Citrus Sinensis ID: 033932

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHcccEEEcHHHHHHHHHcccccEEEcHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccccccEEEEccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHcccccccccccccccHHHHHccEEEEccHHHHHHHHHccccEEEcHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEcccc
Coil and Loop (DISEMBL)
mapkkdkapppsskpaksgggkqkkkkwskgkqkekvnnmvlfDQATYDKLLseapkyklitpsilsdRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
Flexible Loop (DISEMBL)
mapkkdkapppsskpaksgggkqkkkkwskgkqkekvnnmvLFDQATYDKLLSeapkyklitpsilsdrlrINGSLARKAIRELMARGLIRMvsahasqqiytratnt
Low Complexity Region (SEG)
MAPkkdkapppsskpaksgggkqkkkkwskgkqkekVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
Disordered region (IsUnstruct)
**************************************NMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA***********
Disordered Region (DISOPRED)
**********************************EKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT**
Disordered Region (DISEMBL)
*********************************KEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
Disordered Region (DISPRO)
******************************GKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
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)
MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
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]
Q9SIK2	108	40S ribosomal protein S25	yes	no	1.0	1.0	0.925	6e-42
Q9T029	108	40S ribosomal protein S25	yes	no	1.0	1.0	0.916	6e-42
Q8GYL5	108	40S ribosomal protein S25	yes	no	0.990	0.990	0.934	3e-41
P46301	108	40S ribosomal protein S25	N/A	no	1.0	1.0	0.925	1e-40
Q9SIW5	109	40S ribosomal protein S25	no	no	0.981	0.972	0.905	6e-39
Q94G66	114	40S ribosomal protein S25	N/A	no	0.981	0.929	0.785	2e-31
Q8ISN9	123	40S ribosomal protein S25	N/A	no	0.981	0.861	0.605	3e-21
Q9N9V4	120	40S ribosomal protein S25	yes	no	0.824	0.741	0.528	3e-21
Q03409	110	40S ribosomal protein S25	yes	no	0.962	0.945	0.461	3e-21
Q6PBI5	124	40S ribosomal protein S25	yes	no	0.953	0.830	0.596	7e-21

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

 Score =  169 bits (427), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 100/108 (92%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDK PPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLL+EAPK+KL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLTEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDR+RINGSLAR+AIRELMA+GLIRMVSAH+SQQIYTRATNT
Sbjct: 61  ITPSILSDRMRINGSLARRAIRELMAKGLIRMVSAHSSQQIYTRATNT 108

Arabidopsis thaliana (taxid: 3702)

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

 Score =  169 bits (427), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 99/108 (91%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDK PPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLL+EAPK+KL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLTEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDR+RINGSLAR+AIRELMA+G+IRMV+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 =  166 bits (420), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 100/107 (93%), Positives = 105/107 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDK PPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATN 107
           ITPSILSDRLRINGSLAR+AIRELMA+G IRMVSAH+SQQIYTRAT+
Sbjct: 61  ITPSILSDRLRINGSLARRAIRELMAKGTIRMVSAHSSQQIYTRATH 107

Arabidopsis thaliana (taxid: 3702)

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

 Score =  164 bits (416), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 100/108 (92%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKK +APPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFD++TYDKLLSEAPKYKL
Sbjct: 1   MAPKKAQAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDKSTYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPS+LSDRLRI+GSLARKAIR+LMARG IRMVSAHASQQIYTRATNT
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 =  159 bits (401), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 96/106 (90%), Positives = 101/106 (95%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDK PPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKL+SEAPK+KL
Sbjct: 1   MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLMSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106
           ITPSILSDRLRINGSLARKAIR+LM +G IRMVS 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 =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/107 (78%), Positives = 96/107 (89%), Gaps = 1/107 (0%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKS GGKQKKKKWSKGKQKEKVNN+VLFD AT+DKLLSEA K K+
Sbjct: 1   MAPKKDKAPPPSSKPAKS-GGKQKKKKWSKGKQKEKVNNLVLFDNATFDKLLSEAGKQKV 59

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATN 107
           +T + LS+R RINGSLAR+AIREL++RG I+MV  H+S QIYTR+TN
Sbjct: 60  VTAATLSERFRINGSLARRAIRELVSRGAIKMVCHHSSLQIYTRSTN 106

Amaranthus cruentus (taxid: 117272)

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

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 66/109 (60%), Positives = 85/109 (77%), Gaps = 3/109 (2%)

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

Query: 58  YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106
           YKLITPS++S+RL+I GSLAR A++EL ++G+I++VS 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 =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 64/89 (71%)

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

Query: 76  LARKAIRELMARGLIRMVSAHASQQIYTR 104
           +A   +++L    LIR+VS  +  ++YTR
Sbjct: 75  IAAAGLKQLCREKLIRLVSCSSKTRVYTR 103

Leishmania infantum (taxid: 5671)

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

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 70/104 (67%)

Query: 2   APKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLI 61
           A  K K    S   AK   G   +KKWSKG+ +EK+NN +LFD+ TY KLL E P  K+I
Sbjct: 6   AGGKSKQIQASKAAAKGSSGGAGRKKWSKGRSREKLNNAILFDKETYAKLLKEMPTAKVI 65

Query: 62  TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105
           T +++S+R++ NGSLAR+AI+EL+++GLI+ +       +YT+A
Sbjct: 66  TTAVVSERMKCNGSLARRAIKELLSKGLIKQIIKGHGNGVYTKA 109

Dictyostelium discoideum (taxid: 44689)

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

 Score = 99.0 bits (245), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 62/104 (59%), Positives = 79/104 (75%), Gaps = 1/104 (0%)

Query: 4   KKDKAPPPSSK-PAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLIT 62
           KKD       K P    GGK KKKKWSKGK ++K+NN+VLFD+ATYDKL  E P YKLIT
Sbjct: 9   KKDAGKSKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLYKEVPNYKLIT 68

Query: 63  PSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106
           P+++S+RL+I GSLAR A++EL+ +GLI++VS H +Q IYTR T
Sbjct: 69  PAVVSERLKIRGSLARAALQELLGKGLIKLVSKHRAQVIYTRNT 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
255543727	108	40S ribosomal protein S25-1, putative [R	1.0	1.0	0.981	8e-55
313586507	108	40S ribosomal protein S25A [Hevea brasil	1.0	1.0	0.981	9e-55
351725913	108	uncharacterized protein LOC100499810 [Gl	1.0	1.0	0.981	7e-54
359807542	108	40S ribosomal protein S25 [Glycine max]	1.0	1.0	0.981	9e-54
293337351	108	putative 40S ribosomal protein S25-1 [Ga	1.0	1.0	0.972	4e-42
356538747	108	PREDICTED: 40S ribosomal protein S25-2-l	1.0	1.0	0.972	1e-41
388504588	108	unknown [Lotus japonicus] gi|388522993|g	1.0	1.0	0.953	4e-41
388495506	108	unknown [Lotus japonicus]	1.0	1.0	0.953	4e-41
116779097	108	unknown [Picea sitchensis] gi|116779909|	1.0	1.0	0.953	5e-41
255637650	108	unknown [Glycine max]	1.0	1.0	0.962	5e-41

>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 =  217 bits (552), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 106/108 (98%), Positives = 108/108 (100%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLR+NGSLAR+AIRELMARGLIRMVSAHASQQIYTRATNT
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 =  216 bits (551), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 106/108 (98%), Positives = 108/108 (100%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNM+LFDQATYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMILFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLAR+AIRELMARGLIRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARRAIRELMARGLIRMVSAHASQQIYTRATNT 108

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

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 =  214 bits (544), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 106/108 (98%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARKAIRELMARG IRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807542|ref|NP_001241406.1| 40S ribosomal protein S25 [Glycine max] gi|255626191|gb|ACU13440.1| unknown [Glycine max] gi|255647156|gb|ACU24046.1| unknown [Glycine max]

 Score =  213 bits (543), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 106/108 (98%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNN VLFDQATYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNQVLFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARKAIRELMARG IRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|293337351|gb|ADE42971.1| putative 40S ribosomal protein S25-1 [Gardenia jasminoides]

 Score =  174 bits (442), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 105/108 (97%), Positives = 108/108 (100%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFD+ATYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDKATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPS+LSDRLRI+GSLARKAIRELMARGLIRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSVLSDRLRISGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108

Source: Gardenia jasminoides

Species: Gardenia jasminoides

Genus: Gardenia

Family: Rubiaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  173 bits (438), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 105/108 (97%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARKAIRELMARG IRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 103/108 (95%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLR+NGSLAR+AIRELMARG IRMVSAHASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRVNGSLARRAIRELMARGSIRMVSAHASQQIYTRATNT 108

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388495506|gb|AFK35819.1| unknown [Lotus japonicus]

 Score =  171 bits (434), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 103/108 (95%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQ TYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLR+NGSLARKAIRELMARG IRMVS+HASQQIYTRATNT
Sbjct: 61  ITPSILSDRLRVNGSLARKAIRELMARGSIRMVSSHASQQIYTRATNT 108

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

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 =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 103/108 (95%), Positives = 107/108 (99%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARKAI++LMARG IRM+SAH+SQQIYTRATNT
Sbjct: 61  ITPSILSDRLRINGSLARKAIKDLMARGSIRMISAHSSQQIYTRATNT 108

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637650|gb|ACU19149.1| unknown [Glycine max]

 Score =  171 bits (433), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 104/108 (96%), Positives = 106/108 (98%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKV+NMVLFDQ TYDKLLSEAPK+KL
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVSNMVLFDQGTYDKLLSEAPKFKL 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           ITPSILSDRLRINGSLARKAIRELMARG IRMVSAHASQQIYTRATNT
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:2049369	108	AT2G21580 "AT2G21580" [Arabido	0.666	0.666	0.902	1e-29
TAIR|locus:2136348	108	AT4G39200 "AT4G39200" [Arabido	0.666	0.666	0.888	1.6e-29
TAIR|locus:505006559	108	AT4G34555 "AT4G34555" [Arabido	0.657	0.657	0.915	4.4e-29
UNIPROTKB|Q56JX5	125	RPS25 "40S ribosomal protein S	0.648	0.56	0.628	3.5e-20
UNIPROTKB|P62851	125	RPS25 "40S ribosomal protein S	0.648	0.56	0.628	3.5e-20
UNIPROTKB|F2Z5G8	125	RPS25 "Uncharacterized protein	0.648	0.56	0.628	3.5e-20
MGI|MGI:1922867	125	Rps25 "ribosomal protein S25"	0.648	0.56	0.628	3.5e-20
RGD|621043	125	Rps25 "ribosomal protein s25"	0.648	0.56	0.628	3.5e-20
UNIPROTKB|F1NU56	139	RPS25 "Uncharacterized protein	0.648	0.503	0.628	4.4e-20
ZFIN|ZDB-GENE-040426-1788	132	rps25 "ribosomal protein S25"	0.648	0.530	0.628	4.4e-20

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

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 65/72 (90%), Positives = 71/72 (98%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             VNNMVLFDQ TYDKLL+EAPK+KLITPSILSDR+RINGSLAR+AIRELMA+GLIRMVSAH
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

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

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 64/72 (88%), Positives = 72/72 (100%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             VNNMVLFDQATYDKLL+EAPK+KLITPSILSDR+RINGSLAR+AIRELMA+G+IRMV+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:505006559 AT4G34555 "AT4G34555" [Arabidopsis thaliana (taxid:3702)]

 Score = 323 (118.8 bits), Expect = 4.4e-29, P = 4.4e-29
 Identities = 65/71 (91%), Positives = 70/71 (98%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             VNNMVLFDQATYDKLLSEAPK+KLITPSILSDRLRINGSLAR+AIRELMA+G IRMVSAH
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

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

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 44/70 (62%), Positives = 60/70 (85%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+++GLI++VS 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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 44/70 (62%), Positives = 60/70 (85%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+++GLI++VS 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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 44/70 (62%), Positives = 60/70 (85%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+++GLI++VS 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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 44/70 (62%), Positives = 60/70 (85%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+++GLI++VS 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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 44/70 (62%), Positives = 60/70 (85%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+++GLI++VS 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 = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 44/70 (62%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+ +GLI++VS 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 = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 44/70 (62%), Positives = 59/70 (84%)

Query:    37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
             +NN+VLFD+ATYDKL  E P YKLITP+++S+RL+I GSLAR A++EL+ +GLI++VS 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	0.5575	0.9814	0.848	yes	no
P62852	RS25_MOUSE	No assigned EC number	0.5575	0.9814	0.848	yes	no
Q03409	RS25_DICDI	No assigned EC number	0.4615	0.9629	0.9454	yes	no
Q6PBI5	RS25_DANRE	No assigned EC number	0.5961	0.9537	0.8306	yes	no
Q9N9V4	RS25_LEIIN	No assigned EC number	0.5280	0.8240	0.7416	yes	no
Q9SIW5	RS251_ARATH	No assigned EC number	0.9056	0.9814	0.9724	no	no
P52821	RS25_CAEEL	No assigned EC number	0.5753	0.6759	0.6239	yes	no
P48588	RS25_DROME	No assigned EC number	0.4642	0.9814	0.9059	yes	no
P46301	RS25_SOLLC	No assigned EC number	0.9259	1.0	1.0	N/A	no
Q90YP9	RS25_ICTPU	No assigned EC number	0.5625	0.9814	0.8548	N/A	no
Q56JX5	RS25_BOVIN	No assigned EC number	0.5575	0.9814	0.848	yes	no
Q8ISN9	RS25_BRABE	No assigned EC number	0.6055	0.9814	0.8617	N/A	no
Q8GYL5	RS253_ARATH	No assigned EC number	0.9345	0.9907	0.9907	yes	no
Q9T029	RS254_ARATH	No assigned EC number	0.9166	1.0	1.0	yes	no
Q94G66	RS25_AMACR	No assigned EC number	0.7850	0.9814	0.9298	N/A	no
Q6Q311	RS25_SHEEP	No assigned EC number	0.5575	0.9814	0.848	N/A	no
Q9SIK2	RS252_ARATH	No assigned EC number	0.9259	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:
	RPS25A	40S ribosomal protein S25 (RPS25B); 40S ribosomal protein S25 (RPS25B); FUNCTIONS IN- structural constituent of ribosome; INVOLVED IN- translation; LOCATED IN- cytosolic small ribosomal subunit, cytosolic ribosome, ribosome, plasma membrane; EXPRESSED IN- 23 plant structures; EXPRESSED DURING- 13 growth stages; CONTAINS InterPro DOMAIN/s- Ribosomal protein S25 (InterPro-IPR004977); BEST Arabidopsis thaliana protein match is- 40S ribosomal protein S25 (RPS25E) (TAIR-AT4G39200.2); Has 502 Blast hits to 502 proteins in 179 species- Archae - 5; Bacteria - 0; Metazoa - 227; Fungi - 100; Pla [...] (108 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	AT3G04840	40S ribosomal protein S3A (RPS3aA); 40S ribosomal protein S3A (RPS3aA); FUNCTIONS IN- structura [...] (262 aa)				•	•		•		0.964
	AT1G26880	60S ribosomal protein L34 (RPL34A); 60S ribosomal protein L34 (RPL34A); FUNCTIONS IN- structura [...] (120 aa)				•			•		0.960
	ATRPS5B	ATRPS5B (RIBOSOMAL PROTEIN 5B); structural constituent of ribosome; One of two genes encoding t [...] (207 aa)				•	•		•		0.954
	AT2G32060	40S ribosomal protein S12 (RPS12C); 40S ribosomal protein S12 (RPS12C); FUNCTIONS IN- structura [...] (144 aa)				•	•				0.943
	P40	P40; structural constituent of ribosome; acidic protein associated to 40S ribosomal subunit of [...] (298 aa)				•	•		•		0.942
	RPL23AA	RPL23AA (RIBOSOMAL PROTEIN L23AA); RNA binding / nucleotide binding / structural constituent of [...] (154 aa)				•	•				0.937
	RPL17A	60S ribosomal protein L17 (RPL17A); 60S ribosomal protein L17 (RPL17A); FUNCTIONS IN- structura [...] (176 aa)				•	•		•		0.933
	AT4G14320	60S ribosomal protein L36a/L44 (RPL36aB); 60S ribosomal protein L36a/L44 (RPL36aB); FUNCTIONS I [...] (105 aa)				•			•		0.930
	RPL23AB	RPL23AB (RIBOSOMAL PROTEIN L23AB); RNA binding / nucleotide binding / structural constituent of [...] (154 aa)				•	•				0.928
	AT4G15000	60S ribosomal protein L27 (RPL27C); 60S ribosomal protein L27 (RPL27C); FUNCTIONS IN- structura [...] (135 aa)				•					0.926

---

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	9e-49
COG4901	107	COG4901, COG4901, Ribosomal protein S25 [Translati	3e-19
PRK09334	86	PRK09334, PRK09334, 30S ribosomal protein S25e; Pr	1e-06

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

 Score =  150 bits (380), Expect = 9e-49
 Identities = 70/106 (66%), Positives = 83/106 (78%), Gaps = 1/106 (0%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           M PKK +     +  A S GGK KKKKWSKGK K+K+NN VLFD+ATYDKLL E P YKL
Sbjct: 1   MPPKKQQKKAAKAA-AASAGGKAKKKKWSKGKVKDKLNNAVLFDKATYDKLLKEVPTYKL 59

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106
           ITPS+LSDRL+INGSLAR+A+REL  +GLI+ V  H++Q IYTRAT
Sbjct: 60  ITPSVLSDRLKINGSLARRALRELEEKGLIKPVVKHSAQLIYTRAT 105

Length = 105

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

 Score = 75.7 bits (186), Expect = 3e-19
 Identities = 38/104 (36%), Positives = 57/104 (54%)

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

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

Length = 107

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

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 27/84 (32%), Positives = 46/84 (54%)

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

Query: 82  RELMARGLIRMVSAHASQQIYTRA 105
           REL  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:	97.23
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	97.07
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	97.03
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.98
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	96.94
PF14502	48	HTH_41: Helix-turn-helix domain	96.91
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.76
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.61
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.59
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	96.48
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.47
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.26
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	96.18
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.14
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	96.13
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	96.09
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	96.09
PRK13509	251	transcriptional repressor UlaR; Provisional	96.05
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.01
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	95.98
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	95.97
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	95.87
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.86
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	95.85
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	95.83
PRK03837	241	transcriptional regulator NanR; Provisional	95.82
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.8
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.77
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.75
PHA02943	165	hypothetical protein; Provisional	95.74
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	95.69
PRK14165	217	winged helix-turn-helix domain-containing protein/	95.57
PRK14999	241	histidine utilization repressor; Provisional	95.49
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	95.41
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	95.4
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.39
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	95.38
smart00843	63	Ftsk_gamma This domain directs oriented DNA transl	95.38
TIGR03338	212	phnR_burk phosphonate utilization associated trans	95.36
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	95.35
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.3
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.26
PRK11014	141	transcriptional repressor NsrR; Provisional	95.21
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	95.21
PRK04984	239	fatty acid metabolism regulator; Provisional	95.21
COG2188	236	PhnF Transcriptional regulators [Transcription]	95.18
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	95.16
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.09
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	95.03
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	95.03
TIGR03337	231	phnR transcriptional regulator protein. This famil	94.98
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	94.98
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	94.9
PF13730	55	HTH_36: Helix-turn-helix domain	94.9
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	94.82
PRK10079	241	phosphonate metabolism transcriptional regulator P	94.74
COG3355	126	Predicted transcriptional regulator [Transcription	94.7
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	94.67
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.64
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	94.39
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	94.29
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	94.28
PF04157	223	EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP	94.15
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	93.99
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	93.79
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.65
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.64
PRK03573	144	transcriptional regulator SlyA; Provisional	93.62
COG4465	261	CodY Pleiotropic transcriptional repressor [Transc	93.61
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.56
PRK10870	176	transcriptional repressor MprA; Provisional	93.53
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	93.49
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	93.47
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.44
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	93.28
PRK04158	256	transcriptional repressor CodY; Validated	93.27
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.05
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.92
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	92.89
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	92.77
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	92.65
PRK03902	142	manganese transport transcriptional regulator; Pro	92.64
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	92.43
COG1959	150	Predicted transcriptional regulator [Transcription	92.29
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	92.07
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	91.99
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.94
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	91.88
PRK11050	152	manganese transport regulator MntR; Provisional	91.86
COG1802	230	GntR Transcriptional regulators [Transcription]	91.85
COG1846	126	MarR Transcriptional regulators [Transcription]	91.82
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	91.65
COG1725	125	Predicted transcriptional regulators [Transcriptio	91.59
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	91.53
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	91.53
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	91.48
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	91.39
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	91.37
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	91.32
COG2512	258	Predicted membrane-associated trancriptional regul	91.17
PRK09954	362	putative kinase; Provisional	91.09
PRK06266	178	transcription initiation factor E subunit alpha; V	91.01
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	90.98
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	90.94
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	90.91
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	90.81
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	90.76
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	90.66
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	90.61
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	90.5
PRK11169	164	leucine-responsive transcriptional regulator; Prov	90.25
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	90.17
PRK13777	185	transcriptional regulator Hpr; Provisional	90.03
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	89.58
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	89.45
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	89.05
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	88.97
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	88.89
COG2186	241	FadR Transcriptional regulators [Transcription]	88.87
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	88.72
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	88.67
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	88.63
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	88.1
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	88.06
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	87.78
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	87.77
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	87.72
PF12728	51	HTH_17: Helix-turn-helix domain	87.58
TIGR02054	120	MerD mercuric resistence transcriptional repressor	87.56
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	87.55
PRK09462	148	fur ferric uptake regulator; Provisional	87.49
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	87.37
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	87.13
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	87.13
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	87.12
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	87.01
PRK12423	202	LexA repressor; Provisional	86.78
PRK09333	150	30S ribosomal protein S19e; Provisional	86.62
TIGR01764	49	excise DNA binding domain, excisionase family. An	86.5
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	86.37
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	86.24
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	85.82
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	85.73
PRK05472	213	redox-sensing transcriptional repressor Rex; Provi	85.58
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	85.54
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	85.43
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	85.41
PRK13749	121	transcriptional regulator MerD; Provisional	85.38
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	85.15
PRK11569	274	transcriptional repressor IclR; Provisional	84.8
PRK13752	144	putative transcriptional regulator MerR; Provision	84.72
PRK00215	205	LexA repressor; Validated	84.61
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	84.11
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	84.1
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	84.03
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	83.82
PF01090	139	Ribosomal_S19e: Ribosomal protein S19e; InterPro:	83.72
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	83.47
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	83.39
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	83.37
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	83.29
COG1414	246	IclR Transcriptional regulator [Transcription]	83.25
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	83.24
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	83.11
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	83.0
COG1733	120	Predicted transcriptional regulators [Transcriptio	82.91
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	82.74
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	82.63
PRK06474	178	hypothetical protein; Provisional	82.62
KOG2760	432	consensus Vacuolar sorting protein VPS36 [Intracel	82.47
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	82.37
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	82.16
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	82.12
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	81.87
PF13814	191	Replic_Relax: Replication-relaxation	81.82
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	81.77
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	81.77
PRK05638	442	threonine synthase; Validated	81.59
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	81.45
COG3177	348	Fic family protein [Function unknown]	81.36
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	81.33
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	81.31
COG3432	95	Predicted transcriptional regulator [Transcription	81.12
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	80.82
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	80.56
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	80.02

