Citrus Sinensis ID: 023862

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270------
Protein Sequence
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV
Secondary Structure (PSIPRED)
ccccccccEEccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEEHHHHccccHHHHHHHHHHHHHHccccEEEEccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEccccccccEEEccccccccccccccccccccEEEEEEEEEcccccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEccccEEEEEcccccEEEcccccccccccccccccccccccccccEEEEEEccccccccccccEEccccccHHHHHHHHHHHHHcccEEEHHHHHHHccccHHHHHHHHHHHHHHccccEEEcccccEEEEccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHc
Coil and Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfpriqplpfprisgkipgsrvlvpvakastdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADtdgflevsdegdvlyvfpnnyraKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfnifispsdlfwywdpyyyrrrrvqtddddkkmNFIKSVFSFvfgegdpnqgieeKRWKLV
Flexible Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfPRIQPLPFPRISGKIPGSRVLVPVAKAStdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIlssksddddrgrrrrsfdsgfnifispsdlfwywdpYYYRRRRvqtddddkkMNFIKSVFsfvfgegdpnqgieekrwklv
Low Complexity Region (SEG)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfNIFISPSDLFWYWDPyyyrrrrVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV
Disordered region (IsUnstruct)
******CFTTTPKSRFFFTPLR****************LPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL****************DSGFNIFISPSDLFWYWDPYYYRR****************************************
Disordered Region (DISOPRED)
*****TCFTTTPKSRF*********************************************************************RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAII***********************NIFISPSDLFWYWDP********************KSVFSFVFGEGDPNQGIE**RWKL*
Disordered Region (DISEMBL)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSS**********RRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV
Disordered Region (DISPRO)
*TSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSK************FDSGFNIFISPSDLFWYWDPYYYRRRRV******KKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV
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	276	2.2.26 [Sep-21-2011]
Q8GW20	523	Uncharacterized protein A	yes	no	0.989	0.521	0.598	2e-88

>sp|Q8GW20|Y5390_ARATH Uncharacterized protein At5g03900, chloroplastic OS=Arabidopsis thaliana GN=At5g03900 PE=1 SV=2

 Score =  325 bits (834), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRP-SINLKPP---DSFPRIQPLPFPRISGKIPGSRVLV 55
           M  +STC   +P+ ++   +  +P  I L+ P    SFPR+  L    +S +   +R  +
Sbjct: 1   MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query: 56  PVAKAST--DVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
            V KA++   V+  + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct: 59  AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query: 114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
           AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct: 119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query: 174 RVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPY 232
           RV FGTALIASIVIV+T+IIA+LSSKS+DD+R RRR RS+DSGFN +I+P DL WYWDP 
Sbjct: 179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPN 238

Query: 233 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281

Arabidopsis thaliana (taxid: 3702)

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	276
118488331	288	unknown [Populus trichocarpa]	0.974	0.934	0.672	5e-97
255575701	514	conserved hypothetical protein [Ricinus	0.971	0.521	0.690	4e-95
449462964	516	PREDICTED: uncharacterized protein At5g0	0.978	0.523	0.660	1e-93
224077276	374	predicted protein [Populus trichocarpa]	0.786	0.580	0.764	2e-92
225440882	495	PREDICTED: uncharacterized protein At5g0	0.807	0.450	0.743	1e-87
312283379	523	unnamed protein product [Thellungiella h	0.996	0.525	0.588	3e-87
7406400	757	putative protein [Arabidopsis thaliana]	0.989	0.360	0.598	3e-87
26453262	523	unknown protein [Arabidopsis thaliana]	0.989	0.521	0.598	4e-87
21536751	523	unknown [Arabidopsis thaliana]	0.989	0.521	0.598	9e-87
18414392	523	Iron-sulfur assembly-like protein [Arabi	0.989	0.521	0.598	1e-86

>gi|118488331|gb|ABK95984.1| unknown [Populus trichocarpa]

 Score =  360 bits (923), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 189/281 (67%), Positives = 225/281 (80%), Gaps = 12/281 (4%)

