..++.|+|.+....++...|+.
T Consensus         2 ~~i~eva~~~gvs~~----tLR~ye~~Gll~~~r~~~g~R~Y~~   41 (102)
T cd04775           2 YTIGQMSRKFGVSRS----TLLYYESIGLIPSARSEANYRLYSE   41 (102)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCeeeCH
Confidence            588999999988765    5799999999955544456778875

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

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=88.74  E-value=0.8  Score=32.98  Aligned_cols=46  Identities=11%  Similarity=0.203  Sum_probs=39.0

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...++-|+.+    -=++.+.||++++++-+-.+.=++.|++.|+|.-
T Consensus        10 ~D~~Il~~Lq~d----~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179         10 LDRGILEALMEN----ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             HHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            466667777766    3468899999999999999999999999999973

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

Probab=88.66  E-value=1.2  Score=32.40  Aligned_cols=45  Identities=24%  Similarity=0.385  Sum_probs=34.4

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +++|+.|..+.|...+-|+|              ++|+.|++.|+|..+.-..+...|-
T Consensus        40 eei~~~l~~~~p~islaTVY--------------r~L~~l~e~Glv~~~~~~~~~~~y~   84 (145)
T COG0735          40 EELYEELREEGPGISLATVY--------------RTLKLLEEAGLVHRLEFEGGKTRYE   84 (145)
T ss_pred             HHHHHHHHHhCCCCCHhHHH--------------HHHHHHHHCCCEEEEEeCCCEEEEe
Confidence            56778888777776665555              7899999999999997666555564

>PRK09462 fur ferric uptake regulator; Provisional

Probab=88.52  E-value=1.1  Score=32.10  Aligned_cols=43  Identities=14%  Similarity=0.250  Sum_probs=28.2

Q ss_pred             echhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|+..|-+++     .|+.+-.-+.|+.|++.|+|..+.-......|-
T Consensus        34 ~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~   81 (148)
T PRK09462         34 VSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE   81 (148)
T ss_pred             CCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence            4555554444     244455568999999999999986444445554

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=88.04  E-value=1.3  Score=34.16  Aligned_cols=37  Identities=19%  Similarity=0.181  Sum_probs=33.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      -+|.+.||++++++-|-+.++|+.|++.|++.....+
T Consensus        28 ~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~   64 (257)
T PRK15090         28 EIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGES   64 (257)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence            4899999999999999999999999999999875433

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=87.88  E-value=0.95  Score=35.12  Aligned_cols=57  Identities=19%  Similarity=0.369  Sum_probs=43.4

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ...+++|...|      |+-+|=|-..|||+|+|+=++-|-+|+.|+..|+|..   .++-.+|.+
T Consensus        13 ~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~   75 (241)
T COG2186          13 DEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVR   75 (241)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEec
Confidence            44555555554      4567888899999999999999999999999999965   233345553

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=87.75  E-value=0.51  Score=32.12  Aligned_cols=40  Identities=13%  Similarity=0.124  Sum_probs=32.8

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-ceeEEEecc
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAH-ASQQIYTRA  105 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr~  105 (108)
                      |...||+.++|+.    +.||.-++.|||.|.... ++..+|+..
T Consensus         2 ~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~   42 (124)
T COG0789           2 TIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPE   42 (124)
T ss_pred             cHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHH
Confidence            6788999997664    579999999999999655 588999853

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=87.62  E-value=1.2  Score=34.66  Aligned_cols=36  Identities=19%  Similarity=0.343  Sum_probs=33.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +|.+.||++++++-|-+.++|+.|++.|+|......
T Consensus        27 ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~   62 (263)
T PRK09834         27 ATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASD   62 (263)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCC
Confidence            899999999999999999999999999999876433

>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=87.61  E-value=1.8  Score=29.71  Aligned_cols=45  Identities=13%  Similarity=0.146  Sum_probs=34.9

Q ss_pred             echhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           61 ITPSILSDRLR----INGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        61 ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      +|...|.+.+.    +.-+-.+..|+.|+++|+|..-. .++..+|.+..
T Consensus        18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~-~gr~~~Y~p~i   66 (115)
T PF03965_consen   18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK-IGRAYVYSPLI   66 (115)
T ss_dssp             EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE-ETTCEEEEESS
T ss_pred             CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee-cCCceEEEeCC
Confidence            67777776665    66899999999999999999864 46688998653

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 ....

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

Probab=87.41  E-value=0.58  Score=31.54  Aligned_cols=40  Identities=8%  Similarity=0.095  Sum_probs=32.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      +|.+.||+.++|+.+    .||.-++.|+|.++.. .++...|+.
T Consensus         1 ~ti~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~   41 (96)
T cd04768           1 LTIGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSY   41 (96)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCH
Confidence            378899999998876    5899999999999753 556778874

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

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

Probab=87.39  E-value=0.61  Score=33.58  Aligned_cols=40  Identities=18%  Similarity=0.339  Sum_probs=33.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.|...||++++|+.+    .||..+++|+|.+.. .++++.|+.
T Consensus         1 lysI~eVA~~~GVs~~----TLR~wE~~GLl~p~r-~~G~R~Ys~   40 (120)
T cd04767           1 LYPIGVVAELLNIHPE----TLRIWERHGLIKPAR-RNGQRLYSN   40 (120)
T ss_pred             CCCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCcEEECH
Confidence            3688999999998877    477999999999964 478889975

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

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

Probab=87.32  E-value=0.44  Score=32.99  Aligned_cols=40  Identities=10%  Similarity=0.120  Sum_probs=31.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      .|...||++++|+.+    .||+-++.|||.+... .++...|+.
T Consensus         1 ~~I~eva~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~   41 (123)
T cd04770           1 MKIGELAKAAGVSPD----TIRYYERIGLLPPPQRSENGYRLYGE   41 (123)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCCccCCH
Confidence            378899999988765    6899999999997643 456678874

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

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

Probab=87.25  E-value=2.3  Score=28.00  Aligned_cols=34  Identities=21%  Similarity=0.209  Sum_probs=29.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|.+.|.+.++++-|-..+-|+.|++.|+|..-
T Consensus        14 ~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~   47 (80)
T PF13601_consen   14 EATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE   47 (80)
T ss_dssp             EEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4789999999999999999999999999999864

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=86.92  E-value=0.69  Score=34.31  Aligned_cols=42  Identities=29%  Similarity=0.398  Sum_probs=35.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .++|...||.+++|+.+    .||.-++.|||.+....+....|+.
T Consensus        10 ~~~~IgevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y~~   51 (154)
T PRK15002         10 ALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR   51 (154)
T ss_pred             ccccHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECH
Confidence            68999999999999876    5899999999999755566788875

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

Probab=86.89  E-value=0.78  Score=28.20  Aligned_cols=40  Identities=13%  Similarity=0.141  Sum_probs=31.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|...||+.++|+.+    .||..+++|+|.+....+....|+.
T Consensus         1 yti~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~r~y~~   40 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGYRYYSE   40 (69)
T ss_dssp             EEHHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSSEEE-H
T ss_pred             CcHHHHHHHHCcCHH----HHHHHHHhcCcccccccCceeeccH
Confidence            378899999998655    5899999999888765666688874

>PF12728 HTH_17: Helix-turn-helix domain

Probab=86.86  E-value=0.87  Score=26.76  Aligned_cols=40  Identities=15%  Similarity=0.149  Sum_probs=30.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++|+..+|+-|+|+-+-    ++.+..+|.|..+. ..+...|.+
T Consensus         1 ~lt~~e~a~~l~is~~t----v~~~~~~g~i~~~~-~g~~~~~~~   40 (51)
T PF12728_consen    1 YLTVKEAAELLGISRST----VYRWIRQGKIPPFK-IGRKWRIPK   40 (51)
T ss_pred             CCCHHHHHHHHCcCHHH----HHHHHHcCCCCeEE-eCCEEEEeH
Confidence            57999999999986655    66777899998884 555555544

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

Probab=86.52  E-value=1.4  Score=32.92  Aligned_cols=38  Identities=26%  Similarity=0.365  Sum_probs=34.3

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -++=+.|...||+.++++-+--.++|++|++.|+|..+
T Consensus        71 ~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~  108 (165)
T PF05732_consen   71 DNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI  108 (165)
T ss_pred             CCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence            34567899999999999999999999999999999876

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK12423 LexA repressor; Provisional

Probab=86.36  E-value=1.1  Score=33.71  Aligned_cols=50  Identities=14%  Similarity=0.204  Sum_probs=37.7

Q ss_pred             HHHHHHHHhhCCCCee-echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEAPKFKL-ITPSILSDRLRI-NGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~-ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .+.++.|...+-...+ =|...||+.|++ .-+..+..|+.|+++|+|..--
T Consensus         9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~   60 (202)
T PRK12423          9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVP   60 (202)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecC
Confidence            4566666654333322 388899999995 7888899999999999998653

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=86.36  E-value=1.7  Score=31.35  Aligned_cols=32  Identities=22%  Similarity=0.225  Sum_probs=30.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      -+|...||+-++++-.-.-++|++|+++|+|.
T Consensus       149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        149 YATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            37999999999999999999999999999997

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=86.13  E-value=1.1  Score=33.62  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=28.4

Q ss_pred             echhhhhhhhcc--------------cHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRI--------------NGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI--------------~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |....|+..|+.              ++|+.|.+|+.||+-|+|....
T Consensus        68 vGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~  115 (150)
T PRK09333         68 VGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK  115 (150)
T ss_pred             ccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence            566667777776              5899999999999999999765

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=86.01  E-value=2.1  Score=31.65  Aligned_cols=42  Identities=21%  Similarity=0.072  Sum_probs=36.5

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIR   91 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      .++.-++....+|.-.||+.++|+..--|++|..|.+.|||.
T Consensus        18 ~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~   59 (158)
T TIGR00373        18 LVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD   59 (158)
T ss_pred             HHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence            344455656679999999999999999999999999999995

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.

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

Probab=85.84  E-value=1.6  Score=34.80  Aligned_cols=43  Identities=23%  Similarity=0.211  Sum_probs=34.9

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCC-eeEe
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGS-IRMI   93 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGl-Ik~V   93 (108)
                      |+..+..-..++...||++|+|+-+-.++.|+.|++.|+ |.-.
T Consensus         9 il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~   52 (319)
T PRK11886          9 LLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSV   52 (319)
T ss_pred             HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEe
Confidence            333333457889999999999999999999999999999 5443

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

Probab=85.71  E-value=0.85  Score=31.58  Aligned_cols=39  Identities=13%  Similarity=0.144  Sum_probs=31.8

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |...+|++++|+.+    .||.-++.|||.++.......+|+.
T Consensus         2 ~ige~a~~~gvs~~----tLryYe~~GLi~p~~~~~~yR~Y~~   40 (116)
T cd04769           2 YIGELAQQTGVTIK----AIRLYEEKGLLPSPKRSGNYRVYDA   40 (116)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCceeeCH
Confidence            66788999988764    6899999999999865557788875

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

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

Probab=85.53  E-value=0.81  Score=31.87  Aligned_cols=39  Identities=13%  Similarity=0.196  Sum_probs=33.0

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |...+|++++|+.+    .||.-++.|||.++..+++...|+.
T Consensus         2 ~IgevA~~~gvs~~----tlRyYe~~GLl~p~~~~~gyR~Y~~   40 (120)
T cd04781           2 DIAEVARQSGLPAS----TLRYYEEKGLIASIGRRGLRRQYDP   40 (120)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCceecCH
Confidence            67889999998765    5899999999999866678888985

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

>TIGR01764 excise DNA binding domain, excisionase family

Probab=85.48  E-value=1.2  Score=24.96  Aligned_cols=40  Identities=13%  Similarity=0.182  Sum_probs=29.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++|+..+|+.|+|+-    .-|+.|...|.|..+..+ +...|.+
T Consensus         1 ~lt~~e~a~~lgis~----~ti~~~~~~g~i~~~~~g-~~~~~~~   40 (49)
T TIGR01764         1 YLTVEEAAEYLGVSK----DTVYRLIHEGELPAYRVG-RHYRIPR   40 (49)
T ss_pred             CCCHHHHHHHHCCCH----HHHHHHHHcCCCCeEEeC-CeEEEeH
Confidence            478999999998754    457778889998876443 4455554

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

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

Probab=85.40  E-value=0.85  Score=25.35  Aligned_cols=40  Identities=13%  Similarity=0.327  Sum_probs=28.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|...+|+.|+|+-+    -|+.+.++|.+.......+...|+.
T Consensus         1 ~s~~e~a~~lgvs~~----tl~~~~~~g~~~~~~~~~~~~~~~~   40 (49)
T cd04762           1 LTTKEAAELLGVSPS----TLRRWVKEGKLKAIRTPGGHRRFPE   40 (49)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHcCCCCceeCCCCceecCH
Confidence            367889999887654    4677788899876544446666764

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

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=85.31  E-value=0.8  Score=32.70  Aligned_cols=44  Identities=18%  Similarity=0.308  Sum_probs=35.6

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEecc
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTRA  105 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr~  105 (108)
                      |..+|...||++++|+.+    .||.-++.|||.|... .++..+|+..
T Consensus         1 m~~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~~   45 (120)
T TIGR02054         1 MNAYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDDA   45 (120)
T ss_pred             CCCCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCHH
Confidence            346789999999998875    5899999999999843 4678888753

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

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=85.17  E-value=1.4  Score=31.33  Aligned_cols=36  Identities=28%  Similarity=0.460  Sum_probs=31.0

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      =|..|...+|.   ||+-+|+++|           ++|++.|+|....-.
T Consensus        38 RF~eL~r~i~~---Is~k~Ls~~L-----------k~Le~~Glv~R~~~~   73 (120)
T COG1733          38 RFNELRRSIGG---ISPKMLSRRL-----------KELEEDGLVERVVYP   73 (120)
T ss_pred             cHHHHHHHccc---cCHHHHHHHH-----------HHHHHCCCEEeeecC
Confidence            57889999998   9999999985           899999999887543

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

Probab=84.87  E-value=0.89  Score=31.43  Aligned_cols=39  Identities=10%  Similarity=0.092  Sum_probs=32.2

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |...||+.++|+.+    .||.-++.|||.+.-..++...|+.
T Consensus         2 ~i~eva~~~gvs~~----tlR~Ye~~GLl~p~r~~~g~R~Y~~   40 (112)
T cd01282           2 RIGELAARTGVSVR----SLRYYEEQGLLVPERSANGYRDYDE   40 (112)
T ss_pred             CHHHHHHHHCCCHH----HHHHHHHCCCCCCCcCCCCCeecCH
Confidence            67889999988765    5899999999999755667788875

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

>PRK05472 redox-sensing transcriptional repressor Rex; Provisional

Probab=84.82  E-value=1.5  Score=33.06  Aligned_cols=52  Identities=13%  Similarity=0.192  Sum_probs=43.7

Q ss_pred             hccceeCHHHHHHHHhhCCCCe--eechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033931           38 NNMVLFDQATYDKLLSEAPKFK--LITPSILSDRLRINGSLARRAIKDLMARGS   89 (108)
Q Consensus        38 nn~V~~dk~t~dKl~KEVpk~k--~ITps~vserlkI~~SlAr~~Lr~L~~kGl   89 (108)
                      ..+++---+.|.+|+..+....  .||...||+.++|+.+..|+=|..|+..|.
T Consensus         8 ~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~   61 (213)
T PRK05472          8 PEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK   61 (213)
T ss_pred             CHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence            3334444567888888888877  999999999999999999999999999885

>PRK00215 LexA repressor; Validated

Probab=84.72  E-value=1.7  Score=32.34  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=33.8

Q ss_pred             echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEeccccee
Q 033931           61 ITPSILSDRLRI-NGSLARRAIKDLMARGSIRMISAHASQ   99 (108)
Q Consensus        61 ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      +|...||+.+++ .-|-+-+.|+.|+++|+|.......|.
T Consensus        24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~   63 (205)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRA   63 (205)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcce
Confidence            688899999999 889999999999999999887555443

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

Probab=84.45  E-value=0.86  Score=30.22  Aligned_cols=40  Identities=10%  Similarity=0.158  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+..+|+.++|+-+.    |+..++.|+|.+....++..+|+.
T Consensus         1 ~~~~eva~~~gi~~~t----lr~~~~~Gll~~~~~~~g~r~y~~   40 (100)
T cd00592           1 YTIGEVAKLLGVSVRT----LRYYEEKGLLPPERSENGYRLYSE   40 (100)
T ss_pred             CCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCCcccCH
Confidence            3788899999887654    678899999987654456778875

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

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

Probab=84.36  E-value=1.2  Score=30.27  Aligned_cols=39  Identities=13%  Similarity=0.214  Sum_probs=31.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |+..+|++++|+.+    .||.-++.|+|.++-..++..+|+.
T Consensus         2 ~I~e~a~~~gvs~~----tLR~ye~~Gll~p~r~~~g~R~Y~~   40 (96)
T cd04774           2 KVDEVAKRLGLTKR----TLKYYEEIGLVSPERSEGRYRLYSE   40 (96)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEECH
Confidence            77899999987765    4788899999998765667778874

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

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

Probab=84.32  E-value=0.85  Score=31.28  Aligned_cols=39  Identities=10%  Similarity=0.088  Sum_probs=31.5

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc--cceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISA--HASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYtr  104 (108)
                      |...||++++|+.+    .||.-+++|+|.+...  .+....|+.
T Consensus         2 ~i~eva~~~gis~~----tlR~ye~~GLi~p~~~~~~ngyR~Y~~   42 (108)
T cd01107           2 TIGEFAKLSNLSIK----ALRYYDKIGLLKPAYVDPDTGYRYYSA   42 (108)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHcCCCCCCcCCCCCCccccCH
Confidence            67889999998876    5899999999999643  356778875

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

>PRK11569 transcriptional repressor IclR; Provisional

Probab=84.31  E-value=1.9  Score=33.72  Aligned_cols=35  Identities=14%  Similarity=0.301  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|.+.||+++++.-|-+-++|..|++.|++....
T Consensus        43 ~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~   77 (274)
T PRK11569         43 SVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG   77 (274)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            37999999999999999999999999999997653

>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=84.27  E-value=1.5  Score=32.57  Aligned_cols=27  Identities=19%  Similarity=0.315  Sum_probs=22.5

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEecccce
Q 033931           72 INGSLARRAIKDLMARGSIRMISAHAS   98 (108)
Q Consensus        72 I~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      =++|++|.+|++||+-|+|....++.|
T Consensus        92 asg~iiR~~LqqLE~~glv~k~~~~GR  118 (139)
T PF01090_consen   92 ASGSIIRKILQQLEKAGLVEKDPKGGR  118 (139)
T ss_dssp             CHHHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred             CCcHHHHHHHHHHHHCCCEEecCCCCC
Confidence            358899999999999999998854443

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 family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.

>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis

Probab=84.13  E-value=1  Score=32.28  Aligned_cols=34  Identities=21%  Similarity=0.325  Sum_probs=31.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..+.++||.++++-.+++|-++-+|.+.|+|..-
T Consensus        55 ~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~   88 (114)
T PF05331_consen   55 PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVR   88 (114)
T ss_pred             CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEe
Confidence            7899999999999999999999999999999653

The function of these proteins is unknown.

>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=84.01  E-value=0.76  Score=31.10  Aligned_cols=35  Identities=17%  Similarity=0.229  Sum_probs=27.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..+|-..||+.++++..-.|++|..|.+.|+|...
T Consensus        26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~   60 (105)
T PF02002_consen   26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR   60 (105)
T ss_dssp             --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence            57899999999999999999999999999999665

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.

>PF13814 Replic_Relax: Replication-relaxation

Probab=83.68  E-value=1.8  Score=31.30  Aligned_cols=49  Identities=18%  Similarity=0.266  Sum_probs=41.2

Q ss_pred             CCCeeechhhhhhhhcccHH---HHHHHHHHHHHcCCeeEecc------cceeEEEec
Q 033931           56 PKFKLITPSILSDRLRINGS---LARRAIKDLMARGSIRMISA------HASQQIYTR  104 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~S---lAr~~Lr~L~~kGlIk~V~k------~~~q~IYtr  104 (108)
                      -.+.++|...|+.-+.....   -+++.|+.|.+.|+|.....      .+...||.-
T Consensus         5 ~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~L   62 (191)
T PF13814_consen    5 ARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYL   62 (191)
T ss_pred             HHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEE
Confidence            35788999999999999987   79999999999999998865      356678763

>PRK13749 transcriptional regulator MerD; Provisional

Probab=83.38  E-value=0.89  Score=32.64  Aligned_cols=43  Identities=16%  Similarity=0.274  Sum_probs=34.7

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEec
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTR  104 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      |...|...||.+.+|+..    .||.-++.|||.++.. .++...|+.
T Consensus         1 M~~~tIgelA~~~gvS~~----tiR~YE~~GLl~p~~r~~~gyR~Y~~   44 (121)
T PRK13749          1 MSAYTVSRLALDAGVSVH----IVRDYLLRGLLRPVACTTGGYGLFDD   44 (121)
T ss_pred             CCCCcHHHHHHHHCCCHH----HHHHHHHCCCCCCCCcCCCCCccCCH
Confidence            345789999999998874    6899999999999844 467778875

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

Probab=83.08  E-value=1.8  Score=35.74  Aligned_cols=37  Identities=19%  Similarity=0.323  Sum_probs=33.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      +|.+.||++|+|+=....+.|....++|+|+.-..++
T Consensus        27 ltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~   63 (321)
T COG2390          27 LTQSEIAERLGISRATVSRLLAKAREEGIVKISINSP   63 (321)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCC
Confidence            6999999999999999999999999999998765544

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

Probab=83.05  E-value=4.2  Score=28.76  Aligned_cols=48  Identities=21%  Similarity=0.183  Sum_probs=42.6

Q ss_pred             HHHHHHHhhCCCCe-eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           46 ATYDKLLSEAPKFK-LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k-~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +.|.+|..-.+... -||...||+.|..+-==||.+|+.|.+.|.|.-.
T Consensus         4 ~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~   52 (115)
T PF12793_consen    4 EQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQ   52 (115)
T ss_pred             HHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeee
Confidence            46888888888654 4999999999999999999999999999999876

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=82.73  E-value=2.4  Score=33.01  Aligned_cols=36  Identities=19%  Similarity=0.314  Sum_probs=33.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      +|.+.||+++++.-|-+.++|..|++.|++..-..+
T Consensus        20 l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~   55 (246)
T COG1414          20 LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED   55 (246)
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence            899999999999999999999999999999875543

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

Probab=82.59  E-value=1.2  Score=31.13  Aligned_cols=40  Identities=18%  Similarity=0.198  Sum_probs=31.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-cccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI-SAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr  104 (108)
                      +|...+|.+++|+.+    .||..++.|||.+. ...++.+.|+.
T Consensus         1 m~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~   41 (126)
T cd04783           1 LTIGELAKAAGVNVE----TIRYYQRRGLLPEPPRPEGGYRRYPE   41 (126)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence            367889999998876    57999999999954 43556778874

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

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=82.50  E-value=1.4  Score=32.07  Aligned_cols=46  Identities=15%  Similarity=0.175  Sum_probs=35.9

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTRA  105 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr~  105 (108)
                      |....+|...||.+++|+.+    .||.-++.|||.+... .++.++|+..
T Consensus         3 ~~~~~~~IgevAk~~Gvs~~----TLRyYE~~GLl~p~~r~~~gyR~Y~~~   49 (144)
T PRK13752          3 NNLENLTIGVFAKAAGVNVE----TIRFYQRKGLLPEPDKPYGSIRRYGEA   49 (144)
T ss_pred             CCCCcccHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeecCHH
Confidence            34456899999999988765    6999999999987543 4567889753

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=82.45  E-value=1.5  Score=31.91  Aligned_cols=40  Identities=28%  Similarity=0.328  Sum_probs=32.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|...||+.++|+.+    .||.-++.|||.+....++...|+.
T Consensus         2 ~~IgevA~~~Gvs~~----tLRyYE~~GLl~~~r~~~g~R~Y~~   41 (142)
T TIGR01950         2 LTVGELAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR   41 (142)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECH
Confidence            478899999988765    5899999999998655566788875

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

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

Probab=82.43  E-value=1.1  Score=30.26  Aligned_cols=40  Identities=13%  Similarity=0.065  Sum_probs=31.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-ccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS-AHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr  104 (108)
                      .|...||+.++|+.+    .||..++.|+|.|.. ..+....|+.
T Consensus         1 ~~i~eva~~~gvs~~----tlR~ye~~Gll~p~~~~~~gyR~Y~~   41 (97)
T cd04782           1 FTTGEFAKLCGISKQ----TLFHYDKIGLFKPEIVKENGYRYYTL   41 (97)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCccCCH
Confidence            367889999988765    589999999999974 3455677864

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

>PRK06474 hypothetical protein; Provisional

Probab=82.33  E-value=4.2  Score=30.44  Aligned_cols=44  Identities=18%  Similarity=0.360  Sum_probs=36.6

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEeccc----ceeEEEec
Q 033931           61 ITPSILSDRL-RINGSLARRAIKDLMARGSIRMISAH----ASQQIYTR  104 (108)
Q Consensus        61 ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k~----~~q~IYtr  104 (108)
                      .|+..|++.+ +|..+..-+-|+.|++-|+|..+...    .+..+|.-
T Consensus        27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~   75 (178)
T PRK06474         27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAI   75 (178)
T ss_pred             CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEe
Confidence            8999999999 78888899999999999999998642    34456654

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=82.31  E-value=2.8  Score=32.85  Aligned_cols=36  Identities=25%  Similarity=0.014  Sum_probs=32.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|.+.||+++++.-|-+-++|..|++.|++..-.
T Consensus        39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~   74 (271)
T PRK10163         39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS   74 (271)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            348999999999999999999999999999997643

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

Probab=82.19  E-value=1.3  Score=31.37  Aligned_cols=39  Identities=10%  Similarity=0.180  Sum_probs=31.6

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-ceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAH-ASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr  104 (108)
                      |...+|..++|+.+    .||.-++.|||.+.... ++.+.|+.
T Consensus         2 ~IgE~A~~~gvs~~----TLRyYE~~GLl~p~r~~~~gyR~Y~~   41 (133)
T cd04787           2 KVKELANAAGVTPD----TVRFYTRIGLLRPTRDPVNGYRLYSE   41 (133)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeeeCCH
Confidence            67889999988765    68999999999997543 66778874

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

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=82.14  E-value=2.2  Score=30.27  Aligned_cols=32  Identities=13%  Similarity=0.235  Sum_probs=30.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+-++++-...=++|++|+++|+|..
T Consensus       144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~  175 (193)
T TIGR03697       144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI  175 (193)
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999999976

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.