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

Probab=100.00  E-value=2.7e-49  Score=279.44  Aligned_cols=106  Identities=67%  Similarity=0.965  Sum_probs=101.3

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA   80 (108)
Q Consensus         1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~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            78888888877776 45899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEeccccceEEEecccC
Q 033932           81 IRELMARGLIRMVSAHASQQIYTRATN  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=2.6e-49  Score=278.84  Aligned_cols=105  Identities=68%  Similarity=0.995  Sum_probs=79.0

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA   80 (108)
Q Consensus         1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~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            99999888777666 45889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEeccccceEEEeccc
Q 033932           81 IRELMARGLIRMVSAHASQQIYTRAT  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=1.3e-37  Score=219.48  Aligned_cols=106  Identities=40%  Similarity=0.638  Sum_probs=101.4

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA   80 (108)
Q Consensus         1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~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 MAPKSQLSKEKKAEKA-KAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIV   79 (107)
T ss_pred             CcchhHHHHHHHHHHH-HhhhhhhhhccccccccchhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHH
Confidence            9999999998888755 678899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEeccccceEEEecccC
Q 033932           81 IRELMARGLIRMVSAHASQQIYTRATN  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            999999999999999999999999765

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=100.00  E-value=4.6e-36  Score=205.45  Aligned_cols=81  Identities=31%  Similarity=0.454  Sum_probs=76.5

Q ss_pred             ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        25 KKKWsKgk~keK~nn~Vl~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            44456667999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 033932          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=97.23  E-value=0.00034  Score=41.37  Aligned_cols=42  Identities=29%  Similarity=0.417  Sum_probs=32.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   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=97.07  E-value=0.0031  Score=39.37  Aligned_cols=50  Identities=26%  Similarity=0.371  Sum_probs=37.2

Q ss_pred             HHHHHHHhhCCC-----Ceee-chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEAPK-----YKLI-TPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            344555444433     3455 9999999999999999999999999999987654

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=97.03  E-value=0.0012  Score=41.15  Aligned_cols=46  Identities=15%  Similarity=0.289  Sum_probs=38.9

Q ss_pred             HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           49 DKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.98  E-value=0.0036  Score=37.01  Aligned_cols=38  Identities=26%  Similarity=0.347  Sum_probs=32.9

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=96.94  E-value=0.0039  Score=37.50  Aligned_cols=49  Identities=27%  Similarity=0.350  Sum_probs=38.7

Q ss_pred             HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           45 QATYDKLLSEAP------KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        45 k~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +++++.|...+.      .-.+.|...||+.|+|+-+-++++|..|++.|+|...
T Consensus         4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377           4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            456666666632      2344569999999999999999999999999998654

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

>PF14502 HTH_41: Helix-turn-helix domain

Probab=96.91  E-value=0.0019  Score=40.27  Aligned_cols=41  Identities=20%  Similarity=0.240  Sum_probs=37.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   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=96.76  E-value=0.0047  Score=38.79  Aligned_cols=44  Identities=20%  Similarity=0.364  Sum_probs=37.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .=.|+..||+.++|.-+-+..+|+.|+++|+|......  ..+|..
T Consensus        21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~a   64 (68)
T PF01978_consen   21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYRA   64 (68)
T ss_dssp             CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEEE
Confidence            44899999999999999999999999999999988743  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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.61  E-value=0.007  Score=35.40  Aligned_cols=44  Identities=16%  Similarity=0.240  Sum_probs=36.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            357999999999999999999999999999999775544 44454

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

Probab=96.59  E-value=0.0045  Score=39.99  Aligned_cols=38  Identities=16%  Similarity=0.173  Sum_probs=31.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   97 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      -+|...|||.++|+.+-||..|..|+..|.|+.+--.+
T Consensus        15 p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~r   52 (62)
T PF04703_consen   15 PLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRR   52 (62)
T ss_dssp             -EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            38889999999999999999999999999999864333

>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=96.48  E-value=0.0096  Score=38.76  Aligned_cols=46  Identities=26%  Similarity=0.380  Sum_probs=32.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  106 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~  106 (108)
                      ++|.|.|||+++|+-|+--.+||-|++-|+|.--|- .--..|.+..
T Consensus         4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSl-GmKGT~ikvl   49 (61)
T PF08222_consen    4 RLVASKIADRVGITRSVIVNALRKLESAGVIESRSL-GMKGTYIKVL   49 (61)
T ss_dssp             EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEET-TSS-EEEEE-
T ss_pred             eehHHHHHHHhCccHHHHHHHHHHHHhcCceeeccc-CCCceeeeee
Confidence            689999999999999999999999999999984432 1123555443

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.

>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=96.47  E-value=0.013  Score=38.43  Aligned_cols=51  Identities=25%  Similarity=0.357  Sum_probs=39.0

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ..+....+|...||++++++-+..+++|+.|.+.|+|.-....+......+
T Consensus        19 ~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~   69 (83)
T PF02082_consen   19 RHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLAR   69 (83)
T ss_dssp             CTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS
T ss_pred             hCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecC
Confidence            445555699999999999999999999999999999987765444443334

(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.

>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=96.26  E-value=0.011  Score=35.83  Aligned_cols=34  Identities=29%  Similarity=0.466  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

...

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=96.18  E-value=0.017  Score=43.65  Aligned_cols=39  Identities=21%  Similarity=0.292  Sum_probs=35.7

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.++=|-..||++|+|+-...|+||.+|+.+|+|..+-
T Consensus        21 ~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~   59 (230)
T TIGR02018        21 PGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQ   59 (230)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            567888999999999999999999999999999997754

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.

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

Probab=96.14  E-value=0.018  Score=34.30  Aligned_cols=42  Identities=24%  Similarity=0.394  Sum_probs=36.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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 344554

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.

>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=96.13  E-value=0.019  Score=35.26  Aligned_cols=47  Identities=26%  Similarity=0.343  Sum_probs=35.1

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS--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            44568999999999999999999999999999997773  335544443

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=96.09  E-value=0.015  Score=43.60  Aligned_cols=40  Identities=30%  Similarity=0.419  Sum_probs=36.6

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            6678999999999999999999999999999999987643

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.

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=96.09  E-value=0.016  Score=43.83  Aligned_cols=40  Identities=23%  Similarity=0.225  Sum_probs=36.5

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            5678889999999999999999999999999999987643

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

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=96.05  E-value=0.011  Score=46.25  Aligned_cols=50  Identities=24%  Similarity=0.307  Sum_probs=44.7

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.01  E-value=0.013  Score=33.51  Aligned_cols=33  Identities=18%  Similarity=0.329  Sum_probs=30.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=95.98  E-value=0.022  Score=43.51  Aligned_cols=40  Identities=23%  Similarity=0.391  Sum_probs=36.1

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            5567889999999999999999999999999999987654

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=95.97  E-value=0.015  Score=43.56  Aligned_cols=54  Identities=20%  Similarity=0.271  Sum_probs=43.4

Q ss_pred             eCHHHHHHHHhhCCCC-----eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           43 FDQATYDKLLSEAPKY-----KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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 TALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK   66 (224)
T ss_pred             hhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence            3456788888776442     23477899999999999999999999999999876543

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=95.87  E-value=0.024  Score=45.78  Aligned_cols=59  Identities=24%  Similarity=0.369  Sum_probs=50.9

Q ss_pred             hhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           36 KVNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        36 K~nn~Vl~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .++..-+-.-+..++|+.+.... -.++-+.||++++|+-|..|.+|+.|++.|+|.--+
T Consensus       173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            34444455678899999999994 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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.86  E-value=0.044  Score=31.40  Aligned_cols=46  Identities=17%  Similarity=0.291  Sum_probs=37.7

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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    3489999999999999999999999999999986543

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=95.85  E-value=0.015  Score=45.52  Aligned_cols=48  Identities=10%  Similarity=0.195  Sum_probs=43.0

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +-.++|+..+.....+|...||++|+|+-+-+|+=|.+|+++|+|..+
T Consensus         5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            456777777777889999999999999999999999999999999775

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=95.83  E-value=0.027  Score=43.15  Aligned_cols=51  Identities=16%  Similarity=0.186  Sum_probs=41.9

Q ss_pred             HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEAP------KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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

>PRK03837 transcriptional regulator NanR; Provisional

Probab=95.82  E-value=0.019  Score=43.18  Aligned_cols=51  Identities=16%  Similarity=0.241  Sum_probs=41.6

Q ss_pred             HHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        45 k~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ...|+.|...|-.      .++-+-..||++|+|+-+..|.||+.|+..|+|...-+
T Consensus        16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~   72 (241)
T PRK03837         16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG   72 (241)
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            4566666666543      44558999999999999999999999999999988643

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

Probab=95.80  E-value=0.0062  Score=38.84  Aligned_cols=47  Identities=15%  Similarity=0.232  Sum_probs=36.5

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   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            33334455789999999999999999999999999999999986543

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

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=95.77  E-value=0.016  Score=36.60  Aligned_cols=37  Identities=14%  Similarity=0.301  Sum_probs=33.0

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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 ....

>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=95.75  E-value=0.026  Score=34.33  Aligned_cols=37  Identities=22%  Similarity=0.295  Sum_probs=33.7

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>PHA02943 hypothetical protein; Provisional

Probab=95.74  E-value=0.031  Score=42.66  Aligned_cols=54  Identities=22%  Similarity=0.207  Sum_probs=45.1

Q ss_pred             HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           49 DKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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 77788999999999999999999999999999999998776665444

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=95.69  E-value=0.021  Score=43.45  Aligned_cols=39  Identities=23%  Similarity=0.289  Sum_probs=35.8

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            457999999999999999999999999999999998754

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

Probab=95.57  E-value=0.029  Score=43.91  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=42.2

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            34444569999999999999999999999999999998886556676664

>PRK14999 histidine utilization repressor; Provisional

Probab=95.49  E-value=0.028  Score=42.82  Aligned_cols=39  Identities=18%  Similarity=0.303  Sum_probs=35.4

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            567888999999999999999999999999999997643

>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=95.41  E-value=0.028  Score=33.87  Aligned_cols=33  Identities=36%  Similarity=0.493  Sum_probs=30.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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 ....

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=95.40  E-value=0.023  Score=44.50  Aligned_cols=48  Identities=17%  Similarity=0.123  Sum_probs=42.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +=.++|+..+.....||+..||+.|+|+.+-.|+=|++|+++|+|..+
T Consensus         5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~   52 (256)
T PRK10434          5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT   52 (256)
T ss_pred             HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            345677878888888999999999999999999999999999999775

>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=95.39  E-value=0.033  Score=33.51  Aligned_cols=32  Identities=19%  Similarity=0.324  Sum_probs=29.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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            69999999999999999999999999999864

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.

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=95.38  E-value=0.048  Score=41.72  Aligned_cols=50  Identities=18%  Similarity=0.243  Sum_probs=41.5

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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      344555789999999999999999999999999998654

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

Probab=95.38  E-value=0.02  Score=37.31  Aligned_cols=54  Identities=22%  Similarity=0.332  Sum_probs=48.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   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            467899988888888999999999999999999999999999999999975444

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

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=95.36  E-value=0.041  Score=40.67  Aligned_cols=49  Identities=29%  Similarity=0.370  Sum_probs=39.9

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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      44555 889999999999999999999999999997643

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.

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

Probab=95.35  E-value=0.013  Score=38.33  Aligned_cols=58  Identities=16%  Similarity=0.265  Sum_probs=43.2

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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            4567777766667788999999999999999999999999999999998655433343

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.

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

Probab=95.30  E-value=0.055  Score=34.64  Aligned_cols=34  Identities=15%  Similarity=0.155  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +|...||+.++|.-+-++++|..|+++|+|....
T Consensus        23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550       23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            9999999999999999999999999999997754

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

>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=95.26  E-value=0.024  Score=35.09  Aligned_cols=50  Identities=24%  Similarity=0.243  Sum_probs=40.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            55556666665556689999999999999999999999999999988754

...

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=95.21  E-value=0.053  Score=38.63  Aligned_cols=45  Identities=16%  Similarity=0.233  Sum_probs=38.2

Q ss_pred             CCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932           55 APKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ   99 (108)
Q Consensus        55 Vpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      .+.-..++...||++++|+-+-.|++|+.|...|+|..+.+.+..
T Consensus        20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG   64 (141)
T PRK11014         20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGG   64 (141)
T ss_pred             CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCC
Confidence            333458899999999999999999999999999999988655433

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

Probab=95.21  E-value=0.027  Score=44.12  Aligned_cols=49  Identities=18%  Similarity=0.251  Sum_probs=44.3

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +=.++|+..+.....|++..||++|+|+-.-.|+=|++|+++|++..+.
T Consensus         5 eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h   53 (253)
T COG1349           5 ERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH   53 (253)
T ss_pred             HHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence            3457888888889999999999999999999999999999999998754

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=95.21  E-value=0.039  Score=41.64  Aligned_cols=50  Identities=14%  Similarity=0.228  Sum_probs=40.3

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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      345566899999999999999999999999999998653

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=95.18  E-value=0.038  Score=42.54  Aligned_cols=41  Identities=29%  Similarity=0.405  Sum_probs=37.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   96 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      |+.++=|=..||++|+|+-...|+||++|++.|+|....+.
T Consensus        27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~   67 (236)
T COG2188          27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK   67 (236)
T ss_pred             CCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC
Confidence            45789999999999999999999999999999999886543

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=95.16  E-value=0.066  Score=40.75  Aligned_cols=52  Identities=17%  Similarity=0.237  Sum_probs=43.4

Q ss_pred             CHHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           44 DQATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.09  E-value=0.053  Score=38.09  Aligned_cols=47  Identities=23%  Similarity=0.354  Sum_probs=42.7

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            56778888888887    999999999999999999999999999999876

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=95.03  E-value=0.049  Score=41.08  Aligned_cols=51  Identities=14%  Similarity=0.221  Sum_probs=41.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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.

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=95.03  E-value=0.05  Score=37.17  Aligned_cols=52  Identities=12%  Similarity=0.089  Sum_probs=39.9

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEE
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS--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            33334344468999999999999999999999999999999873  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.

>TIGR03337 phnR transcriptional regulator protein

Probab=94.98  E-value=0.075  Score=39.70  Aligned_cols=40  Identities=30%  Similarity=0.363  Sum_probs=36.7

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            6678889999999999999999999999999999987654

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.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=94.98  E-value=0.048  Score=41.03  Aligned_cols=43  Identities=26%  Similarity=0.400  Sum_probs=36.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----cccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS----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    345555554

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=94.90  E-value=0.05  Score=41.62  Aligned_cols=52  Identities=19%  Similarity=0.238  Sum_probs=41.8

Q ss_pred             CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           44 DQATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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      46667899999999999999999999999999986543

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.90  E-value=0.036  Score=33.18  Aligned_cols=31  Identities=29%  Similarity=0.500  Sum_probs=28.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLI   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

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=94.82  E-value=0.042  Score=43.42  Aligned_cols=49  Identities=10%  Similarity=0.094  Sum_probs=43.1

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=94.74  E-value=0.051  Score=41.40  Aligned_cols=50  Identities=20%  Similarity=0.220  Sum_probs=39.9

Q ss_pred             HHHHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEA-PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        46 ~t~dKl~KEV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .+.++|..+. |+.++=|=..||++|+|+-...|+||.+|+.+|+|...-+
T Consensus        20 ~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G   70 (241)
T PRK10079         20 KLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG   70 (241)
T ss_pred             HHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            3444444333 4568889999999999999999999999999999987543

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.70  E-value=0.12  Score=37.72  Aligned_cols=58  Identities=22%  Similarity=0.391  Sum_probs=48.0

Q ss_pred             eCHHHHHHHHh-hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe----ccccceEEEec
Q 033932           43 FDQATYDKLLS-EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV----SAHASQQIYTR  104 (108)
Q Consensus        43 ~dk~t~dKl~K-EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V----~k~~~q~IYtr  104 (108)
                      .|-+.|..|+. +-|    .|.-.|||++++.-|.+.++|+-|.+.|+|...    -+++.-.||-+
T Consensus        28 ~Dv~v~~~LL~~~~~----~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~   90 (126)
T COG3355          28 LDVEVYKALLEENGP----LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKP   90 (126)
T ss_pred             HHHHHHHHHHhhcCC----cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEec
Confidence            57889999994 444    699999999999999999999999999999876    34455567754

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=94.67  E-value=0.068  Score=40.75  Aligned_cols=52  Identities=21%  Similarity=0.203  Sum_probs=42.7

Q ss_pred             CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           44 DQATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            35567777776644      45558899999999999999999999999999997653

>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=94.64  E-value=0.067  Score=34.43  Aligned_cols=35  Identities=20%  Similarity=0.340  Sum_probs=30.8

Q ss_pred             chhhhhhhhccc-HHHHHHHHHHHHHcCCeeEeccc
Q 033932           62 TPSILSDRLRIN-GSLARKAIRELMARGLIRMVSAH   96 (108)
Q Consensus        62 Tps~vserlkI~-~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      |..+|++.|+++ -|-+..-|+.|+++|+|.....-
T Consensus        27 t~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~~   62 (65)
T PF01726_consen   27 TVREIAEALGLKSTSTVQRHLKALERKGYIRRDPGK   62 (65)
T ss_dssp             -HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred             CHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCCC
Confidence            778999999998 99999999999999999886543

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=94.39  E-value=0.095  Score=33.71  Aligned_cols=34  Identities=24%  Similarity=0.300  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            5999999999999999999999999999999874

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=94.29  E-value=0.097  Score=37.10  Aligned_cols=41  Identities=22%  Similarity=0.242  Sum_probs=35.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   97 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      .-..+|...||++++|.....+++|+.|...|+|.-+...+
T Consensus        22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~   62 (135)
T TIGR02010        22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPG   62 (135)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence            34579999999999999999999999999999998754433

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

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=94.28  E-value=0.068  Score=40.04  Aligned_cols=49  Identities=16%  Similarity=0.251  Sum_probs=40.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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 568999999999999999999999999998654

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

Probab=94.15  E-value=0.11  Score=39.85  Aligned_cols=46  Identities=26%  Similarity=0.294  Sum_probs=40.2

Q ss_pred             HHHHHHHhhC--CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           46 ATYDKLLSEA--PKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   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.

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=93.99  E-value=0.089  Score=36.36  Aligned_cols=38  Identities=26%  Similarity=0.380  Sum_probs=34.4

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ++-..+|...||+.++|+.+..+++|+.|...|+|.-.
T Consensus        21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        21 PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            44558899999999999999999999999999998764

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.