Query: 1   MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFP-RIQPLPFPRISGKIPGSRVLVPVA- 58
           M SIST  + +P        L+P + LKPPDS   R Q L   ++S K P  +  +  + 
Sbjct: 1   MASISTPLSYSPSP----VRLKPPVRLKPPDSLLLRTQTLH--KLSFKSPNPKTPIGFSV 54

Query: 59  KASTDVA--VGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116
           KA+ DV   +G+ PG +VE+DKLP+DVRNRAM+AVDAC  RVTIGDVA +AGLKLNEAQK
Sbjct: 55  KATADVTKTMGIRPGSVVETDKLPSDVRNRAMEAVDACGGRVTIGDVASRAGLKLNEAQK 114

Query: 117 ALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVL 176
           ALQALA+DTDGFLEVSDEGDVLYVFP +YR+KLAAKS RLK EP+ +K KAAAEY IRV 
Sbjct: 115 ALQALASDTDGFLEVSDEGDVLYVFPKDYRSKLAAKSLRLKFEPLFEKGKAAAEYLIRVS 174

Query: 177 FGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPYYYR 235
           FGTALIASIVIV+T IIAILSS  D++DRGRRR RSFD+GF  ++SP+DLFWYWDPYYYR
Sbjct: 175 FGTALIASIVIVYTTIIAILSSSRDENDRGRRRSRSFDTGFAFYLSPTDLFWYWDPYYYR 234

Query: 236 RRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           RR+++TD  D KMNFI+SVFSFVFG+GDPNQGIEE+RWKL+
Sbjct: 235 RRQLRTDGGD-KMNFIESVFSFVFGDGDPNQGIEEERWKLI 274

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255575701|ref|XP_002528750.1| conserved hypothetical protein [Ricinus communis] gi|223531844|gb|EEF33662.1| conserved hypothetical protein [Ricinus communis]

 Score =  353 bits (906), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 192/278 (69%), Positives = 226/278 (81%), Gaps = 10/278 (3%)

Query: 1   MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV-PVAK 59
           M SISTCFT +PK+R   T  +PS  LKPPDSF +I      R+S K+   RV    V +
Sbjct: 1   MASISTCFTISPKTRIILTS-KPSCRLKPPDSFTKI------RLSPKLSDPRVYRGSVIR 53

Query: 60  ASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ 119
           A  D+  G+ PG  VESDKL ADVR RAM+AVDA   RVTIGDVA KAGLKLNEAQKALQ
Sbjct: 54  AGIDLPSGIKPGGAVESDKLRADVRKRAMEAVDAFGGRVTIGDVASKAGLKLNEAQKALQ 113

Query: 120 ALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGT 179
           ALAADT+GFLEVSDEGDVLY FP +YR+KLAAKSF++KVEP++DKAKA  EY IRV FGT
Sbjct: 114 ALAADTNGFLEVSDEGDVLYAFPKDYRSKLAAKSFKMKVEPLVDKAKATGEYLIRVSFGT 173

Query: 180 ALIASIVIVFTAIIAILSSKSDDDDRGRR-RRSFDSGFNIFISPSDLFWYWDPYYYRRRR 238
           ALIASIV+V+T IIA+LSS+S++D+RGRR  RS+DSGF  + SP+DLFWYWDPYYYRRR+
Sbjct: 174 ALIASIVLVYTTIIALLSSRSEEDNRGRRGGRSYDSGFTFYFSPTDLFWYWDPYYYRRRQ 233

Query: 239 VQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           ++ DDDD KMNFI+SVFSFVFG+GDPNQGIEE+RWKL+
Sbjct: 234 IKKDDDD-KMNFIESVFSFVFGDGDPNQGIEEERWKLI 270

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462964|ref|XP_004149205.1| PREDICTED: uncharacterized protein At5g03900, chloroplastic-like [Cucumis sativus] gi|449500907|ref|XP_004161226.1| PREDICTED: uncharacterized protein At5g03900, chloroplastic-like [Cucumis sativus]