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

Probab=82.02  E-value=1.4  Score=29.92  Aligned_cols=39  Identities=15%  Similarity=0.231  Sum_probs=31.1

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-cccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMI-SAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr  104 (108)
                      |++.||+.++|+.+    .||..++.|+|.++ ...+....|+.
T Consensus         2 ~i~e~A~~~gvs~~----tlR~Ye~~Gll~~~~r~~~g~R~Y~~   41 (99)
T cd04772           2 RTVDLARAIGLSPQ----TVRNYESLGLIPPAERTANGYRIYTD   41 (99)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHcCCCCCCCcCCCCCeecCH
Confidence            78899999998876    47899999999986 33456778874

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

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

Probab=82.00  E-value=2  Score=32.85  Aligned_cols=33  Identities=18%  Similarity=0.236  Sum_probs=31.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      =+|.+.||++++++-|-+-++|..|++.|++..
T Consensus        24 ~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        24 RLTLTDVAEATGLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            478999999999999999999999999999975

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.

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=81.93  E-value=2.2  Score=31.66  Aligned_cols=33  Identities=12%  Similarity=0.178  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|...||+-++++-.-.-++|++|+++|+|..-
T Consensus       185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            788999999999999888899999999999864

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

Probab=81.77  E-value=1.6  Score=31.50  Aligned_cols=40  Identities=20%  Similarity=0.234  Sum_probs=33.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|...||++++|+.+    .||.-++.|||.+.-..++...|+.
T Consensus         2 ~~I~EvA~~~Gvs~~----tLRyYE~~GLl~p~r~~~g~R~Y~~   41 (139)
T cd01110           2 LSVGEVAKRSGVAVS----ALHFYEQKGLIASWRNAGNQRRYPR   41 (139)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeEECH
Confidence            478899999988875    5899999999998755667788975

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

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

Probab=81.54  E-value=1.3  Score=30.09  Aligned_cols=38  Identities=8%  Similarity=0.139  Sum_probs=29.8

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |...||++++|+.+    .||.-++.|||.|.. .++...|+.
T Consensus         2 ~Ige~a~~~gvs~~----tlRyYe~~GLl~p~~-~~g~r~Y~~   39 (107)
T cd04777           2 KIGKFAKKNNITID----TVRHYIDLGLLIPEK-KGGQYFFDE   39 (107)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCcCCcc-CCCccccCH
Confidence            67889999988765    799999999999954 345567764

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

>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.40  E-value=3.6  Score=35.67  Aligned_cols=51  Identities=22%  Similarity=0.220  Sum_probs=47.2

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -|++.+-.++-+|++....|.+.+|.+++|...||+--|-..|..|+|..=
T Consensus       364 ~~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD  414 (432)
T KOG2760|consen  364 SDEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRD  414 (432)
T ss_pred             chHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeec
Confidence            478888899999999999999999999999999999999999999999763

>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=81.06  E-value=1.9  Score=29.29  Aligned_cols=36  Identities=14%  Similarity=0.167  Sum_probs=32.2

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -.-|...+|++.++++-.-.|..+.+|++-|||.-+
T Consensus        21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~   56 (78)
T PF03444_consen   21 GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ   56 (78)
T ss_pred             CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence            366888899999999999999999999999999654

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

>PRK05638 threonine synthase; Validated

Probab=80.99  E-value=2.8  Score=35.17  Aligned_cols=65  Identities=15%  Similarity=0.067  Sum_probs=44.1

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhc--ccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           33 QKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLR--INGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        33 ~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlk--I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .+|.+...-+ .-..+.-|..+ |    .+.+.|++.++  ++-+...+.|+.|++.|||.......+...|.
T Consensus       363 ~~~~~~~~~~-r~~IL~~L~~~-~----~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~  429 (442)
T PRK05638        363 GREKFTIGGT-KLEILKILSER-E----MYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYK  429 (442)
T ss_pred             chhhhcccch-HHHHHHHHhhC-C----ccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEE
Confidence            3555554322 34444444322 3    68999999998  88889999999999999998653344433453

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=80.95  E-value=1.5  Score=30.86  Aligned_cols=40  Identities=13%  Similarity=0.152  Sum_probs=31.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEecc
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTRA  105 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr~  105 (108)
                      |...||++++|+.    ..||.-++.|||.+... .++...|+..
T Consensus         2 ~I~e~a~~~gvs~----~tlRyYe~~GLl~p~~r~~~gyR~Y~~~   42 (127)
T TIGR02044         2 NIGQVAKLTGLSS----KMIRYYEEKGLIPPPLRSEGGYRTYTQQ   42 (127)
T ss_pred             CHHHHHHHHCcCH----HHHHHHHHCCCCCCCCcCCCCCeecCHH
Confidence            6778999988765    46899999999998743 5677888753

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

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=80.82  E-value=3.3  Score=30.99  Aligned_cols=45  Identities=20%  Similarity=0.296  Sum_probs=36.9

Q ss_pred             HHhhCCCCeee-chhhhhhhh--cccHHHHHHHHHHHHHcCCeeEecc
Q 033931           51 LLSEAPKFKLI-TPSILSDRL--RINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        51 l~KEVpk~k~I-Tps~vserl--kI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.=+|-+..- +|..||.++  +|+..=++.+|.-|++-|+|+.-..
T Consensus        29 ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~   76 (171)
T PF14394_consen   29 IRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD   76 (171)
T ss_pred             HHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence            33334444555 999999999  9999999999999999999998644

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

Probab=80.37  E-value=1.5  Score=27.29  Aligned_cols=39  Identities=8%  Similarity=0.154  Sum_probs=28.7

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHc-CCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMAR-GSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~~~q~IYtr  104 (108)
                      |.+.+|+.++|+-+.    ||..+.+ |++.+.....+...|+.
T Consensus         2 ~i~e~A~~~gVs~~t----lr~ye~~~gl~~~~r~~~g~R~yt~   41 (68)
T cd04763           2 TIGEVALLTGIKPHV----LRAWEREFGLLKPQRSDGGHRLFND   41 (68)
T ss_pred             CHHHHHHHHCcCHHH----HHHHHHhcCCCCCCcCCCCCcccCH
Confidence            788999999988765    5677876 98876543445567874

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

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

Probab=80.32  E-value=1.8  Score=29.49  Aligned_cols=40  Identities=5%  Similarity=0.169  Sum_probs=31.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHc-CCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMAR-GSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~~~q~IYtr  104 (108)
                      .|+..+|+.++|+-+.    ||..+.+ |++.+....++...|+.
T Consensus         1 yti~EvA~~~gVs~~t----LR~ye~~~gli~p~r~~~g~R~Yt~   41 (99)
T cd04765           1 FSIGEVAEILGLPPHV----LRYWETEFPQLKPVKRAGGRRYYRP   41 (99)
T ss_pred             CCHHHHHHHHCcCHHH----HHHHHHHcCCCCCcCCCCCCeeeCH
Confidence            3788999999998775    6788887 88877655667788874

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

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=80.20  E-value=1.6  Score=33.97  Aligned_cols=44  Identities=14%  Similarity=0.080  Sum_probs=37.8

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcC
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARG   88 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kG   88 (108)
                      ++=.++|+.-+.....||+..||+.|+|+..-.|+=|++|+..|
T Consensus         6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~   49 (252)
T PRK10681          6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV   49 (252)
T ss_pred             HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence            34456777777788899999999999999999999999999654

>COG3177 Fic family protein [Function unknown]

Probab=80.03  E-value=2.9  Score=34.32  Aligned_cols=56  Identities=16%  Similarity=0.245  Sum_probs=46.1

Q ss_pred             HHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           47 TYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        47 t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      .++++...+-.. .++|...++--++|.-+-|++-|.+|.+.|++..+..+.+...|
T Consensus       290 ~~~~l~~~~~~~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~  346 (348)
T COG3177         290 RIGQLNVLLFGQEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRSKLY  346 (348)
T ss_pred             hHHHHHHHHhccCCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCceec
Confidence            334344455544 89999999999999999999999999999999999877776665

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	108
3iz6_V	108	Localization Of The Small Subunit Ribosomal Protein		4e-28
3zey_U	113	High-resolution Cryo-electron Microscopy Structure		7e-15
3izb_V	108	Localization Of The Small Subunit Ribosomal Protein		4e-14
2xzm_8	143	Crystal Structure Of The Eukaryotic 40s Ribosomal S		9e-04

>pdb|3IZ6|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 108

Iteration: 1
 Score =  119 bits (298), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 65/71 (91%)
Query: 37  VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
           VNN VLFD+ATYDKLLSE PK+K ITPS+LS+RLRINGSLAR+AIKDL +RG+IR++S H
Sbjct: 37  VNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVH 96
Query: 97  ASQQIYTRATN 107
           +SQ IYTRATN
Sbjct: 97  SSQLIYTRATN 107

>pdb|3ZEY|U Chain U, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 113

Iteration: 1
 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 52/69 (75%)
Query: 37  VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH 96
           + N V+FD+ T DKL+ E PK+K+ITPSI+SDRL+I+ +LA + ++ L  +G IR++S  
Sbjct: 42  LQNAVMFDKETMDKLMKEVPKYKVITPSIISDRLKISVALAGKGLQHLCRQGLIRLVSCS 101
Query: 97  ASQQIYTRA 105
           +  ++YTRA
Sbjct: 102 SKFRVYTRA 110

>pdb|3IZB|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 108

Iteration: 1
 Score = 73.2 bits (178), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 48/71 (67%)
Query: 38  NNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA 97
            + V+ DQ  YD++L E P ++ ++ S+L DRL+I GSLAR A++ L   G I+ IS H+
Sbjct: 37  QHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHS 96
Query: 98  SQQIYTRATNT 108
            Q IYTRAT +
Sbjct: 97  KQAIYTRATAS 107

>pdb|2XZM|8 Chain 8, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 143

Iteration: 1
 Score = 38.5 bits (88), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 37  VNNMVLFDQATYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA 95
           VN+ V  ++   + +++   K  K++T S + ++L++NGSLAR+ ++ +  R  +  ++ 
Sbjct: 39  VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK 98
Query: 96  HASQQIYT 103
           + +Q +Y+
Sbjct: 99  NGNQWVYS 106
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	108
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	1e-39
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	3e-37
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	1e-32

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 108

 Score =  127 bits (319), Expect = 1e-39
 Identities = 90/107 (84%), Positives = 101/107 (94%)

Query: 1   MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60
           MAPKKDKAPPP+SKPAKSGGGKQKKKKWSKGKQKEKVNN VLFD+ATYDKLLSE PK+K 
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSEVPKYKQ 60

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATN 107
           ITPS+LS+RLRINGSLAR+AIKDL +RG+IR++S H+SQ IYTRATN
Sbjct: 61  ITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVHSSQLIYTRATN 107

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z Length = 108

 Score =  120 bits (302), Expect = 3e-37
 Identities = 47/106 (44%), Positives = 66/106 (62%)

Query: 3   PKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLIT 62
           P K +    A   A   GGK+ KKKWSK   K++  + V+ DQ  YD++L E P ++ ++
Sbjct: 2   PPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVS 61

Query: 63  PSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
            S+L DRL+I GSLAR A++ L   G I+ IS H+ Q IYTRAT +
Sbjct: 62  VSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATAS 107

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8 Length = 143

 Score =  110 bits (275), Expect = 1e-32
 Identities = 28/108 (25%), Positives = 58/108 (53%), Gaps = 1/108 (0%)

Query: 2   APKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKF-KL 60
            P   +     +    +   K  KKKW+KGK K+KVN+ V  ++   + +++   K  K+
Sbjct: 4   QPAAGQKKTKEAIAKAAQAKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGKV 63

Query: 61  ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRATNT 108
           +T S + ++L++NGSLAR+ ++ +  R  +  ++ + +Q +Y+     
Sbjct: 64  LTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAKNGNQWVYSVIGGV 111

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	108
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	100.0
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	100.0
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	100.0
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	97.41
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	97.28
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	97.2
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	97.16
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	96.87
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.78
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.67
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.63
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.6
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.57
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.48
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.44
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.34
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.24
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.22
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	96.21
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	96.18
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.17
3by6_A	126	Predicted transcriptional regulator; structural ge	96.16
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.15
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.05
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	96.02
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	96.02
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	96.01
1sfx_A	109	Conserved hypothetical protein AF2008; structural	95.98
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	95.93
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.92
2gxg_A	146	146AA long hypothetical transcriptional regulator;	95.91
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.89
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	95.88
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.86
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.85
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.85
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	95.83
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	95.82
3jth_A	98	Transcription activator HLYU; transcription factor	95.78
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	95.78
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.76
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.74
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.73
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.71
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	95.7
3r0a_A	123	Putative transcriptional regulator; structural gen	95.7
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	95.67
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	95.67
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.67
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.65
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.65
2nnn_A	140	Probable transcriptional regulator; structural gen	95.64
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	95.64
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.63
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	95.62
3eet_A	272	Putative GNTR-family transcriptional regulator; st	95.62
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.61
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.57
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.56
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.55
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	95.53
2h09_A	155	Transcriptional regulator MNTR; transcription regu	95.52
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.5
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.48
2kko_A	108	Possible transcriptional regulatory protein (possi	95.47
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.45
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	95.44
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.42
3s2w_A	159	Transcriptional regulator, MARR family; structural	95.41
2eth_A	154	Transcriptional regulator, putative, MAR family; M	95.4
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	95.4
3c7j_A	237	Transcriptional regulator, GNTR family; structural	95.38
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	95.35
2vn2_A	128	DNAD, chromosome replication initiation protein; D	95.34
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.32
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.3
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	95.27
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.25
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.24
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.23
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.21
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	95.19
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.19
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.17
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	95.11
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.1
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.07
3bja_A	139	Transcriptional regulator, MARR family, putative;	95.02
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	95.02
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	94.96
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	94.95
1y0u_A	96	Arsenical resistance operon repressor, putative; s	94.92
1ylf_A	149	RRF2 family protein; structural genomics, transcri	94.9
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.88
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	94.88
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	94.87
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	94.86
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.84
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.83
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	94.81
3f3x_A	144	Transcriptional regulator, MARR family, putative;	94.77
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	94.77
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	94.73
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.72
2w25_A	150	Probable transcriptional regulatory protein; trans	94.7
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	94.65
3nqo_A	189	MARR-family transcriptional regulator; structural	94.65
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	94.57
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.55
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	94.54
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.5
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.5
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.49
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	94.48
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	94.45
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.37
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.35
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	94.26
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	94.24
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	94.21
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	94.18
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	94.16
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	94.14
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.02
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	93.98
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.97
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	93.96
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	93.95
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.94
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.9
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	93.84
1yyv_A	131	Putative transcriptional regulator; reductive meth	93.79
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	93.68
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.67
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	93.58
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	93.56
1xd7_A	145	YWNA; structural genomics, protein structure initi	93.47
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	93.42
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.41
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	93.35
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	93.32
2fxa_A	207	Protease production regulatory protein HPR; protea	93.31
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	93.19
3k69_A	162	Putative transcription regulator; putative transcr	92.92
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	92.9
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	92.66
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	92.63
3eqx_A	373	FIC domain containing transcriptional regulator; F	92.58
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	92.5
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	92.47
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	92.17
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	92.1
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	92.04
2ra5_A	247	Putative transcriptional regulator; beta structure	91.3
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	91.23
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	90.96
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	90.77
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	90.36
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	90.25
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	90.18
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	90.09
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	89.94
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	89.87
3hh0_A	146	Transcriptional regulator, MERR family; protein st	89.32
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	89.22
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	89.15
1mkm_A	249	ICLR transcriptional regulator; structural genomic	88.98
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	88.95
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	88.73
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	88.65
2ve8_A	73	FTSK, DNA translocase FTSK; nucleotide-binding, ch	88.56
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	88.4
1bia_A	321	BIRA bifunctional protein; transcription regulatio	88.37
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	88.29
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	88.06
2w57_A	150	Ferric uptake regulation protein; gene regulation,	88.05
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	87.94
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	87.83
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	87.81
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	87.58
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	87.48
3gpv_A	148	Transcriptional regulator, MERR family; protein st	87.47
2obp_A	96	Putative DNA-binding protein; structural genomics,	87.45
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	87.19
1hsj_A	487	Fusion protein consisting of staphylococcus access	86.96
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	86.77
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	86.7
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	86.67
3cta_A	230	Riboflavin kinase; structural genomics, transferas	86.62
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	86.54
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	86.44
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	86.27
2o0m_A	345	Transcriptional regulator, SORC family; structural	86.1
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	86.06
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	86.0
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	85.82
1xma_A	145	Predicted transcriptional regulator; southea colla	85.68
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	85.62
2g7u_A	257	Transcriptional regulator; ICLR family, structural	85.23
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	84.87
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	84.78
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	84.71
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	84.65
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	84.54
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	84.44
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	84.41
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	84.22
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	84.21
3b02_A	195	Transcriptional regulator, CRP family; structural	83.99
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	83.98
1ft9_A	222	Carbon monoxide oxidation system transcription reg	83.92
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	83.66
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	83.35
4esf_A	117	PADR-like transcriptional regulator; PADR family,	83.21
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	83.18
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	83.14
1z05_A	429	Transcriptional regulator, ROK family; structural	83.02
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	82.98
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	82.96
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	82.92
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	82.73
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	82.66
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	82.65
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	82.28
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	82.13
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	82.08
1bja_A	95	Transcription regulatory protein MOTA; activation	81.88
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	81.8
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	81.63
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	81.45
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	80.94
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	80.83
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	80.59
2jml_A	81	DNA binding domain/transcriptional regulator; anti	80.09

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=100.00  E-value=4.8e-55  Score=308.80  Aligned_cols=107  Identities=43%  Similarity=0.737  Sum_probs=69.7

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033931            1 MAPKKDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRA   80 (108)
Q Consensus         1 M~~k~~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~   80 (108)
                      ||||+|+++++++++ +++||+++||||||||++||+||+|+||++|||+|++|||+|+|||||+|||||+|+|||||++
T Consensus         1 M~pK~~~sk~~k~~~-a~~ggk~~KKKWsKgk~kdK~nn~VlfDk~t~dkl~KEVpk~KlITpsvlseRlkI~gSLAR~a   79 (108)
T 3u5c_Z            1 MPPKQQLSKAAKAAA-ALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIA   79 (108)
T ss_dssp             ------------------------------------CCSCSSCTTHHHHHHHHHCSSCSSBSHHHHHHTTCCCTTHHHHH
T ss_pred             CCCccccCHHHHHHH-HhcCCCccccccccccHHHHhhcceeeCHHHHHHHHHHccCCeEEeHHHhhhhhhhhHHHHHHH
Confidence            999988888888875 8899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEecccceeEEEecccCC
Q 033931           81 IKDLMARGSIRMISAHASQQIYTRATNT  108 (108)
Q Consensus        81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~~  108 (108)
                      ||||+++|+|++|++||+|.||||++++
T Consensus        80 LreL~~kGlIk~V~kh~~q~IYTr~~~~  107 (108)
T 3u5c_Z           80 LRHLEKEGIIKPISKHSKQAIYTRATAS  107 (108)
T ss_dssp             HHHHSSSSSCEEEECCSSCCEEECCC--
T ss_pred             HHHHHHCCCEEEEecCCCEEEEecCccC
Confidence            9999999999999999999999999864

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=100.00  E-value=9.3e-55  Score=307.33  Aligned_cols=107  Identities=77%  Similarity=1.121  Sum_probs=94.9

Q ss_pred             CCCC-CCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHH
Q 033931            1 MAPK-KDKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARR   79 (108)
Q Consensus         1 M~~k-~~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~   79 (108)
                      |||| +|++++++++ ++++||+++||||||||++||+||+|+||++|||+|++|||+|+|||||+|||||+|+|||||+
T Consensus         1 m~pk~~~~~k~~~~~-~a~~ggk~~KKKWsKgk~kdk~nn~Vl~Dk~t~dkl~KEVpk~KlITpsvlseRlkI~gSLAR~   79 (108)
T 3iz6_V            1 MAPKKDKAPPPSSKP-AKSGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQ   79 (108)
T ss_dssp             --------CCCCCCC-CTTCCCCCCCCSCCCCCCSHHHHSHHHHSSHHHHHHHHHHHHHSSEEEHHHHHHHHTCCHHHHH
T ss_pred             CCCcccccCHHHHHH-HHhcCCCccccccccccHHHHhcCcEeECHHHHHHHHHHccCCeEEeHHHHHhhhcccHHHHHH
Confidence            9999 5555555555 6899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCeeEecccceeEEEecccCC
Q 033931           80 AIKDLMARGSIRMISAHASQQIYTRATNT  108 (108)
Q Consensus        80 ~Lr~L~~kGlIk~V~k~~~q~IYtr~~~~  108 (108)
                      +||||+++|+|++|++||+|.||||++++
T Consensus        80 aLreL~~kGlIk~V~kh~~q~IYTr~~~~  108 (108)
T 3iz6_V           80 AIKDLESRGAIRVVSVHSSQLIYTRATNA  108 (108)
T ss_dssp             HHHHHHHHHTSCEECCCTTSCCEEESCCC
T ss_pred             HHHHHHHCCCEEEEecCCCEEEEecCcCC
Confidence            99999999999999999999999999874

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=100.00  E-value=2.9e-49  Score=290.20  Aligned_cols=105  Identities=28%  Similarity=0.505  Sum_probs=85.4