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

Probab=93.79  E-value=0.13  Score=34.83  Aligned_cols=37  Identities=19%  Similarity=0.283  Sum_probs=34.0

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...-+|++.||+.+++.=+-..++|.+|+++|+|..-
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~   80 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ   80 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            3568999999999999999999999999999999864

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

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.65  E-value=0.092  Score=36.61  Aligned_cols=35  Identities=11%  Similarity=0.289  Sum_probs=32.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..+|...||++++|+-+..+++|+.|++.|+|.-+
T Consensus        24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            46899999999999999999999999999999765

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.64  E-value=0.14  Score=36.13  Aligned_cols=36  Identities=19%  Similarity=0.322  Sum_probs=33.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            446999999999999999999999999999999988

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=93.62  E-value=0.16  Score=35.69  Aligned_cols=41  Identities=15%  Similarity=0.210  Sum_probs=35.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS--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

>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]

Probab=93.61  E-value=0.14  Score=41.35  Aligned_cols=54  Identities=22%  Similarity=0.338  Sum_probs=46.3

Q ss_pred             cceeCHHHHHHHHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           40 MVLFDQATYDKLLSEAPK-YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        40 ~Vl~dk~t~dKl~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+-+-+.++-|..|.-. .=+++.|.||||.+|+-|+-=.|||.|++-|+|.-=
T Consensus       183 LSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSR  237 (261)
T COG4465         183 LSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR  237 (261)
T ss_pred             ccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeec
Confidence            334456778888888876 479999999999999999999999999999999754

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.56  E-value=0.14  Score=39.82  Aligned_cols=46  Identities=17%  Similarity=0.255  Sum_probs=40.4

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4556666767789999999999999999999999999999999763

>PRK10870 transcriptional repressor MprA; Provisional

Probab=93.53  E-value=0.14  Score=38.07  Aligned_cols=35  Identities=34%  Similarity=0.298  Sum_probs=33.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            46899999999999999999999999999999998

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=93.49  E-value=0.046  Score=41.13  Aligned_cols=48  Identities=17%  Similarity=0.096  Sum_probs=42.0

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

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

Probab=93.47  E-value=0.11  Score=40.11  Aligned_cols=58  Identities=17%  Similarity=0.204  Sum_probs=45.3

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            6778888888889999999999999999999999999999999999988899999974

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

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.44  E-value=0.2  Score=31.84  Aligned_cols=34  Identities=29%  Similarity=0.448  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=93.28  E-value=0.2  Score=33.45  Aligned_cols=44  Identities=18%  Similarity=0.380  Sum_probs=37.0

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   91 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      |...+.-|..+    .-+|.+.||+.++++-+-+++.|+.|++.|+|.
T Consensus         5 D~~il~~L~~~----~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        5 DRKILEELQKD----ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            45555555544    248999999999999999999999999999998

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

>PRK04158 transcriptional repressor CodY; Validated

Probab=93.27  E-value=0.11  Score=42.05  Aligned_cols=61  Identities=21%  Similarity=0.334  Sum_probs=52.6

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           33 QKEKVNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        33 ~keK~nn~Vl~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +++-++..-+-.-+..+-|..|.... =+++.|-||||.+|+-||-=.|||-||+-|+|.-=
T Consensus       173 V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIESr  234 (256)
T PRK04158        173 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR  234 (256)
T ss_pred             HHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceeec
Confidence            45556666666778889999999885 79999999999999999999999999999999743

>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=93.05  E-value=0.24  Score=30.91  Aligned_cols=32  Identities=19%  Similarity=0.379  Sum_probs=30.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIR   91 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      -+|...||+-++++-.-.-++|++|+++|+|.
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            47899999999999999999999999999998

...

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

Probab=92.92  E-value=0.15  Score=33.27  Aligned_cols=32  Identities=19%  Similarity=0.395  Sum_probs=29.5

Q ss_pred             hhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           63 PSILSDRLRINGSLARKAIRELMARGLIRMVS   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            56899999999999999999999999998754

iron dependent repressor

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=92.89  E-value=0.19  Score=37.80  Aligned_cols=46  Identities=20%  Similarity=0.192  Sum_probs=38.1

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=92.77  E-value=0.26  Score=33.60  Aligned_cols=35  Identities=20%  Similarity=0.215  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            46999999999999999999999999999999987

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=92.65  E-value=0.24  Score=32.22  Aligned_cols=44  Identities=20%  Similarity=0.189  Sum_probs=31.5

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   92 (108)
Q Consensus        48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      +-.|++.+. ..-.+++.|+...+++.+.+.+.|++|+++|+|..
T Consensus         8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~   51 (77)
T PF14947_consen    8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK   51 (77)
T ss_dssp             HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence            334454443 34567899999999999999999999999999943

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.64  E-value=0.27  Score=34.88  Aligned_cols=36  Identities=14%  Similarity=0.104  Sum_probs=32.6

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

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

Probab=92.43  E-value=0.17  Score=29.07  Aligned_cols=40  Identities=18%  Similarity=0.228  Sum_probs=30.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            378899999998766    5788899999986544457778874

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=92.29  E-value=0.25  Score=36.18  Aligned_cols=46  Identities=17%  Similarity=0.238  Sum_probs=39.1

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ...+|...||++++|+-+.-+++|..|.+.|+|+-+-....-..-.
T Consensus        23 ~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~La   68 (150)
T COG1959          23 GGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLA   68 (150)
T ss_pred             CCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCC
Confidence            3489999999999999999999999999999999987655544333

>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=92.07  E-value=0.31  Score=28.71  Aligned_cols=33  Identities=24%  Similarity=0.371  Sum_probs=29.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIR   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 ....

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=91.99  E-value=0.31  Score=35.62  Aligned_cols=41  Identities=17%  Similarity=0.238  Sum_probs=36.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ   99 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      ..+|..+||++++|+-+.-+++|..|...|+|.-+...+.-
T Consensus        23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GG   63 (153)
T PRK11920         23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGG   63 (153)
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCC
Confidence            46799999999999999999999999999999987654433

>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=91.94  E-value=0.61  Score=27.71  Aligned_cols=28  Identities=32%  Similarity=0.487  Sum_probs=26.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcC
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARG   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 ....

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

Probab=91.88  E-value=0.31  Score=27.80  Aligned_cols=30  Identities=23%  Similarity=0.418  Sum_probs=25.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLI   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            577889999999999999999999999997

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 ....

>PRK11050 manganese transport regulator MntR; Provisional

Probab=91.86  E-value=0.32  Score=35.38  Aligned_cols=34  Identities=21%  Similarity=0.317  Sum_probs=31.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRM   92 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      .-+|+..||++|+|+-|-..++|+.|++.|+|..
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r   83 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEM   83 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3479999999999999999999999999999865

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.85  E-value=0.27  Score=37.08  Aligned_cols=55  Identities=20%  Similarity=0.319  Sum_probs=45.6

Q ss_pred             cceeCHHHHHHHHhhCCCCe-----eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           40 MVLFDQATYDKLLSEAPKYK-----LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        40 ~Vl~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

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=91.82  E-value=0.4  Score=31.17  Aligned_cols=30  Identities=27%  Similarity=0.496  Sum_probs=29.3

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           64 SILSDRLRINGSLARKAIRELMARGLIRMV   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            999999999999999999999999999987

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

Probab=91.65  E-value=0.25  Score=34.23  Aligned_cols=47  Identities=26%  Similarity=0.287  Sum_probs=37.5

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            34444444444468899999999999999999999999999998743

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=91.59  E-value=0.41  Score=34.83  Aligned_cols=46  Identities=22%  Similarity=0.354  Sum_probs=39.7

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 PGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET---KRGKGTFVT   76 (125)
T ss_pred             CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCeeEEEc
Confidence            6689999999999999999999999999999999965   345556654

>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=91.53  E-value=0.27  Score=28.53  Aligned_cols=37  Identities=16%  Similarity=0.203  Sum_probs=25.5

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCe-eEeccccceEEE
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLI-RMVSAHASQQIY  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 TIGEVAKLLGVSPR----TLRYYEREGLLPPPERTEGGYRRY   38 (38)
T ss_dssp             EHHHHHHHHTS-HH----HHHHHHHTTSS-SSEETTTS-EEE
T ss_pred             CHHHHHHHHCCCHH----HHHHHHHCCCCCCCccCCCCeecC
Confidence            56788999988764    69999999999 555433444444

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 ....

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=91.53  E-value=0.19  Score=30.87  Aligned_cols=40  Identities=13%  Similarity=0.140  Sum_probs=30.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV-SAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr  104 (108)
                      .|+..+|+.++|+-+.    |+.++++|+|.+. ...++...|+.
T Consensus         1 ~s~~eva~~~gvs~~t----lr~~~~~gli~~~~~~~~g~r~y~~   41 (70)
T smart00422        1 YTIGEVAKLAGVSVRT----LRYYERIGLLPPPIRTEGGYRLYSD   41 (70)
T ss_pred             CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCEecCH
Confidence            4788999999987654    6788899999987 44556677864

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

Probab=91.48  E-value=0.49  Score=31.91  Aligned_cols=45  Identities=20%  Similarity=0.296  Sum_probs=36.7

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            457999999998     688889999999999999999996544445553

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.

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=91.39  E-value=0.49  Score=35.05  Aligned_cols=49  Identities=10%  Similarity=0.213  Sum_probs=39.2

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +.+.-|..-.-+--.++...||++|+|.-+-+..+|+.|++.|+|..+-
T Consensus        10 dYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~   58 (154)
T COG1321          10 DYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP   58 (154)
T ss_pred             HHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence            3344444333356789999999999999999999999999999998753

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

Probab=91.37  E-value=0.2  Score=33.36  Aligned_cols=41  Identities=20%  Similarity=0.291  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc-ceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA-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            46899999999988765    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.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=91.32  E-value=0.61  Score=29.18  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=31.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .+|...||++++|+-+..++.|+.|++.|+.....
T Consensus        13 ~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~   47 (69)
T TIGR00122        13 PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV   47 (69)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            36789999999999999999999999999965544

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.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=91.17  E-value=0.62  Score=37.33  Aligned_cols=80  Identities=19%  Similarity=0.172  Sum_probs=58.8

Q ss_pred             ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        25 KKKWsKgk~keK~nn~Vl~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            34577754444455545555554444333333445899999999999999999999999999999999988888877554

>PRK09954 putative kinase; Provisional

Probab=91.09  E-value=0.25  Score=39.53  Aligned_cols=42  Identities=29%  Similarity=0.409  Sum_probs=36.3

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   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            455555555689999999999999999999999999999984

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=91.01  E-value=0.25  Score=37.41  Aligned_cols=50  Identities=16%  Similarity=0.092  Sum_probs=43.4

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>TIGR00498 lexA SOS regulatory protein LexA

Probab=90.98  E-value=0.34  Score=35.90  Aligned_cols=53  Identities=13%  Similarity=0.135  Sum_probs=39.4

Q ss_pred             CHHHHHHHHhhCCCC-eeechhhhhhhhccc-HHHHHHHHHHHHHcCCeeEeccc
Q 033932           44 DQATYDKLLSEAPKY-KLITPSILSDRLRIN-GSLARKAIRELMARGLIRMVSAH   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            445566666432211 126677999999999 89999999999999999987543

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.

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=90.94  E-value=0.47  Score=35.30  Aligned_cols=42  Identities=19%  Similarity=0.199  Sum_probs=36.2

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   97 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      +.-..+|...||++++|.....+++|+.|.+.|+|.-....+
T Consensus        21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~   62 (164)
T PRK10857         21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPG   62 (164)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCC
Confidence            344679999999999999999999999999999999754433

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

Probab=90.91  E-value=0.28  Score=32.58  Aligned_cols=41  Identities=12%  Similarity=0.183  Sum_probs=32.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            36899999999998765    788899999998754456677864

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.

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

Probab=90.81  E-value=0.26  Score=33.47  Aligned_cols=41  Identities=20%  Similarity=0.271  Sum_probs=32.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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    678899999998644557788874

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.

>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=90.76  E-value=0.49  Score=38.95  Aligned_cols=67  Identities=16%  Similarity=0.255  Sum_probs=43.6

Q ss_pred             hhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEec
Q 033932           36 KVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV--SAHASQQIYTR  104 (108)
Q Consensus        36 K~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr  104 (108)
                      |++..---+.-.|+-|. + -+.+=|....|-.+.++.-+.-.++|+.|++++||+.|  .+|+...||.-
T Consensus        78 k~~~l~~~e~lvy~~I~-~-ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml  146 (327)
T PF05158_consen   78 KLKGLSDEERLVYQLIE-E-AGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYML  146 (327)
T ss_dssp             ---SSSCCHHHHHHHHH-H-HTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEE
T ss_pred             hhcCCCHHHHHHHHHHH-H-hCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEE
Confidence            34444334444555554 2 23456778899999999999999999999999999999  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.

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=90.66  E-value=0.43  Score=38.95  Aligned_cols=50  Identities=20%  Similarity=0.272  Sum_probs=39.5

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            34455555554      345666788999999999999999999999999997543

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

Probab=90.61  E-value=1.1  Score=30.68  Aligned_cols=54  Identities=30%  Similarity=0.427  Sum_probs=39.8

Q ss_pred             HHhhCCCCeeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           51 LLSEAPKYKLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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            3444455  67888888877     466667789999999999999998777777776543

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 ....

>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=90.50  E-value=0.39  Score=32.28  Aligned_cols=33  Identities=21%  Similarity=0.237  Sum_probs=29.5

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLI   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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=90.25  E-value=0.61  Score=34.04  Aligned_cols=43  Identities=26%  Similarity=0.333  Sum_probs=35.7

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            4444444445578899999999999999999999999999974

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=90.17  E-value=0.74  Score=32.85  Aligned_cols=44  Identities=16%  Similarity=0.170  Sum_probs=34.9

Q ss_pred             echhhhhhh----hcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932           61 ITPSILSDR----LRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA  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            488885544    578999999999999999999775 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=90.03  E-value=0.53  Score=35.89  Aligned_cols=36  Identities=19%  Similarity=0.084  Sum_probs=32.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

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

Probab=89.58  E-value=0.31  Score=33.23  Aligned_cols=40  Identities=23%  Similarity=0.210  Sum_probs=32.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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=89.45  E-value=0.38  Score=32.76  Aligned_cols=40  Identities=20%  Similarity=0.300  Sum_probs=31.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            588999999998876    5799999999955544456778874

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=89.05  E-value=0.74  Score=33.15  Aligned_cols=46  Identities=11%  Similarity=0.238  Sum_probs=39.2

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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    3478999999999999999999999999999973

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=88.97  E-value=0.88  Score=32.94  Aligned_cols=41  Identities=17%  Similarity=0.259  Sum_probs=34.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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  3345555

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=88.89  E-value=0.39  Score=32.70  Aligned_cols=41  Identities=15%  Similarity=0.176  Sum_probs=33.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEecc
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTRA  105 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr~  105 (108)
                      .|...||+.++|+.    +.||.-++.|||.|.... ++.++|+..
T Consensus         1 ~~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~   42 (124)
T COG0789           1 YTIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPE   42 (124)
T ss_pred             CcHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHH
Confidence            36788999997765    569999999999999666 588999853

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=88.87  E-value=0.78  Score=35.59  Aligned_cols=57  Identities=19%  Similarity=0.420  Sum_probs=43.4

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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

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

Probab=88.72  E-value=0.32  Score=33.68  Aligned_cols=40  Identities=15%  Similarity=0.194  Sum_probs=31.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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            378899999998865    6899999999997644 456677874

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.

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

Probab=88.67  E-value=0.43  Score=32.14  Aligned_cols=40  Identities=13%  Similarity=0.169  Sum_probs=32.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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            378899999999876    5899999999999854 566778874

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.

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=88.63  E-value=1.1  Score=34.48  Aligned_cols=36  Identities=17%  Similarity=0.194  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      -+|.+.||++++++-|-+.++|+.|++.|++.....
T Consensus        28 ~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~   63 (257)
T PRK15090         28 EIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE   63 (257)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            489999999999999999999999999999977543

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

Probab=88.10  E-value=0.52  Score=33.90  Aligned_cols=40  Identities=23%  Similarity=0.423  Sum_probs=33.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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    467999999999964 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

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=88.06  E-value=1.1  Score=34.88  Aligned_cols=36  Identities=17%  Similarity=0.341  Sum_probs=33.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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=87.78  E-value=1.8  Score=29.70  Aligned_cols=45  Identities=13%  Similarity=0.191  Sum_probs=34.9

Q ss_pred             echhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           61 ITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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 46788998653

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 ....

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=87.77  E-value=0.58  Score=34.71  Aligned_cols=42  Identities=29%  Similarity=0.444  Sum_probs=35.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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    5899999999999755566788874

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

Probab=87.72  E-value=0.66  Score=28.50  Aligned_cols=40  Identities=18%  Similarity=0.216  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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    5899999999888775666688874

>PF12728 HTH_17: Helix-turn-helix domain

Probab=87.58  E-value=0.77  Score=26.98  Aligned_cols=40  Identities=15%  Similarity=0.131  Sum_probs=30.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 555555543

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=87.56  E-value=0.49  Score=33.77  Aligned_cols=43  Identities=21%  Similarity=0.332  Sum_probs=35.4

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  104 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      |..+|...||++++|+.+    .||.-++.|||.|... .++..+|+.
T Consensus         1 m~~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~   44 (120)
T TIGR02054         1 MNAYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDD   44 (120)
T ss_pred             CCCCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCH
Confidence            346799999999999875    5899999999999844 467888875

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.

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

Probab=87.55  E-value=0.6  Score=32.35  Aligned_cols=39  Identities=18%  Similarity=0.230  Sum_probs=32.2

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            67789999998765    5899999999999866667788874

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.

>PRK09462 fur ferric uptake regulator; Provisional

Probab=87.49  E-value=1.4  Score=31.57  Aligned_cols=43  Identities=12%  Similarity=0.274  Sum_probs=28.7

Q ss_pred             echhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            4555555544     244555668999999999999986544445554

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

Probab=87.37  E-value=2.2  Score=28.08  Aligned_cols=34  Identities=21%  Similarity=0.242  Sum_probs=29.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

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

Probab=87.13  E-value=1.2  Score=33.23  Aligned_cols=37  Identities=22%  Similarity=0.401  Sum_probs=33.8

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +.=+.|-..||+.++++-+--.++|.+|++.|+|..+
T Consensus        72 N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~  108 (165)
T PF05732_consen   72 NAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI  108 (165)
T ss_pred             CeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence            4567899999999999999999999999999999876

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

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

Probab=87.13  E-value=0.6  Score=32.52  Aligned_cols=39  Identities=15%  Similarity=0.258  Sum_probs=33.3

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            67889999998865    5899999999999866678888975

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

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

Probab=87.12  E-value=1.7  Score=31.61  Aligned_cols=45  Identities=22%  Similarity=0.401  Sum_probs=33.9

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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~islaTV--------------Yr~L~~l~e~Glv~~~~~~~~~~~y~   84 (145)
T COG0735          40 EELYEELREEGPGISLATV--------------YRTLKLLEEAGLVHRLEFEGGKTRYE   84 (145)
T ss_pred             HHHHHHHHHhCCCCCHhHH--------------HHHHHHHHHCCCEEEEEeCCCEEEEe
Confidence            5677777777777665554              47899999999999997666555564

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

Probab=87.01  E-value=1.3  Score=35.40  Aligned_cols=42  Identities=29%  Similarity=0.253  Sum_probs=34.5

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCC-eeE
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGL-IRM   92 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGl-Ik~   92 (108)
                      |+..+..-..++...||++|+|+-+-.++.|+.|++.|+ |.-
T Consensus         9 il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~   51 (319)
T PRK11886          9 LLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS   51 (319)
T ss_pred             HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence            333333457889999999999999999999999999999 543

>PRK12423 LexA repressor; Provisional

Probab=86.78  E-value=1.1  Score=33.88  Aligned_cols=49  Identities=20%  Similarity=0.255  Sum_probs=37.3

Q ss_pred             HHHHHHHHhhCCCCee-echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEe
Q 033932           45 QATYDKLLSEAPKYKL-ITPSILSDRLRI-NGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~-ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .+.++.|...+-..-+ =|...||+.|++ +-+..+..|+.|+++|+|..-
T Consensus         9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~   59 (202)
T PRK12423          9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV   59 (202)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence            4566666654333322 388899999995 788889999999999999864

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=86.62  E-value=0.98  Score=33.97  Aligned_cols=34  Identities=24%  Similarity=0.338  Sum_probs=28.7

Q ss_pred             echhhhhhhhcc--------------cHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRI--------------NGSLARKAIRELMARGLIRMVS   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            566677777777              5899999999999999999765

>TIGR01764 excise DNA binding domain, excisionase family

Probab=86.50  E-value=1  Score=25.26  Aligned_cols=40  Identities=13%  Similarity=0.169  Sum_probs=29.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 YLTVEEAAEYLGVSKD----TVYRLIHEGELPAYRVG-RHYRIPR   40 (49)
T ss_pred             CCCHHHHHHHHCCCHH----HHHHHHHcCCCCeEEeC-CeEEEeH
Confidence            4789999999987544    57777889998876443 4455543

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=86.37  E-value=0.72  Score=25.65  Aligned_cols=40  Identities=13%  Similarity=0.324  Sum_probs=28.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            377889999988655    4677788899876644446666754

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.

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

Probab=86.24  E-value=0.7  Score=31.95  Aligned_cols=39  Identities=15%  Similarity=0.169  Sum_probs=32.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            67889999998865    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.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=85.82  E-value=1.7  Score=31.25  Aligned_cols=32  Identities=28%  Similarity=0.260  Sum_probs=30.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIR   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

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

Probab=85.73  E-value=0.67  Score=31.77  Aligned_cols=39  Identities=15%  Similarity=0.165  Sum_probs=31.6

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc--ccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA--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            67899999998876    5899999999999643  256778875

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.