 Score =  348 bits (893), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 185/280 (66%), Positives = 227/280 (81%), Gaps = 10/280 (3%)

Query: 1   MTSISTCFTTTPKSRFFFTPL---RPSINLKPPD-SFPRIQPLPFPRISGKIPGSRVLVP 56
           M SIST F  +  SR +F PL   +PSI +KP   +FP    LP  RI+     +R  VP
Sbjct: 1   MASISTYFAISQSSRLYFHPLITLKPSICVKPSTITFP---ALP-TRIAPPESRARGFVP 56

Query: 57  VAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116
             +A  D+   + PG +VESDKLP+DVR R M+AV+AC  RVTIGDVA +AGLKLNEAQK
Sbjct: 57  TVRAGIDIPSDIRPGNVVESDKLPSDVRKRTMEAVEACGGRVTIGDVASRAGLKLNEAQK 116

Query: 117 ALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVL 176
           ALQALAADTDGFLEVSDEGDVLYVFP +YR+KLAAKSF +K EP+I+K+KAAAEY +RV 
Sbjct: 117 ALQALAADTDGFLEVSDEGDVLYVFPKDYRSKLAAKSFWIKFEPLIEKSKAAAEYLVRVS 176

Query: 177 FGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRR 236
           FGTALIASIV+V+T IIA++SS+S++D+RGRR RS+DSGF  ++SP+DLFWYWDPYYYRR
Sbjct: 177 FGTALIASIVLVYTTIIALISSRSEEDNRGRRSRSYDSGFTFYLSPTDLFWYWDPYYYRR 236

Query: 237 RRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           RR+QT+D+  KMNFI+S+FSFVFG+GDPNQGIEE+RWKL+
Sbjct: 237 RRLQTEDN--KMNFIESIFSFVFGDGDPNQGIEEERWKLI 274

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077276|ref|XP_002305197.1| predicted protein [Populus trichocarpa] gi|222848161|gb|EEE85708.1| predicted protein [Populus trichocarpa]

 Score =  345 bits (884), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 169/221 (76%), Positives = 196/221 (88%), Gaps = 4/221 (1%)

Query: 59  KASTDVA--VGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQK 116
           KA+ DV   +G+ PG +VE+DKLP+DVRNRAM+AVDAC  RVTIGDVA +AGLKLNEAQK
Sbjct: 5   KATADVTKTMGIRPGSVVETDKLPSDVRNRAMEAVDACGGRVTIGDVASRAGLKLNEAQK 64

Query: 117 ALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVL 176
           ALQALA+DTDGFLEVSDEGDVLYVFP +YR+KLAAKS RLK EP+ +K KAAAEY IRV 
Sbjct: 65  ALQALASDTDGFLEVSDEGDVLYVFPKDYRSKLAAKSLRLKFEPLFEKGKAAAEYLIRVS 124

Query: 177 FGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPYYYR 235
           FGTALIASIVIV+T IIAILSS  D++DRGRRR RSFD+GF  ++SP+DLFWYWDPYYYR
Sbjct: 125 FGTALIASIVIVYTTIIAILSSSRDENDRGRRRSRSFDTGFAFYLSPTDLFWYWDPYYYR 184

Query: 236 RRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           RR+++TD  D KMNFI+SVFSFVFG+GDPNQGIEE+RWKL+
Sbjct: 185 RRQLRTDGGD-KMNFIESVFSFVFGDGDPNQGIEEERWKLI 224

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440882|ref|XP_002276711.1| PREDICTED: uncharacterized protein At5g03900, chloroplastic-like [Vitis vinifera]

 Score =  329 bits (843), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 168/226 (74%), Positives = 201/226 (88%), Gaps = 3/226 (1%)

Query: 52  RVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKL 111
           +V VPV +A  DVA G+ PG IVE+DKLP++VR RAMDAVDAC  RVTIGDVA K GLKL
Sbjct: 28  QVFVPVVRAGLDVASGIRPGGIVETDKLPSNVRKRAMDAVDACGGRVTIGDVASKGGLKL 87