Q ss_pred             CCCCC-CCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHH
Q 033931            1 MAPKK-DKAPPPASKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKF-KLITPSILSDRLRINGSLAR   78 (108)
Q Consensus         1 M~~k~-~~~k~~~~~~~~~~g~k~~KKKWsKgk~keK~nn~V~~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr   78 (108)
                      ||||. ++++++++ ++++ +|+++||||||||+|||+||+|+||++|||+|++|||+| +|||||+|||||+||+||||
T Consensus         4 mppk~~~k~k~~~~-~~a~-~gk~kKKKWSKgKvkdK~nn~VlfDk~tydKL~KEVpk~gKlITpsvlseRlkI~gSLAR   81 (143)
T 2xzm_8            4 QPAAGQKKTKEAIA-KAAQ-AKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLAR   81 (143)
T ss_dssp             ---------------------CCCCSSCCCSSCCCCCCCCBSCCCHHHHHHHHTCCTTSCSEECHHHHHHHHCBCHHHHH
T ss_pred             CCCcccccchhHHH-Hhhc-cCccccCCcccchHHHHHhcceeecHHHHHHHHHHhcccceeecHHHHHHHhcchHHHHH
Confidence            89995 55544444 3344 488889999999999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHHcCCeeEecccceeEEEecccC
Q 033931           79 RAIKDLMARGSIRMISAHASQQIYTRATN  107 (108)
Q Consensus        79 ~~Lr~L~~kGlIk~V~k~~~q~IYtr~~~  107 (108)
                      ++||||+++|+|++|++||+|.||||+++
T Consensus        82 kaLreL~~kGlIk~V~kh~~q~IYTra~~  110 (143)
T 2xzm_8           82 QLMRTMADRKLVEKVAKNGNQWVYSVIGG  110 (143)
T ss_dssp             HHHHHHHHTTSEEEEEEETTEEEEEETTC
T ss_pred             HHHHHHHHCCCEEEEecCCCeEEEecCCc
Confidence            99999999999999999999999999874

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

Probab=97.41  E-value=8.8e-05  Score=48.43  Aligned_cols=46  Identities=11%  Similarity=0.068  Sum_probs=41.9

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           48 YDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ++.|+..+.....+|.+.||+.|+|+-+..|+-|.+|+++|+|..+
T Consensus         4 L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            4 LIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4567777777789999999999999999999999999999999998

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=97.28  E-value=0.00021  Score=48.08  Aligned_cols=54  Identities=24%  Similarity=0.308  Sum_probs=43.2

Q ss_pred             HHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEE
Q 033931           48 YDKLLSEA-PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQI  101 (108)
Q Consensus        48 ~dKl~KEV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~I  101 (108)
                      .+.|+.++ |+..+.|...||++|+|+-+..|.+|+.|++.|+|..... +++..|
T Consensus        30 ~~~I~~~l~~g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~gG~~G~~V   85 (102)
T 2b0l_A           30 IEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYI   85 (102)
T ss_dssp             HHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSCEEE
T ss_pred             HHHHHhhhcCCCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeCCCCcEEE
Confidence            56666555 4567779999999999999999999999999999987663 244444

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

Probab=97.20  E-value=0.00014  Score=48.68  Aligned_cols=47  Identities=19%  Similarity=0.154  Sum_probs=41.7

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           48 YDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++.|+..+.....+|++.||+.|+|+-+..|+-|.+|+++|+|..+.
T Consensus         4 L~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            4 LMEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             THHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            45666666667889999999999999999999999999999999984

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

Probab=97.16  E-value=0.00022  Score=46.48  Aligned_cols=45  Identities=11%  Similarity=0.051  Sum_probs=38.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      --+|...||+.|+|+-+-+|+-|..|+++|+|..+-..++...+.
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~ggr~~~~~~   67 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVNAGKGVPGLW   67 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESCSSSSCCEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCCCCcHHHH
Confidence            348999999999999999999999999999999987655544443

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=96.87  E-value=0.0025  Score=43.57  Aligned_cols=51  Identities=20%  Similarity=0.159  Sum_probs=42.3

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|      |+.++-|-..||++|+|+-+..|.+|+.|++.|+|....+
T Consensus        16 ~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g   72 (125)
T 3neu_A           16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecC
Confidence            44566666655      4567778999999999999999999999999999987654

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

Probab=96.78  E-value=0.0037  Score=39.27  Aligned_cols=43  Identities=12%  Similarity=0.090  Sum_probs=35.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-ccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS-AHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYt  103 (108)
                      +|...||+.++|+-+-+++.|+.|++.|+|.... +..+...|.
T Consensus        15 ~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~   58 (81)
T 2htj_A           15 GKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWF   58 (81)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEE
Confidence            8999999999999999999999999999998652 333333443

>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=96.67  E-value=0.0027  Score=42.15  Aligned_cols=44  Identities=14%  Similarity=0.190  Sum_probs=37.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--cccceeEEEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI--SAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYt  103 (108)
                      =||+..|++++++.-+..-++|+.|+++|+|+.+  ..+.+..+|.
T Consensus        36 gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~~~~~~~~rKvy~   81 (91)
T 2dk5_A           36 GIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYM   81 (91)
T ss_dssp             CEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCCcEEEE
Confidence            5999999999999999999999999999999977  3334555654

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=96.63  E-value=0.0032  Score=40.49  Aligned_cols=43  Identities=9%  Similarity=0.055  Sum_probs=35.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      .-+|++.||+++++.-|-.-++|..|+++|+| ....++|...|
T Consensus        29 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv-~~~~d~R~~~v   71 (95)
T 2qvo_A           29 NDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV-ECELEGRTKII   71 (95)
T ss_dssp             CCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE-EEEEETTEEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc-cCCCCCCeEEE
Confidence            35899999999999999999999999999999 44445554443

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=96.60  E-value=0.0038  Score=41.86  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=39.4

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..|+.|...|      |..++-|...||++|+|+-+..|.+|+.|++.|+|..+.
T Consensus        13 ~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           13 QLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            4555555543      345666999999999999999999999999999987654

>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=96.57  E-value=0.0031  Score=41.32  Aligned_cols=57  Identities=9%  Similarity=0.098  Sum_probs=44.8

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHH-HHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGS-LARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~S-lAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .++-++|+.-+.+.-=.|...||+.|+|+.+ -+|+.|..|++.|+|.....++-  +|.
T Consensus        10 ~~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~~~gRP--~w~   67 (79)
T 1xmk_A           10 AEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTPP--IWH   67 (79)
T ss_dssp             HHHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECSSSC--EEE
T ss_pred             hhHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEecCCCCC--CeE
Confidence            4566666655555555899999999999999 99999999999999986644442  665

>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=96.48  E-value=0.0049  Score=42.29  Aligned_cols=49  Identities=14%  Similarity=0.226  Sum_probs=40.4

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..|+.|...|      |+.+|-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus        18 QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~~~   72 (134)
T 4ham_A           18 QIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVK   72 (134)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            3455555443      667888999999999999999999999999999997654

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=96.44  E-value=0.0083  Score=37.65  Aligned_cols=56  Identities=13%  Similarity=0.092  Sum_probs=43.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +--+|+..+-...-+|+..||++++|+-|-..+.|+.|++.|+|..... ++...|.
T Consensus        25 ~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~-~r~~~y~   80 (99)
T 3cuo_A           25 KRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRD-AQRILYS   80 (99)
T ss_dssp             HHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC-SSCEEEE
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec-CCEEEEE
Confidence            3344555554444689999999999999999999999999999988753 4445554

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=96.34  E-value=0.0076  Score=37.93  Aligned_cols=36  Identities=22%  Similarity=0.338  Sum_probs=33.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|+..||+.++|.-+-..++|+.|++.|+|....
T Consensus        35 ~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           35 KPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            348999999999999999999999999999999874

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

Probab=96.24  E-value=0.0071  Score=37.71  Aligned_cols=45  Identities=13%  Similarity=0.229  Sum_probs=38.8

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|++++     +|..+-..+.|+.|++.|+|..+....+...|-
T Consensus        32 ~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y~   81 (83)
T 2fu4_A           32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE   81 (83)
T ss_dssp             SSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEee
Confidence            368999999999     999999999999999999999987655555563

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=96.22  E-value=0.0043  Score=41.18  Aligned_cols=43  Identities=26%  Similarity=0.344  Sum_probs=36.3

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++..+.... +|++.||+++++.-|-..++|+.|+++|+|....
T Consensus        43 iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~   85 (146)
T 3tgn_A           43 ILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSK   85 (146)
T ss_dssp             HHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEecc
Confidence            444555556 9999999999999999999999999999998764

>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=96.21  E-value=0.0097  Score=39.30  Aligned_cols=45  Identities=20%  Similarity=0.112  Sum_probs=37.9

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           48 YDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +-.|+.-+...  ++++.||+.++++-+.++..|+.|+++|+|....
T Consensus        10 i~~IL~~i~~~--~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~   54 (95)
T 1r7j_A           10 IQAILEACKSG--SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG   54 (95)
T ss_dssp             HHHHHHHHTTC--BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHcC--CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC
Confidence            33455555543  9999999999999999999999999999998863

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=96.18  E-value=0.011  Score=44.49  Aligned_cols=44  Identities=9%  Similarity=0.231  Sum_probs=37.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEE
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQI  101 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I  101 (108)
                      |+.++=|-..||++|+|+-...|+||++|+++|+|..  ++++..|
T Consensus        32 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~--~g~Gt~V   75 (248)
T 3f8m_A           32 IGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER--RGRTTVV   75 (248)
T ss_dssp             TTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE--ETTEEEE
T ss_pred             CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--CCCEEEE
Confidence            4456669999999999999999999999999999988  4444433

>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=96.17  E-value=0.012  Score=36.60  Aligned_cols=45  Identities=13%  Similarity=0.198  Sum_probs=37.9

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           60 LITPSILSDRLR----INGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        60 ~ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      -+|+..|+++++    +.-|-...+|+.|+++|+|..... ++..+|...
T Consensus        23 ~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~-gr~~~y~~~   71 (82)
T 1p6r_A           23 SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE-GRVFVYTPN   71 (82)
T ss_dssp             SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEES
T ss_pred             CCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec-CCEEEEEee
Confidence            489999999998    578899999999999999998754 556788654

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=96.16  E-value=0.0093  Score=40.89  Aligned_cols=51  Identities=24%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..+|+.|...|      |+.++-|...||++|+|+-+..|.+|+.|+..|+|....+
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   70 (126)
T 3by6_A           14 LQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPG   70 (126)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence            34555555544      3445569999999999999999999999999999976543

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

Probab=96.15  E-value=0.0032  Score=41.10  Aligned_cols=50  Identities=22%  Similarity=0.222  Sum_probs=39.8

Q ss_pred             HHHHHHHHh---hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLS---EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~K---EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .++..+|+.   |.+-=+-+|...||++|+|.-+-.++.|..|++.|+|..+.
T Consensus         9 ~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g   61 (81)
T 1qbj_A            9 QDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             hHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            344444443   44433479999999999999999999999999999999885

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=96.05  E-value=0.0098  Score=39.44  Aligned_cols=50  Identities=12%  Similarity=0.057  Sum_probs=40.8

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      ++-.+|+.-....- +|...||++|+|+-+-.|+-|..|++.|+|.....+
T Consensus        17 ~~~~~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~~   66 (82)
T 1oyi_A           17 EIVCEAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDI   66 (82)
T ss_dssp             HHHHHHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSSS
T ss_pred             HHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC
Confidence            55666654444333 999999999999999999999999999999887544

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=96.02  E-value=0.0053  Score=42.07  Aligned_cols=51  Identities=10%  Similarity=0.094  Sum_probs=40.7

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..+|+.|...|      |+.++-|-..||++|+|+-+-.|.||+.|++.|+|....+
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~~   70 (126)
T 3ic7_A           14 LQIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNKRG   70 (126)
T ss_dssp             THHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEETT
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEcC
Confidence            45677776665      3456668899999999999999999999999999977643

>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=96.02  E-value=0.016  Score=43.01  Aligned_cols=50  Identities=14%  Similarity=0.129  Sum_probs=41.9

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|      |+.+| +-..||++|+|+-+--|.||+.|+..|+|...-+
T Consensus        31 ~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~   86 (239)
T 2hs5_A           31 TRVAGILRDAIIDGTFRPGARL-SEPDICAALDVSRNTVREAFQILIEDRLVAHELN   86 (239)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHcCCCCCcCEe-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            45666666554      66788 9999999999999999999999999999987643

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=96.01  E-value=0.0035  Score=40.90  Aligned_cols=51  Identities=10%  Similarity=0.053  Sum_probs=40.5

Q ss_pred             CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           44 DQATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        44 dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+.+++.|...|-.      ..+-|...||++|+|+-+..|++|+.|++.|+|..+.
T Consensus        13 ~~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           13 YADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             HHHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            34566666665544      3444999999999999999999999999999997653

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

Probab=95.98  E-value=0.031  Score=34.89  Aligned_cols=34  Identities=24%  Similarity=0.366  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+.++++-+-..+.|+.|+++|+|....
T Consensus        35 ~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~   68 (109)
T 1sfx_A           35 MRVSEIARELDLSARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            8999999999999999999999999999998874

>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=95.93  E-value=0.016  Score=42.21  Aligned_cols=51  Identities=14%  Similarity=0.196  Sum_probs=41.3

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|      |+.++=|-..||++|+|+-+-.|.||+.|+..|+|....+
T Consensus        10 ~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~g   66 (239)
T 1hw1_A           10 GFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG   66 (239)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecC
Confidence            34555555554      5566669999999999999999999999999999987543

>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=95.92  E-value=0.022  Score=37.91  Aligned_cols=44  Identities=11%  Similarity=0.111  Sum_probs=38.8

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .++..+-...-+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        40 ~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   83 (140)
T 3hsr_A           40 IVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRT   83 (140)
T ss_dssp             HHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEec
Confidence            34555656677999999999999999999999999999999987

>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=95.91  E-value=0.014  Score=38.46  Aligned_cols=37  Identities=16%  Similarity=0.125  Sum_probs=34.1

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..-+|++.||+++++.-|-...+|+.|+++|+|....
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   84 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVR   84 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeec
Confidence            4558999999999999999999999999999999873

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

Probab=95.89  E-value=0.022  Score=36.37  Aligned_cols=44  Identities=23%  Similarity=0.222  Sum_probs=39.7

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++.+-+.-.-+|+..||++++|.-+-.++.|..|+++|+|..+.
T Consensus        22 ~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           22 FLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            46677766679999999999999999999999999999999885

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=95.88  E-value=0.0081  Score=38.04  Aligned_cols=46  Identities=11%  Similarity=0.187  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      |+++||=|..   +-=+|-.+-++.+|+|.=..--.+|+.|+++|||++
T Consensus        12 e~~lL~yIr~---sGGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           12 ERELLDYIVN---NGGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHHH---TTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHH---cCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCeec
Confidence            4444444432   236899999999999999999999999999999986

>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=95.86  E-value=0.016  Score=38.09  Aligned_cols=34  Identities=15%  Similarity=0.181  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        47 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   80 (139)
T 3eco_A           47 GLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRY   80 (139)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            5899999999999999999999999999999987

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=95.85  E-value=0.016  Score=37.88  Aligned_cols=45  Identities=13%  Similarity=0.132  Sum_probs=37.1

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           60 LITPSILSDRLR----INGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        60 ~ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      -+|++.|+++++    ++-|-..++|+.|+++|+|..... .+..+|..-
T Consensus        24 ~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~-~rr~~~~~l   72 (123)
T 1okr_A           24 YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD-NKIFQYYSL   72 (123)
T ss_dssp             SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE-TTEEEEEES
T ss_pred             CcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec-CCeEEEEEe
Confidence            489999999999    779999999999999999998754 444555443

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

Probab=95.85  E-value=0.016  Score=37.90  Aligned_cols=35  Identities=26%  Similarity=0.280  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||++++++-+-..++|+.|+++|+|....
T Consensus        45 ~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~   79 (142)
T 3bdd_A           45 PLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKR   79 (142)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            38999999999999999999999999999998873

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=95.83  E-value=0.016  Score=37.37  Aligned_cols=42  Identities=19%  Similarity=0.298  Sum_probs=36.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|++.||++++++-+-..+.|+.|++.|+|..... ++...|.
T Consensus        35 ~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~-gr~~~y~   76 (114)
T 2oqg_A           35 QSASSLATRLPVSRQAIAKHLNALQACGLVESVKV-GREIRYR   76 (114)
T ss_dssp             BCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec-CCEEEEE
Confidence            79999999999999999999999999999987654 3444554

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=95.82  E-value=0.013  Score=40.42  Aligned_cols=50  Identities=16%  Similarity=0.116  Sum_probs=39.9

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           46 ATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        46 ~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .+|+.|...|      |+.++-|-..||++|+|+-+..|.+|+.|+..|+|....+
T Consensus         8 ~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g   63 (129)
T 2ek5_A            8 QIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRG   63 (129)
T ss_dssp             HHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETT
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            4455555443      4556669999999999999999999999999999977543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=95.78  E-value=0.025  Score=36.05  Aligned_cols=57  Identities=16%  Similarity=0.145  Sum_probs=44.5

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++--+|+..+-. .-+|.+.|++.++|.-|...+-|+.|++.|+|..... .+...|.-
T Consensus        23 ~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~-g~~~~y~l   79 (98)
T 3jth_A           23 ERRLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKE-AQTVYYTL   79 (98)
T ss_dssp             HHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC-TTCCEEEE
T ss_pred             HHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEE
Confidence            344456666655 5689999999999999999999999999999987643 44555653

>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=95.78  E-value=0.019  Score=37.62  Aligned_cols=43  Identities=19%  Similarity=0.287  Sum_probs=36.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEEE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQIY  102 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IY  102 (108)
                      -+|++.||++++++-+-.-++|+.|+++|+|....  .++|...|
T Consensus        48 ~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~   92 (138)
T 1jgs_A           48 CITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLV   92 (138)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEE
T ss_pred             CCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccCceeEe
Confidence            37999999999999999999999999999999873  34444433

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

Probab=95.76  E-value=0.024  Score=35.40  Aligned_cols=45  Identities=13%  Similarity=0.141  Sum_probs=36.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEEEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IYt  103 (108)
                      .-+|++.||+.++++-|-.-+.|+.|++.|+|....  ..++...|.
T Consensus        29 ~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~   75 (100)
T 1ub9_A           29 RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVE   75 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEE
Confidence            358999999999999999999999999999998643  234444443

>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=95.74  E-value=0.014  Score=38.11  Aligned_cols=33  Identities=18%  Similarity=0.268  Sum_probs=31.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|...||+.|+|+-+-.+.+|+.|++.|+|...
T Consensus        34 ~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           34 MTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             BCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            699999999999999999999999999999876

>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=95.73  E-value=0.021  Score=36.31  Aligned_cols=44  Identities=14%  Similarity=0.113  Sum_probs=36.4

Q ss_pred             Ceeechhhh----hhhhcccHHHHHHHHHHHHHcCCeeEecccceeEE
Q 033931           58 FKLITPSIL----SDRLRINGSLARRAIKDLMARGSIRMISAHASQQI  101 (108)
Q Consensus        58 ~k~ITps~v----serlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I  101 (108)
                      ..-+|++.|    |++++++-+-.-++|+.|+++|+|......+...+
T Consensus        20 ~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~   67 (99)
T 1tbx_A           20 NEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRL   67 (99)
T ss_dssp             CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEE
T ss_pred             cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEE
Confidence            345799999    99999999999999999999999988754444333

>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=95.71  E-value=0.019  Score=37.65  Aligned_cols=35  Identities=11%  Similarity=0.064  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~   84 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKV   84 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeC
Confidence            48999999999999999999999999999998873

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=95.70  E-value=0.017  Score=38.29  Aligned_cols=36  Identities=11%  Similarity=0.060  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~   85 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREI   85 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccC
Confidence            458999999999999999999999999999998873

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

Probab=95.70  E-value=0.024  Score=38.31  Aligned_cols=48  Identities=25%  Similarity=0.426  Sum_probs=37.7

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +-..|.-|... +. ..+|++.||+++++.-|-..+.|+.|+++|+|...
T Consensus        28 e~~il~~L~~~-~~-~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           28 DLNVMKSFLNE-PD-RWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHHHS-TT-CCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHC-CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            33445555432 22 13899999999999999999999999999999875

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=95.67  E-value=0.024  Score=42.43  Aligned_cols=39  Identities=18%  Similarity=0.363  Sum_probs=34.7

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.++=|-..||++|+|+-+..|+||+.|+++|+|....
T Consensus        30 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   68 (243)
T 2wv0_A           30 PDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLK   68 (243)
T ss_dssp             TTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEeC
Confidence            456676999999999999999999999999999997654

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=95.67  E-value=0.016  Score=42.60  Aligned_cols=48  Identities=27%  Similarity=0.265  Sum_probs=40.5

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +..|+.|...|      |+.++-+-..||++|+|+-+-.|.||+.|+..|+|..
T Consensus         7 ~~v~~~L~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~L~~~GlV~~   60 (239)
T 2di3_A            7 ESVMDWVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTIST   60 (239)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEe
Confidence            45566666555      5667778889999999999999999999999999986

>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=95.67  E-value=0.012  Score=37.45  Aligned_cols=41  Identities=5%  Similarity=-0.052  Sum_probs=34.4

Q ss_pred             eechhhhhhhhcccHHH-HHHHHHHHHHcCCeeEecccceeE
Q 033931           60 LITPSILSDRLRINGSL-ARRAIKDLMARGSIRMISAHASQQ  100 (108)
Q Consensus        60 ~ITps~vserlkI~~Sl-Ar~~Lr~L~~kGlIk~V~k~~~q~  100 (108)
                      -+|++.||+.+++.-+- .-++|+.|+++|+|..-..+++..
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~   71 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVK   71 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEE
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeE
Confidence            37999999999999999 999999999999999433444443

>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=95.65  E-value=0.018  Score=38.28  Aligned_cols=35  Identities=17%  Similarity=0.225  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+++++.-+-..++|+.|+++|+|....
T Consensus        54 ~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~   88 (152)
T 3bj6_A           54 GATAPQLGAALQMKRQYISRILQEVQRAGLIERRT   88 (152)
T ss_dssp             TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence            48999999999999999999999999999999873

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=95.65  E-value=0.024  Score=36.99  Aligned_cols=36  Identities=17%  Similarity=0.182  Sum_probs=33.2

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        42 ~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~   77 (138)
T 3bpv_A           42 PGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQ   77 (138)
T ss_dssp             TTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeec
Confidence            347999999999999999999999999999999873

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

Probab=95.64  E-value=0.025  Score=36.86  Aligned_cols=34  Identities=15%  Similarity=0.172  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.++++-|-.-++|+.|+++|+|...
T Consensus        52 ~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~   85 (140)
T 2nnn_A           52 PCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRS   85 (140)
T ss_dssp             SBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            5899999999999999999999999999999986

>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=95.64  E-value=0.023  Score=37.48  Aligned_cols=35  Identities=26%  Similarity=0.318  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.+++.-|-.-++|+.|+++|+|....
T Consensus        43 ~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~   77 (144)
T 1lj9_A           43 GIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE   77 (144)
T ss_dssp             TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeec
Confidence            48999999999999999999999999999999873

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

Probab=95.63  E-value=0.015  Score=39.10  Aligned_cols=38  Identities=8%  Similarity=0.097  Sum_probs=33.2

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      -..+|...||++++|+-+..+++|+.|.+.|+|.-+..
T Consensus        24 ~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~g   61 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRG   61 (129)
T ss_dssp             SCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecCC
Confidence            35689999999999999999999999999999977643

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.62  E-value=0.027  Score=36.83  Aligned_cols=34  Identities=15%  Similarity=0.133  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||++++++-+-..++|+.|+++|+|....
T Consensus        51 ~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~   84 (142)
T 2fbi_A           51 MESYQLANQACILRPSMTGVLARLERDGIVRRWK   84 (142)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeec
Confidence            9999999999999999999999999999998873

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=95.62  E-value=0.023  Score=43.45  Aligned_cols=40  Identities=25%  Similarity=0.326  Sum_probs=35.3

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |+.++=|-..||++|+|+-...|+||+.|+++|+|....+
T Consensus        49 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g   88 (272)
T 3eet_A           49 PHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGRSG   88 (272)
T ss_dssp             TTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCC
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            4467779999999999999999999999999999977543

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.61  E-value=0.02  Score=37.62  Aligned_cols=36  Identities=19%  Similarity=0.332  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+.+++.-|-..++|+.|+++|+|....
T Consensus        51 ~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~   86 (146)
T 2fbh_A           51 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLA   86 (146)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecC
Confidence            348999999999999999999999999999999873

>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=95.57  E-value=0.027  Score=36.92  Aligned_cols=33  Identities=24%  Similarity=0.329  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||++++++-|-.-++|+.|+++|+|...
T Consensus        42 ~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           42 LTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            899999999999999999999999999999987

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=95.56  E-value=0.02  Score=38.36  Aligned_cols=35  Identities=20%  Similarity=0.229  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||++++|.-+-..++|+.|+++|+|....
T Consensus        61 ~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   95 (153)
T 2pex_A           61 ERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTR   95 (153)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecC
Confidence            48999999999999999999999999999999873