>PRK05472 redox-sensing transcriptional repressor Rex; Provisional

Probab=85.58  E-value=1.3  Score=33.39  Aligned_cols=53  Identities=15%  Similarity=0.204  Sum_probs=44.2

Q ss_pred             hhccceeCHHHHHHHHhhCCCCe--eechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033932           37 VNNMVLFDQATYDKLLSEAPKYK--LITPSILSDRLRINGSLARKAIRELMARGL   89 (108)
Q Consensus        37 ~nn~Vl~dk~t~dKl~KEVpk~k--~ITps~vserlkI~~SlAr~~Lr~L~~kGl   89 (108)
                      +..+++---+.|.+|++.+....  .||...||+.++|+.+..|+=|..|+..|.
T Consensus         7 ~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~   61 (213)
T PRK05472          7 IPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK   61 (213)
T ss_pred             CCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence            33344444677888888888877  999999999999999999999999999885

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=85.54  E-value=2.2  Score=31.53  Aligned_cols=42  Identities=26%  Similarity=0.139  Sum_probs=36.5

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   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            345556656679999999999999999999999999999995

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.

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

Probab=85.43  E-value=0.98  Score=30.62  Aligned_cols=39  Identities=13%  Similarity=0.253  Sum_probs=31.6

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      |+..+|++++|+.+.    ||.-++.|+|.++-..++..+|+.
T Consensus         2 ~I~e~a~~~gvs~~t----LR~ye~~Gll~p~r~~~g~R~Y~~   40 (96)
T cd04774           2 KVDEVAKRLGLTKRT----LKYYEEIGLVSPERSEGRYRLYSE   40 (96)
T ss_pred             CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCEEECH
Confidence            788999999887664    788899999998765667778874

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.

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

Probab=85.41  E-value=0.73  Score=30.54  Aligned_cols=40  Identities=15%  Similarity=0.233  Sum_probs=30.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            3788999999988665    678899999987654456677875

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.

>PRK13749 transcriptional regulator MerD; Provisional

Probab=85.38  E-value=0.65  Score=33.34  Aligned_cols=43  Identities=21%  Similarity=0.310  Sum_probs=34.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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            345789999999998875    6899999999999844 367778875

>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=85.15  E-value=0.85  Score=32.66  Aligned_cols=34  Identities=21%  Similarity=0.369  Sum_probs=31.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=84.80  E-value=1.7  Score=34.00  Aligned_cols=35  Identities=14%  Similarity=0.326  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            48999999999999999999999999999997643

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=84.72  E-value=1  Score=32.84  Aligned_cols=46  Identities=20%  Similarity=0.229  Sum_probs=36.1

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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            34456899999999998875    5999999999987643 4567889753

>PRK00215 LexA repressor; Validated

Probab=84.61  E-value=1.7  Score=32.30  Aligned_cols=39  Identities=18%  Similarity=0.299  Sum_probs=33.7

Q ss_pred             echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEeccccce
Q 033932           61 ITPSILSDRLRI-NGSLARKAIRELMARGLIRMVSAHASQ   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 889999999999999999887554443

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=84.11  E-value=1.2  Score=32.45  Aligned_cols=40  Identities=28%  Similarity=0.376  Sum_probs=32.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            478899999998875    5899999999998654566788874

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=84.10  E-value=0.85  Score=30.76  Aligned_cols=40  Identities=15%  Similarity=0.127  Sum_probs=31.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  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            377899999998765    5899999999999743 355677764

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.

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

Probab=84.03  E-value=1  Score=31.95  Aligned_cols=39  Identities=15%  Similarity=0.259  Sum_probs=31.8

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-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            67889999998865    68999999999997543 67788874

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

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

Probab=83.82  E-value=1  Score=31.51  Aligned_cols=40  Identities=23%  Similarity=0.272  Sum_probs=31.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV-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            377899999999876    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.

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

Probab=83.72  E-value=1.6  Score=32.44  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=22.5

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932           72 INGSLARKAIRELMARGLIRMVSAHAS   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.

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

Probab=83.47  E-value=1.3  Score=32.02  Aligned_cols=40  Identities=23%  Similarity=0.283  Sum_probs=33.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            478899999998876    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.

>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=83.39  E-value=0.83  Score=30.90  Aligned_cols=35  Identities=23%  Similarity=0.305  Sum_probs=27.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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.

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

Probab=83.37  E-value=1.2  Score=30.31  Aligned_cols=39  Identities=21%  Similarity=0.280  Sum_probs=31.2

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMV-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~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~   41 (99)
T cd04772           2 RTVDLARAIGLSPQT----VRNYESLGLIPPAERTANGYRIYTD   41 (99)
T ss_pred             CHHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCCeecCH
Confidence            788999999988764    7899999999986 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.

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=83.29  E-value=1.1  Score=31.55  Aligned_cols=39  Identities=18%  Similarity=0.212  Sum_probs=31.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr  104 (108)
                      |...||++++|+.+    .||.-++.|||.+..+ .++.+.|+.
T Consensus         2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~   41 (127)
T TIGR02044         2 NIGQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQ   41 (127)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence            67889999888765    6899999999998743 567788875

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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=83.25  E-value=2.2  Score=33.21  Aligned_cols=36  Identities=17%  Similarity=0.320  Sum_probs=33.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            899999999999999999999999999999875433

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

Probab=83.24  E-value=1  Score=30.57  Aligned_cols=39  Identities=13%  Similarity=0.232  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|...+|++++|+.+    .||.-++.|||.|.. .++...|+.
T Consensus         1 m~Ige~a~~~gvs~~----tlRyYe~~GLl~p~~-~~g~r~Y~~   39 (107)
T cd04777           1 MKIGKFAKKNNITID----TVRHYIDLGLLIPEK-KGGQYFFDE   39 (107)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCcCCcc-CCCccccCH
Confidence            367889999998865    799999999999954 345556763

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.

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

Probab=83.11  E-value=4.1  Score=28.78  Aligned_cols=48  Identities=19%  Similarity=0.214  Sum_probs=42.6

Q ss_pred             HHHHHHHhhCCCCe-eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYK-LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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 4899999999999999999999999999999876

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=83.00  E-value=2.4  Score=33.18  Aligned_cols=35  Identities=17%  Similarity=0.034  Sum_probs=32.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|.+.||+++++.-|-+-++|..|++.|++..-
T Consensus        39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~   73 (271)
T PRK10163         39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD   73 (271)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            34899999999999999999999999999999764

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=82.91  E-value=2  Score=30.52  Aligned_cols=35  Identities=34%  Similarity=0.548  Sum_probs=30.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      =|..|..++|.   ||+-+|+++|           ++|++.|+|....-
T Consensus        38 RF~eL~r~i~~---Is~k~Ls~~L-----------k~Le~~Glv~R~~~   72 (120)
T COG1733          38 RFNELRRSIGG---ISPKMLSRRL-----------KELEEDGLVERVVY   72 (120)
T ss_pred             cHHHHHHHccc---cCHHHHHHHH-----------HHHHHCCCEEeeec
Confidence            57889999998   9999999985           89999999988754

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

Probab=82.74  E-value=1.7  Score=33.23  Aligned_cols=33  Identities=15%  Similarity=0.233  Sum_probs=31.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            479999999999999999999999999999975

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.

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

Probab=82.63  E-value=1.9  Score=35.56  Aligned_cols=37  Identities=16%  Similarity=0.358  Sum_probs=33.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   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            6999999999999999999999999999998766544

>PRK06474 hypothetical protein; Provisional

Probab=82.62  E-value=4  Score=30.57  Aligned_cols=44  Identities=18%  Similarity=0.375  Sum_probs=36.7

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc----ccceEEEec
Q 033932           61 ITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA----HASQQIYTR  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 7988999999999999999999864    234456654

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

Probab=82.47  E-value=3.1  Score=36.03  Aligned_cols=51  Identities=24%  Similarity=0.268  Sum_probs=47.2

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            478888899999999999999999999999999999999999999999753

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

Probab=82.37  E-value=1.4  Score=30.03  Aligned_cols=40  Identities=10%  Similarity=0.174  Sum_probs=31.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAHASQQIYTR  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 88877655667888874

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.

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

Probab=82.16  E-value=1.1  Score=31.31  Aligned_cols=39  Identities=21%  Similarity=0.348  Sum_probs=31.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|+..||+.++|+.+    .||.-++.|||.|.. ..+...|+.
T Consensus         1 ~~Igeva~~~gvs~~----tlRyYe~~GLl~p~r-~~gyR~Y~~   39 (118)
T cd04776           1 YTISELAREFDVTPR----TLRFYEDKGLLSPER-RGQTRVYSR   39 (118)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCccccCH
Confidence            367889999988875    589999999999964 447888875

Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

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

Probab=82.12  E-value=1.2  Score=27.71  Aligned_cols=39  Identities=13%  Similarity=0.229  Sum_probs=28.8

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAHASQQIYTR  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            788999999998775    5677876 98876543445567864

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

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

Probab=81.87  E-value=1.4  Score=30.88  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=31.6

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  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~~r~~~gyR~Y~~   41 (127)
T cd04784           2 KIGELAKKTGCSVE----TIRYYEKEGLLPAPARSANNYRLYDE   41 (127)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence            67889999998765    6999999999997643 467788875

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PF13814 Replic_Relax: Replication-relaxation

Probab=81.82  E-value=2.3  Score=30.75  Aligned_cols=49  Identities=16%  Similarity=0.275  Sum_probs=41.0

Q ss_pred             CCCeeechhhhhhhhcccHH---HHHHHHHHHHHcCCeeEecc------ccceEEEec
Q 033932           56 PKYKLITPSILSDRLRINGS---LARKAIRELMARGLIRMVSA------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            35688999999999999987   79999999999999998865      356678763

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=81.77  E-value=4.2  Score=26.50  Aligned_cols=39  Identities=21%  Similarity=0.292  Sum_probs=30.2

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -.+.+.|+|+-+-+|.+|--|.++|++...-.+ +...|.
T Consensus        27 i~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~G-r~~~Y~   65 (70)
T PF07848_consen   27 IRLLAAFGVSESAVRTALSRLVRRGWLESERRG-RRSYYR   65 (70)
T ss_dssp             HHHHCCTT--HHHHHHHHHHHHHTTSEEEECCC-TEEEEE
T ss_pred             HHHHHHcCCChHHHHHHHHHHHHcCceeeeecC-ccceEe
Confidence            356789999999999999999999999986544 455664

PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.

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

Probab=81.77  E-value=1.5  Score=30.11  Aligned_cols=40  Identities=20%  Similarity=0.272  Sum_probs=31.8

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTR  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~~~~~~g~R~Y~~   41 (108)
T cd04773           1 MTIGELAHLLGVPPS----TLRHWEKEGLLSPDREPETGYRVYDP   41 (108)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCceeeCH
Confidence            378899999988765    58889999999987543 56778875

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>PRK05638 threonine synthase; Validated

Probab=81.59  E-value=2.6  Score=35.40  Aligned_cols=65  Identities=17%  Similarity=0.105  Sum_probs=44.6

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhc--ccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           33 QKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLR--INGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        33 ~keK~nn~Vl~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            4566554422 34444444432 3    68999999998  88889999999999999998653444443453

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=81.45  E-value=1.4  Score=31.24  Aligned_cols=40  Identities=18%  Similarity=0.276  Sum_probs=32.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  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~~~gyR~Y~~   42 (131)
T TIGR02043         2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTD   42 (131)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCH
Confidence            578999999998876    6899999999999644 456778874

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>COG3177 Fic family protein [Function unknown]

Probab=81.36  E-value=2.4  Score=34.73  Aligned_cols=58  Identities=16%  Similarity=0.269  Sum_probs=46.8

Q ss_pred             HHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           46 ATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        46 ~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      ..++++...+-.. .++|...++--++|.-+-|++-|.+|.+.|++..+..+.+...|.
T Consensus       289 ~~~~~l~~~~~~~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~~  347 (348)
T COG3177         289 ERIGQLNVLLFGQEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRSKLYS  347 (348)
T ss_pred             hhHHHHHHHHhccCCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCceecc
Confidence            3344344455543 899999999999999999999999999999999998777766653

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=81.33  E-value=3.1  Score=31.12  Aligned_cols=45  Identities=22%  Similarity=0.338  Sum_probs=37.0

Q ss_pred             HHhhCCCCeee-chhhhhhhh--cccHHHHHHHHHHHHHcCCeeEecc
Q 033932           51 LLSEAPKYKLI-TPSILSDRL--RINGSLARKAIRELMARGLIRMVSA   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

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=81.31  E-value=2.3  Score=31.48  Aligned_cols=33  Identities=9%  Similarity=0.212  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            788999999999999888899999999999863

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=81.12  E-value=3.8  Score=28.68  Aligned_cols=41  Identities=22%  Similarity=0.091  Sum_probs=31.2

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS   98 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      ..-+.|.-|.=.-|++..+|+..|++|++.|+|.....+++
T Consensus        29 ~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~   69 (95)
T COG3432          29 EGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRR   69 (95)
T ss_pred             CCCCCceeeeeecCcCHHHHHHHHHHHHhCCCEEeccCCcc
Confidence            34455566666778999999999999999997777654433

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=80.82  E-value=2.6  Score=29.90  Aligned_cols=32  Identities=9%  Similarity=0.258  Sum_probs=30.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=80.56  E-value=1.7  Score=31.30  Aligned_cols=40  Identities=15%  Similarity=0.203  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR  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~~~gyR~Y~~   42 (140)
T PRK09514          2 YRIGELAKLAEVTPD----TLRFYEKQGLMDPEVRTEGGYRLYTE   42 (140)
T ss_pred             CcHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCCeeeCH
Confidence            578999999998765    6899999999999643 456788875

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

Probab=80.02  E-value=2  Score=28.81  Aligned_cols=39  Identities=15%  Similarity=0.264  Sum_probs=31.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVS-AHASQQIYTR  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~~~gyR~Y~~   41 (96)
T cd04788           2 KIGELARRTGLSVR----TLHHYDHIGLLSPSQRTEGGHRLYDR   41 (96)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCH
Confidence            67889999998765    589999999999863 3466788875

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

---

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		2e-27
3zey_U	113	High-resolution Cryo-electron Microscopy Structure		8e-17
3izb_V	108	Localization Of The Small Subunit Ribosomal Protein		2e-15
2xzm_8	143	Crystal Structure Of The Eukaryotic 40s Ribosomal S		3e-05

>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 =  117 bits (293), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 64/71 (90%)
Query: 37  VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
           VNN VLFD+ATYDKLLSE PKYK ITPS+LS+RLRINGSLAR+AI++L +RG IR+VS 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 = 82.0 bits (201), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 37/69 (53%), Positives = 53/69 (76%)
Query: 37  VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96
           + N V+FD+ T DKL+ E PKYK+ITPSI+SDRL+I+ +LA K ++ L  +GLIR+VS  
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 = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 34/71 (47%), Positives = 49/71 (69%)
Query: 38  NNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97
            + V+ DQ  YD++L E P Y+ ++ S+L DRL+I GSLAR A+R L   G+I+ +S 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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 37  VNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95
           VN+ V  ++   + +++   K  K++T S + ++L++NGSLAR+ +R +  R L+  V+ 
Sbjct: 39  VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK 98
Query: 96  HASQQIYT 103
           + +Q +Y+
Sbjct: 99  NGNQWVYS 106

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	3e-41
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	2e-38
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	6e-34

>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 =  130 bits (329), Expect = 3e-41
 Identities = 91/107 (85%), Positives = 100/107 (93%)

Query: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKL 60
           MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNN VLFD+ATYDKLLSE PKYK 
Sbjct: 1   MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSEVPKYKQ 60

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATN 107
           ITPS+LS+RLRINGSLAR+AI++L +RG IR+VS 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 =  123 bits (311), Expect = 2e-38
 Identities = 47/106 (44%), Positives = 67/106 (63%)

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

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

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

 Score =  113 bits (284), Expect = 6e-34
 Identities = 31/108 (28%), Positives = 59/108 (54%), Gaps = 1/108 (0%)

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

Query: 61  ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRATNT 108
           +T S + ++L++NGSLAR+ +R +  R L+  V+ + +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;	97.31
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	97.18
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	97.15
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	96.89
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.8
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.67
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.63
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.63
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.62
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.51
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.38
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.32
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.31
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	96.27
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	96.24
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.23
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.2
3by6_A	126	Predicted transcriptional regulator; structural ge	96.17
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.13
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	96.09
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.07
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.03
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	96.01
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.98
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	95.97
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	95.97
2gxg_A	146	146AA long hypothetical transcriptional regulator;	95.96
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	95.92
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	95.88
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.88
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.87
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.86
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.82
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.82
3jth_A	98	Transcription activator HLYU; transcription factor	95.81
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	95.81
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	95.78
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	95.76
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.75
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.74
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.73
3r0a_A	123	Putative transcriptional regulator; structural gen	95.7
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.67
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	95.67
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.67
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	95.66
3eet_A	272	Putative GNTR-family transcriptional regulator; st	95.63
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.62
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	95.62
2nnn_A	140	Probable transcriptional regulator; structural gen	95.61
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.6
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	95.56
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.55
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.54
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.53
2h09_A	155	Transcriptional regulator MNTR; transcription regu	95.51
2kko_A	108	Possible transcriptional regulatory protein (possi	95.5
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	95.48
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	95.47
3c7j_A	237	Transcriptional regulator, GNTR family; structural	95.46
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.44
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.44
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.43
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.43
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	95.4
2eth_A	154	Transcriptional regulator, putative, MAR family; M	95.4
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.38
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	95.38
3s2w_A	159	Transcriptional regulator, MARR family; structural	95.36
2vn2_A	128	DNAD, chromosome replication initiation protein; D	95.35
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.3
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.27
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.25
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.21
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	95.2
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.18
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.16
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.13
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	95.12
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.12
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.08
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	95.04
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.04
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.03
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	95.01
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.01
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	94.98
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	94.97
3bja_A	139	Transcriptional regulator, MARR family, putative;	94.96
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.95
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.9
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	94.86
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	94.84
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	94.74
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.7
2w25_A	150	Probable transcriptional regulatory protein; trans	94.66
3f3x_A	144	Transcriptional regulator, MARR family, putative;	94.66
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.66
3nqo_A	189	MARR-family transcriptional regulator; structural	94.65
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	94.58
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	94.54
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.54
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.53
1ylf_A	149	RRF2 family protein; structural genomics, transcri	94.51
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.49
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	94.48
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	94.46
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.45
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	94.44
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	94.43
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	94.36
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.35
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	94.27
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	94.24
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	94.23
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.15
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	94.14
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.12
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	94.1
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	94.03
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	94.02
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	94.0
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	93.96
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.94
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	93.94
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.89
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	93.82
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	93.71
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	93.7
1yyv_A	131	Putative transcriptional regulator; reductive meth	93.67
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	93.59
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.59
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	93.59
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	93.47
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	93.27
2fxa_A	207	Protease production regulatory protein HPR; protea	93.21
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	93.12
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.11
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	92.86
3eqx_A	373	FIC domain containing transcriptional regulator; F	92.83
1xd7_A	145	YWNA; structural genomics, protein structure initi	92.79
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	92.69
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	92.58
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	92.51
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	92.29
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	92.22
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	92.04
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	91.97
3k69_A	162	Putative transcription regulator; putative transcr	91.89
2ra5_A	247	Putative transcriptional regulator; beta structure	91.61
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	91.42
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	91.36
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	91.06
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	90.93
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	90.3
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	90.3
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	90.24
3hh0_A	146	Transcriptional regulator, MERR family; protein st	90.11
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	89.98
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	89.5
1mkm_A	249	ICLR transcriptional regulator; structural genomic	89.41
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	89.35
2ve8_A	73	FTSK, DNA translocase FTSK; nucleotide-binding, ch	89.23
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	89.2
1bia_A	321	BIRA bifunctional protein; transcription regulatio	89.15
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	89.04
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	88.98
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	88.97
3gpv_A	148	Transcriptional regulator, MERR family; protein st	88.65
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	88.43
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	88.42
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	88.36
2w57_A	150	Ferric uptake regulation protein; gene regulation,	88.2
2obp_A	96	Putative DNA-binding protein; structural genomics,	88.07
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	87.84
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	87.72
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	87.59
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	87.47
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	87.21
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	87.13
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	86.99
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	86.82
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	86.4
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	86.37
3cta_A	230	Riboflavin kinase; structural genomics, transferas	86.31
2o0m_A	345	Transcriptional regulator, SORC family; structural	86.24
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	86.14
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	86.09
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	86.08
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	85.97
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	85.96
1hsj_A	487	Fusion protein consisting of staphylococcus access	85.94
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	85.8
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	85.68
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	85.64
2g7u_A	257	Transcriptional regulator; ICLR family, structural	85.62
1xma_A	145	Predicted transcriptional regulator; southea colla	85.18
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	85.17
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	85.12
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	85.09
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	84.99
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	84.88
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	84.78
1z05_A	429	Transcriptional regulator, ROK family; structural	84.17
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	83.93
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	83.88
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	83.76
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	83.71
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	83.62
4esf_A	117	PADR-like transcriptional regulator; PADR family,	83.38
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	83.38
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	83.27
1ft9_A	222	Carbon monoxide oxidation system transcription reg	83.1
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	83.06
3b02_A	195	Transcriptional regulator, CRP family; structural	83.03
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	82.39
3u5c_T	144	40S ribosomal protein S19-A; translation, ribosome	82.38
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	82.21
3iz6_S	146	40S ribosomal protein S19 (S19E); eukaryotic ribos	82.11
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	82.08
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	81.9
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	81.83
2jml_A	81	DNA binding domain/transcriptional regulator; anti	81.71
1bja_A	95	Transcription regulatory protein MOTA; activation	81.64
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	81.33
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	81.19
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	80.93
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	80.9
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	80.83
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	80.78
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	80.2
3qph_A	342	TRMB, A global transcription regulator; transcript	80.1