Query: 112 NEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEY 171
           NEAQKALQALAADT+GFLEVSDEGDVLYVFP +YR+KLAAKSFR+K+EP ++KAK+AAEY
Sbjct: 88  NEAQKALQALAADTNGFLEVSDEGDVLYVFPKDYRSKLAAKSFRIKLEPFVEKAKSAAEY 147

Query: 172 SIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRR-RRSFDSGFNIFISPSDLFWYWD 230
            +RV FGTALIASIV+V+T IIA+LSS+SD+D+RGRR  RS+DSGF  +++P+DLFWYWD
Sbjct: 148 LVRVSFGTALIASIVLVYTTIIALLSSRSDEDNRGRRGGRSYDSGFTFYLNPADLFWYWD 207

Query: 231 PYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           PYYYRRRR+Q +DD   MNFI+SVFSFVFG+GDPNQGIE++RWKL+
Sbjct: 208 PYYYRRRRIQKEDD--GMNFIESVFSFVFGDGDPNQGIEDERWKLI 251

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312283379|dbj|BAJ34555.1| unnamed protein product [Thellungiella halophila]

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 166/282 (58%), Positives = 210/282 (74%), Gaps = 7/282 (2%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRPSINLKPP----DSFPRIQPLPFPRISGKIPGSRVLV 55
           MT +STC   +PK ++  F+  +P I L+ P     +FP I    FP    +     + V
Sbjct: 1   MTCVSTCLIVSPKLTQSGFSSKKPVIRLRSPVDRCYAFPGIFTKRFPSSRREFTSHGIAV 60

Query: 56  PVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQ 115
             A +   V+  +  G +VESDKLP DVR RAM+AVD C RRVT+GDVA +AGLK+ EAQ
Sbjct: 61  VRAASIDKVSGAIKLGGLVESDKLPTDVRKRAMEAVDECGRRVTVGDVASRAGLKVTEAQ 120

Query: 116 KALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRV 175
           KALQA+AADTDGFLEVSDEGDVLYVFP +YR+KLA KS R+++EP ++KAK A +Y  RV
Sbjct: 121 KALQAIAADTDGFLEVSDEGDVLYVFPRDYRSKLATKSLRIQIEPFLEKAKGAVDYLTRV 180

Query: 176 LFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPYYY 234
            FGTALIASIVIV+T II +LSS+S+DD+R RRR R +DSGFN FI+P DLFWYWDP YY
Sbjct: 181 SFGTALIASIVIVYTTIIVLLSSRSEDDNRQRRRGRGYDSGFNFFINPVDLFWYWDPNYY 240

Query: 235 RRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
            RRR + +D+ K MNFI+SVFSFVFG+GDPN+G EE+RW+++
Sbjct: 241 SRRRAR-EDEGKGMNFIESVFSFVFGDGDPNEGTEEERWQMI 281

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7406400|emb|CAB85510.1| putative protein [Arabidopsis thaliana]

 Score =  327 bits (838), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRP-SINLKPP---DSFPRIQPLPFPRISGKIPGSRVLV 55
           M  +STC   +P+ ++   +  +P  I L+ P    SFPR+  L    +S +   +R  +
Sbjct: 1   MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query: 56  PVAKAST--DVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
            V KA++   V+  + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct: 59  AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query: 114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
           AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct: 119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query: 174 RVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPY 232
           RV FGTALIASIVIV+T+IIA+LSSKS+DD+R RRR RS+DSGFN +I+P DL WYWDP 
Sbjct: 179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPN 238

Query: 233 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|26453262|dbj|BAC43704.1| unknown protein [Arabidopsis thaliana]