>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=95.55  E-value=0.019  Score=38.01  Aligned_cols=35  Identities=26%  Similarity=0.228  Sum_probs=32.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+.++|+-+-..++|+.|+++|+|...
T Consensus        49 ~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~   83 (147)
T 2hr3_A           49 GDVTPSELAAAERMRSSNLAALLRELERGGLIVRH   83 (147)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeC
Confidence            34899999999999999999999999999999887

>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=95.53  E-value=0.02  Score=41.52  Aligned_cols=51  Identities=24%  Similarity=0.289  Sum_probs=42.8

Q ss_pred             eCHHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           43 FDQATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        43 ~dk~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +....|+.|...|      |+.++ +-..||++|+|+-+--|.||+.|+..|+|...-
T Consensus        13 l~~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~   69 (218)
T 3sxy_A           13 VRTKVYNLLKEMILNHELKLGEKL-NVRELSEKLGISFTPVRDALLQLATEGLVKVVP   69 (218)
T ss_dssp             -CHHHHHHHHHHHHTTSSCTTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEET
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCEe-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            4456777777665      55677 999999999999999999999999999998764

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=95.52  E-value=0.011  Score=40.47  Aligned_cols=49  Identities=16%  Similarity=0.178  Sum_probs=37.4

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..++.|+.-+-...-+|++.||+.|+|+-+-.+++|+.|+++|+|....
T Consensus        40 ~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           40 DYVELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEec
Confidence            3444444333222347999999999999999999999999999987653

>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=95.50  E-value=0.017  Score=38.18  Aligned_cols=35  Identities=9%  Similarity=0.072  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        51 ~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~   85 (142)
T 2bv6_A           51 PVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRER   85 (142)
T ss_dssp             EEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeec
Confidence            48999999999999999999999999999998874

>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=95.48  E-value=0.03  Score=36.82  Aligned_cols=35  Identities=26%  Similarity=0.198  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.+++.-+-.-.+|+.|+++|+|....
T Consensus        47 ~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~   81 (145)
T 2a61_A           47 PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP   81 (145)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecC
Confidence            48999999999999999999999999999999873

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.47  E-value=0.024  Score=37.33  Aligned_cols=43  Identities=14%  Similarity=0.172  Sum_probs=36.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -+|+..||++++|+-|...+.|+.|++.|+|..... ++...|.
T Consensus        38 ~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~-gr~~~y~   80 (108)
T 2kko_A           38 ERAVEAIATATGMNLTTASANLQALKSGGLVEARRE-GTRQYYR   80 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEE-TTEEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEE
Confidence            369999999999999999999999999999987653 4445564

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=95.45  E-value=0.028  Score=37.95  Aligned_cols=34  Identities=24%  Similarity=0.158  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||++++|.-+-..++|+.|+++|+|...
T Consensus        66 ~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   99 (162)
T 3cjn_A           66 GLPIGTLGIFAVVEQSTLSRALDGLQADGLVRRE   99 (162)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            4899999999999999999999999999999887

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=95.44  E-value=0.02  Score=40.21  Aligned_cols=47  Identities=13%  Similarity=0.192  Sum_probs=38.8

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----ccceeEEEe
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS----AHASQQIYT  103 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYt  103 (108)
                      +...+||..||+++++..+-.-++|+.|+++|+|..-.    .+.+..+|.
T Consensus        48 g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~yd   98 (135)
T 2v79_A           48 GSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYS   98 (135)
T ss_dssp             TCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEE
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEee
Confidence            34789999999999999999999999999999999842    234445564

>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=95.42  E-value=0.029  Score=37.43  Aligned_cols=36  Identities=14%  Similarity=0.144  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   85 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTH   85 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecC
Confidence            358999999999999999999999999999998873

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=95.41  E-value=0.028  Score=38.08  Aligned_cols=34  Identities=32%  Similarity=0.375  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        64 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   97 (159)
T 3s2w_A           64 GINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQ   97 (159)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3899999999999999999999999999999887

>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=95.40  E-value=0.029  Score=37.80  Aligned_cols=34  Identities=15%  Similarity=0.079  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||++++++-+-.-++|+.|+++|+|...
T Consensus        58 ~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   91 (154)
T 2eth_A           58 PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   91 (154)
T ss_dssp             CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999987

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=95.40  E-value=0.026  Score=37.42  Aligned_cols=35  Identities=14%  Similarity=0.208  Sum_probs=32.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        56 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~   90 (150)
T 2rdp_A           56 DLTVGELSNKMYLACSTTTDLVDRMERNGLVARVR   90 (150)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecC
Confidence            48999999999999999999999999999998863

>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=95.38  E-value=0.023  Score=42.32  Aligned_cols=48  Identities=19%  Similarity=0.216  Sum_probs=39.9

Q ss_pred             HHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           47 TYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        47 t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .|+.|...|      |+.++ +...||++|+|+-+-.|.+|+.|+..|+|....+
T Consensus        31 v~~~L~~~I~~g~l~pG~~L-~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~~   84 (237)
T 3c7j_A           31 IEEKLRNAIIDGSLPSGTAL-RQQELATLFGVSRMPVREALRQLEAQSLLRVETH   84 (237)
T ss_dssp             HHHHHHHHHHTSSSCTTCBC-CHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHhCCCCCcCee-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            566665554      44566 9999999999999999999999999999987643

>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=95.35  E-value=0.012  Score=38.56  Aligned_cols=60  Identities=17%  Similarity=0.228  Sum_probs=55.2

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.++..+...|...|++.-..||..|+++-..+-.-|++|++.|.|.=|.-.+.-.||.-
T Consensus         6 ~~ll~~Fi~yIk~~Kvv~LedLA~~F~l~t~~~i~RI~~Le~~g~ltGViDDRGKfIyIs   65 (72)
T 1wi9_A            6 SGFLTEFINYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             CCHHHHHHHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHHHHHHHcCeeeHHHHHHHhCCChHHHHHHHHHHHHCCCeEEEEeCCCCEEEec
Confidence            456788888888999999999999999999999999999999999999988899999974

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=95.34  E-value=0.013  Score=40.12  Aligned_cols=37  Identities=19%  Similarity=0.405  Sum_probs=33.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..+||+.||+++++..+-..++|+.|+++|+|.....
T Consensus        50 ~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           50 LFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             SSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC-
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeE
Confidence            4489999999999999999999999999999998643

>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=95.32  E-value=0.031  Score=36.90  Aligned_cols=43  Identities=16%  Similarity=0.160  Sum_probs=36.2

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--cceeEEEe
Q 033931           61 ITPSILSDRL-RINGSLARRAIKDLMARGSIRMISA--HASQQIYT  103 (108)
Q Consensus        61 ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      +|++.|++.+ +|.-+..-..|+.|++.|+|.....  +++...|.
T Consensus        36 ~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~   81 (112)
T 1z7u_A           36 KRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYT   81 (112)
T ss_dssp             BCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEE
T ss_pred             CCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEE
Confidence            7999999999 9999999999999999999988742  34554553

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=95.30  E-value=0.025  Score=37.82  Aligned_cols=32  Identities=31%  Similarity=0.404  Sum_probs=31.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|++.||+.+++.-|-.-++|+.|+++|+|..
T Consensus        56 ~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           56 ISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            89999999999999999999999999999987

>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=95.27  E-value=0.024  Score=38.63  Aligned_cols=42  Identities=24%  Similarity=0.368  Sum_probs=35.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQI  101 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~I  101 (108)
                      =+|++.||+++++.-+-.-++|+.|+++|+|....  .++|...
T Consensus        60 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~  103 (162)
T 3k0l_A           60 NLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRIL  103 (162)
T ss_dssp             TCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeE
Confidence            48999999999999999999999999999999873  3444443

>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=95.25  E-value=0.025  Score=39.22  Aligned_cols=34  Identities=18%  Similarity=0.214  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        69 ~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~  102 (166)
T 3deu_A           69 QSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQT  102 (166)
T ss_dssp             EEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeC
Confidence            9999999999999999999999999999999873

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

Probab=95.24  E-value=0.019  Score=38.10  Aligned_cols=33  Identities=15%  Similarity=0.180  Sum_probs=32.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||+.+++.-|-.-++|+.|+++|+|...
T Consensus        46 ~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   78 (145)
T 3g3z_A           46 RTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQ   78 (145)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            999999999999999999999999999999986

>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=95.23  E-value=0.03  Score=38.27  Aligned_cols=46  Identities=13%  Similarity=0.261  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus         7 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            7 DLNIIEELKKD----SRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHC----SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            34455555443    33899999999999999999999999999999864

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

Probab=95.21  E-value=0.029  Score=38.19  Aligned_cols=36  Identities=17%  Similarity=0.110  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~  101 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSI  101 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            358999999999999999999999999999999873

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=95.19  E-value=0.036  Score=37.05  Aligned_cols=58  Identities=5%  Similarity=0.028  Sum_probs=44.8

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcc----cHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRI----NGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI----~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      ..-..++-|..+-    =+|+..|++++..    .-+-...+|+.|+++|+|.... .++..+|+..
T Consensus        36 ~e~~VL~~L~~~~----~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~-~gR~~~Y~p~   97 (99)
T 2k4b_A           36 AELIVMRVIWSLG----EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEK-EGRKFVYRPL   97 (99)
T ss_dssp             SCSHHHHHHHHHS----CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEE-ETTEEEEECC
T ss_pred             HHHHHHHHHHhCC----CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEe-CCCEEEEEEe
Confidence            3445677776533    3799999999985    4678889999999999999875 4667788764

>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=95.19  E-value=0.033  Score=37.08  Aligned_cols=41  Identities=22%  Similarity=0.323  Sum_probs=35.6

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRL-RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|++.|++.+ +|+-+..-+.|+.|++.|+|.....  +...|.
T Consensus        43 ~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~--r~~~y~   84 (111)
T 3df8_A           43 QNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG--QITTYA   84 (111)
T ss_dssp             BCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES--SSEEEE
T ss_pred             CCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec--CcEEEE
Confidence            6699999999 9999999999999999999988654  455554

>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=95.17  E-value=0.024  Score=37.54  Aligned_cols=35  Identities=14%  Similarity=0.225  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        54 ~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~   88 (147)
T 1z91_A           54 TLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKR   88 (147)
T ss_dssp             EEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCB
T ss_pred             CCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEecc
Confidence            68999999999999999999999999999998763

>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=95.11  E-value=0.046  Score=35.81  Aligned_cols=44  Identities=20%  Similarity=0.238  Sum_probs=36.4

Q ss_pred             eechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--cceeEEEe
Q 033931           60 LITPSILSDRL-RINGSLARRAIKDLMARGSIRMISA--HASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      -+|++.|++++ +|+-+..-..|+.|++.|+|.....  .++...|.
T Consensus        27 ~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~   73 (107)
T 2hzt_A           27 KKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYE   73 (107)
T ss_dssp             CBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEE
Confidence            37999999999 9999999999999999999987632  24444554

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=95.10  E-value=0.022  Score=38.32  Aligned_cols=35  Identities=14%  Similarity=0.152  Sum_probs=32.2

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeC
Confidence            44899999999999999999999999999999887

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.07  E-value=0.038  Score=37.89  Aligned_cols=49  Identities=24%  Similarity=0.346  Sum_probs=41.2

Q ss_pred             ceeCHHHHHHHHhhCCCCeeechhhhhhhh--cccHHHHHHHHHHHHHcCCeeEe
Q 033931           41 VLFDQATYDKLLSEAPKFKLITPSILSDRL--RINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        41 V~~dk~t~dKl~KEVpk~k~ITps~vserl--kI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...|..+++-|..+-    -+||+.||+.+  +|+-+-.++-|+.|++.|+|...
T Consensus        12 d~~d~~IL~~L~~~g----~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           12 TIWDDRILEIIHEEG----NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CHHHHHHHHHHHHHS----CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CHHHHHHHHHHHHcC----CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            344666777666554    48999999999  99999999999999999999985

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

Probab=95.02  E-value=0.024  Score=36.95  Aligned_cols=34  Identities=15%  Similarity=0.083  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.+++.-|-.-++|+.|+++|+|...
T Consensus        47 ~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   80 (139)
T 3bja_A           47 KVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTE   80 (139)
T ss_dssp             SEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeec
Confidence            4899999999999999999999999999999886

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=95.02  E-value=0.036  Score=38.50  Aligned_cols=46  Identities=26%  Similarity=0.312  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...++-|..+-+    +|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        12 ~~~il~~L~~~~~----~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           12 DIKILQVLQENGR----LTNVELSERVALSPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHCTT----CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEeee
Confidence            3455555554433    799999999999999999999999999999864

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=94.96  E-value=0.047  Score=35.50  Aligned_cols=42  Identities=17%  Similarity=0.212  Sum_probs=36.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|+..||+.++|+-|...+.|+.|++.|+|..... ++...|.
T Consensus        40 ~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~-gr~~~y~   81 (106)
T 1r1u_A           40 ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQ-GQSMIYS   81 (106)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEE
Confidence            69999999999999999999999999999988653 3445554

>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=94.95  E-value=0.072  Score=39.62  Aligned_cols=48  Identities=15%  Similarity=0.135  Sum_probs=38.0

Q ss_pred             HHHHHHh-hC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           47 TYDKLLS-EA-PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        47 t~dKl~K-EV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +.++|.. +. |+.++=|-..||++|+|+-+..|+||+.|+++|+|....
T Consensus        14 l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~   63 (239)
T 3bwg_A           14 IETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVR   63 (239)
T ss_dssp             HHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeC
Confidence            3344443 33 345666999999999999999999999999999998754

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

Probab=94.92  E-value=0.031  Score=35.68  Aligned_cols=47  Identities=17%  Similarity=0.078  Sum_probs=38.1

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++-.+|+..+ . .-+|+..||++++|+-+..++.|+.|++.|+|....
T Consensus        31 ~~r~~Il~~L-~-~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           31 PVRRKILRML-D-KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHHHH-H-TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHH-c-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            3334555555 2 338999999999999999999999999999998765

>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=94.90  E-value=0.032  Score=38.87  Aligned_cols=45  Identities=13%  Similarity=0.184  Sum_probs=35.8

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ..+|...||++++|+-+..+++|..|.+.|+|.-+.+ +....-+|
T Consensus        29 ~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG-~GGy~L~~   73 (149)
T 1ylf_A           29 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG-PGGAGLLK   73 (149)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----CCEEESS
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC-CCceEeCC
Confidence            5789999999999999999999999999999987765 43333333

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=94.88  E-value=0.029  Score=37.37  Aligned_cols=36  Identities=14%  Similarity=0.165  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||++++|+-|-..++|+.|+++|+|....
T Consensus        30 ~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            458999999999999999999999999999998754

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=94.88  E-value=0.046  Score=37.60  Aligned_cols=34  Identities=21%  Similarity=0.235  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        59 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   92 (168)
T 2nyx_A           59 PINLATLATLLGVQPSATGRMVDRLVGAELIDRL   92 (168)
T ss_dssp             SEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            3899999999999999999999999999999886

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

Probab=94.87  E-value=0.057  Score=33.25  Aligned_cols=45  Identities=9%  Similarity=0.039  Sum_probs=35.9

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ..+++-|..+   -..+|...||++++|.-+...++|..|++.|+|..
T Consensus        13 ~~IL~~L~~~---~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           13 QKILQVLSDD---GGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHH---CSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHc---CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            3455544422   14599999999999999999999999999999754

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=94.86  E-value=0.067  Score=37.26  Aligned_cols=49  Identities=10%  Similarity=0.074  Sum_probs=39.3

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.-..+|...||++++|+-+..+++|..|.+.|+|.-+.+.+....-.|
T Consensus        24 ~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   72 (143)
T 3t8r_A           24 EGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRGAKGGYQLRV   72 (143)
T ss_dssp             TTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSSSSSEEEESS
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCCCCCCeeecC
Confidence            4446899999999999999999999999999999987755443333333

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.84  E-value=0.043  Score=35.98  Aligned_cols=44  Identities=11%  Similarity=0.136  Sum_probs=37.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      -+|++.||+.++|+-|-..+.|+.|++.|+|.... ..+...|+-
T Consensus        45 ~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~-~~r~~~~~~   88 (119)
T 2lkp_A           45 PLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDR-AGRSIVYSL   88 (119)
T ss_dssp             CCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEE-ETTEEEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe-cCCEEEEEE
Confidence            47999999999999999999999999999998754 445556664

>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=94.83  E-value=0.07  Score=34.88  Aligned_cols=42  Identities=12%  Similarity=0.263  Sum_probs=35.5

Q ss_pred             echhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRLR----INGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|+..|+++++    +.-|-...+|+-|+++|+|...... +..+|.
T Consensus        25 ~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~-r~~~~~   70 (126)
T 1sd4_A           25 VSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSE-NIYFYS   70 (126)
T ss_dssp             EEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEET-TEEEEE
T ss_pred             CCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCC-CeEEEE
Confidence            89999999998    5789999999999999999997644 455664

>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=94.81  E-value=0.041  Score=41.06  Aligned_cols=39  Identities=15%  Similarity=0.187  Sum_probs=33.2

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +.++=|-..||++|+|+-...|+||+.|+++|+|....+
T Consensus        30 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g   68 (236)
T 3edp_A           30 GMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNG   68 (236)
T ss_dssp             CC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEECC
Confidence            456669999999999999999999999999999987643

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=94.77  E-value=0.062  Score=35.54  Aligned_cols=32  Identities=28%  Similarity=0.380  Sum_probs=31.3

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        52 ~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~   83 (144)
T 3f3x_A           52 SMVYLANRYFVTQSAITAAVDKLEAKGLVRRI   83 (144)
T ss_dssp             EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            99999999999999999999999999999987

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=94.77  E-value=0.037  Score=37.08  Aligned_cols=43  Identities=16%  Similarity=0.162  Sum_probs=36.4

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ++..+....-+|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        48 iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~   90 (155)
T 3cdh_A           48 VLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRV   90 (155)
T ss_dssp             HHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            3334444445899999999999999999999999999999876

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=94.73  E-value=0.074  Score=38.15  Aligned_cols=50  Identities=10%  Similarity=0.069  Sum_probs=40.6

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      +.-..+|...||++++|+-+..+++|..|.+.|+|.-+.+.+....-+|.
T Consensus        40 ~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar~   89 (159)
T 3lwf_A           40 IGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRGAHGGYVLNGD   89 (159)
T ss_dssp             TTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSTTCEEEECSC
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCCCceEecCC
Confidence            34457999999999999999999999999999999987655444444443

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=94.72  E-value=0.035  Score=37.22  Aligned_cols=34  Identities=12%  Similarity=0.099  Sum_probs=32.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||++++|+-|-..++|+.|+++|+|...
T Consensus        22 ~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~   55 (142)
T 1on2_A           22 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_dssp             SCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3899999999999999999999999999999875

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=94.70  E-value=0.05  Score=37.20  Aligned_cols=46  Identities=22%  Similarity=0.257  Sum_probs=37.2

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...+.-|..+    .-+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus         9 ~~~iL~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            9 DRILVRELAAD----GRATLSELATRAGLSVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHC----TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            33455555433    23899999999999999999999999999999765

>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=94.65  E-value=0.024  Score=37.94  Aligned_cols=33  Identities=12%  Similarity=0.186  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        55 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~   87 (150)
T 3fm5_A           55 VNQRGVAATMGLDPSQIVGLVDELEERGLVVRT   87 (150)
T ss_dssp             CCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-
T ss_pred             cCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            899999999999999999999999999999876

>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=94.65  E-value=0.049  Score=38.53  Aligned_cols=36  Identities=14%  Similarity=0.223  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        56 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~   91 (189)
T 3nqo_A           56 EETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIP   91 (189)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            358999999999999999999999999999999873

>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=94.57  E-value=0.084  Score=34.43  Aligned_cols=44  Identities=18%  Similarity=0.215  Sum_probs=35.9

Q ss_pred             eechhhhhhhhc-ccHHHHHHHHHHHHHcCCeeEecc--cceeEEEe
Q 033931           60 LITPSILSDRLR-INGSLARRAIKDLMARGSIRMISA--HASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserlk-I~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      -+|++.|++.+. |.-+..-..|+.|++.|+|.....  .++...|.
T Consensus        38 ~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~   84 (107)
T 2fsw_A           38 IIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYS   84 (107)
T ss_dssp             CEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEE
Confidence            479999999995 999999999999999999987632  34444453

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=94.55  E-value=0.029  Score=37.25  Aligned_cols=35  Identities=20%  Similarity=0.228  Sum_probs=32.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        53 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            36899999999999999999999999999999876

>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=94.54  E-value=0.034  Score=37.07  Aligned_cols=35  Identities=14%  Similarity=0.019  Sum_probs=32.8

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   86 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKK   86 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCB
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            45899999999999999999999999999999875

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=94.50  E-value=0.052  Score=37.08  Aligned_cols=46  Identities=26%  Similarity=0.213  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        11 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           11 DMQLVKILSEN----SRLTYRELADILNTTRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHC----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            44455545443    34899999999999999999999999999999864

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.50  E-value=0.056  Score=38.50  Aligned_cols=46  Identities=33%  Similarity=0.315  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...++-|..+-    -+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        19 d~~IL~~L~~~~----~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           19 DRNILRLLKKDA----RLTISELSEQLKKPESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHCT----TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcC----CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            345555555442    3899999999999999999999999999999754

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=94.49  E-value=0.056  Score=36.24  Aligned_cols=44  Identities=11%  Similarity=0.212  Sum_probs=35.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      -+|.+.||+.++|.-|-..+.|+.|++.|+|.... .++...|+-
T Consensus        56 ~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~-~gr~~~y~l   99 (122)
T 1u2w_A           56 ELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK-EGKLALYSL   99 (122)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CCEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-ECCEEEEEE
Confidence            37999999999999999999999999999998754 344556654

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=94.48  E-value=0.038  Score=39.80  Aligned_cols=32  Identities=25%  Similarity=0.364  Sum_probs=29.9

Q ss_pred             hhhhhhhhc--------------ccHHHHHHHHHHHHHcCCeeEec
Q 033931           63 PSILSDRLR--------------INGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        63 ps~vserlk--------------I~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...|++.|+              ++.+..|.||+.|++.|+|....
T Consensus        70 ~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~  115 (150)
T 2v7f_A           70 IERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVP  115 (150)
T ss_dssp             HHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEeC
Confidence            389999999              99999999999999999998764

>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=94.45  E-value=0.043  Score=37.10  Aligned_cols=36  Identities=14%  Similarity=0.093  Sum_probs=33.8

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+=|+..+|..++++.-...-++|+.||.+|+|+.|
T Consensus        51 n~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~V   86 (95)
T 2yu3_A           51 NKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   86 (95)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEe
Confidence            355899999999999999999999999999999999

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=94.37  E-value=0.056  Score=37.05  Aligned_cols=46  Identities=11%  Similarity=0.187  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        10 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A           10 DRGILEALMGN----ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHC----TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceE
Confidence            34455545443    34899999999999999999999999999999864

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

Probab=94.35  E-value=0.025  Score=37.54  Aligned_cols=35  Identities=20%  Similarity=0.234  Sum_probs=28.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~   85 (142)
T 3ech_A           51 GLNLQDLGRQMCRDKALITRKIRELEGRNLVRRER   85 (142)
T ss_dssp             TCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC--
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeecc
Confidence            38999999999999999999999999999998763

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=94.24  E-value=0.06  Score=36.81  Aligned_cols=35  Identities=23%  Similarity=0.193  Sum_probs=30.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.+++.-+-.-++|+.|+++|+|....
T Consensus        62 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   96 (168)
T 3u2r_A           62 GMATLQIADRLISRAPDITRLIDRLDDRGLVLRTR   96 (168)
T ss_dssp             CEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecC
Confidence            58999999999999999999999999999999873

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=94.21  E-value=0.079  Score=36.06  Aligned_cols=35  Identities=14%  Similarity=0.243  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+++++.-|-.-++|..|+++|+|....
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~   85 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRP   85 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEee
Confidence            48999999999999999999999999999999873

>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=94.18  E-value=0.083  Score=38.25  Aligned_cols=50  Identities=18%  Similarity=0.325  Sum_probs=40.7

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEA------PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|      |+.++- -..||++|+|+-+--|.||+.|+..|+|....+
T Consensus        19 ~~v~~~l~~~I~~g~l~pG~~L~-E~~La~~lgVSRtpVREAl~~L~~eGlv~~~~~   74 (222)
T 3ihu_A           19 DTVFFGIMSGLELGTFVPGQRLV-ETDLVAHFGVGRNSVREALQRLAAEGIVDLQRH   74 (222)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEEC-HHHHHHHHTCCHHHHHHHHHHHHHTTSEEECST
T ss_pred             HHHHHHHHHHHHhCCCCCCCccC-HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            45666666554      445665 999999999999999999999999999987643