>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=1.2e-54  Score=306.53  Aligned_cols=107  Identities=44%  Similarity=0.766  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA   80 (108)
Q Consensus         1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~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            999988888887774 5899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEeccccceEEEecccCC
Q 033932           81 IRELMARGLIRMVSAHASQQIYTRATNT  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=1.4e-54  Score=306.19  Aligned_cols=108  Identities=84%  Similarity=1.211  Sum_probs=94.3

Q ss_pred             CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA   80 (108)
Q Consensus         1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~   80 (108)
                      ||||.++..+++.++++++||+++||||||||++||+||+|+||++|||+|++|||+|+|||||+|||||+|++||||++
T Consensus         1 m~pk~~~~~k~~~~~~a~~ggk~~KKKWsKgk~kdk~nn~Vl~Dk~t~dkl~KEVpk~KlITpsvlseRlkI~gSLAR~a   80 (108)
T 3iz6_V            1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQA   80 (108)
T ss_dssp             --------CCCCCCCCTTCCCCCCCCSCCCCCCSHHHHSHHHHSSHHHHHHHHHHHHHSSEEEHHHHHHHHTCCHHHHHH
T ss_pred             CCCcccccCHHHHHHHHhcCCCccccccccccHHHHhcCcEeECHHHHHHHHHHccCCeEEeHHHHHhhhcccHHHHHHH
Confidence            99995444444444466899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHcCCeeEeccccceEEEecccCC
Q 033932           81 IRELMARGLIRMVSAHASQQIYTRATNT  108 (108)
Q Consensus        81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~~  108 (108)
                      ||||+++|+|++|++||+|.||||++++
T Consensus        81 LreL~~kGlIk~V~kh~~q~IYTr~~~~  108 (108)
T 3iz6_V           81 IKDLESRGAIRVVSVHSSQLIYTRATNA  108 (108)
T ss_dssp             HHHHHHHHTSCEECCCTTSCCEEESCCC
T ss_pred             HHHHHHCCCEEEEecCCCEEEEecCcCC
Confidence            9999999999999999999999999874

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

Probab=100.00  E-value=4.4e-49  Score=289.07  Aligned_cols=105  Identities=30%  Similarity=0.520  Sum_probs=85.5

Q ss_pred             CCCCC-CCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHH
Q 033932            1 MAPKK-DKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLAR   78 (108)
Q Consensus         1 M~pk~-~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~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-KAA-QAKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLAR   81 (143)
T ss_dssp             ---------------------CCCCSSCCCSSCCCCCCCCBSCCCHHHHHHHHTCCTTSCSEECHHHHHHHHCBCHHHHH
T ss_pred             CCCcccccchhHHH-Hhh-ccCccccCCcccchHHHHHhcceeecHHHHHHHHHHhcccceeecHHHHHHHhcchHHHHH
Confidence            89995 55444444 343 4488889999999999999999999999999999999999 99999999999999999999


Q ss_pred             HHHHHHHHcCCeeEeccccceEEEecccC
Q 033932           79 KAIRELMARGLIRMVSAHASQQIYTRATN  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            99999999999999999999999999875

>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=9e-05  Score=48.36  Aligned_cols=46  Identities=9%  Similarity=0.063  Sum_probs=41.7

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4566766767789999999999999999999999999999999988

>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=97.31  E-value=0.00018  Score=48.37  Aligned_cols=54  Identities=26%  Similarity=0.354  Sum_probs=43.2

Q ss_pred             HHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEE
Q 033932           48 YDKLLSEA-PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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 4557779999999999999999999999999999987663 244444

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

Probab=97.18  E-value=0.00014  Score=48.66  Aligned_cols=47  Identities=17%  Similarity=0.139  Sum_probs=41.5

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            45566666667899999999999999999999999999999999884

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

Probab=97.15  E-value=0.00022  Score=46.42  Aligned_cols=45  Identities=13%  Similarity=0.074  Sum_probs=38.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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=96.89  E-value=0.0023  Score=43.79  Aligned_cols=51  Identities=20%  Similarity=0.178  Sum_probs=42.1

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            34566666654      4567778999999999999999999999999999977543

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

Probab=96.80  E-value=0.0036  Score=39.29  Aligned_cols=43  Identities=12%  Similarity=0.135  Sum_probs=35.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS-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

>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=96.67  E-value=0.003  Score=40.60  Aligned_cols=43  Identities=7%  Similarity=0.098  Sum_probs=35.8

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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

>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=96.63  E-value=0.0026  Score=41.67  Aligned_cols=57  Identities=7%  Similarity=0.054  Sum_probs=45.2

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHH-HHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGS-LARKAIRELMARGLIRMVSAHASQQIYT  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            4666676655555555899999999999999 99999999999999986654442  664

>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=96.63  E-value=0.0033  Score=41.72  Aligned_cols=44  Identities=18%  Similarity=0.228  Sum_probs=37.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV--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

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

Probab=96.62  E-value=0.0035  Score=42.05  Aligned_cols=49  Identities=18%  Similarity=0.173  Sum_probs=39.2

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            4455555543      345666999999999999999999999999999987654

>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=96.51  E-value=0.0043  Score=42.59  Aligned_cols=49  Identities=20%  Similarity=0.265  Sum_probs=40.3

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=96.38  E-value=0.0068  Score=38.16  Aligned_cols=51  Identities=20%  Similarity=0.283  Sum_probs=38.8

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ....+.-|..=.....-+|+..||+.++|+-|-..++|+.|++.|+|....
T Consensus        20 ~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           20 TDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             CHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            444444443222113348999999999999999999999999999999874

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

Probab=96.32  E-value=0.012  Score=36.94  Aligned_cols=56  Identities=14%  Similarity=0.139  Sum_probs=43.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            3345555554444689999999999999999999999999999988753 4445554

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

Probab=96.31  E-value=0.0067  Score=37.83  Aligned_cols=45  Identities=11%  Similarity=0.252  Sum_probs=39.0

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            369999999999     999999999999999999999987655555563

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

Probab=96.27  E-value=0.0088  Score=45.03  Aligned_cols=44  Identities=14%  Similarity=0.251  Sum_probs=37.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEE
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQI  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            4456669999999999999999999999999999987  4454443

>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=96.24  E-value=0.0092  Score=39.40  Aligned_cols=45  Identities=16%  Similarity=0.149  Sum_probs=38.1

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            34455555543  9999999999999999999999999999998863

>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=96.23  E-value=0.0028  Score=41.38  Aligned_cols=50  Identities=20%  Similarity=0.207  Sum_probs=39.6

Q ss_pred             HHHHHHHHh---hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLS---EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            334444443   44433379999999999999999999999999999999885

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

Probab=96.20  E-value=0.0045  Score=41.10  Aligned_cols=43  Identities=26%  Similarity=0.390  Sum_probs=36.4

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=96.17  E-value=0.0087  Score=41.04  Aligned_cols=50  Identities=24%  Similarity=0.258  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...|+.|...|      |+.++-|-..||++|+|+-+..|.+|+.|+..|+|....
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   69 (126)
T 3by6_A           14 LQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIP   69 (126)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            34555555544      344556999999999999999999999999999997654

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

Probab=96.13  E-value=0.0082  Score=39.80  Aligned_cols=50  Identities=12%  Similarity=0.090  Sum_probs=40.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            56666654444434 999999999999999999999999999999886443

>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=96.09  E-value=0.014  Score=43.39  Aligned_cols=50  Identities=16%  Similarity=0.188  Sum_probs=41.8

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            45666666544      66787 9999999999999999999999999999987643

>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=96.07  E-value=0.015  Score=36.23  Aligned_cols=45  Identities=13%  Similarity=0.192  Sum_probs=37.9

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932           60 LITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYTRA  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 SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHK-EGRVFVYTPN   71 (82)
T ss_dssp             SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEE-ETTEEEEEES
T ss_pred             CCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEe-cCCEEEEEee
Confidence            489999999998    57899999999999999999875 3556788643

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

Probab=96.03  E-value=0.013  Score=36.62  Aligned_cols=34  Identities=21%  Similarity=0.433  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=96.01  E-value=0.0046  Score=42.36  Aligned_cols=50  Identities=8%  Similarity=0.104  Sum_probs=40.3

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..+|+.|...|      |+.++-|-..||++|+|+-+-.|.+|+.|++.|+|....
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   69 (126)
T 3ic7_A           14 LQIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNKR   69 (126)
T ss_dssp             THHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEET
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEc
Confidence            45667776665      345666889999999999999999999999999997764

>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=95.98  E-value=0.019  Score=36.68  Aligned_cols=44  Identities=20%  Similarity=0.205  Sum_probs=39.5

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=95.97  E-value=0.0032  Score=41.05  Aligned_cols=50  Identities=10%  Similarity=0.119  Sum_probs=39.9

Q ss_pred             HHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        45 k~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..+++.|...|-.      ..+-|...||++|+|+-+..|++|+.|++.|+|..+.
T Consensus        14 ~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           14 ADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             HHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            4566666655544      3444999999999999999999999999999997643

>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=95.97  E-value=0.014  Score=42.47  Aligned_cols=50  Identities=14%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ...|+.|...|      |+.++=|-..||++|+|+-+-.|.||+.|+..|+|....
T Consensus        10 ~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~   65 (239)
T 1hw1_A           10 GFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH   65 (239)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEec
Confidence            34555555554      556666999999999999999999999999999998754

>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=95.96  E-value=0.014  Score=38.47  Aligned_cols=37  Identities=22%  Similarity=0.198  Sum_probs=34.1

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=95.92  E-value=0.0075  Score=38.18  Aligned_cols=46  Identities=15%  Similarity=0.239  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            4444544442   235899999999999999999999999999999986

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

Probab=95.88  E-value=0.016  Score=37.40  Aligned_cols=42  Identities=26%  Similarity=0.351  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            79999999999999999999999999999987644 4444554

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

Probab=95.88  E-value=0.017  Score=37.86  Aligned_cols=35  Identities=20%  Similarity=0.289  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=95.87  E-value=0.024  Score=37.76  Aligned_cols=44  Identities=9%  Similarity=0.146  Sum_probs=38.8

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=95.86  E-value=0.016  Score=37.84  Aligned_cols=45  Identities=13%  Similarity=0.176  Sum_probs=37.3

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932           60 LITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYTRA  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 445566543

>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=95.82  E-value=0.012  Score=38.37  Aligned_cols=33  Identities=21%  Similarity=0.333  Sum_probs=31.7

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            799999999999999999999999999999876

>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=95.82  E-value=0.017  Score=38.01  Aligned_cols=34  Identities=21%  Similarity=0.249  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

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

Probab=95.81  E-value=0.028  Score=35.80  Aligned_cols=57  Identities=18%  Similarity=0.189  Sum_probs=44.6

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRK-EAQTVYYTL   79 (98)
T ss_dssp             HHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-CTTCCEEEE
T ss_pred             HHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEE
Confidence            344456666655 568999999999999999999999999999998764 344555653

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

Probab=95.81  E-value=0.012  Score=40.60  Aligned_cols=49  Identities=16%  Similarity=0.165  Sum_probs=39.5

Q ss_pred             HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        46 ~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..|+.|...|      |+.++-|-..||++|+|+-+..|.+|+.|+..|+|....
T Consensus         8 ~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~   62 (129)
T 2ek5_A            8 QIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKR   62 (129)
T ss_dssp             HHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEET
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence            3455555443      455666899999999999999999999999999997654

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

Probab=95.78  E-value=0.013  Score=43.01  Aligned_cols=48  Identities=29%  Similarity=0.284  Sum_probs=40.4

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            44566666555      5667778889999999999999999999999999986

>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=95.76  E-value=0.02  Score=37.55  Aligned_cols=43  Identities=16%  Similarity=0.283  Sum_probs=35.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS--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

>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=95.75  E-value=0.012  Score=37.54  Aligned_cols=41  Identities=7%  Similarity=0.003  Sum_probs=34.5

Q ss_pred             eechhhhhhhhcccHHH-HHHHHHHHHHcCCeeEeccccceE
Q 033932           60 LITPSILSDRLRINGSL-ARKAIRELMARGLIRMVSAHASQQ  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

>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=95.74  E-value=0.024  Score=35.40  Aligned_cols=45  Identities=18%  Similarity=0.208  Sum_probs=36.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS--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

>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=95.73  E-value=0.02  Score=37.58  Aligned_cols=35  Identities=14%  Similarity=0.135  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=95.70  E-value=0.022  Score=38.48  Aligned_cols=47  Identities=19%  Similarity=0.427  Sum_probs=37.3

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -..|.-|... +. ..+|++.||+++++.-|-..+.|+.|+++|+|...
T Consensus        29 ~~il~~L~~~-~~-~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           29 LNVMKSFLNE-PD-RWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHHS-TT-CCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHC-CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            3445555432 22 13999999999999999999999999999999875

>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=95.67  E-value=0.019  Score=38.27  Aligned_cols=35  Identities=20%  Similarity=0.276  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=0.022  Score=42.57  Aligned_cols=39  Identities=21%  Similarity=0.377  Sum_probs=34.6

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            456666899999999999999999999999999997643

>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=95.67  E-value=0.022  Score=36.27  Aligned_cols=42  Identities=12%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             Ceeechhhh----hhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932           58 YKLITPSIL----SDRLRINGSLARKAIRELMARGLIRMVSAHASQ   99 (108)
Q Consensus        58 ~k~ITps~v----serlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q   99 (108)
                      ..-+|++.|    |++++++-+-.-++|+.|+++|+|......+..
T Consensus        20 ~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~   65 (99)
T 1tbx_A           20 NEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEK   65 (99)
T ss_dssp             CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEE
T ss_pred             cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCce
Confidence            345799999    999999999999999999999999887544433

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

Probab=95.66  E-value=0.018  Score=38.23  Aligned_cols=36  Identities=11%  Similarity=0.107  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            458999999999999999999999999999998763

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=95.63  E-value=0.021  Score=43.61  Aligned_cols=39  Identities=26%  Similarity=0.399  Sum_probs=34.8

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      |+.++=|-..||++|+|+-...|+||..|+++|+|....
T Consensus        49 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   87 (272)
T 3eet_A           49 PHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGRS   87 (272)
T ss_dssp             TTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            456777999999999999999999999999999997654

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

Probab=95.62  E-value=0.023  Score=37.06  Aligned_cols=36  Identities=17%  Similarity=0.240  Sum_probs=33.2

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=95.62  E-value=0.017  Score=41.90  Aligned_cols=51  Identities=27%  Similarity=0.348  Sum_probs=42.7

Q ss_pred             eCHHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           43 FDQATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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 999999999999999999999999999997764

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

Probab=95.61  E-value=0.025  Score=36.90  Aligned_cols=34  Identities=18%  Similarity=0.237  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            5899999999999999999999999999999886

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.60  E-value=0.02  Score=37.61  Aligned_cols=36  Identities=19%  Similarity=0.345  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            358999999999999999999999999999999873

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.56  E-value=0.027  Score=36.84  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=32.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+.++++-+-..++|+.|+++|+|....
T Consensus        50 ~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~   84 (142)
T 2fbi_A           50 EMESYQLANQACILRPSMTGVLARLERDGIVRRWK   84 (142)
T ss_dssp             SEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeec
Confidence            39999999999999999999999999999998873

>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=95.55  E-value=0.027  Score=36.90  Aligned_cols=34  Identities=24%  Similarity=0.351  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|++.||++++++-|-.-++|+.|+++|+|...
T Consensus        41 ~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           41 PLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3899999999999999999999999999999887

>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=95.54  E-value=0.019  Score=37.97  Aligned_cols=35  Identities=34%  Similarity=0.317  Sum_probs=32.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=95.53  E-value=0.02  Score=38.33  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=95.51  E-value=0.011  Score=40.40  Aligned_cols=48  Identities=17%  Similarity=0.211  Sum_probs=36.9

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ..++.|...+-...-+|++.||+.|+|+-+-.+++|+.|+++|+|...
T Consensus        40 ~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~   87 (155)
T 2h09_A           40 DYVELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMI   87 (155)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEe
Confidence            344444433322234799999999999999999999999999998765

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.50  E-value=0.024  Score=37.33  Aligned_cols=43  Identities=16%  Similarity=0.229  Sum_probs=36.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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 ERAVEAIATATGMNLTTASANLQALKSGGLVEARR-EGTRQYYR   80 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE-ETTEEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEE
Confidence            36999999999999999999999999999998765 34455564

>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=95.48  E-value=0.025  Score=37.33  Aligned_cols=34  Identities=21%  Similarity=0.358  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||+.++++-|-.-++|+.|+++|+|...
T Consensus        43 ~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~   76 (144)
T 1lj9_A           43 GIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999987

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=95.47  E-value=0.018  Score=40.42  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=38.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----cccceEEEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS----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    234445554

>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=95.46  E-value=0.019  Score=42.69  Aligned_cols=48  Identities=23%  Similarity=0.290  Sum_probs=39.9

Q ss_pred             HHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           47 TYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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      45566 9999999999999999999999999999987643

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

Probab=95.44  E-value=0.021  Score=38.37  Aligned_cols=37  Identities=8%  Similarity=0.152  Sum_probs=33.1

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -..+|...||++++|+-+..+++|+.|.+.|+|.-+.
T Consensus        24 ~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~   60 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIR   60 (129)
T ss_dssp             SCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecC
Confidence            3568999999999999999999999999999987654

>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=95.44  E-value=0.029  Score=37.40  Aligned_cols=36  Identities=17%  Similarity=0.206  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=95.43  E-value=0.029  Score=37.93  Aligned_cols=34  Identities=24%  Similarity=0.189  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999886

>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=95.43  E-value=0.031  Score=36.80  Aligned_cols=35  Identities=23%  Similarity=0.223  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=0.027  Score=37.41  Aligned_cols=35  Identities=20%  Similarity=0.275  Sum_probs=32.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=0.03  Score=37.73  Aligned_cols=34  Identities=18%  Similarity=0.140  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999887

>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=95.38  E-value=0.019  Score=37.95  Aligned_cols=35  Identities=9%  Similarity=0.142  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=95.38  E-value=0.011  Score=38.58  Aligned_cols=60  Identities=17%  Similarity=0.211  Sum_probs=55.2

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            456788888889999999999999999999999999999999999999988899999974

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=95.36  E-value=0.029  Score=38.00  Aligned_cols=34  Identities=29%  Similarity=0.385  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999887

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=95.35  E-value=0.012  Score=40.28  Aligned_cols=37  Identities=22%  Similarity=0.481  Sum_probs=33.5

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            4589999999999999999999999999999998643

>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=37.77  Aligned_cols=32  Identities=34%  Similarity=0.452  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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            99999999999999999999999999999987

>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=95.27  E-value=0.033  Score=36.76  Aligned_cols=43  Identities=23%  Similarity=0.242  Sum_probs=36.1

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--ccceEEEe
Q 033932           61 ITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA--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 9999999999999999999987732  34554453

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

Probab=95.25  E-value=0.02  Score=38.01  Aligned_cols=33  Identities=15%  Similarity=0.238  Sum_probs=32.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            999999999999999999999999999999976

>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=95.21  E-value=0.031  Score=38.18  Aligned_cols=46  Identities=15%  Similarity=0.317  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            34455555544    34899999999999999999999999999999854

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=95.20  E-value=0.037  Score=36.97  Aligned_cols=57  Identities=5%  Similarity=0.078  Sum_probs=44.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcc----cHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRI----NGSLARKAIRELMARGLIRMVSAHASQQIYTRA  105 (108)
Q Consensus        44 dk~t~dKl~KEVpk~k~ITps~vserlkI----~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~  105 (108)
                      .-..++-|..+-    =+|+..|++++..    .-+-...+|+.|+++|+|.... .++..+|...
T Consensus        37 e~~VL~~L~~~~----~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~-~gR~~~Y~p~   97 (99)
T 2k4b_A           37 ELIVMRVIWSLG----EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEK-EGRKFVYRPL   97 (99)
T ss_dssp             CSHHHHHHHHHS----CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEE-ETTEEEEECC
T ss_pred             HHHHHHHHHhCC----CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEe-CCCEEEEEEe
Confidence            445677776533    3799999999985    4688889999999999999864 4667888764

>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=95.18  E-value=0.026  Score=39.12  Aligned_cols=34  Identities=18%  Similarity=0.258  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=95.16  E-value=0.024  Score=37.47  Aligned_cols=35  Identities=14%  Similarity=0.291  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=95.13  E-value=0.036  Score=36.89  Aligned_cols=41  Identities=17%  Similarity=0.339  Sum_probs=35.4

Q ss_pred             echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRL-RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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 9999999999999999999987654  445554

>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=95.12  E-value=0.025  Score=38.55  Aligned_cols=41  Identities=24%  Similarity=0.370  Sum_probs=35.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS--AHASQQ  100 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~  100 (108)
                      =+|++.||+++++.-+-.-++|+.|+++|+|....  .++|..
T Consensus        60 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~  102 (162)
T 3k0l_A           60 NLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRI  102 (162)
T ss_dssp             TCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCee
Confidence            48999999999999999999999999999999873  344443

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

Probab=95.12  E-value=0.03  Score=38.07  Aligned_cols=36  Identities=17%  Similarity=0.155  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            358999999999999999999999999999998873

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.08  E-value=0.037  Score=37.91  Aligned_cols=49  Identities=22%  Similarity=0.368  Sum_probs=41.2

Q ss_pred             ceeCHHHHHHHHhhCCCCeeechhhhhhhh--cccHHHHHHHHHHHHHcCCeeEe
Q 033932           41 VLFDQATYDKLLSEAPKYKLITPSILSDRL--RINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        41 Vl~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  99999999999999999999885

>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=95.04  E-value=0.049  Score=35.64  Aligned_cols=44  Identities=23%  Similarity=0.274  Sum_probs=36.3

Q ss_pred             eechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--ccceEEEe
Q 033932           60 LITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA--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  24444454

>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=95.04  E-value=0.047  Score=35.51  Aligned_cols=42  Identities=17%  Similarity=0.269  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            69999999999999999999999999999987653 4455554

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=95.03  E-value=0.023  Score=38.21  Aligned_cols=35  Identities=11%  Similarity=0.190  Sum_probs=32.2

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            34899999999999999999999999999999877

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=95.01  E-value=0.037  Score=38.45  Aligned_cols=46  Identities=22%  Similarity=0.330  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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    799999999999999999999999999999854

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

Probab=95.01  E-value=0.029  Score=35.82  Aligned_cols=47  Identities=17%  Similarity=0.070  Sum_probs=38.1

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

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

Probab=94.98  E-value=0.046  Score=33.64  Aligned_cols=34  Identities=6%  Similarity=0.034  Sum_probs=31.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRM   92 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      ..+|...||++++|.-+...++|..|++.|+|..
T Consensus        24 ~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           24 GPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             SCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            4599999999999999999999999999999754

>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=94.97  E-value=0.067  Score=39.76  Aligned_cols=48  Identities=19%  Similarity=0.139  Sum_probs=37.9

Q ss_pred             HHHHHHh-hC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           47 TYDKLLS-EA-PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            3444443 33 345665999999999999999999999999999997653

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

Probab=94.96  E-value=0.024  Score=36.93  Aligned_cols=34  Identities=15%  Similarity=0.119  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=94.95  E-value=0.024  Score=37.75  Aligned_cols=36  Identities=17%  Similarity=0.230  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            458999999999999999999999999999998654

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=94.90  E-value=0.044  Score=35.93  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=37.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            47999999999999999999999999999997754 455566664

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=94.86  E-value=0.047  Score=37.57  Aligned_cols=34  Identities=21%  Similarity=0.264  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.84  E-value=0.038  Score=41.23  Aligned_cols=38  Identities=16%  Similarity=0.215  Sum_probs=32.7

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      +.++=|-..||++|+|+-...|+||+.|+++|+|....
T Consensus        30 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   67 (236)
T 3edp_A           30 GMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKN   67 (236)
T ss_dssp             CC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            45666999999999999999999999999999987754

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=94.74  E-value=0.038  Score=37.02  Aligned_cols=43  Identities=19%  Similarity=0.210  Sum_probs=36.4

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            3334444456899999999999999999999999999999876

>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=94.70  E-value=0.035  Score=37.17  Aligned_cols=34  Identities=15%  Similarity=0.137  Sum_probs=32.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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=94.66  E-value=0.053  Score=37.09  Aligned_cols=46  Identities=24%  Similarity=0.296  Sum_probs=37.2

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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    23899999999999999999999999999999755

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=94.66  E-value=0.063  Score=35.50  Aligned_cols=32  Identities=28%  Similarity=0.435  Sum_probs=31.3

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMV   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            99999999999999999999999999999887

>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=94.66  E-value=0.076  Score=34.71  Aligned_cols=42  Identities=12%  Similarity=0.298  Sum_probs=35.6

Q ss_pred             echhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYT  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 VSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS-ENIYFYS   70 (126)
T ss_dssp             EEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             CCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC-CCeEEEE
Confidence            89999999998    578999999999999999998764 4455664

>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=0.05  Score=38.48  Aligned_cols=36  Identities=8%  Similarity=0.200  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=94.58  E-value=0.025  Score=37.85  Aligned_cols=33  Identities=18%  Similarity=0.253  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            899999999999999999999999999999875

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=94.54  E-value=0.035  Score=40.01  Aligned_cols=32  Identities=31%  Similarity=0.430  Sum_probs=29.8

Q ss_pred             hhhhhhhhc--------------ccHHHHHHHHHHHHHcCCeeEec
Q 033932           63 PSILSDRLR--------------INGSLARKAIRELMARGLIRMVS   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

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=94.54  E-value=0.028  Score=37.30  Aligned_cols=35  Identities=14%  Similarity=0.235  Sum_probs=32.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.53  E-value=0.053  Score=36.36  Aligned_cols=44  Identities=14%  Similarity=0.250  Sum_probs=35.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 344556653

>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=94.51  E-value=0.044  Score=38.14  Aligned_cols=37  Identities=19%  Similarity=0.307  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      ..+|...||++++|+-+..+++|..|.+.|+|.-+..
T Consensus        29 ~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG   65 (149)
T 1ylf_A           29 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG   65 (149)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC
Confidence            5789999999999999999999999999999987654

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=94.49  E-value=0.057  Score=38.46  Aligned_cols=46  Identities=30%  Similarity=0.333  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.48  E-value=0.036  Score=36.96  Aligned_cols=35  Identities=14%  Similarity=0.051  Sum_probs=32.8

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.46  E-value=0.089  Score=34.30  Aligned_cols=44  Identities=18%  Similarity=0.271  Sum_probs=35.8

Q ss_pred             eechhhhhhhhc-ccHHHHHHHHHHHHHcCCeeEecc--ccceEEEe
Q 033932           60 LITPSILSDRLR-INGSLARKAIRELMARGLIRMVSA--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  24444453

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=94.45  E-value=0.055  Score=36.96  Aligned_cols=46  Identities=24%  Similarity=0.224  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            34455555443    34899999999999999999999999999999854

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=94.43  E-value=0.095  Score=36.46  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=36.4

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   97 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      +.-..+|...||++++|+-+..+++|..|.+.|+|.-+...+
T Consensus        24 ~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~   65 (143)
T 3t8r_A           24 EGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRGAK   65 (143)
T ss_dssp             TTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSSSS
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCCCC
Confidence            444689999999999999999999999999999988764433

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=94.36  E-value=0.099  Score=37.46  Aligned_cols=49  Identities=8%  Similarity=0.111  Sum_probs=39.4

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +.-..+|...||++++|+-+..+++|..|.+.|+|.-+...+.-..-.|
T Consensus        40 ~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   88 (159)
T 3lwf_A           40 IGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRGAHGGYVLNG   88 (159)
T ss_dssp             TTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSTTCEEEECS
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCCCceEecC
Confidence            3445799999999999999999999999999999988754444333334

>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=94.35  E-value=0.057  Score=36.99  Aligned_cols=46  Identities=11%  Similarity=0.228  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            34455555444    34899999999999999999999999999999864

>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=94.27  E-value=0.072  Score=38.59  Aligned_cols=50  Identities=18%  Similarity=0.374  Sum_probs=40.5

Q ss_pred             HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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            45566666554      445655 999999999999999999999999999987643

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=94.24  E-value=0.089  Score=34.87  Aligned_cols=42  Identities=21%  Similarity=0.115  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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 4555565

>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=94.23  E-value=0.05  Score=36.75  Aligned_cols=36  Identities=19%  Similarity=0.156  Sum_probs=34.0

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            345899999999999999999999999999999999

>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=94.15  E-value=0.025  Score=37.49  Aligned_cols=34  Identities=26%  Similarity=0.319  Sum_probs=28.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      -+|++.||++++++-|-.-++|+.|+++|+|...
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           51 GLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             TCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeec
Confidence            3899999999999999999999999999999876

>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=94.14  E-value=0.088  Score=35.55  Aligned_cols=53  Identities=17%  Similarity=0.224  Sum_probs=40.9

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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-SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK-QGRHVYYQL  102 (122)
T ss_dssp             HHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE-ETTEEEEEE
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEE
Confidence            34444432 347999999999999999999999999999998754 345556664

>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=94.12  E-value=0.089  Score=38.45  Aligned_cols=43  Identities=28%  Similarity=0.258  Sum_probs=36.3

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=94.10  E-value=0.084  Score=35.94  Aligned_cols=35  Identities=17%  Similarity=0.308  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=94.03  E-value=0.05  Score=36.61  Aligned_cols=35  Identities=29%  Similarity=0.387  Sum_probs=32.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=94.02  E-value=0.05  Score=36.47  Aligned_cols=45  Identities=18%  Similarity=0.290  Sum_probs=35.9

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      ...+.-|..+ +   -+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus         7 ~~il~~L~~~-~---~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            7 KIILEILEKD-A---RTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHC-T---TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            3445544433 2   3599999999999999999999999999999744

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=94.00  E-value=0.11  Score=35.28  Aligned_cols=43  Identities=12%  Similarity=0.176  Sum_probs=35.3

Q ss_pred             eechhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           60 LITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYT  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    899999999999999999998754 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=93.96  E-value=0.07  Score=34.16  Aligned_cols=43  Identities=14%  Similarity=0.215  Sum_probs=36.6

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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

>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=93.94  E-value=0.28  Score=32.00  Aligned_cols=53  Identities=21%  Similarity=0.318  Sum_probs=46.1

Q ss_pred             CHHHHHHH---HhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           44 DQATYDKL---LSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            56788877   556677788999999999999999999999999999999888543

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=93.94  E-value=0.063  Score=36.69  Aligned_cols=35  Identities=23%  Similarity=0.237  Sum_probs=30.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=93.89  E-value=0.029  Score=37.56  Aligned_cols=36  Identities=11%  Similarity=0.380  Sum_probs=33.2

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=93.82  E-value=0.062  Score=36.55  Aligned_cols=43  Identities=16%  Similarity=0.172  Sum_probs=35.1

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      |+..+....-+|...||++++++-|-.++.|+.|++.|+|..+
T Consensus         8 il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            8 ILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            3333333334899999999999999999999999999999863

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

Probab=93.71  E-value=0.03  Score=37.62  Aligned_cols=34  Identities=15%  Similarity=0.256  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999876

>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=93.70  E-value=0.057  Score=40.86  Aligned_cols=46  Identities=9%  Similarity=-0.002  Sum_probs=37.6

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ...||++.++++|++...+|+..|.+|+.+|++..=..... .-|.+
T Consensus       166 ~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D~~~eg-~~y~p  211 (218)
T 3cuq_B          166 KGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSVEG-LRFYP  211 (218)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEESSSC-EEEEE
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCCCc-eEEeh
Confidence            45899999999999999999999999999999977543333 33444

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=93.67  E-value=0.13  Score=35.32  Aligned_cols=45  Identities=16%  Similarity=0.197  Sum_probs=36.6

Q ss_pred             eeechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--ccceEEEe
Q 033932           59 KLITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA--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  24444553

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=93.59  E-value=0.061  Score=36.86  Aligned_cols=36  Identities=19%  Similarity=0.335  Sum_probs=29.3

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            348999999999999999999999999999996543

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=93.59  E-value=0.11  Score=35.71  Aligned_cols=34  Identities=18%  Similarity=0.214  Sum_probs=32.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            5689999999999999999999999999999876

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=93.47  E-value=0.077  Score=40.84  Aligned_cols=35  Identities=11%  Similarity=0.257  Sum_probs=32.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCee-Ee
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIR-MV   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            449999999999999999999999999999997 55

>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=93.27  E-value=0.028  Score=37.55  Aligned_cols=34  Identities=18%  Similarity=0.158  Sum_probs=26.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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=93.21  E-value=0.093  Score=38.01  Aligned_cols=35  Identities=20%  Similarity=0.103  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      -+|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        62 ~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~   96 (207)
T 2fxa_A           62 GASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK   96 (207)
T ss_dssp             SEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            38999999999999999999999999999998873

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=93.12  E-value=0.2  Score=33.70  Aligned_cols=51  Identities=16%  Similarity=0.132  Sum_probs=42.4

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            3456777766644 34588999999999999999999999999999999754

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=93.11  E-value=0.21  Score=36.62  Aligned_cols=37  Identities=14%  Similarity=0.216  Sum_probs=34.0

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      ..-+|+..||++|+++-+-..++|+.|+++|+|....
T Consensus        18 ~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~   54 (214)
T 3hrs_A           18 HNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDK   54 (214)
T ss_dssp             CSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEec
Confidence            4579999999999999999999999999999997753

>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=92.86  E-value=0.18  Score=34.96  Aligned_cols=35  Identities=17%  Similarity=0.302  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            47999999999999999999999999999998863

>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=92.83  E-value=0.088  Score=42.36  Aligned_cols=45  Identities=11%  Similarity=0.132  Sum_probs=37.9

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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~~~~~gR-~~~y~  353 (373)
T 3eqx_A          309 QPYCRIQNLVESGLAKRQTASVYLKQLCDIGVLEEVQSGK-EKLFV  353 (373)
T ss_dssp             CSEEEHHHHHHTSSSCHHHHHHHHHHHHHTTSCEEC--CC-SCEEE
T ss_pred             CCCccHHHHHHHhCcCHHHHHHHHHHHHHCCcEEEeCCCC-ceEee
Confidence            4589999999999999999999999999999999986544 45664

>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=92.79  E-value=0.1  Score=36.03  Aligned_cols=34  Identities=18%  Similarity=0.316  Sum_probs=32.0

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      |...||++++|+.+..+++|..|.+.|+|.-+..
T Consensus        25 s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG   58 (145)
T 1xd7_A           25 SSEIIADSVNTNPVVVRRMISLLKKADILTSRAG   58 (145)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecC
Confidence            9999999999999999999999999999987755

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=92.69  E-value=0.13  Score=35.91  Aligned_cols=43  Identities=14%  Similarity=0.243  Sum_probs=34.7

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            3333333334699999999999999999999999999999843

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=92.58  E-value=0.21  Score=35.14  Aligned_cols=57  Identities=18%  Similarity=0.159  Sum_probs=43.7

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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-GEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRK-DGRFRYYRL  114 (151)
T ss_dssp             HHHHHHHHHGGG-CCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEE-ETTEEEEEE
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe-cCCEEEEEE
Confidence            444455555542 338999999999999999999999999999999865 344556653

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=92.51  E-value=0.25  Score=34.37  Aligned_cols=44  Identities=16%  Similarity=0.128  Sum_probs=36.3

Q ss_pred             eechhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc--ccceEEEe
Q 033932           60 LITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA--HASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYt  103 (108)
                      -.+++.|++.+ +|+-+.--..|++|++.|+|.....  .++...|.
T Consensus        39 ~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~   85 (131)
T 4a5n_A           39 KKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYS   85 (131)
T ss_dssp             CBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEE
Confidence            47999999999 9999999999999999999987632  33455554

>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=92.29  E-value=0.066  Score=36.70  Aligned_cols=45  Identities=18%  Similarity=0.185  Sum_probs=36.6

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            3445544443    24899999999999999999999999999999764

>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=92.04  E-value=0.14  Score=37.35  Aligned_cols=44  Identities=7%  Similarity=0.079  Sum_probs=36.8

Q ss_pred             echh-h-hhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932           61 ITPS-I-LSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA  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

>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=91.97  E-value=0.28  Score=36.14  Aligned_cols=43  Identities=23%  Similarity=0.238  Sum_probs=36.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc----cceEEEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH----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

>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=91.89  E-value=0.12  Score=36.90  Aligned_cols=39  Identities=15%  Similarity=0.253  Sum_probs=34.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   97 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~   97 (108)
                      ..+|...||++++|+-+..+++|..|.+.|+|.-+...+
T Consensus        27 ~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~rG~~   65 (162)
T 3k69_A           27 SKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGKN   65 (162)
T ss_dssp             SCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEECSTT
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCC
Confidence            569999999999999999999999999999997664433

>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=91.61  E-value=0.043  Score=41.08  Aligned_cols=49  Identities=22%  Similarity=0.234  Sum_probs=5.1

Q ss_pred             HHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAP------KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            34444444443      34555899999999999999999999999999997653

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=91.42  E-value=0.28  Score=36.39  Aligned_cols=42  Identities=21%  Similarity=0.184  Sum_probs=38.0

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ   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            556899999999999999999999999999999999776654

>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=91.36  E-value=0.17  Score=36.30  Aligned_cols=34  Identities=21%  Similarity=0.178  Sum_probs=31.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            7899999999999999999999999999997653

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=91.06  E-value=0.25  Score=37.52  Aligned_cols=33  Identities=18%  Similarity=0.113  Sum_probs=32.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=90.93  E-value=0.18  Score=37.01  Aligned_cols=34  Identities=24%  Similarity=0.559  Sum_probs=31.5

Q ss_pred             ech--hhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITP--SILSDRLRINGSLARKAIRELMARGLIRMVS   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  9999999999999999999999999998754

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=90.30  E-value=0.029  Score=39.24  Aligned_cols=35  Identities=20%  Similarity=0.316  Sum_probs=31.8

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            3444 9999999999999999999999999999984

>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=90.30  E-value=0.53  Score=40.46  Aligned_cols=53  Identities=9%  Similarity=0.018  Sum_probs=43.4

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhc-------ccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLR-------INGSLARKAIRELMARGLIRMVSAHA   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            455666665445567999999999999       99999999999999999997764444

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

Probab=90.24  E-value=0.48  Score=32.08  Aligned_cols=45  Identities=16%  Similarity=0.378  Sum_probs=37.9

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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     899999999999999999999997655555564

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=90.11  E-value=0.19  Score=35.35  Aligned_cols=41  Identities=15%  Similarity=0.152  Sum_probs=34.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS-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            6899999999999876    588999999999984 3467788875

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=89.98  E-value=0.41  Score=35.41  Aligned_cols=35  Identities=11%  Similarity=0.165  Sum_probs=32.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            47999999999999999999999999999998753

>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=89.50  E-value=0.26  Score=38.04  Aligned_cols=46  Identities=22%  Similarity=0.299  Sum_probs=37.6

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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            4679999999999999999999999999999998554443333444

>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=89.41  E-value=0.52  Score=34.86  Aligned_cols=34  Identities=18%  Similarity=0.200  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4799999999999999999999999999999875

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

Probab=89.35  E-value=0.56  Score=32.33  Aligned_cols=45  Identities=11%  Similarity=0.166  Sum_probs=37.6

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            358999999998     788999999999999999999997655555564

>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=89.23  E-value=0.09  Score=34.27  Aligned_cols=58  Identities=16%  Similarity=0.283  Sum_probs=46.7

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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            4567776666666778899999999999999999999999999999998544433343

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=89.20  E-value=0.079  Score=36.83  Aligned_cols=34  Identities=29%  Similarity=0.394  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999876

>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=89.15  E-value=0.59  Score=36.26  Aligned_cols=50  Identities=16%  Similarity=0.124  Sum_probs=40.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   96 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      ...+|+.-+..-..+|...||++|+|+-+-.++-|+.|++.|++..-..+
T Consensus         6 r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~~~g   55 (321)
T 1bia_A            6 VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPG   55 (321)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETT
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEEecC
Confidence            34455555556678999999999999999999999999999998654333

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=89.04  E-value=0.43  Score=36.14  Aligned_cols=44  Identities=14%  Similarity=0.280  Sum_probs=36.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc-----eEEEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS-----QQIYT  103 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~-----q~IYt  103 (108)
                      -+|++.||+.++++-+.....|+.|++.|+|......++     ...|.
T Consensus        25 ~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~   73 (232)
T 2qlz_A           25 ECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYK   73 (232)
T ss_dssp             TTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEE
Confidence            379999999999999999999999999999998544444     55555

>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=88.98  E-value=0.59  Score=35.00  Aligned_cols=44  Identities=23%  Similarity=0.185  Sum_probs=36.7

Q ss_pred             HHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           51 LLSEAPK-YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=88.97  E-value=0.34  Score=35.62  Aligned_cols=32  Identities=16%  Similarity=0.367  Sum_probs=29.5

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMV   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            44999999999999999999999999999874

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=88.65  E-value=0.24  Score=34.75  Aligned_cols=45  Identities=16%  Similarity=0.242  Sum_probs=33.8

Q ss_pred             CCCe--eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           56 PKYK--LITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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    5889999999986543 467788875

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=88.43  E-value=0.89  Score=31.59  Aligned_cols=44  Identities=14%  Similarity=0.231  Sum_probs=37.3

Q ss_pred             eechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           60 LITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            68899999888     688889999999999999999997655556664

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=88.42  E-value=0.65  Score=31.60  Aligned_cols=45  Identities=9%  Similarity=0.210  Sum_probs=36.5

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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     788888999999999999999987544445564