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=94.16  E-value=0.091  Score=34.83  Aligned_cols=42  Identities=19%  Similarity=0.084  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|++.||+.++|.-+-..+-|+.|++.|+|..... ++...|.
T Consensus        32 ~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~-gr~~~y~   73 (118)
T 3f6o_A           32 ATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQ-GRVRTCA   73 (118)
T ss_dssp             EEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEec-CCEEEEE
Confidence            69999999999999999999999999999987644 4455564

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=94.14  E-value=0.1  Score=35.44  Aligned_cols=43  Identities=12%  Similarity=0.128  Sum_probs=35.3

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           60 LITPSILSDRLR----INGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -+|+..|++++.    +.-|-...+|..|+++|+|..... ++..+|.
T Consensus        24 ~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~-~r~~~~~   70 (138)
T 2g9w_A           24 PQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD-DRAHRYA   70 (138)
T ss_dssp             CEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC----CCEEE
T ss_pred             CCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEec-CCeEEEE
Confidence            489999999998    899999999999999999999864 4455554

>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=94.02  E-value=0.073  Score=34.11  Aligned_cols=43  Identities=14%  Similarity=0.168  Sum_probs=36.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+..|++.++|.-+.....|+.|++.|+|..... .+...|.-
T Consensus        37 ~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~-g~~~~y~l   79 (102)
T 3pqk_A           37 FSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRN-IKQIFYRL   79 (102)
T ss_dssp             BCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECS-SSCCEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEE
Confidence            79999999999999999999999999999987543 44455653

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

Probab=93.98  E-value=0.029  Score=37.70  Aligned_cols=34  Identities=15%  Similarity=0.206  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        62 ~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~   95 (160)
T 3boq_A           62 GLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKA   95 (160)
T ss_dssp             CEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC
T ss_pred             CCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999886

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

Probab=93.97  E-value=0.032  Score=37.37  Aligned_cols=36  Identities=14%  Similarity=0.356  Sum_probs=33.2

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ...-+|++.||+++++.-|-.-++|+.|+++|+|..
T Consensus        48 ~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           48 SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            345599999999999999999999999999999986

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=93.96  E-value=0.053  Score=36.48  Aligned_cols=35  Identities=31%  Similarity=0.348  Sum_probs=32.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+.++|.-+-.-++|+.|+++|+|...
T Consensus        62 ~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~   96 (162)
T 2fa5_A           62 PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRE   96 (162)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeee
Confidence            35899999999999999999999999999999875

>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=93.95  E-value=0.095  Score=35.41  Aligned_cols=53  Identities=13%  Similarity=0.164  Sum_probs=40.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|+..+-. .-.|.+.||+.++|.-|...+.|+.|++.|+|..... ++...|+-
T Consensus        50 ~IL~~L~~-~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~~-gr~~~y~l  102 (122)
T 1r1t_A           50 RLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ-GRHVYYQL  102 (122)
T ss_dssp             HHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEE
Confidence            34444432 3479999999999999999999999999999987543 44556664

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=93.94  E-value=0.047  Score=36.60  Aligned_cols=46  Identities=20%  Similarity=0.285  Sum_probs=36.3

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...+.-|..+ +   -+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus         6 ~~~il~~L~~~-~---~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            6 DKIILEILEKD-A---RTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHHC-T---TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            33455544433 2   2599999999999999999999999999999754

>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=93.90  E-value=0.29  Score=31.98  Aligned_cols=53  Identities=19%  Similarity=0.317  Sum_probs=46.3

Q ss_pred             CHHHHHHH---HhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           44 DQATYDKL---LSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        44 dk~t~dKl---~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      |-+.|+.+   ..+.|--..+|...||-+|++.=+-+.++|-.|+++|.+..+..+
T Consensus        10 ~~~~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~   65 (75)
T 1sfu_A           10 DAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   65 (75)
T ss_dssp             SHHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             hHHHHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCC
Confidence            66788888   556677788999999999999999999999999999999988543

>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=93.84  E-value=0.1  Score=38.15  Aligned_cols=43  Identities=26%  Similarity=0.209  Sum_probs=36.3

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|+..+.+ .-+|.+.||++++++-+-.++-|+.|++.|+|...
T Consensus        24 ~IL~~L~~-~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           24 KILKLLRN-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            34444443 34899999999999999999999999999999987

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=93.79  E-value=0.12  Score=35.45  Aligned_cols=45  Identities=13%  Similarity=0.158  Sum_probs=36.7

Q ss_pred             eeechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--cceeEEEe
Q 033931           59 KLITPSILSDRL-RINGSLARRAIKDLMARGSIRMISA--HASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      .-+|++.|++.+ +|.-+..-+.|+.|++.|+|.....  .++...|.
T Consensus        47 g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~   94 (131)
T 1yyv_A           47 GTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYS   94 (131)
T ss_dssp             CCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEE
T ss_pred             CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEE
Confidence            347999999999 7999999999999999999987632  24555554

>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=93.68  E-value=0.067  Score=36.39  Aligned_cols=34  Identities=21%  Similarity=0.206  Sum_probs=31.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|...||++++++-|-.++.|+.|++.|+|..+
T Consensus        17 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A           17 KYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            4899999999999999999999999999999863

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=93.67  E-value=0.058  Score=36.97  Aligned_cols=36  Identities=19%  Similarity=0.303  Sum_probs=29.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+++++.-+-.-++|..|+++|+|...+
T Consensus        51 ~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~~~   86 (148)
T 4fx0_A           51 IDLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMA   86 (148)
T ss_dssp             ---CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC---
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeC
Confidence            348999999999999999999999999999996554

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=93.58  E-value=0.072  Score=41.00  Aligned_cols=35  Identities=20%  Similarity=0.239  Sum_probs=32.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCee-Ee
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIR-MI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk-~V   93 (108)
                      .-+|...||++|+|+-+..|+-|.+|+++|+|. .+
T Consensus        20 ~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A           20 QDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEe
Confidence            449999999999999999999999999999998 55

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=93.56  E-value=0.1  Score=35.84  Aligned_cols=34  Identities=18%  Similarity=0.172  Sum_probs=32.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .+|++.||++++|.-|-.-++|..|+++|+|...
T Consensus        46 ~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~   79 (151)
T 4aik_A           46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRH   79 (151)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEee
Confidence            4689999999999999999999999999999876

>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=93.47  E-value=0.072  Score=36.86  Aligned_cols=42  Identities=17%  Similarity=0.228  Sum_probs=35.5

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |...||++++|+-+..+++|..|.+.|+|.-+.. +....-.|
T Consensus        25 s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG-~GGy~Lar   66 (145)
T 1xd7_A           25 SSEIIADSVNTNPVVVRRMISLLKKADILTSRAG-VPGASLKK   66 (145)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS-SSSCEESS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecC-CCCceecC
Confidence            8999999999999999999999999999988765 44433333

>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=93.42  E-value=0.068  Score=40.47  Aligned_cols=47  Identities=9%  Similarity=-0.031  Sum_probs=38.0

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      ...||++.++++|++...+|+..|.+|+.+|++-.=.... ..-|.++
T Consensus       166 ~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D~~~e-g~~y~pn  212 (218)
T 3cuq_B          166 KGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSVE-GLRFYPN  212 (218)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEESSS-CEEEEEC
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCCC-ceEEehh
Confidence            4689999999999999999999999999999997754333 2335443

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=93.41  E-value=0.17  Score=37.06  Aligned_cols=38  Identities=13%  Similarity=0.183  Sum_probs=34.4

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...-+|++.||++|++.-+-...+|+.|+++|+|....
T Consensus        17 ~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~   54 (214)
T 3hrs_A           17 RHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDK   54 (214)
T ss_dssp             SCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEec
Confidence            34679999999999999999999999999999998754

>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=93.35  E-value=0.027  Score=37.60  Aligned_cols=34  Identities=18%  Similarity=0.141  Sum_probs=26.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        57 ~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           57 GIIQKDLAQFFGRRGASITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             CCCHHHHHHC------CHHHHHHHHHHTTSBCCC
T ss_pred             CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999877

>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=93.31  E-value=0.09  Score=38.09  Aligned_cols=34  Identities=24%  Similarity=0.116  Sum_probs=32.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        63 ~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~   96 (207)
T 2fxa_A           63 ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK   96 (207)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            8999999999999999999999999999998874

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=93.19  E-value=0.2  Score=33.72  Aligned_cols=51  Identities=16%  Similarity=0.089  Sum_probs=42.6

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      ++..++|...+-. .-.++..+++++++.-+.++.+|+.|.+.|.|.++..+
T Consensus         6 ~~l~~~i~~~~~~-~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~   56 (121)
T 2pjp_A            6 QAIWQKAEPLFGD-EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKD   56 (121)
T ss_dssp             HHHHHHHGGGCSS-SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETT
T ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            4566777776644 34588999999999999999999999999999999754

>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=92.92  E-value=0.077  Score=37.89  Aligned_cols=46  Identities=13%  Similarity=0.142  Sum_probs=37.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ..+|...||++++|+-+..+++|+.|.+.|+|.-+.+.+.-..-.|
T Consensus        27 ~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   72 (162)
T 3k69_A           27 SKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGKNGGYQLDL   72 (162)
T ss_dssp             SCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEECSTTCEEECCS
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeEecC
Confidence            5699999999999999999999999999999977655443333333

>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=92.90  E-value=0.19  Score=34.83  Aligned_cols=35  Identities=11%  Similarity=0.264  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.|+++++|.-+..-+.|+.|++.|+|....
T Consensus        37 ~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~   71 (146)
T 2f2e_A           37 LTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVP   71 (146)
T ss_dssp             CCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            47999999999999999999999999999999874

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=92.66  E-value=0.23  Score=34.55  Aligned_cols=45  Identities=11%  Similarity=0.055  Sum_probs=36.8

Q ss_pred             eeechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--cceeEEEe
Q 033931           59 KLITPSILSDRL-RINGSLARRAIKDLMARGSIRMISA--HASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      .-.+++.|++.+ +|+-+.--..|++|++.|+|.....  .++...|.
T Consensus        38 g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~   85 (131)
T 4a5n_A           38 GKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYS   85 (131)
T ss_dssp             SCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEE
Confidence            347999999999 9999999999999999999987732  33455564

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=92.63  E-value=0.22  Score=35.02  Aligned_cols=57  Identities=14%  Similarity=0.099  Sum_probs=43.5

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++--+|+..+-. .=.|+..||+.++|.-|-...-|+.|++.|+|..... .+..+|.-
T Consensus        58 p~R~~IL~~L~~-~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~l  114 (151)
T 3f6v_A           58 PTRRRLVQLLTS-GEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKD-GRFRYYRL  114 (151)
T ss_dssp             HHHHHHHHHGGG-CCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec-CCEEEEEE
Confidence            444455555542 3389999999999999999999999999999998654 44456653

>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=92.58  E-value=0.1  Score=42.02  Aligned_cols=45  Identities=11%  Similarity=0.101  Sum_probs=37.8

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ..++|...+++.++++-.-|++.|++|.+.|+|..+..+ +..+|.
T Consensus       309 ~p~~t~~~~~~~~~~S~~TA~r~L~~L~e~GiL~~~~~g-R~~~y~  353 (373)
T 3eqx_A          309 QPYCRIQNLVESGLAKRQTASVYLKQLCDIGVLEEVQSG-KEKLFV  353 (373)
T ss_dssp             CSEEEHHHHHHTSSSCHHHHHHHHHHHHHTTSCEEC--C-CSCEEE
T ss_pred             CCCccHHHHHHHhCcCHHHHHHHHHHHHHCCcEEEeCCC-CceEee
Confidence            458999999999999999999999999999999998654 345664

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=92.50  E-value=0.13  Score=35.96  Aligned_cols=43  Identities=16%  Similarity=0.215  Sum_probs=34.7

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |+.....---+|...||++++++-+-.++-|+.|++.|+|..+
T Consensus         8 il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            8 ILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeec
Confidence            3333333333699999999999999999999999999999843

>1u5t_B Defective in vacuolar protein sorting; VPS36P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=92.47  E-value=0.19  Score=36.74  Aligned_cols=44  Identities=7%  Similarity=0.110  Sum_probs=36.8

Q ss_pred             echh-h-hhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           61 ITPS-I-LSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        61 ITps-~-vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      +|.+ . +++++++...+|+..|.+++++|++-.=..... .-|-.|
T Consensus       119 vt~~~~~la~~~~ws~~~a~e~L~~~e~~G~l~~D~~~~G-~~y~~N  164 (169)
T 1u5t_B          119 LTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLSG-IYYYKN  164 (169)
T ss_dssp             HHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECSSC-EEEEEC
T ss_pred             ccHHHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCCCc-ceEEee
Confidence            8999 9 999999999999999999999999987654444 345444

>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=92.17  E-value=0.063  Score=36.83  Aligned_cols=45  Identities=16%  Similarity=0.145  Sum_probs=36.6

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...++-|..+    .-+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus        10 ~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A           10 KKIIKILQND----GKAPLREISKITGLAESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHC----TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3445544433    34899999999999999999999999999999764

>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=92.04  E-value=0.28  Score=36.17  Aligned_cols=43  Identities=19%  Similarity=0.158  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc----ceeEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH----ASQQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~----~~q~IYt  103 (108)
                      .|++.|+++++++-|.....|+.|++.|+|......    ++..+|.
T Consensus        29 ~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~   75 (202)
T 2p4w_A           29 YFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYM   75 (202)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEE
Confidence            799999999999999999999999999999886432    4444554

>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=91.30  E-value=0.049  Score=40.80  Aligned_cols=49  Identities=20%  Similarity=0.186  Sum_probs=5.2

Q ss_pred             HHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           46 ATYDKLLSEAP------KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        46 ~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..++.|...|-      +.++=|-..||++|+|+-+..|+||+.|+++|+|....
T Consensus        20 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   74 (247)
T 2ra5_A           20 QLSQQLEAAIEHGALTPGSLLGNEIELAARLGLSRPTVRQAIQSLVDKGLLVRRR   74 (247)
T ss_dssp             ------------------------------------------------CEEEEEC
T ss_pred             HHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            34455544443      34555899999999999999999999999999997653

>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=91.23  E-value=0.17  Score=36.31  Aligned_cols=34  Identities=21%  Similarity=0.155  Sum_probs=31.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .|...||+.|+++-+-+++.|+.|+++|+|....
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~~   58 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIERKN   58 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC-
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEecC
Confidence            7899999999999999999999999999998753

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=90.96  E-value=0.36  Score=35.84  Aligned_cols=42  Identities=19%  Similarity=0.172  Sum_probs=37.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccee
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQ   99 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      .--.|.|.|+..++++-|-|+-+|..|+.+|+|..|..+...
T Consensus        22 ~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~a   63 (165)
T 2vxz_A           22 DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVA   63 (165)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEE
T ss_pred             hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEE
Confidence            556899999999999999999999999999999999766644

>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=90.77  E-value=0.21  Score=36.70  Aligned_cols=34  Identities=21%  Similarity=0.487  Sum_probs=31.6

Q ss_pred             ech--hhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITP--SILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITp--s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|+  ..||+++++.-+-...+|+.|+++|+|....
T Consensus        23 ~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~   58 (230)
T 1fx7_A           23 VTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG   58 (230)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            677  9999999999999999999999999998864

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

Probab=90.36  E-value=0.49  Score=32.03  Aligned_cols=45  Identities=16%  Similarity=0.358  Sum_probs=37.7

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|.+++     +|..+-.-+.|+.|++.|+|..+.-......|-
T Consensus        25 ~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~   74 (131)
T 2o03_A           25 DFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDTGESVYR   74 (131)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTTSCEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCCCceEEE
Confidence            358999999998     788999999999999999999997655555564

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=90.25  E-value=0.036  Score=38.72  Aligned_cols=35  Identities=17%  Similarity=0.226  Sum_probs=31.8

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +.++ |...||++|+++-+-.|.+|+.|++.|+|..
T Consensus        25 ~~~l-s~~eLa~~lgvSr~~vr~al~~L~~~Gli~~   59 (163)
T 2gqq_A           25 DGRI-SNVELSKRVGLSPTPCLERVRRLERQGFIQG   59 (163)
T ss_dssp             CSSC-CTTGGGTSSSCCTTTSSSTHHHHHHHTSEEE
T ss_pred             CCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            4444 9999999999999999999999999999985

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=90.18  E-value=0.46  Score=36.01  Aligned_cols=33  Identities=15%  Similarity=0.051  Sum_probs=32.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|.+.||+++++.-|-..+.|+.|++.|+|...
T Consensus       167 ~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          167 TGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            899999999999999999999999999999886

>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=90.09  E-value=0.45  Score=35.17  Aligned_cols=35  Identities=11%  Similarity=0.137  Sum_probs=32.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|.+.||+++++.-|-+.++|+.|++.|+|....
T Consensus        21 ~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~   55 (241)
T 2xrn_A           21 GLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALG   55 (241)
T ss_dssp             CEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECG
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            47999999999999999999999999999998754

>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=89.94  E-value=0.62  Score=40.08  Aligned_cols=53  Identities=9%  Similarity=0.033  Sum_probs=43.5

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhc-------ccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLR-------INGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlk-------I~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      .....+|+.-+.....||...|+++|+       +...+|+.+|.+|+.+|++-.=....
T Consensus       493 ~~~~~~il~l~~~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~~~e~eG~l~rDd~~~  552 (566)
T 1w7p_D          493 DVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLS  552 (566)
T ss_dssp             HHHHHHHHHHHTTSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCccccCcccHHHHHHHHHHHHHcCCEEEECCCC
Confidence            455666665455568999999999999       99999999999999999997764444

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=89.87  E-value=0.06  Score=37.43  Aligned_cols=34  Identities=26%  Similarity=0.322  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.++|+-+-.-++|+.|+++|+|...
T Consensus        86 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~  119 (181)
T 2fbk_A           86 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERR  119 (181)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEec
Confidence            4899999999999999999999999999999886

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=89.32  E-value=0.24  Score=34.86  Aligned_cols=41  Identities=10%  Similarity=0.079  Sum_probs=34.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-ccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS-AHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr  104 (108)
                      .+|+..||+.++|+.+    .||.-++.|+|.++. ..++...|+.
T Consensus         4 ~~tI~evA~~~Gvs~~----tLR~ye~~GLl~p~~r~~~g~R~Y~~   45 (146)
T 3hh0_A            4 AWLISEFASVGDVTVR----ALRYYDKINLLKPSDYTEGGHRLYTK   45 (146)
T ss_dssp             CBCHHHHHHHHTCCHH----HHHHHHHTTSSCCSEECTTSCEEBCH
T ss_pred             CCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCeECCCCCEeeCH
Confidence            6899999999998875    589999999999984 3467788875

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

Probab=89.22  E-value=0.57  Score=32.29  Aligned_cols=45  Identities=7%  Similarity=0.102  Sum_probs=37.2

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|.+++     +|..+-.-+.|+.|++.|+|..+.-..+...|-
T Consensus        36 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   85 (145)
T 2fe3_A           36 AHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFD   85 (145)
T ss_dssp             SCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTTSCCEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCCCceEEE
Confidence            358899999998     788899999999999999999996655555564

>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=89.15  E-value=0.29  Score=37.83  Aligned_cols=46  Identities=20%  Similarity=0.242  Sum_probs=37.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      ..-+||++.|++.+++....|+.+|.+|+..|++-.=........|
T Consensus       165 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD~q~~ge~~Y  210 (234)
T 3cuq_A          165 KNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHY  210 (234)
T ss_dssp             TTSEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEESSSSSSCEE
T ss_pred             hcCcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEeCCCCCccee
Confidence            4679999999999999999999999999999998654443333444

>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=88.98  E-value=0.59  Score=34.55  Aligned_cols=34  Identities=15%  Similarity=0.137  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        23 ~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           23 DVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            4799999999999999999999999999999876

>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=88.95  E-value=0.36  Score=35.43  Aligned_cols=32  Identities=13%  Similarity=0.289  Sum_probs=29.6

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           62 TPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +++.||+++++.-+-...+|+.|+++|+|...
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            44999999999999999999999999999875

>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=88.73  E-value=0.69  Score=34.63  Aligned_cols=44  Identities=20%  Similarity=0.147  Sum_probs=36.8

Q ss_pred             HHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           51 LLSEAPK-FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        51 l~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.-+-. -.-+|.+.||+++++.-|-+-++|+.|++.|+|....
T Consensus        11 IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~   55 (260)
T 3r4k_A           11 LLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVE   55 (260)
T ss_dssp             HHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            4444443 2578999999999999999999999999999998754

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=88.65  E-value=0.4  Score=36.36  Aligned_cols=43  Identities=14%  Similarity=0.281  Sum_probs=36.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccce-----eEEEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHAS-----QQIYT  103 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~-----q~IYt  103 (108)
                      +|++.||+.++++-+.....|+.|++.|+|.......+     ...|.
T Consensus        26 ~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~   73 (232)
T 2qlz_A           26 CYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYK   73 (232)
T ss_dssp             TCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEE
Confidence            79999999999999999999999999999998544444     55555

>2ve8_A FTSK, DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA-binding, winged helix, bacterial cell division; HET: DNA; 1.4A {Pseudomonas aeruginosa} SCOP: a.4.5.67 PDB: 2ve9_A* 2j5o_A*

Probab=88.56  E-value=0.11  Score=33.93  Aligned_cols=58  Identities=17%  Similarity=0.281  Sum_probs=46.5

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      .++|+....=|-...-.+.|.|=-||+|-..-|-+++..||+.|+|-+-..+..-.|+
T Consensus         9 D~Ly~~A~~~V~~~~~aS~S~lQR~lrIGYnRAArlid~lE~~GiVgp~~gsk~ReVL   66 (73)
T 2ve8_A            9 DPLYDEAVRFVTESRRASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMNTNGSREVI   66 (73)
T ss_dssp             CTTHHHHHHHHHHHCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCCTTSCCCBC
T ss_pred             cHHHHHHHHHHHhcCCccHHHHHHHHccChHHHHHHHHHHHHCCcCCcccCCCCceEe
Confidence            4566766666666678889999999999999999999999999999998654433343

>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=88.40  E-value=0.76  Score=31.36  Aligned_cols=33  Identities=18%  Similarity=0.121  Sum_probs=31.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-+-.-++|++|+++|+|..
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            478999999999999999999999999999985

>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=88.37  E-value=0.74  Score=35.71  Aligned_cols=49  Identities=14%  Similarity=0.102  Sum_probs=40.1

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...+|+.-+..-..+|...||++|+|+-+-.++-|+.|++.|++..-..
T Consensus         6 r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~~~   54 (321)
T 1bia_A            6 VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVP   54 (321)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEET
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEEec
Confidence            3445555555667899999999999999999999999999999864433

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=88.29  E-value=0.66  Score=31.57  Aligned_cols=45  Identities=9%  Similarity=0.175  Sum_probs=36.2

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|+..|.+++     .|..+-.-+.|+.|++.|+|..+.-......|-
T Consensus        33 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   82 (136)
T 1mzb_A           33 RHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFE   82 (136)
T ss_dssp             CSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEE
T ss_pred             CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            357888888888     788888899999999999999986544444554

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=88.06  E-value=0.91  Score=31.55  Aligned_cols=44  Identities=16%  Similarity=0.216  Sum_probs=36.9

Q ss_pred             eechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           60 LITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -+|...|.+++     .|..+-.-+.|+.|++.|+|..+.-..+...|-
T Consensus        42 ~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   90 (150)
T 2xig_A           42 HLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSKSGRRYE   90 (150)
T ss_dssp             CBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETTTEEEEE
T ss_pred             CCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            58889998888     688888999999999999999986655555664

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=88.05  E-value=0.91  Score=31.54  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=35.4

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|.+++     .|..+-.-+.|+.|++.|+|..+.-......|-
T Consensus        32 ~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   81 (150)
T 2w57_A           32 QHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFE   81 (150)
T ss_dssp             SSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGGGCEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            357888888887     678888889999999999999986544445564

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=87.94  E-value=0.76  Score=31.55  Aligned_cols=32  Identities=22%  Similarity=0.217  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999999984

>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=87.83  E-value=0.58  Score=35.41  Aligned_cols=35  Identities=14%  Similarity=0.155  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+++++.-|-.=++|..|+++|+|....
T Consensus       174 ~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~  208 (250)
T 1p4x_A          174 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKER  208 (250)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeC
Confidence            48999999999999999999999999999999873