>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=88.36  E-value=0.93  Score=26.21  Aligned_cols=40  Identities=20%  Similarity=0.314  Sum_probs=31.4

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIY  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            478999999999     999998887777   45899 66555555556

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=88.20  E-value=0.91  Score=31.54  Aligned_cols=44  Identities=11%  Similarity=0.245  Sum_probs=35.5

Q ss_pred             eechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           60 LITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -+|+..|.+++     .|..+-.-+.|+.|++.|+|..+.-......|-
T Consensus        33 h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   81 (150)
T 2w57_A           33 HISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFE   81 (150)
T ss_dssp             SEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGGGCEEEE
T ss_pred             CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            57888888887     688888899999999999999986544555564

>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=88.07  E-value=0.53  Score=31.55  Aligned_cols=38  Identities=18%  Similarity=0.243  Sum_probs=34.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            5444 4999999999999999999999999999999753

>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=87.84  E-value=0.82  Score=31.21  Aligned_cols=33  Identities=15%  Similarity=0.168  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=87.72  E-value=0.61  Score=35.25  Aligned_cols=35  Identities=11%  Similarity=0.145  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=87.59  E-value=0.59  Score=29.97  Aligned_cols=42  Identities=7%  Similarity=0.194  Sum_probs=35.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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-VLKRN-RQGLEIYYSI   83 (99)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEE-EETTEEEEEC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhhe-EeCcEEEEEE
Confidence            799999999999999999999999999 87754 4455566653

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=87.47  E-value=0.8  Score=31.45  Aligned_cols=32  Identities=28%  Similarity=0.253  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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            78999999999999999999999999999984

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=87.21  E-value=0.79  Score=31.68  Aligned_cols=32  Identities=16%  Similarity=0.374  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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            68899999999999999999999999999975

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=87.13  E-value=0.94  Score=31.14  Aligned_cols=33  Identities=18%  Similarity=0.400  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            479999999999999999999999999999974

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=86.99  E-value=0.87  Score=33.98  Aligned_cols=36  Identities=8%  Similarity=0.122  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=86.82  E-value=1  Score=30.90  Aligned_cols=34  Identities=15%  Similarity=0.220  Sum_probs=31.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=86.40  E-value=1.4  Score=33.07  Aligned_cols=51  Identities=18%  Similarity=0.201  Sum_probs=41.8

Q ss_pred             ceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           41 VLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        41 Vl~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            455666776766666 2 45999999999999999999999999999999653

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=86.37  E-value=0.52  Score=33.34  Aligned_cols=42  Identities=29%  Similarity=0.444  Sum_probs=34.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .++|...+|+.++|+.+    .||.-++.|+|.+.-..++.+.|+.
T Consensus        10 ~~~~i~e~A~~~gvs~~----TLR~ye~~Gll~p~r~~~g~R~Y~~   51 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR   51 (154)
T ss_dssp             CCBCHHHHHHHHTSCHH----HHHHHHHTTSSCCEECTTSCEEBCT
T ss_pred             cCCCHHHHHHHHCcCHH----HHHHHHHcCCCCcccCCCCCEEeCH
Confidence            47999999999999865    5899999999998644466778875

>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=86.31  E-value=1.2  Score=32.40  Aligned_cols=37  Identities=30%  Similarity=0.330  Sum_probs=33.3

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            3456789999999999999999999999999999775

>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=86.24  E-value=0.14  Score=40.01  Aligned_cols=42  Identities=21%  Similarity=0.210  Sum_probs=0.0

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR   91 (108)
Q Consensus        50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      .|+..+-...-+|...||++|+++-+-.|+.|+.|+++|+|.
T Consensus        24 ~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~   65 (345)
T 2o0m_A           24 QILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQLNLIE   65 (345)
T ss_dssp             ------------------------------------------
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            455555556779999999999999999999999999999997

>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=86.14  E-value=1.6  Score=29.08  Aligned_cols=42  Identities=12%  Similarity=0.148  Sum_probs=31.9

Q ss_pred             chhhhhhhh--------cccHHHHHHHHHHHHHcCCeeEec----cccceEEEe
Q 033932           62 TPSILSDRL--------RINGSLARKAIRELMARGLIRMVS----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            566777666        799999999999999999999873    234555664

>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=86.09  E-value=0.72  Score=35.50  Aligned_cols=46  Identities=20%  Similarity=0.317  Sum_probs=37.2

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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            4678999999999999999999999999999998554343223344

>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=86.08  E-value=0.44  Score=37.74  Aligned_cols=41  Identities=12%  Similarity=0.138  Sum_probs=35.6

Q ss_pred             CCCCeeechhhhhhhh--cccHHHHHHHHHHHHHcCCeeEecc
Q 033932           55 APKYKLITPSILSDRL--RINGSLARKAIRELMARGLIRMVSA   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            4455679999999999  8888999999999999999987543

>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=85.97  E-value=0.84  Score=31.09  Aligned_cols=33  Identities=15%  Similarity=0.316  Sum_probs=30.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=85.96  E-value=0.42  Score=32.06  Aligned_cols=58  Identities=12%  Similarity=0.106  Sum_probs=50.1

Q ss_pred             hhccceeCHHHHHHHHhhCCC----CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           37 VNNMVLFDQATYDKLLSEAPK----YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        37 ~nn~Vl~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    3679999999999999999999999999999998874

>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=85.94  E-value=0.5  Score=37.23  Aligned_cols=34  Identities=15%  Similarity=0.115  Sum_probs=32.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=85.80  E-value=1.2  Score=30.94  Aligned_cols=32  Identities=22%  Similarity=0.392  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=85.68  E-value=0.99  Score=28.81  Aligned_cols=34  Identities=21%  Similarity=0.242  Sum_probs=31.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =.|.-+||.+|+.....||.+|+.|.+.|-+..-
T Consensus        18 GMTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRKR   51 (68)
T 3i71_A           18 GMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKR   51 (68)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cccHHHHHHHhCCcHHHHHHHHHHHHhcchhhhh
Confidence            4699999999999999999999999999998764

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=85.64  E-value=0.56  Score=30.89  Aligned_cols=40  Identities=8%  Similarity=0.112  Sum_probs=32.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS-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    578889999999875 3466678875

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=85.62  E-value=0.81  Score=34.04  Aligned_cols=44  Identities=14%  Similarity=0.063  Sum_probs=36.5

Q ss_pred             HHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           50 KLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            345455432 45899999999999999999999999999999874

>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=85.18  E-value=1.8  Score=30.13  Aligned_cols=43  Identities=16%  Similarity=0.149  Sum_probs=33.8

Q ss_pred             echhhhhhhh--------cccHHHHHHHHHHHHHcCCeeEecc----ccceEEEe
Q 033932           61 ITPSILSDRL--------RINGSLARKAIRELMARGLIRMVSA----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        5999999999999999999987732    34455563

>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=85.17  E-value=0.95  Score=31.34  Aligned_cols=32  Identities=19%  Similarity=0.373  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=85.12  E-value=1.2  Score=34.72  Aligned_cols=36  Identities=8%  Similarity=0.227  Sum_probs=33.4

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=85.09  E-value=0.87  Score=32.42  Aligned_cols=45  Identities=13%  Similarity=0.186  Sum_probs=36.4

Q ss_pred             HHHHHhhCC-CCeeechhhhhhhhcccHHHHHHHHHHHHHcCC-eeE
Q 033932           48 YDKLLSEAP-KYKLITPSILSDRLRINGSLARKAIRELMARGL-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            444554444 235699999999999999999999999999999 753

>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=84.99  E-value=0.96  Score=31.54  Aligned_cols=33  Identities=9%  Similarity=0.190  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=84.88  E-value=1.5  Score=29.98  Aligned_cols=45  Identities=13%  Similarity=0.303  Sum_probs=36.2

Q ss_pred             eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  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     588888899999999999999997655555664

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=84.78  E-value=0.85  Score=34.14  Aligned_cols=43  Identities=14%  Similarity=0.100  Sum_probs=35.8

Q ss_pred             HHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           51 LLSEAPK-YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=84.17  E-value=1.1  Score=35.57  Aligned_cols=44  Identities=20%  Similarity=0.148  Sum_probs=36.8

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            33333334458999999999999999999999999999999874

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=83.93  E-value=1.1  Score=33.86  Aligned_cols=43  Identities=21%  Similarity=0.201  Sum_probs=35.8

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEE
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQI  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            35679999999999999999999999999999983 44444433

>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=83.88  E-value=1.6  Score=31.53  Aligned_cols=33  Identities=15%  Similarity=0.168  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            368899999999999999999999999999975

>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=83.76  E-value=1.8  Score=29.83  Aligned_cols=44  Identities=20%  Similarity=0.212  Sum_probs=33.8

Q ss_pred             eechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           60 LITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT  103 (108)
Q Consensus        60 ~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt  103 (108)
                      -+|...|-+++     .|+.+---+.|+.|++.|+|..+.-..+..-|-
T Consensus        33 h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~   81 (145)
T 3eyy_A           33 HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYH   81 (145)
T ss_dssp             SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            35777777766     577777889999999999999997655555564

>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=83.71  E-value=1.1  Score=31.80  Aligned_cols=33  Identities=6%  Similarity=0.230  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   92 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      -+|-..||+.++++-.-.-++|++|+++|+|..
T Consensus       193 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          193 KLSHQAIAEAIGSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEE
Confidence            368899999999999999999999999999985

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

Probab=83.62  E-value=0.73  Score=34.90  Aligned_cols=35  Identities=17%  Similarity=0.119  Sum_probs=30.8

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            48999999999999999999999999999998753

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=83.38  E-value=2.5  Score=28.34  Aligned_cols=43  Identities=9%  Similarity=0.171  Sum_probs=33.5

Q ss_pred             echhhhhhhh------cccHHHHHHHHHHHHHcCCeeEecc----ccceEEEe
Q 033932           61 ITPSILSDRL------RINGSLARKAIRELMARGLIRMVSA----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            5778888887      7999999999999999999998742    23455664

>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=83.38  E-value=1.2  Score=30.92  Aligned_cols=33  Identities=9%  Similarity=0.192  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=83.27  E-value=1.2  Score=30.80  Aligned_cols=33  Identities=6%  Similarity=0.080  Sum_probs=30.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            378899999999999999999999999999965

>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=83.10  E-value=1.1  Score=31.16  Aligned_cols=32  Identities=16%  Similarity=0.244  Sum_probs=30.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=83.06  E-value=0.77  Score=30.21  Aligned_cols=40  Identities=13%  Similarity=0.179  Sum_probs=32.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS-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            578899999998865    578899999999875 3456778874

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=83.03  E-value=1.1  Score=30.55  Aligned_cols=33  Identities=18%  Similarity=0.223  Sum_probs=30.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=82.39  E-value=1.4  Score=31.32  Aligned_cols=32  Identities=3%  Similarity=0.169  Sum_probs=30.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=82.38  E-value=1.1  Score=32.37  Aligned_cols=23  Identities=26%  Similarity=0.547  Sum_probs=20.4

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEec
Q 033932           72 INGSLARKAIRELMARGLIRMVS   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

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=82.21  E-value=3.1  Score=27.09  Aligned_cols=37  Identities=14%  Similarity=0.154  Sum_probs=27.9

Q ss_pred             hhhhcccHHHHHHHHHHHHHcCCeeEecc---ccceEEEe
Q 033932           67 SDRLRINGSLARKAIRELMARGLIRMVSA---HASQQIYT  103 (108)
Q Consensus        67 serlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt  103 (108)
                      ++.++|+-+.--.+|+.|++.|+|.....   .++..+|.
T Consensus        33 ~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~   72 (108)
T 3l7w_A           33 KLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYH   72 (108)
T ss_dssp             TTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEE
T ss_pred             HHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEE
Confidence            33468999999999999999999988732   23455563

>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=82.11  E-value=1.2  Score=32.33  Aligned_cols=24  Identities=21%  Similarity=0.517  Sum_probs=21.2

Q ss_pred             cccHHHHHHHHHHHHHcCCeeEec
Q 033932           71 RINGSLARKAIRELMARGLIRMVS   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            346899999999999999999864

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

Probab=82.08  E-value=1.5  Score=32.51  Aligned_cols=33  Identities=12%  Similarity=0.135  Sum_probs=31.4

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=81.90  E-value=1.3  Score=31.12  Aligned_cols=33  Identities=24%  Similarity=0.230  Sum_probs=30.6

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            379999999999999999999999999999974

>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=81.83  E-value=1.1  Score=34.93  Aligned_cols=44  Identities=11%  Similarity=0.136  Sum_probs=37.6

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=81.71  E-value=1  Score=28.08  Aligned_cols=41  Identities=17%  Similarity=0.331  Sum_probs=31.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccc-cceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAH-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

>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=81.64  E-value=0.79  Score=30.82  Aligned_cols=35  Identities=20%  Similarity=0.399  Sum_probs=32.4

Q ss_pred             CCeeechhhhhh-hhcccHHHHHHHHHHHHHcCCee
Q 033932           57 KYKLITPSILSD-RLRINGSLARKAIRELMARGLIR   91 (108)
Q Consensus        57 k~k~ITps~vse-rlkI~~SlAr~~Lr~L~~kGlIk   91 (108)
                      +...+|++.|+| .+.+.-|.--+.|+-|+++|+|.
T Consensus        27 ~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           27 KKDFITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             HSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             HCCCCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee
Confidence            334899999999 99999999999999999999998

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=81.33  E-value=0.46  Score=34.84  Aligned_cols=48  Identities=17%  Similarity=0.111  Sum_probs=41.5

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            345677777777889999999999999999999999999999887654

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=81.19  E-value=1.4  Score=29.15  Aligned_cols=43  Identities=19%  Similarity=0.274  Sum_probs=32.6

Q ss_pred             echhhhhhhhc--------ccH-HHHHHHHHHHHHcCCeeEecc---ccceEEEe
Q 033932           61 ITPSILSDRLR--------ING-SLARKAIRELMARGLIRMVSA---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            57888888874        776 777889999999999988742   34455664

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C

Probab=80.93  E-value=2.5  Score=27.18  Aligned_cols=40  Identities=20%  Similarity=0.307  Sum_probs=35.0

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            3467899999999999999999999999987777777774

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

Probab=80.90  E-value=1.8  Score=32.53  Aligned_cols=44  Identities=16%  Similarity=0.180  Sum_probs=37.3

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .++|-|. +-    -+|+..||+++++.-...+++||.|..-|++....
T Consensus        29 glf~~l~-~g----~~t~~elA~~~~~~~~~l~rlLr~l~~~gl~~~~~   72 (332)
T 3i53_A           29 RVADHIA-AG----HRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDG   72 (332)
T ss_dssp             THHHHHH-TT----CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             ChHHHHh-cC----CCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEecC
Confidence            4566664 32    38999999999999999999999999999998764

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=80.83  E-value=0.32  Score=41.27  Aligned_cols=61  Identities=15%  Similarity=0.103  Sum_probs=0.0

Q ss_pred             eCHHHH-HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           43 FDQATY-DKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        43 ~dk~t~-dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      +|..-+ +.|+.-+..+.-||-+.|++.++++..-|+++|+.|.++|+|..+-.+ +-.-|..
T Consensus       512 ~~~~~~~~~I~~~l~~~g~it~~di~~l~~ls~~qa~~~L~~Lv~~G~l~~~G~g-r~t~Y~~  573 (583)
T 3lmm_A          512 TDQAELTNAAMLWLSEVGDLATSDLMAMCGVSRGTAKACVDGLVDEERVVAVGGG-RSRRYRL  573 (583)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             CChhHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeCCC-CceEEEE
Confidence            344333 345555666788999999999999999999999999999999987543 3344543

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=80.78  E-value=1.4  Score=32.37  Aligned_cols=43  Identities=19%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc--ccceEEEecc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA--HASQQIYTRA  105 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYtr~  105 (108)
                      +++|...+|+.++|+.    +.||.-++.|||.+...  .++.+.|+..
T Consensus         4 ~~~~i~e~a~~~gvs~----~tlr~y~~~gll~p~~~d~~~g~R~y~~~   48 (278)
T 1r8e_A            4 SYYSIGEVSKLANVSI----KALRYYDKIDLFKPAYVDPDTSYRYYTDS   48 (278)
T ss_dssp             CEEEHHHHHHHHTCCH----HHHHHHHHTTSSCCSEECTTTCCEEEETG
T ss_pred             CcEeHHHHHHHHCcCH----HHHHHHHHCCCCCCCccCCCCCccccCHH
Confidence            5789999999999875    46899999999998753  5677889864

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=80.20  E-value=4.1  Score=27.07  Aligned_cols=43  Identities=14%  Similarity=0.143  Sum_probs=33.4

Q ss_pred             echhhhhhhhc------ccHHHHHHHHHHHHHcCCeeEecc----ccceEEEe
Q 033932           61 ITPSILSDRLR------INGSLARKAIRELMARGLIRMVSA----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    23455564

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=80.10  E-value=0.31  Score=38.49  Aligned_cols=42  Identities=19%  Similarity=0.298  Sum_probs=35.4

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      .|++.||++++|.-|-+..+|+.|+++|+|.....  +-..|..
T Consensus        33 ~t~~eia~~~gv~~~~Vy~~L~~L~~~GlV~~~~g--~p~~y~a   74 (342)
T 3qph_A           33 STAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEG--TPKVYAA   74 (342)
T ss_dssp             HHHSCCSSSTTSSSCSCCHHHHHHHHHTSEEEECC--TTCEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC--ceeEEEE
Confidence            58999999999999999999999999999998632  3345653

---

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	97.23
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	97.15
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	96.74
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.34
d2b0la1	91	GTP-sensing transcriptional pleiotropic repressor	96.21
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.18
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.14
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.12
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.94
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.92
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.84
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	95.61
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	95.51
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	95.51
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	95.47
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	95.39
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	95.32
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	95.25
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	95.0
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.91
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.82
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.67
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.63
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	94.62
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.6
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	94.47
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	94.44
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.38
d1okra_	120	Methicillin resistance regulatory protein MecI {St	94.3
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	94.26
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	94.13
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	94.08
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	94.06
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	94.01
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	93.99
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	93.84
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	93.82
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	93.79
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.77
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	93.72
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.58
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.48
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	93.46
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	93.41
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	93.37
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	92.95
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	92.75
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	92.58
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	92.49
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	92.18
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	92.16
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	91.99
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	91.8
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	91.66
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	90.58
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	90.58
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	90.13
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	90.03
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	89.48
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	89.36
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	89.22
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	88.76
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	88.71
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	88.23
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	88.04
d1zyba1	73	Probable transcription regulator BT4300, C-termina	87.88
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	87.66
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	87.61
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	87.54
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	86.51
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	86.02
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	85.85
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	85.83
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	85.69
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	85.36
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	84.81
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	84.71
d2v7fa1	149	Ribosomal protein S19e {Pyrococcus abyssi [TaxId:	84.33
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	83.67
d1iuya_	92	Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 1	82.97
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	80.89
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	80.8
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	80.49
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	80.42
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	80.32

>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=97.23  E-value=0.0004  Score=42.18  Aligned_cols=39  Identities=18%  Similarity=0.268  Sum_probs=35.0

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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=97.15  E-value=0.00043  Score=42.82  Aligned_cols=57  Identities=12%  Similarity=0.219  Sum_probs=44.0

Q ss_pred             HHHHHHHHhhC--CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           45 QATYDKLLSEA--PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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        10 e~i~~~I~~g~~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~---g~G~~V~   68 (74)
T d1hw1a1          10 EYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH---GKPTKVN   68 (74)
T ss_dssp             HHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET---TEEEEEC
T ss_pred             HHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEe---CceEEEC
Confidence            34555665554  566787889999999999999999999999999997653   3345544

>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=96.74  E-value=0.0012  Score=40.68  Aligned_cols=39  Identities=23%  Similarity=0.210  Sum_probs=35.1

Q ss_pred             CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            456777999999999999999999999999999998753

>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=96.34  E-value=0.0029  Score=37.78  Aligned_cols=51  Identities=16%  Similarity=0.126  Sum_probs=40.8

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   96 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~   96 (108)
                      ++.-+|+.-...-.++|...||++|+|+-+-.++-|+.|++.|++..-..+
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~~~~g   55 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPG   55 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETT
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEEEeCC
Confidence            344456666666789999999999999999999999999999985443333

>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=96.21  E-value=0.0037  Score=40.75  Aligned_cols=62  Identities=21%  Similarity=0.322  Sum_probs=51.9

Q ss_pred             hHHhhhccceeCHHHHHHHHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           33 QKEKVNNMVLFDQATYDKLLSEAPK-YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        33 ~keK~nn~Vl~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            4444555555567788899999985 4799999999999999999999999999999998654

>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=96.18  E-value=0.0072  Score=37.72  Aligned_cols=47  Identities=32%  Similarity=0.333  Sum_probs=38.8

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEE
Q 033932           54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQI  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

>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=96.14  E-value=0.0056  Score=39.22  Aligned_cols=46  Identities=20%  Similarity=0.322  Sum_probs=38.6

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV--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            34799999999999999999999999999999865  34556666764

>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=96.12  E-value=0.0054  Score=38.97  Aligned_cols=34  Identities=21%  Similarity=0.397  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      =+|++.||++++|+-|-..++|+.|+++|+|...
T Consensus        36 ~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~   69 (109)
T d2d1ha1          36 PITSEELADIFKLSKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEe
Confidence            3799999999999999999999999999999876