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=87.81  E-value=0.86  Score=31.33  Aligned_cols=33  Identities=15%  Similarity=0.338  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-+-.-++|++|+++|+|..
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            479999999999999999999999999999975

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=87.58  E-value=0.73  Score=31.87  Aligned_cols=32  Identities=19%  Similarity=0.340  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-+-.-++|++|+++|+|..
T Consensus       179 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  210 (227)
T 3dkw_A          179 VAKQLVAGHLSIQPETFSRIMHRLGDEGIIHL  210 (227)
T ss_dssp             SCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEe
Confidence            78999999999999999999999999999975

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=87.48  E-value=0.93  Score=31.07  Aligned_cols=34  Identities=18%  Similarity=0.210  Sum_probs=31.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      --+|...||+.++++-+-.-++|++|+++|+|..
T Consensus       162 ~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          162 FQIRHHELAALAGTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            4479999999999999999999999999999975

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=87.47  E-value=0.32  Score=34.12  Aligned_cols=45  Identities=11%  Similarity=0.203  Sum_probs=33.7

Q ss_pred             CCCe--eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEec
Q 033931           56 PKFK--LITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTR  104 (108)
Q Consensus        56 pk~k--~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      +.|.  .+|...||+.++|+.+    .||.-++.|||.++.. .+....|+.
T Consensus        10 k~M~~~~~~I~evA~~~gvs~~----tLR~Ye~~Gll~p~~r~~~g~R~Y~~   57 (148)
T 3gpv_A           10 KRMNDMYYTIGQVAKMQHLTIS----QIRYYDKQGLFPFLQRNEKGDRIFNE   57 (148)
T ss_dssp             -----CCBCHHHHHHHTTCCHH----HHHHHHHTTCCTTCEECTTCCEEBCH
T ss_pred             CccccCceeHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCH
Confidence            4455  7999999999999865    5889999999986533 467788875

>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=87.45  E-value=0.61  Score=31.24  Aligned_cols=38  Identities=18%  Similarity=0.193  Sum_probs=34.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |.-. ++++.|++++.+..|--.+.|..|+..|||....
T Consensus        33 ~g~~-~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~   70 (96)
T 2obp_A           33 GATP-WSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSV   70 (96)
T ss_dssp             TCCC-CBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCC-cCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeec
Confidence            5544 4999999999999999999999999999999763

>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=87.19  E-value=1.1  Score=25.85  Aligned_cols=40  Identities=20%  Similarity=0.282  Sum_probs=30.9

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      ..+|...|++.|     +|+.+-.++-|+   +-|+| .+........|
T Consensus        18 ~~~t~~el~~~l~~~~~~vs~~Tv~R~L~---~lg~v-~~~~~~~~~~Y   62 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYKVTQATVSRDIK---ELHLV-KVPTNNGSYKY   62 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCCCCHHHHHHHHH---HHTCE-EEEETTTEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCcCHHHHHHHHH---HcCCE-EEecCCCceee
Confidence            468999999999     999988887777   55899 66555555556

>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=86.96  E-value=0.47  Score=37.39  Aligned_cols=34  Identities=9%  Similarity=0.040  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|+..||+++++.-+-.-++|..|+++|+|...
T Consensus       420 ~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~  453 (487)
T 1hsj_A          420 EISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKK  453 (487)
T ss_dssp             EEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            4899999999999999999999999999999887

>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=86.77  E-value=0.72  Score=31.43  Aligned_cols=33  Identities=18%  Similarity=0.282  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+-++++-.-.-++|++|+++|+|..
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  196 (207)
T 2oz6_A          164 KITRQEIGRIVGCSREMVGRVLKSLEEQGLVHV  196 (207)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            479999999999999999999999999999975

>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=86.70  E-value=1.3  Score=33.24  Aligned_cols=51  Identities=16%  Similarity=0.148  Sum_probs=41.7

Q ss_pred             ceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           41 VLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        41 V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..+..+-|=++.-+. + .-|+...||++|+++-+-.+.+|+.|.++|+|..-
T Consensus        13 ls~s~EdYLk~I~~L-~-~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~   63 (200)
T 2p8t_A           13 PEYTVEDVLAVIFLL-K-EPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSK   63 (200)
T ss_dssp             -CCCHHHHHHHHHHT-T-SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHHHH-c-CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            455666676666666 2 45999999999999999999999999999999653

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=86.67  E-value=0.71  Score=29.60  Aligned_cols=42  Identities=7%  Similarity=0.160  Sum_probs=35.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|++.||+++++.-|-..+-|+.|++. +|..-. .++...|.-
T Consensus        42 ~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~-~gr~~~y~l   83 (99)
T 2zkz_A           42 LNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNR-QGLEIYYSI   83 (99)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEE-ETTEEEEEC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheE-eCcEEEEEE
Confidence            799999999999999999999999999 887644 455566653

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=86.62  E-value=1.2  Score=32.43  Aligned_cols=37  Identities=35%  Similarity=0.334  Sum_probs=33.4

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...-+|.+.+|++++|+-|-.-+.|+.||+.|||...
T Consensus        24 ~~~~~s~s~aA~~L~isq~avSr~I~~LE~~~L~~R~   60 (230)
T 3cta_A           24 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT   60 (230)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            3456789999999999999999999999999999875

>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=86.54  E-value=1.1  Score=31.12  Aligned_cols=32  Identities=22%  Similarity=0.382  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-.-.-++|++|.++|+|..
T Consensus       178 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          178 LTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999999976

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=86.44  E-value=0.99  Score=33.68  Aligned_cols=36  Identities=11%  Similarity=0.113  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|.+.||+++++.-|-+.++|+.|++.|+|....
T Consensus        37 ~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~   72 (260)
T 2o0y_A           37 PTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRA   72 (260)
T ss_dssp             SSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            458999999999999999999999999999998753

>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=86.27  E-value=0.59  Score=37.05  Aligned_cols=41  Identities=15%  Similarity=0.101  Sum_probs=35.5

Q ss_pred             CCCCeeechhhhhhhh--cccHHHHHHHHHHHHHcCCeeEecc
Q 033931           55 APKFKLITPSILSDRL--RINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        55 Vpk~k~ITps~vserl--kI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +-...-|+..+||++|  +++-.-.|+-|.+||+.|+|..+..
T Consensus        31 l~~~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~Hg   73 (338)
T 1stz_A           31 IENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHT   73 (338)
T ss_dssp             HHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             HHcCCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEccC
Confidence            4455779999999999  8888899999999999999988543

>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=86.10  E-value=0.14  Score=39.94  Aligned_cols=43  Identities=19%  Similarity=0.149  Sum_probs=0.0

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      .|+..+-...-+|...||++|++.-+-.|+.|+.|+++|+|..
T Consensus        24 ~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~   66 (345)
T 2o0m_A           24 QILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQLNLIEP   66 (345)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4555555567799999999999999999999999999999973

>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=86.06  E-value=0.81  Score=31.69  Aligned_cols=32  Identities=22%  Similarity=0.329  Sum_probs=30.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-+-.-++|++|+++|+|..
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  219 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLHA  219 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            68999999999999999999999999999985

>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=86.00  E-value=1.6  Score=29.03  Aligned_cols=42  Identities=14%  Similarity=0.111  Sum_probs=31.7

Q ss_pred             chhhhhhhh--------cccHHHHHHHHHHHHHcCCeeEec----ccceeEEEe
Q 033931           62 TPSILSDRL--------RINGSLARRAIKDLMARGSIRMIS----AHASQQIYT  103 (108)
Q Consensus        62 Tps~vserl--------kI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYt  103 (108)
                      +.|.|..++        .|+-+.-..+|+.|++.|+|....    ..++..+|.
T Consensus        27 ~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~   80 (116)
T 3f8b_A           27 YVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYR   80 (116)
T ss_dssp             CHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEE
Confidence            566776665        799999999999999999999873    234555664

>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=85.82  E-value=0.83  Score=31.86  Aligned_cols=33  Identities=12%  Similarity=0.172  Sum_probs=31.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       180 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          180 YLSREELATLSNMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEee
Confidence            479999999999999999999999999999975

>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=85.68  E-value=1.8  Score=30.16  Aligned_cols=43  Identities=16%  Similarity=0.131  Sum_probs=33.9

Q ss_pred             echhhhhhhh--------cccHHHHHHHHHHHHHcCCeeEecc----cceeEEEe
Q 033931           61 ITPSILSDRL--------RINGSLARRAIKDLMARGSIRMISA----HASQQIYT  103 (108)
Q Consensus        61 ITps~vserl--------kI~~SlAr~~Lr~L~~kGlIk~V~k----~~~q~IYt  103 (108)
                      .+.+.|++.+        .|+-+.--.+|+.|++.|+|.....    .++-.+|.
T Consensus        55 ~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~  109 (145)
T 1xma_A           55 SYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYR  109 (145)
T ss_dssp             EEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEE
T ss_pred             CCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEE
Confidence            6888888887        5999999999999999999988732    34555663

>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=85.62  E-value=0.79  Score=35.29  Aligned_cols=46  Identities=15%  Similarity=0.278  Sum_probs=37.3

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      ..-+||++.|++.+++....|+.+|.+|+..|++=.=........|
T Consensus       178 ~~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD~q~~~e~~Y  223 (233)
T 1u5t_A          178 ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALY  223 (233)
T ss_dssp             TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEE
T ss_pred             hcCcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCCCccce
Confidence            4678999999999999999999999999999998554443223444

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=85.23  E-value=0.88  Score=33.84  Aligned_cols=44  Identities=16%  Similarity=0.052  Sum_probs=36.5

Q ss_pred             HHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           50 KLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        50 Kl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|+..+-.. .-+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        18 ~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           18 AVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             HHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            344444432 45899999999999999999999999999999874

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=84.87  E-value=1.6  Score=29.95  Aligned_cols=45  Identities=16%  Similarity=0.349  Sum_probs=35.8

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           59 KLITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .-+|...|.+++     +|+.+---+.|+.|++.|+|..+.-.....-|-
T Consensus        28 ~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~   77 (139)
T 3mwm_A           28 EFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAEGESVYR   77 (139)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTTSCEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCceEEE
Confidence            367888888887     578888889999999999999986655555564

>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=84.78  E-value=0.97  Score=32.19  Aligned_cols=32  Identities=13%  Similarity=0.256  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       194 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          194 LSHQAIAEAIGSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEE
Confidence            68999999999999999999999999999985

>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=84.71  E-value=1.5  Score=31.70  Aligned_cols=33  Identities=18%  Similarity=0.121  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  249 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRILKMLEDQNLISA  249 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            378999999999999999999999999999985

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=84.65  E-value=0.67  Score=30.50  Aligned_cols=40  Identities=5%  Similarity=0.055  Sum_probs=32.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-ccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS-AHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr  104 (108)
                      +|+..+|+.++|+.+    .||..++.|+|.+.. ..++...|+.
T Consensus         3 ~~i~e~A~~~gvs~~----tLR~ye~~Gll~p~~~~~~g~R~Y~~   43 (109)
T 1r8d_A            3 YQVKQVAEISGVSIR----TLHHYDNIELLNPSALTDAGYRLYSD   43 (109)
T ss_dssp             BCHHHHHHHHSCCHH----HHHHHHHTTSSCCSEECTTCCEEBCH
T ss_pred             ccHHHHHHHHCcCHH----HHHHHHHCCCCCCCeECCCCCeeeCH
Confidence            689999999998865    578899999999875 3566678875

>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=84.54  E-value=1.4  Score=34.30  Aligned_cols=36  Identities=11%  Similarity=0.164  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|.+.||++++++-+-.-+++++|++.|+|..+.
T Consensus        32 ~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~~~   67 (380)
T 2hoe_A           32 SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEK   67 (380)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            348999999999999999999999999999999874

>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=84.44  E-value=1.1  Score=31.29  Aligned_cols=33  Identities=15%  Similarity=0.164  Sum_probs=31.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-.-.-++|++|.++|+|..
T Consensus       175 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          175 PLGTQDIMARTSSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            379999999999999999999999999999975

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=84.41  E-value=0.93  Score=33.92  Aligned_cols=43  Identities=16%  Similarity=0.082  Sum_probs=35.8

Q ss_pred             HHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           51 LLSEAPK-FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        51 l~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |+.-+-. -.-+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        26 iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~   69 (265)
T 2ia2_A           26 VIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD   69 (265)
T ss_dssp             HHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES
T ss_pred             HHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            4444432 245899999999999999999999999999999874

>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=84.22  E-value=1.1  Score=31.94  Aligned_cols=45  Identities=13%  Similarity=0.164  Sum_probs=36.5

Q ss_pred             HHHHHhhCC-CCeeechhhhhhhhcccHHHHHHHHHHHHHcCC-eeE
Q 033931           48 YDKLLSEAP-KFKLITPSILSDRLRINGSLARRAIKDLMARGS-IRM   92 (108)
Q Consensus        48 ~dKl~KEVp-k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGl-Ik~   92 (108)
                      ..+|+..+. +-..+|...||++|+|+-+-.++=|+.|++.|+ |.-
T Consensus        23 ~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           23 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            444555444 235699999999999999999999999999999 753

>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=84.21  E-value=1.1  Score=31.12  Aligned_cols=33  Identities=9%  Similarity=0.056  Sum_probs=30.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+-++++-.-.-++|++|+++|+|..
T Consensus       167 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          167 GLNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             SSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            378999999999999999999999999999965

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=83.99  E-value=1  Score=30.86  Aligned_cols=33  Identities=15%  Similarity=0.179  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       139 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          139 TVSHEEIADATASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             ECCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            378999999999999999999999999999975

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=83.98  E-value=1.2  Score=33.60  Aligned_cols=43  Identities=19%  Similarity=0.198  Sum_probs=35.8

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEE
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQI  101 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I  101 (108)
                      ..-.|+..||+++++.-+.-...|.+|.+.|+|+. .+..+..|
T Consensus       176 ~~~~t~~~la~~~~l~~~~V~~~l~~L~~~~~v~~-~~~~~~~~  218 (232)
T 2qlz_A          176 NGRATVEELSDRLNLKEREVREKISEMARFVPVKI-INDNTVVL  218 (232)
T ss_dssp             SSEEEHHHHHHHHTCCHHHHHHHHHHHTTTSCEEE-ETTTEEEE
T ss_pred             cCCCCHHHHHHHhCcCHHHHHHHHHHHHhcCCeEE-ecCCeEEe
Confidence            36679999999999999999999999999999983 44444433

>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=83.92  E-value=0.99  Score=31.43  Aligned_cols=32  Identities=16%  Similarity=0.230  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            79999999999999999999999999999976

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=83.66  E-value=0.65  Score=31.12  Aligned_cols=58  Identities=12%  Similarity=0.078  Sum_probs=50.0

Q ss_pred             hhccceeCHHHHHHHHhhCCC----CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           37 VNNMVLFDQATYDKLLSEAPK----FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        37 ~nn~V~~dk~t~dKl~KEVpk----~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +..-++|..++|+++...+-.    ..-||++.+-|.++++-..|-.+|+.|-+.|+...+.
T Consensus        53 i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~lg~sRK~ai~lLE~~Dr~g~TrR~g  114 (121)
T 2pjp_A           53 IVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRG  114 (121)
T ss_dssp             EETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEET
T ss_pred             ecCCceECHHHHHHHHHHHHHHHHHCCCccHHHHHHHHCCcHHHHHHHHHHHhhcCCeEeeC
Confidence            345678889999888877765    3779999999999999999999999999999999874

>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=83.35  E-value=1.2  Score=31.63  Aligned_cols=32  Identities=6%  Similarity=0.147  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       178 ~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~  209 (250)
T 3e6c_C          178 LSQKSIGEITGVHHVTVSRVLASLKRENILDK  209 (250)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEe
Confidence            69999999999999999999999999999976

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=83.21  E-value=2.5  Score=28.30  Aligned_cols=43  Identities=7%  Similarity=0.112  Sum_probs=33.5

Q ss_pred             echhhhhhhh------cccHHHHHHHHHHHHHcCCeeEecc----cceeEEEe
Q 033931           61 ITPSILSDRL------RINGSLARRAIKDLMARGSIRMISA----HASQQIYT  103 (108)
Q Consensus        61 ITps~vserl------kI~~SlAr~~Lr~L~~kGlIk~V~k----~~~q~IYt  103 (108)
                      .+.|.|..++      .|+-+.--.+|+.|++.|+|.....    .++..+|.
T Consensus        25 ~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~   77 (117)
T 4esf_A           25 TYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYS   77 (117)
T ss_dssp             BCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEE
T ss_pred             CCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEE
Confidence            5678888887      7999999999999999999998742    23455664

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=83.18  E-value=1.9  Score=29.77  Aligned_cols=43  Identities=21%  Similarity=0.189  Sum_probs=32.8

Q ss_pred             echhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           61 ITPSILSDRL-----RINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        61 ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +|...|-+++     .|+.+---+.|+.|++.|+|..+.-..+..-|-
T Consensus        34 ~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~   81 (145)
T 3eyy_A           34 ATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYH   81 (145)
T ss_dssp             BCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            5777776666     567777789999999999999996555555564

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

Probab=83.14  E-value=0.82  Score=34.64  Aligned_cols=35  Identities=14%  Similarity=0.047  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|.+.||+++++.-|-+-++|+.|++.|++....
T Consensus        45 ~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~   79 (275)
T 3mq0_A           45 DLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA   79 (275)
T ss_dssp             CEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            48999999999999999999999999999998754

>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=83.02  E-value=1.2  Score=35.16  Aligned_cols=44  Identities=11%  Similarity=0.063  Sum_probs=36.9

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+..+-...-+|.+.||++++++-+-..+++++|++.|+|....
T Consensus        44 il~~l~~~~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           44 VYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            33333344458999999999999999999999999999999874

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=82.98  E-value=1.5  Score=27.96  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=30.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .|.-.||.+|+.....||.+|..|.+.|-+..-
T Consensus        19 MTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRKR   51 (68)
T 3i71_A           19 MTAGEVAAHFGWPLEKARNALEQLFSAGTLRKR   51 (68)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHhcchhhhh
Confidence            589999999999999999999999999998764

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=82.96  E-value=3  Score=27.15  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=28.4

Q ss_pred             hhhhhcccHHHHHHHHHHHHHcCCeeEecc---cceeEEEe
Q 033931           66 LSDRLRINGSLARRAIKDLMARGSIRMISA---HASQQIYT  103 (108)
Q Consensus        66 vserlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt  103 (108)
                      |++.++|+-+.--.+|+.|++.|+|.....   .++..+|.
T Consensus        32 l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~   72 (108)
T 3l7w_A           32 IKLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYH   72 (108)
T ss_dssp             HTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEE
T ss_pred             HHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEE
Confidence            333468999999999999999999988732   23455664

>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=82.92  E-value=1.2  Score=31.44  Aligned_cols=33  Identities=15%  Similarity=0.160  Sum_probs=30.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       186 ~~t~~~lA~~lG~sr~tvsR~l~~l~~~glI~~  218 (232)
T 1zyb_A          186 KVKMDDLARCLDDTRLNISKTLNELQDNGLIEL  218 (232)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEE
T ss_pred             cCCHHHHHHHhCCChhHHHHHHHHHHHCCCEEe
Confidence            379999999999999999999999999999975

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C

Probab=82.73  E-value=2.1  Score=27.50  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=35.1

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           64 SILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ..++.||..+.+.-++.|+.|-+++.|.....+.....|.
T Consensus        37 ~ql~~rF~p~~~~IKk~IE~LIereYl~R~~~~~~~y~Y~   76 (77)
T 3tdu_C           37 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYL   76 (77)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEEC
T ss_pred             HHHhCcCCCCHHHHHHHHHHHHhhhHhhcCCCCCceEEEe
Confidence            4567899999999999999999999999987777777774

>3u5c_T 40S ribosomal protein S19-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_S 3o30_M 3o2z_M 3u5g_T 3jyv_T*

Probab=82.66  E-value=1.1  Score=32.47  Aligned_cols=23  Identities=22%  Similarity=0.458  Sum_probs=20.4

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEec
Q 033931           72 INGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        72 I~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      =++|++|.+|+.||+-|+|....
T Consensus        96 asg~iiR~~LQqLE~~g~vek~~  118 (144)
T 3u5c_T           96 ASGSINRKVLQALEKIGIVEISP  118 (144)
T ss_dssp             CCHHHHHHHHHHHHHTTSEECCS
T ss_pred             cCcHHHHHHHHHHHHCCCeeecC
Confidence            36799999999999999998764

>3iz6_S 40S ribosomal protein S19 (S19E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=82.65  E-value=1.2  Score=32.43  Aligned_cols=24  Identities=21%  Similarity=0.423  Sum_probs=21.2

Q ss_pred             cccHHHHHHHHHHHHHcCCeeEec
Q 033931           71 RINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        71 kI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +=++|++|.+|++||+-|+|....
T Consensus        97 ~asg~iiR~~LQqLE~~g~Vek~~  120 (146)
T 3iz6_S           97 KSSGAISRNILQQLQKMGIIDVDP  120 (146)
T ss_dssp             CCCHHHHHHHHHHHHHHTSEEEET
T ss_pred             CCCcHHHHHHHHHHHHCCCeEecC
Confidence            346899999999999999998864

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=82.28  E-value=0.99  Score=31.86  Aligned_cols=43  Identities=28%  Similarity=0.387  Sum_probs=35.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEecc
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRA  105 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      .++|...+|+.++|+.+    .||.-++.|+|.+.-..++...|+..
T Consensus        10 ~~~~i~e~A~~~gvs~~----TLR~ye~~Gll~p~r~~~g~R~Y~~~   52 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKRD   52 (154)
T ss_dssp             CCBCHHHHHHHHTSCHH----HHHHHHHTTSSCCEECTTSCEEBCTT
T ss_pred             cCCCHHHHHHHHCcCHH----HHHHHHHcCCCCcccCCCCCEEeCHH
Confidence            47999999999999865    68999999999986444667788753

>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=82.13  E-value=1.1  Score=35.02  Aligned_cols=44  Identities=5%  Similarity=0.102  Sum_probs=37.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|+.-+-...-+|-+.||++++++-+-...++++|++.|+|..+
T Consensus        20 ~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~~   63 (406)
T 1z6r_A           20 AVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   63 (406)
T ss_dssp             HHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEee
Confidence            34444445556999999999999999999999999999999986

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=82.08  E-value=1.4  Score=29.18  Aligned_cols=43  Identities=23%  Similarity=0.263  Sum_probs=32.8

Q ss_pred             echhhhhhhhc--------ccH-HHHHHHHHHHHHcCCeeEecc---cceeEEEe
Q 033931           61 ITPSILSDRLR--------ING-SLARRAIKDLMARGSIRMISA---HASQQIYT  103 (108)
Q Consensus        61 ITps~vserlk--------I~~-SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt  103 (108)
                      .+.|.|++.+.        |+- +.--.+|+.|++.|+|.....   ..+..+|.
T Consensus        27 ~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~   81 (118)
T 2esh_A           27 SHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYR   81 (118)
T ss_dssp             BCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEE
T ss_pred             CCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEE
Confidence            57888888884        777 777899999999999988742   34455664

>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=81.88  E-value=0.79  Score=30.83  Aligned_cols=38  Identities=18%  Similarity=0.297  Sum_probs=33.6

Q ss_pred             CCeeechhhhhh-hhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           57 KFKLITPSILSD-RLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        57 k~k~ITps~vse-rlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +...+|++.|+| .+.+.-|.--+.|+-|+++|+|. .+.
T Consensus        27 ~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe-~~~   65 (95)
T 1bja_A           27 KKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE-KSG   65 (95)
T ss_dssp             HSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE-EET
T ss_pred             HCCCCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee-cCC
Confidence            334899999999 99999999999999999999998 443

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=81.80  E-value=0.27  Score=36.14  Aligned_cols=48  Identities=17%  Similarity=0.064  Sum_probs=41.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +=.+.|+..+.....+|...||+.|+++.+-.|+=|.||...||+..+
T Consensus        12 eR~~~i~~~l~~~~~~~~~~la~~~~vs~~TiRrDl~eL~~~~l~~r~   59 (190)
T 4a0z_A           12 KRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRI   59 (190)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHCCCEeHHHHHHHHCCCHHHHHHHHHHhcCcchhhHh
Confidence            345677777888899999999999999999999999999999987654