>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=95.94  E-value=0.0065  Score=35.95  Aligned_cols=47  Identities=11%  Similarity=0.242  Sum_probs=38.7

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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~~~-~---r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           6 LDRGILEALMGN-A---RTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHHC-T---TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            355666666655 3   3599999999999999999999999999999854

>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=95.92  E-value=0.0062  Score=39.82  Aligned_cols=35  Identities=23%  Similarity=0.310  Sum_probs=33.0

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      =+|++.||+++++.-|-+-.+|+.|++.|+|..+.
T Consensus        41 plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~   75 (151)
T d1ku9a_          41 PLTISDIMEELKISKGNVSMSLKKLEELGFVRKVW   75 (151)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEE
Confidence            39999999999999999999999999999999873

>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=95.84  E-value=0.0075  Score=38.99  Aligned_cols=39  Identities=15%  Similarity=0.160  Sum_probs=34.7

Q ss_pred             hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      +.|+ .-||+..||++++++-|-+-++|+.|+++|+|...
T Consensus        40 ~~~~-~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~   78 (135)
T d3broa1          40 RNKN-KEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   78 (135)
T ss_dssp             HTTT-SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HcCC-CCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHH
Confidence            3343 56899999999999999999999999999999877

>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=95.61  E-value=0.0074  Score=36.07  Aligned_cols=43  Identities=21%  Similarity=0.140  Sum_probs=35.9

Q ss_pred             HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=95.51  E-value=0.011  Score=38.56  Aligned_cols=33  Identities=18%  Similarity=0.168  Sum_probs=32.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            799999999999999999999999999999987

>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=95.51  E-value=0.0031  Score=40.52  Aligned_cols=50  Identities=12%  Similarity=0.137  Sum_probs=41.6

Q ss_pred             HHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   95 (108)
Q Consensus        46 ~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k   95 (108)
                      .+++.|...|-.      .+|-|-..||+.|+|+-+..|+||+.|+++|+|....+
T Consensus        13 qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   68 (100)
T d1v4ra1          13 DVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGA   68 (100)
T ss_dssp             HHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETT
T ss_pred             HHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecC
Confidence            456667666654      56779999999999999999999999999999986543

>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=95.47  E-value=0.013  Score=37.15  Aligned_cols=47  Identities=19%  Similarity=0.211  Sum_probs=40.2

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEec
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV--SAHASQQIYTR  104 (108)
Q Consensus        58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr  104 (108)
                      -+=|....|-.+.++.-+.-.++|+.||++++|+.|  .+++...+|.-
T Consensus        27 ~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~VksV~~~~rK~YmL   75 (78)
T d2dk5a1          27 NKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYML   75 (78)
T ss_dssp             TTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEE
T ss_pred             ccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceeecccCCCCeEEEEe
Confidence            346778899999999999999999999999999999  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=95.39  E-value=0.014  Score=37.95  Aligned_cols=34  Identities=24%  Similarity=0.225  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=38.18  Aligned_cols=34  Identities=26%  Similarity=0.360  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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=95.25  E-value=0.021  Score=35.48  Aligned_cols=64  Identities=14%  Similarity=0.122  Sum_probs=44.5

Q ss_pred             ccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-c-cccceEEEe
Q 033932           39 NMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV-S-AHASQQIYT  103 (108)
Q Consensus        39 n~Vl~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 24444433334899999999999999999999999999999865 2 245555554

>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=95.00  E-value=0.016  Score=36.34  Aligned_cols=61  Identities=16%  Similarity=0.216  Sum_probs=55.3

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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

>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=94.91  E-value=0.017  Score=37.44  Aligned_cols=36  Identities=17%  Similarity=0.201  Sum_probs=33.0

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      .-+|++.|+++++|.-+-.-++|+.|+++|+|..+.
T Consensus        45 ~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~   80 (140)
T d3deua1          45 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQT   80 (140)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecc
Confidence            368999999999999999999999999999998773

>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=94.82  E-value=0.016  Score=38.00  Aligned_cols=34  Identities=35%  Similarity=0.337  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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=94.67  E-value=0.016  Score=34.44  Aligned_cols=33  Identities=15%  Similarity=0.161  Sum_probs=30.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=32.59  Aligned_cols=47  Identities=15%  Similarity=0.325  Sum_probs=38.5

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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    3499999999999999999999999999999753

>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=94.62  E-value=0.016  Score=37.76  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=34.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS   98 (108)
Q Consensus        61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~   98 (108)
                      +|..+||+.++++-+.-|++|+.|.+.|+|.-+-..+.
T Consensus        19 ~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG~~G   56 (127)
T d1xd7a_          19 TSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPG   56 (127)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSS
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCCCCC
Confidence            79999999999999999999999999999997755443

>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=94.60  E-value=0.019  Score=33.38  Aligned_cols=47  Identities=19%  Similarity=0.214  Sum_probs=38.7

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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-G---KAPLREISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHHC-T---TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            456666666665 2   3499999999999999999999999999999743

>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=94.47  E-value=0.027  Score=36.25  Aligned_cols=34  Identities=21%  Similarity=0.349  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.44  E-value=0.038  Score=35.67  Aligned_cols=33  Identities=15%  Similarity=0.178  Sum_probs=32.0

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=94.38  E-value=0.036  Score=33.50  Aligned_cols=38  Identities=24%  Similarity=0.400  Sum_probs=32.2

Q ss_pred             echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEeccccc
Q 033932           61 ITPSILSDRLRI-NGSLARKAIRELMARGLIRMVSAHAS   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 57789999999999999999854443

>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=94.30  E-value=0.034  Score=35.72  Aligned_cols=45  Identities=13%  Similarity=0.178  Sum_probs=38.0

Q ss_pred             echhhhhhhh----cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           61 ITPSILSDRL----RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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 ASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDR-KKDNKIFQYYSLV   70 (120)
T ss_dssp             EEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEE-EEETTEEEEEESS
T ss_pred             CCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEE-EecCCceEEeecC
Confidence            7899888887    5899999999999999999986 4467778998753

>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=94.26  E-value=0.035  Score=36.39  Aligned_cols=34  Identities=21%  Similarity=0.403  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=94.13  E-value=0.0056  Score=37.88  Aligned_cols=60  Identities=15%  Similarity=0.272  Sum_probs=47.0

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            345666666566667789999999999999999999999999999999865443334443

>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=94.08  E-value=0.028  Score=36.46  Aligned_cols=35  Identities=14%  Similarity=0.304  Sum_probs=33.1

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            45899999999999999999999999999999887

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.06  E-value=0.034  Score=33.57  Aligned_cols=35  Identities=17%  Similarity=0.184  Sum_probs=32.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      .-+|++.||+.+++.-|-+.++|..|++.|++...
T Consensus        19 ~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~   53 (75)
T d1mkma1          19 GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   53 (75)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            35999999999999999999999999999999875

>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=94.01  E-value=0.044  Score=35.59  Aligned_cols=34  Identities=21%  Similarity=0.366  Sum_probs=32.2

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999865

>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=93.99  E-value=0.042  Score=35.66  Aligned_cols=34  Identities=18%  Similarity=0.230  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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=93.84  E-value=0.031  Score=33.46  Aligned_cols=33  Identities=18%  Similarity=0.377  Sum_probs=30.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRM   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            478899999999999999999999999999964

>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=93.82  E-value=0.027  Score=36.49  Aligned_cols=36  Identities=8%  Similarity=0.116  Sum_probs=33.3

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=93.79  E-value=0.041  Score=32.42  Aligned_cols=34  Identities=9%  Similarity=0.262  Sum_probs=32.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=93.77  E-value=0.025  Score=36.34  Aligned_cols=42  Identities=14%  Similarity=0.070  Sum_probs=35.7

Q ss_pred             HhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           52 LSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=93.72  E-value=0.014  Score=36.29  Aligned_cols=60  Identities=13%  Similarity=0.248  Sum_probs=49.2

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 D~ly~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~~~~~ReVL~~   65 (69)
T d2j5pa1           6 DPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLAP   65 (69)
T ss_dssp             CTTHHHHHHHHHHTTEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSBCCCCSSSEEEBCSC
T ss_pred             cHHHHHHHHHHHHhCcccHHHHHHHHhccchHHHHHHHHHHHCCcCCCCCCCCCCeEcCC
Confidence            457777777777788899999999999999999999999999999998755444344443

>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=93.58  E-value=0.013  Score=34.42  Aligned_cols=46  Identities=20%  Similarity=0.302  Sum_probs=37.3

Q ss_pred             eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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-A---RTPFTEIAKKLGISETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHHHC-T---TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            355555555554 3   359999999999999999999999999999963

>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=93.48  E-value=0.054  Score=31.83  Aligned_cols=40  Identities=15%  Similarity=0.209  Sum_probs=35.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY  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  34566665

>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=93.46  E-value=0.029  Score=36.03  Aligned_cols=34  Identities=15%  Similarity=0.115  Sum_probs=32.5

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4999999999999999999999999999999876

>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=93.41  E-value=0.039  Score=32.92  Aligned_cols=46  Identities=11%  Similarity=0.115  Sum_probs=40.7

Q ss_pred             HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=93.37  E-value=0.03  Score=32.99  Aligned_cols=43  Identities=12%  Similarity=0.205  Sum_probs=35.7

Q ss_pred             HHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033932           47 TYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGL   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            344555555443 5899999999999999999999999999997

>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=92.95  E-value=0.035  Score=36.10  Aligned_cols=34  Identities=18%  Similarity=0.112  Sum_probs=32.9

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>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=92.75  E-value=0.073  Score=31.53  Aligned_cols=40  Identities=8%  Similarity=0.157  Sum_probs=35.4

Q ss_pred             CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932           58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA   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            4455778999999999999999999999999999997654

>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=92.58  E-value=0.072  Score=34.76  Aligned_cols=34  Identities=12%  Similarity=0.151  Sum_probs=32.3

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            4899999999999999999999999999999776

>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=92.49  E-value=0.075  Score=34.79  Aligned_cols=38  Identities=18%  Similarity=0.289  Sum_probs=33.2

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            46899999999999999999999999999999887664

>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=92.18  E-value=0.074  Score=33.94  Aligned_cols=43  Identities=16%  Similarity=0.142  Sum_probs=34.9

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEecc
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV--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            47899999999998865    58999999999874  345667889854

>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=92.16  E-value=0.12  Score=34.98  Aligned_cols=58  Identities=26%  Similarity=0.273  Sum_probs=42.6

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----cccceEEEecc
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS----AHASQQIYTRA  105 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYtr~  105 (108)
                      +--+|+.-.-. .=.|.+.||+.+++.-+....-|+.|++.|+|..+.    .++.+.+|..+
T Consensus        20 ~R~~Il~~L~~-~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~   81 (190)
T d1ulya_          20 TRRKILKLLRN-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRT   81 (190)
T ss_dssp             HHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEES
T ss_pred             HHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEc
Confidence            33445544432 236999999999999999999999999999997652    22346677643

>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=91.99  E-value=0.048  Score=33.54  Aligned_cols=36  Identities=22%  Similarity=0.337  Sum_probs=32.6

Q ss_pred             CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            346899999999999999999999999999998744

>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=91.80  E-value=0.2  Score=31.47  Aligned_cols=53  Identities=17%  Similarity=0.234  Sum_probs=41.8

Q ss_pred             HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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            4454554434 699999999999999999999999999999874 4556666763

>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=91.66  E-value=0.19  Score=32.07  Aligned_cols=45  Identities=24%  Similarity=0.407  Sum_probs=34.1

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--cceEEEe
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH--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            4468889999987   899999998           6899999999876322  2334465

>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=90.58  E-value=0.21  Score=32.26  Aligned_cols=46  Identities=11%  Similarity=0.158  Sum_probs=35.3

Q ss_pred             eechhhhhhhh----cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           60 LITPSILSDRL----RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  106 (108)
Q Consensus        60 ~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~~~-~~gr~~~Y~~~i   71 (122)
T d2g9wa1          22 PQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI-RDDRAHRYAPVH   71 (122)
T ss_dssp             CEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE-C---CCEEEESS
T ss_pred             CccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEe-ecCCeEEEEeCC
Confidence            36888887777    57889999999999999999975 456677998753

>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=90.58  E-value=0.083  Score=33.32  Aligned_cols=40  Identities=8%  Similarity=0.121  Sum_probs=33.1

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-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            48999999999875    56999999999998744 366788875

>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=90.13  E-value=0.64  Score=28.53  Aligned_cols=53  Identities=21%  Similarity=0.307  Sum_probs=44.6

Q ss_pred             CHHHHHHHHh---hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932           44 DQATYDKLLS---EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH   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            5566665554   5667799999999999999999999999999999999887654

>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=90.03  E-value=0.3  Score=31.57  Aligned_cols=45  Identities=11%  Similarity=0.243  Sum_probs=36.9

Q ss_pred             echhhhhhhh----cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           61 ITPSILSDRL----RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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 6677888998753

>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=89.48  E-value=0.32  Score=29.77  Aligned_cols=45  Identities=11%  Similarity=0.168  Sum_probs=35.5

Q ss_pred             echhhhhhh----hcccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932           61 ITPSILSDR----LRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT  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    47788899999999999999986 5567788998754

>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=89.36  E-value=0.21  Score=31.41  Aligned_cols=34  Identities=18%  Similarity=0.233  Sum_probs=29.1

Q ss_pred             eeechhhhhhhhcc--cHHHHHHHHHHHHHcCCeeE
Q 033932           59 KLITPSILSDRLRI--NGSLARKAIRELMARGLIRM   92 (108)
Q Consensus        59 k~ITps~vserlkI--~~SlAr~~Lr~L~~kGlIk~   92 (108)
                      .=|+-..|++.+++  +-+-.|..|.+|+++|+|..
T Consensus        22 ~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~   57 (87)
T d1stza1          22 KPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ   57 (87)
T ss_dssp             SCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC
T ss_pred             CccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC
Confidence            34778889999666  58889999999999999976

>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=89.22  E-value=0.2  Score=33.82  Aligned_cols=34  Identities=21%  Similarity=0.149  Sum_probs=32.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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            7999999999999999999999999999998763

>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=88.76  E-value=0.44  Score=32.52  Aligned_cols=33  Identities=27%  Similarity=0.220  Sum_probs=31.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV   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

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.71  E-value=0.31  Score=29.55  Aligned_cols=42  Identities=21%  Similarity=0.262  Sum_probs=36.0

Q ss_pred             HHhhCCCCeeechhhhhhhh-cccHHHHHHHHHHHHHcCCeeE
Q 033932           51 LLSEAPKYKLITPSILSDRL-RINGSLARKAIRELMARGLIRM   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            44566766778999999999 7999999999999999999843

>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=88.23  E-value=0.49  Score=29.56  Aligned_cols=44  Identities=30%  Similarity=0.431  Sum_probs=32.4

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--cceEEEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH--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            457888888886   8899998885           899999999866322  2334464

>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=88.04  E-value=0.39  Score=30.64  Aligned_cols=44  Identities=14%  Similarity=0.246  Sum_probs=35.1

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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

>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=87.88  E-value=0.36  Score=28.72  Aligned_cols=32  Identities=25%  Similarity=0.259  Sum_probs=30.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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=87.66  E-value=0.32  Score=28.66  Aligned_cols=32  Identities=9%  Similarity=0.196  Sum_probs=30.3

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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            78899999999999999999999999999974

>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=87.61  E-value=0.047  Score=37.02  Aligned_cols=35  Identities=29%  Similarity=0.385  Sum_probs=32.7

Q ss_pred             eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS   94 (108)
Q Consensus        60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~   94 (108)
                      =+|++.||++++|.-+-.-++|..|+++|+|....
T Consensus        79 ~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          79 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             CcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeec
Confidence            37999999999999999999999999999999884

>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=87.54  E-value=0.23  Score=31.78  Aligned_cols=35  Identities=20%  Similarity=0.288  Sum_probs=32.7

Q ss_pred             eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV   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            35899999999999999999999999999999877

>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=86.51  E-value=0.37  Score=28.54  Aligned_cols=32  Identities=3%  Similarity=0.169  Sum_probs=30.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=86.02  E-value=0.52  Score=28.65  Aligned_cols=45  Identities=24%  Similarity=0.251  Sum_probs=37.8

Q ss_pred             HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=85.85  E-value=0.74  Score=28.58  Aligned_cols=43  Identities=16%  Similarity=0.254  Sum_probs=36.5

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR  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 4556666653

>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=85.83  E-value=0.47  Score=29.54  Aligned_cols=45  Identities=22%  Similarity=0.220  Sum_probs=37.5

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA   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

>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=85.69  E-value=0.45  Score=28.18  Aligned_cols=34  Identities=15%  Similarity=0.219  Sum_probs=31.2

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS   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

>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=85.36  E-value=0.28  Score=29.35  Aligned_cols=47  Identities=17%  Similarity=0.275  Sum_probs=37.1

Q ss_pred             CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM   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            3455556664432  2368999999999999999999999999999865

>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=84.71  E-value=0.71  Score=28.89  Aligned_cols=40  Identities=20%  Similarity=0.307  Sum_probs=35.7

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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

>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=84.33  E-value=0.42  Score=33.09  Aligned_cols=24  Identities=38%  Similarity=0.632  Sum_probs=21.0

Q ss_pred             ccHHHHHHHHHHHHHcCCeeEecc
Q 033932           72 INGSLARKAIRELMARGLIRMVSA   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

>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=83.67  E-value=0.59  Score=29.40  Aligned_cols=32  Identities=19%  Similarity=0.196  Sum_probs=29.9

Q ss_pred             echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRINGSLARKAIRELMARGLIRM   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

>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=82.97  E-value=0.75  Score=28.73  Aligned_cols=40  Identities=18%  Similarity=0.230  Sum_probs=34.9

Q ss_pred             hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932           64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT  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            3446689999999999999999999999988888888885

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=80.89  E-value=0.52  Score=30.14  Aligned_cols=39  Identities=21%  Similarity=0.234  Sum_probs=32.4

Q ss_pred             chhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932           62 TPSILSDRLRINGSLARKAIRELMARGLIRMVS-AHASQQIYTR  104 (108)
Q Consensus        62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr  104 (108)
                      |.+.||..++|+.+    .||.-++.|||.|.. ..+..+.|+.
T Consensus         2 ~Ige~A~~~gvs~~----TlR~Ye~~GLl~p~~r~~~gyR~Y~~   41 (127)
T d1q06a_           2 NISDVAKITGLTSK----AIRFYEEKGLVTPPMRSENGYRTYTQ   41 (127)
T ss_dssp             CHHHHHHHHTCCHH----HHHHHHHTTCSCCCEECTTSCEECCH
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHcCCCCCCccCCcCcccchH
Confidence            56889999998875    589999999999974 3577888875

>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=80.80  E-value=1.3  Score=27.87  Aligned_cols=32  Identities=22%  Similarity=0.168  Sum_probs=28.8

Q ss_pred             echhhhhhhhccc-HHHHHHHHHHHHHcCCeeE
Q 033932           61 ITPSILSDRLRIN-GSLARKAIRELMARGLIRM   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            6889999999995 6777889999999999985

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=80.49  E-value=1.6  Score=27.44  Aligned_cols=53  Identities=19%  Similarity=0.293  Sum_probs=38.5

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccH---HHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRING---SLARKAIRELMARGLIRMVSAHASQQIYTR  104 (108)
Q Consensus        47 t~dKl~KEVpk~k~ITps~vserlkI~~---SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr  104 (108)
                      ++|-|...-   .=+|+..||++.++..   ..-.++||-|...|++..+....  ..|..
T Consensus        34 i~d~l~~~~---~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~gi~~~~~~~~--~~Y~l   89 (101)
T d1fp2a1          34 IPNIIQNHG---KPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITKEE--ESYAL   89 (101)
T ss_dssp             HHHHHHHHT---SCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEEESSS--EEEEE
T ss_pred             cHHHHHHcC---CCCCHHHHHHHcCCCCccchHHHHHHHHHHhCCceeeecCCC--CeEec
Confidence            455554321   2489999999999754   56789999999999998875543  45664

>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=80.42  E-value=1.5  Score=27.81  Aligned_cols=34  Identities=32%  Similarity=0.492  Sum_probs=27.4

Q ss_pred             HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932           46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV   93 (108)
Q Consensus        46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V   93 (108)
                      --|..|.+.+|+   ||+.+|++||           ++|++.|+|...
T Consensus        33 ~RF~el~~~l~g---IS~~~Ls~rL-----------k~L~~~glv~R~   66 (108)
T d1z7ua1          33 KRNGELMRALDG---ITQRVLTDRL-----------REMEKDGLVHRE   66 (108)
T ss_dssp             BCHHHHHHHSTT---CCHHHHHHHH-----------HHHHHHTSEEEE
T ss_pred             CCHHHHHHHCcC---CChhHHHHHH-----------HHHHHCCcceee
Confidence            346778888876   8888888875           899999999765

>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=80.32  E-value=1.6  Score=28.03  Aligned_cols=43  Identities=19%  Similarity=0.343  Sum_probs=30.9

Q ss_pred             HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc--cceEEEe
Q 033932           47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH--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            46777777776   7788887774           899999999877432  3345565