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=81.63  E-value=0.96  Score=29.76  Aligned_cols=40  Identities=10%  Similarity=0.122  Sum_probs=31.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-ccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS-AHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr  104 (108)
                      +|+..+|+.++|+.+    .||.-++.|+|.+.. ..++...|+.
T Consensus         2 ~~i~e~A~~~gvs~~----tLR~ye~~Gll~p~~r~~~g~R~Y~~   42 (108)
T 2vz4_A            2 YSVGQVAGFAGVTVR----TLHHYDDIGLLVPSERSHAGHRRYSD   42 (108)
T ss_dssp             BCHHHHHHHHTCCHH----HHHHHHHHTSSCCSEECSSCCEEBCH
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeecCH
Confidence            578899999998765    578899999999875 3456778875

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=81.45  E-value=0.29  Score=41.49  Aligned_cols=54  Identities=9%  Similarity=0.084  Sum_probs=0.0

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+.-+..+.-||-+.|++.++++..-|+++|+.|.++|+|..+-.. +-.-|..
T Consensus       520 ~I~~~l~~~g~it~~di~~l~~ls~~qa~~~L~~Lv~~G~l~~~G~g-r~t~Y~~  573 (583)
T 3lmm_A          520 AAMLWLSEVGDLATSDLMAMCGVSRGTAKACVDGLVDEERVVAVGGG-RSRRYRL  573 (583)
T ss_dssp             -------------------------------------------------------
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeCCC-CceEEEE
Confidence            45555566788999999999999999999999999999999987543 4445543

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=80.94  E-value=3.7  Score=27.30  Aligned_cols=43  Identities=12%  Similarity=0.084  Sum_probs=33.6

Q ss_pred             echhhhhhhhc------ccHHHHHHHHHHHHHcCCeeEecc----cceeEEEe
Q 033931           61 ITPSILSDRLR------INGSLARRAIKDLMARGSIRMISA----HASQQIYT  103 (108)
Q Consensus        61 ITps~vserlk------I~~SlAr~~Lr~L~~kGlIk~V~k----~~~q~IYt  103 (108)
                      .+.|.|++++.      |+-+.--.+|+.|++.|+|.....    .++..+|.
T Consensus        23 ~~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~   75 (115)
T 4esb_A           23 VYGYELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYH   75 (115)
T ss_dssp             EEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEE
T ss_pred             CCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEE
Confidence            47788888875      899999999999999999987632    34455664

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

Probab=80.83  E-value=1.8  Score=32.11  Aligned_cols=33  Identities=12%  Similarity=0.091  Sum_probs=31.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      =+|+..||+++++.-.+.++.||.|...|++..
T Consensus        39 ~~t~~ela~~~~~~~~~l~r~L~~L~~~g~l~~   71 (335)
T 2r3s_A           39 IESSQSLAQKCQTSERGMRMLCDYLVIIGFMTK   71 (335)
T ss_dssp             EECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHhCCCchHHHHHHHHHHhcCCeEe
Confidence            489999999999999999999999999999975

>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=80.59  E-value=1.3  Score=33.50  Aligned_cols=34  Identities=18%  Similarity=0.085  Sum_probs=32.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|+..|++++.+.-+--=.+|..|+++|+|...
T Consensus        50 ~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~   83 (250)
T 1p4x_A           50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKV   83 (250)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEE
T ss_pred             CcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence            4799999999999999999999999999999887

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=80.09  E-value=1.2  Score=27.66  Aligned_cols=41  Identities=15%  Similarity=0.281  Sum_probs=31.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccc-ceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMAR-GSIRMISAH-ASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~-~~q~IYtr  104 (108)
                      .+|+..+|+.++|+.+    .||.-+++ |++.+.-.. ++...|+.
T Consensus         5 ~~~i~e~A~~~gvs~~----tlR~ye~~~gl~~p~r~~~~g~R~Y~~   47 (81)
T 2jml_A            5 TLRIRTIARMTGIREA----TLRAWERRYGFPRPLRSEGNNYRVYSR   47 (81)
T ss_dssp             CEEHHHHHHTTSTTHH----HHHHHHHHTCCSCCBSSSCSSSCEECH
T ss_pred             cccHHHHHHHHCcCHH----HHHHHHHhCCCCCCcCCCCCCeeecCH
Confidence            5899999999998865    57788997 999886433 56677874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	108
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	97.19
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	97.06
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	96.71
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.17
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.16
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.13
d2b0la1	91	GTP-sensing transcriptional pleiotropic repressor	96.12
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.11
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.93
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.91
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.88
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	95.56
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	95.53
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	95.51
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	95.48
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	95.48
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	95.32
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	95.31
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	95.03
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.0
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	94.9
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	94.89
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.87
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.72
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	94.7
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.63
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.55
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	94.5
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	94.36
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.33
d1okra_	120	Methicillin resistance regulatory protein MecI {St	94.18
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	94.15
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	94.13
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	93.94
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	93.93
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	93.91
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.84
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	93.73
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	93.72
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.69
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	93.67
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.46
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	93.45
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	93.39
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.08
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	93.06
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	92.77
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	92.7
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	92.52
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	92.14
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	92.14
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	91.97
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	91.79
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	91.71
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	91.47
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	91.25
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	90.97
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	89.85
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	89.65
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	89.47
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	89.42
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	89.08
d1zyba1	73	Probable transcription regulator BT4300, C-termina	88.48
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	88.4
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	88.3
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	87.76
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	87.73
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	87.47
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	86.99
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	86.57
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	85.98
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	85.43
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	85.39
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	84.97
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	84.75
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	84.58
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	84.31
d1iuya_	92	Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 1	83.54
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	83.43
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	83.19
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	82.2
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	82.08
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	82.02
d2p5ka1	63	Arginine repressor (ArgR), N-terminal DNA-binding	81.67

>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=97.19  E-value=0.00059  Score=41.40  Aligned_cols=39  Identities=15%  Similarity=0.192  Sum_probs=35.1

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |..++ +...||++|+++-+..|.||+.|+++|+|...-+
T Consensus        22 ~G~~l-~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1          22 PGARL-SEPDICAALDVSRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             TTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CcCcc-CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            56776 7899999999999999999999999999987643

>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=97.06  E-value=0.00057  Score=42.29  Aligned_cols=50  Identities=14%  Similarity=0.222  Sum_probs=41.2

Q ss_pred             HHHHHHHHhhC--CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEA--PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEV--pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +.+.+.|....  |+.+|=+-..||++|+|+-+.+|++|+.|+++|+|....
T Consensus        10 e~i~~~I~~g~~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          10 EYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             HHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEe
Confidence            44555666554  566887889999999999999999999999999997753

>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=0.0013  Score=40.40  Aligned_cols=39  Identities=18%  Similarity=0.205  Sum_probs=35.2

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           56 PKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |..+|-|-..||+.|+|+-+..|.||+.|++.|+|...-
T Consensus        18 ~G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          18 QGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             TTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            456777999999999999999999999999999998764

>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=96.17  E-value=0.0042  Score=37.04  Aligned_cols=47  Identities=15%  Similarity=0.120  Sum_probs=39.3

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ++--+|+.-...-.++|...||++|+|+-+-.++-|+.|++.|++..
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~   51 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF   51 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCE
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEE
Confidence            34445666666678899999999999999999999999999998543

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.16  E-value=0.0057  Score=39.18  Aligned_cols=46  Identities=22%  Similarity=0.272  Sum_probs=38.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--cccceeEEEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI--SAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr  104 (108)
                      .-+|++.||+.++|.-|-...+|..|+++|+|...  ..+++..+|..
T Consensus        33 g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a   80 (109)
T d1sfxa_          33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSA   80 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEE
T ss_pred             CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccC
Confidence            34699999999999999999999999999999865  34556666764

>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=96.13  E-value=0.0085  Score=37.40  Aligned_cols=47  Identities=36%  Similarity=0.335  Sum_probs=38.7

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEE
Q 033931           54 EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQI  101 (108)
Q Consensus        54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I  101 (108)
                      +..+-.-||++.||+++++.-|-.-++|..|++.|+|..-. ++|...
T Consensus        15 ~~~~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~-D~R~~~   61 (85)
T d3ctaa1          15 EASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTV-TKRGQI   61 (85)
T ss_dssp             TTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE-ETTEEE
T ss_pred             hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeec-cccccc
Confidence            34445689999999999999999999999999999999854 444433

>d2b0la1 a.4.5.66 (A:167-257) GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CodY HTH domain
domain: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=96.12  E-value=0.0044  Score=40.40  Aligned_cols=62  Identities=19%  Similarity=0.281  Sum_probs=51.4

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           33 QKEKVNNMVLFDQATYDKLLSEAPK-FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        33 ~keK~nn~V~~dk~t~dKl~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ++--++..-+-+-+..+.|..|... .=++..|.||||.+|+-|+-=.+||.||+-|+|.-=|
T Consensus         6 v~~Ai~tLSySEleAv~hIf~eL~g~EGllvASkiADrvgiTRSVIVNALRK~ESAGvIEsrS   68 (91)
T d2b0la1           6 VQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   68 (91)
T ss_dssp             HHHHHHTSCHHHHHHHHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHcCCCcceEeehhhhhhhCchHHHHHHHHHHhhhcceeeecc
Confidence            3444455555566788899999985 4799999999999999999999999999999998653

>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=96.11  E-value=0.0049  Score=39.16  Aligned_cols=33  Identities=21%  Similarity=0.358  Sum_probs=31.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||++++|.-|-...+|+.|+++|+|...
T Consensus        37 ~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~   69 (109)
T d2d1ha1          37 ITSEELADIFKLSKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEe
Confidence            799999999999999999999999999999876

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=95.93  E-value=0.0065  Score=35.96  Aligned_cols=46  Identities=11%  Similarity=0.192  Sum_probs=38.2

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |...+.-|..+ +   -+|...||++++++.+..+.=|+.|++.|+|..+
T Consensus         7 D~~IL~~L~~~-~---r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           7 DRGILEALMGN-A---RTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHC-T---TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            55666666655 3   3489999999999999999999999999999854

>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=95.91  E-value=0.0063  Score=39.77  Aligned_cols=34  Identities=24%  Similarity=0.287  Sum_probs=32.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+++++.-|-+-.+|+.|++.|+|..+.
T Consensus        42 lt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~   75 (151)
T d1ku9a_          42 LTISDIMEELKISKGNVSMSLKKLEELGFVRKVW   75 (151)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             cCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEE
Confidence            9999999999999999999999999999999873

>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=95.88  E-value=0.0066  Score=39.27  Aligned_cols=35  Identities=14%  Similarity=0.104  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-||+..||++++++-|-+-++|+.|+++|+|...
T Consensus        44 ~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~   78 (135)
T d3broa1          44 KEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   78 (135)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHH
Confidence            55899999999999999999999999999999877

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=95.56  E-value=0.0079  Score=35.94  Aligned_cols=43  Identities=12%  Similarity=0.053  Sum_probs=35.8

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           51 LLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |+.-+-...-+|-+.||+.++++-+-+..+|++|++.|+|..+
T Consensus        11 Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1          11 VYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3333333445999999999999999999999999999999876

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=95.53  E-value=0.0035  Score=40.32  Aligned_cols=51  Identities=12%  Similarity=0.087  Sum_probs=42.2

Q ss_pred             HHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           45 QATYDKLLSEAPK------FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        45 k~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      +.+++.|...|-.      .+|-|-..||+.|+|+-+..|.||+.|+++|+|....+
T Consensus        12 ~qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1          12 ADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             HHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETT
T ss_pred             HHHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecC
Confidence            3466667666654      56779999999999999999999999999999987643

>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=95.51  E-value=0.012  Score=37.27  Aligned_cols=46  Identities=15%  Similarity=0.189  Sum_probs=39.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--cccceeEEEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI--SAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr  104 (108)
                      +=|....|-.+.++.-+.-.++|+.||.+++|+.|  .+|+...+|.-
T Consensus        28 ~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~VksV~~~~rK~YmL   75 (78)
T d2dk5a1          28 KGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYML   75 (78)
T ss_dssp             TCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEE
T ss_pred             cceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceeecccCCCCeEEEEe
Confidence            45777889999999999999999999999999999  45556778863

>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=95.48  E-value=0.013  Score=38.09  Aligned_cols=34  Identities=26%  Similarity=0.200  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        44 ~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~   77 (139)
T d2a61a1          44 PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   77 (139)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCCcccchHHHHHHHhcCeeeee
Confidence            3699999999999999999999999999999877

>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=95.48  E-value=0.011  Score=38.51  Aligned_cols=33  Identities=15%  Similarity=0.104  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||++++|.-|-+-++++.|+++|+|...
T Consensus        47 ~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~   79 (140)
T d2etha1          47 KKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   79 (140)
T ss_dssp             BCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            799999999999999999999999999999988

>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=95.32  E-value=0.014  Score=38.19  Aligned_cols=34  Identities=21%  Similarity=0.284  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        51 ~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~   84 (141)
T d1lnwa_          51 LNLQDLGRQMCRDKALITRKIRELEGRNLVRRER   84 (141)
T ss_dssp             CBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCccHhHHHHHHHHHHHhhceeeec
Confidence            7999999999999999999999999999998773

>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=95.31  E-value=0.02  Score=35.55  Aligned_cols=64  Identities=11%  Similarity=0.074  Sum_probs=44.5

Q ss_pred             ccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--ccceeEEEe
Q 033931           39 NMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS--AHASQQIYT  103 (108)
Q Consensus        39 n~V~~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IYt  103 (108)
                      +.++.|+.-+ .|+.-+-...-+|++.|++.++|+-+..-+.|+.|++.|+|....  .+++..+|.
T Consensus        10 ~~~l~~p~r~-~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~   75 (100)
T d1ub9a_          10 SHILGNPVRL-GIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVE   75 (100)
T ss_dssp             CHHHHSHHHH-HHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             HHhcCCHHHH-HHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCcccccc
Confidence            3344444322 244444333348999999999999999999999999999997652  245555564

>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=95.03  E-value=0.011  Score=38.61  Aligned_cols=39  Identities=18%  Similarity=0.225  Sum_probs=35.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccee
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQ   99 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      +|..+||+.++++-+.-|++|+.|.+.|+|.-+-+.+..
T Consensus        19 ~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG~~GG   57 (127)
T d1xd7a_          19 TSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGA   57 (127)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSSC
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCCCCCc
Confidence            799999999999999999999999999999987665443

>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=95.00  E-value=0.016  Score=37.57  Aligned_cols=35  Identities=17%  Similarity=0.150  Sum_probs=33.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.|+++++|.-+-.-++|+.|+++|+|..+
T Consensus        45 ~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~   79 (140)
T d3deua1          45 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQ   79 (140)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEec
Confidence            36899999999999999999999999999999877

>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=94.90  E-value=0.021  Score=36.87  Aligned_cols=34  Identities=21%  Similarity=0.336  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.+++.-|..-+++..|+++|+|...
T Consensus        43 ~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~   76 (137)
T d2fbha1          43 SPTQRELAQSVGVEGPTLARLLDGLESQGLVRRL   76 (137)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHHHcCCcccc
Confidence            3799999999999999999999999999999987

>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=94.89  E-value=0.018  Score=36.14  Aligned_cols=61  Identities=16%  Similarity=0.233  Sum_probs=55.2

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      .++..+...|...|+|.--.||..|+++-..+..=|++|++.|.|.=|.-.+.-.||.--+
T Consensus         7 ~lL~~FI~~Ik~~Kvv~LedLAa~F~lktqd~i~RIq~Le~~g~ltGViDDRGKfIyIS~s   67 (72)
T d1wi9a_           7 GFLTEFINYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPS   67 (72)
T ss_dssp             CHHHHHHHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECCCS
T ss_pred             HHHHHHHHHHHHCCEeeHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeEEcCCCCEEEEcCC
Confidence            4567778888889999999999999999999999999999999999998889999998544

>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=94.87  E-value=0.015  Score=38.13  Aligned_cols=34  Identities=26%  Similarity=0.245  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+++++..|-+-++|..|+.+|+|...
T Consensus        49 ~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~   82 (145)
T d2hr3a1          49 DVTPSELAAAERMRSSNLAALLRELERGGLIVRH   82 (145)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEee
Confidence            4999999999999999999999999999999876

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=94.72  E-value=0.016  Score=34.54  Aligned_cols=33  Identities=12%  Similarity=0.129  Sum_probs=30.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -++.+.||++|+|.-+-+-.+|+.|+++|+|..
T Consensus        21 ~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~   53 (61)
T d2ev0a1          21 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            478899999999999999999999999999864

>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=94.70  E-value=0.028  Score=36.92  Aligned_cols=34  Identities=26%  Similarity=0.370  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        44 ~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~   77 (144)
T d1lj9a_          44 IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE   77 (144)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCccHhhHHHHHHHHHhhhcccccC
Confidence            7999999999999999999999999999998773

>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=94.63  E-value=0.037  Score=32.62  Aligned_cols=47  Identities=13%  Similarity=0.270  Sum_probs=38.4

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|...++-|+.+-    =+|.+.||+.++++-+-...=|+.|++.|+|.-+
T Consensus         6 ~D~~IL~~L~~n~----r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           6 IDLNIIEELKKDS----RLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHHCS----CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcC----CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence            3556666666542    3489999999999999999999999999999754

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.55  E-value=0.02  Score=33.36  Aligned_cols=47  Identities=17%  Similarity=0.179  Sum_probs=38.6

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|...++-|.++    --+|...||++++++.+-...-|+.|++.|+|.-+
T Consensus         4 ~D~~Il~~L~~n----~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           4 IDKKIIKILQND----GKAPLREISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHHC----TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            456666666665    23499999999999999999999999999999743

>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=94.50  E-value=0.039  Score=35.62  Aligned_cols=33  Identities=15%  Similarity=0.135  Sum_probs=32.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +|++.||++++|.-+-.-.+|+.|+++|+|...
T Consensus        45 ~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~   77 (136)
T d2fbia1          45 MESYQLANQACILRPSMTGVLARLERDGIVRRW   77 (136)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            799999999999999999999999999999877

>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=94.36  E-value=0.023  Score=36.87  Aligned_cols=36  Identities=8%  Similarity=0.037  Sum_probs=33.3

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..=+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        46 ~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~   81 (136)
T d2bv6a1          46 ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRE   81 (136)
T ss_dssp             SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEe
Confidence            345799999999999999999999999999999877

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=94.33  E-value=0.038  Score=33.39  Aligned_cols=38  Identities=24%  Similarity=0.368  Sum_probs=32.1

Q ss_pred             echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEecccce
Q 033931           61 ITPSILSDRLRI-NGSLARRAIKDLMARGSIRMISAHAS   98 (108)
Q Consensus        61 ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      .|...|++.|++ +-|-++..|..|+++|+|......+|
T Consensus        25 Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~~~~R   63 (71)
T d1jhfa1          25 PTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASR   63 (71)
T ss_dssp             CCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECSSSSS
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCCCCCc
Confidence            467789999999 57789999999999999999854444

>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=94.18  E-value=0.037  Score=35.56  Aligned_cols=45  Identities=13%  Similarity=0.121  Sum_probs=37.8

Q ss_pred             echhhhhhhh----cccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           61 ITPSILSDRL----RINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        61 ITps~vserl----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      +|+..|++.+    .+..|--..+|+-|+++|+|..- ++++..+|++..
T Consensus        22 ~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~-~~gr~~~Y~~~~   70 (120)
T d1okra_          22 ASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK-KDNKIFQYYSLV   70 (120)
T ss_dssp             EEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE-EETTEEEEEESS
T ss_pred             CCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEE-ecCCceEEeecC
Confidence            7899988887    58899999999999999999874 456777998754

>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=94.15  E-value=0.026  Score=36.65  Aligned_cols=35  Identities=14%  Similarity=0.238  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .=+|++.||+++++.-+-.-+++..|+++|+|...
T Consensus        46 ~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~   80 (137)
T d1z91a1          46 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   80 (137)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEe
Confidence            45899999999999999999999999999999988

>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=94.13  E-value=0.04  Score=35.83  Aligned_cols=34  Identities=24%  Similarity=0.371  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.++|.-+.+-+++..|+++|+|...
T Consensus        48 ~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~   81 (138)
T d1jgsa_          48 CITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEe
Confidence            3899999999999999999999999999999865

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.94  E-value=0.033  Score=33.66  Aligned_cols=36  Identities=14%  Similarity=0.121  Sum_probs=33.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.||+.+++.-|-+.++|..|++.|++....
T Consensus        19 ~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~   54 (75)
T d1mkma1          19 GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK   54 (75)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            358999999999999999999999999999998753

>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=93.93  E-value=0.042  Score=35.66  Aligned_cols=34  Identities=15%  Similarity=0.165  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|+..||+++++.-+-+-+++..|+++|+|...
T Consensus        49 ~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~   82 (143)
T d1s3ja_          49 SLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   82 (143)
T ss_dssp             EEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheee
Confidence            3799999999999999999999999999999877

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.91  E-value=0.029  Score=33.57  Aligned_cols=33  Identities=15%  Similarity=0.312  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      .++.+.||++|+|.-+-+-.+++.|.++|+|..
T Consensus        23 ~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          23 TPLRARIAERLDQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            478899999999999999999999999999965

>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=93.84  E-value=0.022  Score=36.62  Aligned_cols=42  Identities=14%  Similarity=0.033  Sum_probs=35.7

Q ss_pred             HhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           52 LSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        52 ~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +-+-|.- -+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        42 l~~~~~~-~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~   83 (115)
T d2frha1          42 ISENKEK-EYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   83 (115)
T ss_dssp             HHHTCCS-EEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             HHcCCCC-CCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeee
Confidence            3344442 37999999999999999999999999999999883

>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=93.73  E-value=0.042  Score=32.36  Aligned_cols=34  Identities=12%  Similarity=0.195  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ||-+.||+.+++..+-...++++|++.|+|....
T Consensus        13 isr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1          13 VSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            7999999999999999999999999999999874

>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=93.72  E-value=0.026  Score=36.30  Aligned_cols=34  Identities=9%  Similarity=0.040  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|++.||+++++.-|-.=++|..|+++|+|...
T Consensus        48 ~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~   81 (115)
T d1hsja1          48 EISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKK   81 (115)
T ss_dssp             EEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEE
Confidence            4999999999999999999999999999999877

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.69  E-value=0.051  Score=31.98  Aligned_cols=40  Identities=18%  Similarity=0.171  Sum_probs=35.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIY  102 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY  102 (108)
                      +|...||+-++++-.-.-++|++|+++|+|..  .+++..||
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~~--~~~~I~I~   69 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLISA--HGKTIVVY   69 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--ETTEEEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--cCCEEEEC
Confidence            79999999999999999999999999999974  35666665

>d2ve8a1 a.4.5.67 (A:745-811) DNA translocase FtsK {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.67  E-value=0.0076  Score=37.25  Aligned_cols=60  Identities=17%  Similarity=0.270  Sum_probs=46.7

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .++|++...=|-...-.+.|.|--+|+|-..-|-+++..||+.|+|-+-..+..-.|.++
T Consensus         3 D~ly~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~g~~~ReVL~~   62 (67)
T d2ve8a1           3 DPLYDEAVRFVTESRRASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMNTNGSREVIAP   62 (67)
T ss_dssp             CTTHHHHHHHHHHHCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCCTTSCCCBCSC
T ss_pred             cHHHHHHHHHHHHhCcccHHHHHHHHhcchHHHHHHHHHHHHCcCCCCCCCCCCCeEeCC
Confidence            345666665555566788999999999999999999999999999999865444344443

>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=93.46  E-value=0.013  Score=34.34  Aligned_cols=46  Identities=20%  Similarity=0.262  Sum_probs=37.2

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           43 FDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...+.-|..+    -=+|...||++++++.+....-|+.|++.|+|.-
T Consensus         4 ~D~kIl~~L~~n----~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1           4 RDKIILEILEKD----ARTPFTEIAKKLGISETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHHHC----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            355555555544    2359999999999999999999999999999964

>d2j5pa1 a.4.5.67 (A:1261-1329) DNA translocase FtsK {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Escherichia coli [TaxId: 562]

Probab=93.45  E-value=0.018  Score=35.77  Aligned_cols=59  Identities=15%  Similarity=0.233  Sum_probs=48.7

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      .++|++...=|-...-.+.|.|--||+|-..-|-+++..||+.|+|-+-..+..-.|+.
T Consensus         6 D~ly~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~~~~~ReVL~   64 (69)
T d2j5pa1           6 DPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLA   64 (69)
T ss_dssp             CTTHHHHHHHHHHTTEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSBCCCCSSSEEEBCS
T ss_pred             cHHHHHHHHHHHHhCcccHHHHHHHHhccchHHHHHHHHHHHCCcCCCCCCCCCCeEcC
Confidence            35677777777778889999999999999999999999999999999875554444444

>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=93.39  E-value=0.04  Score=32.90  Aligned_cols=46  Identities=4%  Similarity=0.083  Sum_probs=40.8

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           48 YDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...|+.-+....-+|-+.||+.++++.+-...++++|.+.|+|...
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            3456666777888999999999999999999999999999999876

>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=93.08  E-value=0.035  Score=36.07  Aligned_cols=34  Identities=18%  Similarity=0.085  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|+..||+++++.-|-.-++|+.|+++|+|..+
T Consensus        50 ~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~   83 (125)
T d1p4xa1          50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKV   83 (125)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEE
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCceee
Confidence            5999999999999999999999999999999998

>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=93.06  E-value=0.036  Score=32.67  Aligned_cols=43  Identities=12%  Similarity=0.184  Sum_probs=36.0

Q ss_pred             HHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033931           47 TYDKLLSEAPKF-KLITPSILSDRLRINGSLARRAIKDLMARGS   89 (108)
Q Consensus        47 t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGl   89 (108)
                      -..+|+..+... ..||...||++|+|+-.-.|+=|.+|++.|+
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            345555555444 5799999999999999999999999999997

>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=92.77  E-value=0.067  Score=35.06  Aligned_cols=38  Identities=16%  Similarity=0.239  Sum_probs=33.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      ..+|...||++++|+-...+++|+.|.+.|+|.-..++
T Consensus        22 ~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG~   59 (138)
T d1ylfa1          22 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGP   59 (138)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecCC
Confidence            46899999999999999999999999999999888765

>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=92.70  E-value=0.077  Score=31.45  Aligned_cols=40  Identities=10%  Similarity=0.130  Sum_probs=35.6

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033931           58 FKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHA   97 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      +.--|...|++.+++.-..+|.+|+.|.+.|.+..|+..+
T Consensus        21 ~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~~d~   60 (64)
T d1lvaa3          21 WQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEF   60 (64)
T ss_dssp             TSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSB
T ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecccc
Confidence            4556778999999999999999999999999999997654

>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=92.52  E-value=0.071  Score=34.80  Aligned_cols=34  Identities=15%  Similarity=0.162  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.+++.-|-.-++++.|+++|+|...
T Consensus        49 ~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~   82 (125)
T d1p4xa2          49 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE   82 (125)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             CccHHHHHHHHCCCcchHHHHHHHHHhccCEeee
Confidence            4899999999999999999999999999999876

>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=92.14  E-value=0.046  Score=33.67  Aligned_cols=36  Identities=17%  Similarity=0.295  Sum_probs=32.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           57 KFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ..=+||++.|-+.|+-.-.-|+.+|++|..+|+.=.
T Consensus        14 ~~G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~Wv   49 (68)
T d1u5ta2          14 ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWI   49 (68)
T ss_dssp             TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEE
T ss_pred             HcCceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEE
Confidence            346899999999999999999999999999998743

>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=92.14  E-value=0.15  Score=32.52  Aligned_cols=45  Identities=24%  Similarity=0.358  Sum_probs=34.0

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--ceeEEEe
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH--ASQQIYT  103 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~--~~q~IYt  103 (108)
                      .--|..|.+.+|+   ||+.+||+|           |++|++.|+|....-+  .....|.
T Consensus        33 ~~rF~el~~~l~g---Is~~~Ls~r-----------LkeL~~~glv~r~~~~~~p~~veY~   79 (102)
T d2fswa1          33 IIRYGELKRAIPG---ISEKMLIDE-----------LKFLCGKGLIKKKQYPEVPPRVEYS   79 (102)
T ss_dssp             CEEHHHHHHHSTT---CCHHHHHHH-----------HHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCCHHHHHhhCcc---cchhHHHHH-----------HHHHHHCCceeecccCCCCCeehhh
Confidence            3457888888887   899999998           6899999999876432  2334565

>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=91.97  E-value=0.15  Score=34.45  Aligned_cols=59  Identities=24%  Similarity=0.231  Sum_probs=42.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----ccceeEEEecc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS----AHASQQIYTRA  105 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYtr~  105 (108)
                      ++--+|+.-.-. .=.|.+.||+.+++.-+.+..-|+.|++.|+|..+.    .++.+.+|..+
T Consensus        19 p~R~~Il~~L~~-~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~   81 (190)
T d1ulya_          19 DTRRKILKLLRN-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRT   81 (190)
T ss_dssp             HHHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEES
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEc
Confidence            333445544432 236999999999999999999999999999997652    22346677644

>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=91.79  E-value=0.093  Score=33.12  Aligned_cols=42  Identities=19%  Similarity=0.216  Sum_probs=32.4

Q ss_pred             eeechhhhhhhhcc--cHHHHHHHHHHHHHcCCeeEecccceeEE
Q 033931           59 KLITPSILSDRLRI--NGSLARRAIKDLMARGSIRMISAHASQQI  101 (108)
Q Consensus        59 k~ITps~vserlkI--~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I  101 (108)
                      .=|+-..|++.+++  +-+-.|..|.+|+++|+|.. .+.++..|
T Consensus        22 ~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~-~h~s~Gri   65 (87)
T d1stza1          22 KPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ-PHTSAGRI   65 (87)
T ss_dssp             SCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC-CSSCSCBE
T ss_pred             CccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC-CCCCCCCc
Confidence            44778889999666  57889999999999999987 44444433

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=91.71  E-value=0.092  Score=33.48  Aligned_cols=43  Identities=12%  Similarity=0.072  Sum_probs=34.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--cccceeEEEecc
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI--SAHASQQIYTRA  105 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr~  105 (108)
                      .+.|...||+.++|+.+    .||+-++.|||.|-  ...++.+.|+..
T Consensus         2 ~yytI~evA~~~gvs~~----tlR~Ye~~GLl~P~~~r~~~gyR~Y~~~   46 (118)
T d1r8ea1           2 SYYSIGEVSKLANVSIK----ALRYYDKIDLFKPAYVDPDTSYRYYTDS   46 (118)
T ss_dssp             CEEEHHHHHHHHTCCHH----HHHHHHHTTSSCCSEECTTTCCEEEETG
T ss_pred             CcccHHHHHHHHCcCHH----HHHHHHHcCCcccccccCCCCcccccHH
Confidence            47899999999998765    58999999999874  345667889864

>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=91.47  E-value=0.21  Score=31.37  Aligned_cols=53  Identities=13%  Similarity=0.177  Sum_probs=41.5

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           50 KLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|+..+-.-. .|++.|++.++++-|..-.=|+.|++-|+|..- +.++...|.-
T Consensus        27 ~Il~~L~~~~-~~v~ela~~l~is~stvS~HL~~L~~aglV~~~-r~G~~~~Y~l   79 (98)
T d1r1ta_          27 RLLSLLARSE-LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYR-KQGRHVYYQL   79 (98)
T ss_dssp             HHHHHHTTCC-BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-EETTEEEEEE
T ss_pred             HHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE-EECCEEEEEE
Confidence            4444444434 699999999999999999999999999999874 4555666653

>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=91.25  E-value=0.23  Score=30.44  Aligned_cols=45  Identities=11%  Similarity=0.178  Sum_probs=35.4

Q ss_pred             echhhhhhh----hcccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           61 ITPSILSDR----LRINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        61 ITps~vser----lkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      +|...|.+.    ..+.-+-.+..|+.|+++|+|.. .+.++..+|++..
T Consensus        24 ~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~-~k~gr~~~Y~p~i   72 (82)
T d1p6ra_          24 INTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNH-HKEGRVFVYTPNI   72 (82)
T ss_dssp             EEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEESC
T ss_pred             CCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEE-EecCCeEEEEecC
Confidence            577776544    46788899999999999999986 4567788998754

>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=90.97  E-value=0.19  Score=32.50  Aligned_cols=45  Identities=11%  Similarity=0.133  Sum_probs=35.0

Q ss_pred             echhhhhhhh----cccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           61 ITPSILSDRL----RINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        61 ITps~vserl----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      +|+..|.+.|    .+..|-.+..|+.|+++|+|... +.++..+|++..
T Consensus        23 ~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~-~~gr~~~Y~~~i   71 (122)
T d2g9wa1          23 QTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI-RDDRAHRYAPVH   71 (122)
T ss_dssp             EEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE-C---CCEEEESS
T ss_pred             ccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEe-ecCCeEEEEeCC
Confidence            6888888777    57789999999999999999975 456677998753

>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=89.85  E-value=0.31  Score=31.56  Aligned_cols=45  Identities=11%  Similarity=0.204  Sum_probs=36.8

Q ss_pred             echhhhhhhh----cccHHHHHHHHHHHHHcCCeeEecccceeEEEeccc
Q 033931           61 ITPSILSDRL----RINGSLARRAIKDLMARGSIRMISAHASQQIYTRAT  106 (108)
Q Consensus        61 ITps~vserl----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      +|+..|.+.+    .+..+-.+..|+-|+++|+|.. .+.++..+|++..
T Consensus        21 ~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~-~~~gr~~~Y~~~v   69 (122)
T d1sd4a_          21 VSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKR-YKSENIYFYSSNI   69 (122)
T ss_dssp             EEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEECS
T ss_pred             CCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceee-eccCCeEEEeecC
Confidence            6888766664    7788999999999999999985 5667788998753

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=89.65  E-value=0.11  Score=32.68  Aligned_cols=40  Identities=8%  Similarity=0.081  Sum_probs=33.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-cceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISA-HASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      .|...||+.++|+.    ..||.-++.|||.|+.. .++...|+.
T Consensus         3 ytI~e~A~~~gvs~----~tlR~Ye~~GLl~p~~r~~~gyR~Y~~   43 (109)
T d1r8da_           3 YQVKQVAEISGVSI----RTLHHYDNIELLNPSALTDAGYRLYSD   43 (109)
T ss_dssp             BCHHHHHHHHSCCH----HHHHHHHHTTSSCCSEECTTCCEEBCH
T ss_pred             ccHHHHHHHHCcCH----HHHHHHHHcCCcCCcccCCcccccccH
Confidence            48899999999874    57999999999998744 467788875

>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=89.47  E-value=0.77  Score=28.18  Aligned_cols=53  Identities=19%  Similarity=0.306  Sum_probs=45.0

Q ss_pred             CHHHHHHHHh---hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033931           44 DQATYDKLLS---EAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH   96 (108)
Q Consensus        44 dk~t~dKl~K---EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      |.++|+-+.+   +.|.-..+|.-.||-+|+|.-+=+-+.|=.|+++|.+..+..+
T Consensus         5 ~~~i~~lvk~~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~t   60 (70)
T d1sfua_           5 DAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   60 (70)
T ss_dssp             SHHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHHHHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCCc
Confidence            5666665555   5566789999999999999999999999999999999988654

>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=89.42  E-value=0.2  Score=33.90  Aligned_cols=34  Identities=24%  Similarity=0.116  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||+.+++.-+-.-++++.|+++|+|....
T Consensus        56 ~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~   89 (162)
T d2fxaa1          56 ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK   89 (162)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             cCHHHHHHHHcCCchhhHHHHHHHHHCCCceeec
Confidence            7999999999999999999999999999999763

>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=89.08  E-value=0.4  Score=30.03  Aligned_cols=44  Identities=27%  Similarity=0.395  Sum_probs=32.1

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--ceeEEEe
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH--ASQQIYT  103 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~--~~q~IYt  103 (108)
                      --|+.|...+|+   ||+.+||+||           ++|++.|+|....-+  .....|.
T Consensus        25 ~rF~el~~~l~g---is~~~Ls~rL-----------k~Le~~glv~r~~~~~~p~~veY~   70 (95)
T d2hzta1          25 KRTSELKRLMPN---ITQKMLTQQL-----------RELEADGVINRIVYNQVPPKVEYE   70 (95)
T ss_dssp             BCHHHHHHHCTT---SCHHHHHHHH-----------HHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCHHHHHHHhhc---CChhHHHHHH-----------HHHHHhHHHhheeccccccchhhh
Confidence            347778888875   7888888885           899999999876332  2334465

>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=88.48  E-value=0.34  Score=28.88  Aligned_cols=32  Identities=16%  Similarity=0.186  Sum_probs=30.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+-++++-.-.-++|++|+++|+|..
T Consensus        28 lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~~   59 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISKTLNELQDNGLIEL   59 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            69999999999999999999999999999973

>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=88.40  E-value=0.28  Score=29.01  Aligned_cols=32  Identities=13%  Similarity=0.177  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+-++++-.-.-++|++|+++|+|..
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            78999999999999999999999999999974

>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=88.30  E-value=0.45  Score=32.47  Aligned_cols=33  Identities=21%  Similarity=0.115  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .|++.||++|+|+-+-.+.=|+.|++.|+|...
T Consensus        29 ~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~   61 (194)
T d2p4wa1          29 YFVSELSRELGVGQKAVLEHLRILEEAGLIESR   61 (194)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            699999999999999999999999999999865

>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=87.76  E-value=0.052  Score=36.81  Aligned_cols=34  Identities=26%  Similarity=0.367  Sum_probs=32.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|++.||++++|.-+-.-++|..|+++|+|....
T Consensus        80 lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          80 LRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             BCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             cCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeec
Confidence            7999999999999999999999999999999884

>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=87.73  E-value=0.4  Score=29.05  Aligned_cols=42  Identities=21%  Similarity=0.271  Sum_probs=35.8

Q ss_pred             HHhhCCCCeeechhhhhhhh-cccHHHHHHHHHHHHHcCCeeE
Q 033931           51 LLSEAPKFKLITPSILSDRL-RINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +.+..|.-.=|....|..+| ++..+-.+.++++|...|.|=.
T Consensus        14 ~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_          14 LIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             HHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCceec
Confidence            44566666678999999999 7999999999999999999843

>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=87.47  E-value=0.45  Score=30.32  Aligned_cols=44  Identities=11%  Similarity=0.208  Sum_probs=35.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           60 LITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      =.|++.|++.+++.-|..-.=|+.|.+-|+|..- +.++...|.-
T Consensus        45 ~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~-r~G~~~~Y~l   88 (108)
T d1u2wa1          45 ELCVCDIANILGVTIANASHHLRTLYKQGVVNFR-KEGKLALYSL   88 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CCEEEE
T ss_pred             CccHHHHHHHHccChhHHHHHHHHHHHCCeeEEE-EECCEEEEEE
Confidence            3889999999999999999999999999999874 4455556653

>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=86.99  E-value=0.34  Score=28.74  Aligned_cols=32  Identities=6%  Similarity=0.147  Sum_probs=30.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+-++++-.-.-++|.+|.+.|+|..
T Consensus        31 lt~~elA~~~g~sretvsr~l~~l~~~glI~~   62 (80)
T d3e5ua1          31 LSQKSIGEITGVHHVTVSRVLASLKRENILDK   62 (80)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence            78999999999999999999999999999963

>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=86.57  E-value=0.28  Score=31.39  Aligned_cols=35  Identities=17%  Similarity=0.228  Sum_probs=32.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033931           59 KLITPSILSDRLRINGSLARRAIKDLMARGSIRMI   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .=+|-..||+.++|+...-|++|-.|.+.||+.-+
T Consensus        32 ~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~   66 (88)
T d1q1ha_          32 TEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (88)
T ss_dssp             SCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEE
Confidence            45899999999999999999999999999999877

>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=85.98  E-value=0.44  Score=28.27  Aligned_cols=34  Identities=15%  Similarity=0.202  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|...||+-++++-.-.=++|++|.++|+|..-.
T Consensus        31 ~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~~   64 (80)
T d1ft9a1          31 FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG   64 (80)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEECS
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
Confidence            6888999999999999999999999999997643

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.39  E-value=0.62  Score=29.20  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=35.7

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           64 SILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ..+..+|..+.+.-++.|..|-++|.|.....++...+|.
T Consensus        50 ~~l~~~F~p~~~~iK~~Ie~LIereYi~R~~~~~~~y~Yv   89 (90)
T d1ldja1          50 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYL   89 (90)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSSTTEEEEC
T ss_pred             HHHhccCCCCHHHHHHHHHHHHhhHHHhcCCCCCceeeee
Confidence            4567789999999999999999999999988888888885

>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=84.97  E-value=0.81  Score=28.40  Aligned_cols=43  Identities=16%  Similarity=0.198  Sum_probs=36.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEec
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|++.|++.++++-|..-.=|+.|.+-|+|..- +.++...|.-
T Consensus        32 ~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~-r~G~~~~Y~l   74 (94)
T d1r1ua_          32 ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAK-RQGQSMIYSL   74 (94)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-EETTEEEEEE
T ss_pred             ccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEE-EECCEEEEEE
Confidence            579999999999999999999999999999864 4455556653

>d2v7fa1 a.4.5.84 (A:2-150) Ribosomal protein S19e {Pyrococcus abyssi [TaxId: 29292]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rps19E-like
domain: Ribosomal protein S19e
species: Pyrococcus abyssi [TaxId: 29292]

Probab=84.75  E-value=0.41  Score=33.17  Aligned_cols=24  Identities=29%  Similarity=0.544  Sum_probs=20.9

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEecc
Q 033931           72 INGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        72 I~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      =.++++|.+|++||+-|+|..+.+
T Consensus        92 ~Sg~iiR~~LQqLE~~glVek~~~  115 (149)
T d2v7fa1          92 AGGSIIRKALQQLEAAGFVEKVPG  115 (149)
T ss_dssp             HHHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CccHHHHHHHHHHHhCCCeeEcCC
Confidence            357999999999999999998754

>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=84.58  E-value=0.67  Score=28.11  Aligned_cols=45  Identities=22%  Similarity=0.200  Sum_probs=37.8

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033931           45 QATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMIS   94 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      =.++|.|. +-|    +|...||++.++.-..-+++||.|..-|++....
T Consensus        24 L~ifd~l~-~gp----~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~   68 (85)
T d1tw3a1          24 LRLVDHIL-AGA----RTVKALAARTDTRPEALLRLIRHLVAIGLLEEDA   68 (85)
T ss_dssp             TTHHHHHH-TTC----CBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCcHHHhc-cCC----CCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecC
Confidence            34667774 334    7999999999999999999999999999997654

>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=84.31  E-value=0.63  Score=28.94  Aligned_cols=45  Identities=22%  Similarity=0.190  Sum_probs=37.5

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033931           46 ATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISA   95 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .++|.|. +-|    +|...||++.++.-....++||.|.+-|++.....
T Consensus        31 ~ifd~L~-~gp----~t~~eLA~~~g~~~~~l~rLlr~L~a~gll~~~~d   75 (92)
T d1qzza1          31 RLVDHLL-AGA----DTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEK   75 (92)
T ss_dssp             THHHHHH-TTC----CSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECCCC
T ss_pred             CchHHHh-CCC----CCHHHHHHHHCcCchHHHHHHHHHHHCCCeeeecC
Confidence            3556664 434    79999999999999999999999999999987543

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.54  E-value=0.72  Score=28.85  Aligned_cols=40  Identities=15%  Similarity=0.219  Sum_probs=35.0

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           64 SILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ..+..+|....+.-++.|..|-++|.|..-..+....+|.
T Consensus        52 ~~l~~~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y~   91 (92)
T d1iuya_          52 QQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYV   91 (92)
T ss_dssp             HHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSCSSEEEEC
T ss_pred             HHHhCcCCCCHHHHHHHHHHHHhhhhhhcCCCCCCeeeee
Confidence            3456789999999999999999999999988888888885

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=83.43  E-value=0.61  Score=29.33  Aligned_cols=32  Identities=25%  Similarity=0.163  Sum_probs=29.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ++++-|.-+-|++-+.+.+.|..|+++|+|..
T Consensus        19 ~~kT~i~~~aNLs~~~~~kyl~~L~~~GLI~~   50 (90)
T d1r7ja_          19 SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQ   50 (90)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCccHHHHHcCCCHHHHHHHHHHHHHCCCeee
Confidence            46899999999999999999999999999975

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.19  E-value=0.4  Score=28.69  Aligned_cols=47  Identities=17%  Similarity=0.297  Sum_probs=36.9

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033931           44 DQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      .-++=+||..-+-  .=+++-.+|.+|+|.-|-+-+.|+...+-|.|.|
T Consensus        16 s~DLR~Riv~~~~--~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~P   62 (63)
T d1k78a1          16 PDVVRQRIVELAH--QGVRPCDISRQLRVSHGCVSKILGRYYETGSIKP   62 (63)
T ss_dssp             CHHHHHHHHHHHH--TTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCC
T ss_pred             CHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCC
Confidence            3345556654332  2368999999999999999999999999999865

>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=82.20  E-value=1.2  Score=28.33  Aligned_cols=43  Identities=26%  Similarity=0.390  Sum_probs=30.5

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--ceeEEEe
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH--ASQQIYT  103 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~--~~q~IYt  103 (108)
                      -|..|.+.+|+   ||+.+|++||           ++|++.|+|......  .....|.
T Consensus        34 RF~el~~~l~g---IS~~~Ls~rL-----------k~L~~~glv~R~~~~~~p~~veY~   78 (108)
T d1z7ua1          34 RNGELMRALDG---ITQRVLTDRL-----------REMEKDGLVHRESFNELPPRVEYT   78 (108)
T ss_dssp             CHHHHHHHSTT---CCHHHHHHHH-----------HHHHHHTSEEEEEECCSSCEEEEE
T ss_pred             CHHHHHHHCcC---CChhHHHHHH-----------HHHHHCCcceeeccCCCcceehhh
Confidence            46777777775   7888888875           899999999875322  2334465

>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=82.08  E-value=1.2  Score=28.55  Aligned_cols=43  Identities=16%  Similarity=0.302  Sum_probs=30.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--ceeEEEe
Q 033931           47 TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAH--ASQQIYT  103 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~--~~q~IYt  103 (108)
                      -|..|.+.+|+   ||+.+||+||           ++|++.|+|......  .....|.
T Consensus        39 RF~el~~~l~g---is~~~Ls~rL-----------~~Le~~glv~R~~~~~~p~~veY~   83 (114)
T d1yyva1          39 RFSDLRRKMGG---VSEKMLAQSL-----------QALEQDGFLNRVSYPVVPPHVEYS   83 (114)
T ss_dssp             EHHHHHHHSTT---CCHHHHHHHH-----------HHHHHHTCEEEEEECSSSCEEEEE
T ss_pred             CHHHHHHHccc---cchhHHHHHH-----------HHHHHHHHHhhcccCCCCchhHhH
Confidence            36667777775   7777777774           899999999877433  3445575

>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=82.02  E-value=1.2  Score=28.10  Aligned_cols=32  Identities=25%  Similarity=0.155  Sum_probs=28.8

Q ss_pred             echhhhhhhhccc-HHHHHHHHHHHHHcCCeeE
Q 033931           61 ITPSILSDRLRIN-GSLARRAIKDLMARGSIRM   92 (108)
Q Consensus        61 ITps~vserlkI~-~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +|...||+-+++. -.-.-++|++|.++|+|..
T Consensus        32 lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~   64 (100)
T d2bgca1          32 LTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY   64 (100)
T ss_dssp             CCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEE
Confidence            7889999999995 6777889999999999985

>d2p5ka1 a.4.5.3 (A:2-64) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=81.67  E-value=1.4  Score=25.99  Aligned_cols=49  Identities=16%  Similarity=0.304  Sum_probs=31.6

Q ss_pred             hhccceeCHH-HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccceeEEEe
Q 033931           37 VNNMVLFDQA-TYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIKDLMARGSIRMISAHASQQIYT  103 (108)
Q Consensus        37 ~nn~V~~dk~-t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      +.+.-+-.++ +.+-|.++  ++. +|.++||              |+|.+-|+++ |.......+|+
T Consensus        13 i~~~~i~tQ~eL~~~L~~~--G~~-vTQaTlS--------------RDL~eLg~vK-v~~~~g~~~Y~   62 (63)
T d2p5ka1          13 ITSNEIETQDELVDMLKQD--GYK-VTQATVS--------------RDIKELHLVK-VPTNNGSYKYS   62 (63)
T ss_dssp             HHHSCCCSHHHHHHHHHHT--TCC-CCHHHHH--------------HHHHHHTCEE-EEETTTEEEEE
T ss_pred             HHhCCCCCHHHHHHHHHHc--CCC-eeHHHHH--------------HHHHHhCCEE-eeCCCCcEEee
Confidence            3333344444 44444444  665 8999888              8888999999 44455566885