 Score =  327 bits (837), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 217/284 (76%), Gaps = 11/284 (3%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRP-SINLKPP---DSFPRIQPLPFPRISGKIPGSRVLV 55
           M  +STC   +P+ ++   +  +P  I L+ P    SFPR+  L    +S +   +R  +
Sbjct: 1   MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query: 56  PVAKAST--DVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
            V KA++   V+  + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct: 59  AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query: 114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
           AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct: 119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query: 174 RVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPY 232
           RV FGTALIASIVIV+T+IIA+LSSKS+DD+R RRR RS+DSGFN +I+P+DL WYWDP 
Sbjct: 179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPADLLWYWDPN 238

Query: 233 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21536751|gb|AAM61083.1| unknown [Arabidopsis thaliana]

 Score =  325 bits (834), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRP-SINLKPP---DSFPRIQPLPFPRISGKIPGSRVLV 55
           M  +STC   +P+ ++   +  +P  I L+ P    SFPR+  L    +S +   +R  +
Sbjct: 1   MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query: 56  PVAKAST--DVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
            V KA++   V+  + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct: 59  AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query: 114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
           AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct: 119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query: 174 RVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPY 232
           RV FGTALIASIVIV+T+IIA+LSSKS+DD+R RRR RS+DSGFN +I+P DL WYWDP 
Sbjct: 179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPN 238

Query: 233 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18414392|ref|NP_568129.1| Iron-sulfur assembly-like protein [Arabidopsis thaliana] gi|88909724|sp|Q8GW20.2|Y5390_ARATH RecName: Full=Uncharacterized protein At5g03900, chloroplastic; Flags: Precursor gi|332003286|gb|AED90669.1| Iron-sulfur assembly-like protein [Arabidopsis thaliana]

 Score =  325 bits (834), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

Query: 1   MTSISTCFTTTPK-SRFFFTPLRP-SINLKPP---DSFPRIQPLPFPRISGKIPGSRVLV 55
           M  +STC   +P+ ++   +  +P  I L+ P    SFPR+  L    +S +   +R  +
Sbjct: 1   MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query: 56  PVAKAST--DVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
            V KA++   V+  + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct: 59  AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query: 114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
           AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct: 119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query: 174 RVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRR-RSFDSGFNIFISPSDLFWYWDPY 232
           RV FGTALIASIVIV+T+IIA+LSSKS+DD+R RRR RS+DSGFN +I+P DL WYWDP 
Sbjct: 179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPN 238

Query: 233 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	276
TAIR|locus:2150560	523	AT5G03900 "AT5G03900" [Arabido	0.989	0.521	0.535	1e-68

TAIR|locus:2150560 AT5G03900 "AT5G03900" [Arabidopsis thaliana (taxid:3702)]

 Score = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 152/284 (53%), Positives = 192/284 (67%)

Query:     1 MTSISTCFTTTPK-SRFFFTPLRPS-INLKPP-D--SFPRIQPLPFPRISGKIPGSRVLV 55
             M  +STC   +P+ ++   +  +P  I L+ P D  SFPR+  L    +S +   +R  +
Sbjct:     1 MACVSTCLILSPRLTQVGLSSKKPFLIRLRSPVDRYSFPRM--LTERCLSTRRKFNRHGI 58

Query:    56 PVAKA-STDVAVG-VGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNE 113
              V KA S D   G + PG +VESDKLP DVR RAMDAVD C RRVT+GDVA + GLK+ E
Sbjct:    59 AVVKAASLDKVSGAIKPGGLVESDKLPTDVRKRAMDAVDECGRRVTVGDVASRGGLKVTE 118

Query:   114 AQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSI 173
             AQ ALQA+AADTDGFLEVSDEGDVLYVFP +YR KLAAKS R+++EP ++KAK A +Y  
Sbjct:   119 AQTALQAIAADTDGFLEVSDEGDVLYVFPRDYRTKLAAKSLRIQIEPFLEKAKGAVDYLA 178

Query:   174 RVLFGTALIASIVIVFTAIIAILXXXXXXXXXXXXXXXXXXXX-NIFISPSDLFWYWDPX 232
             RV FGTALIASIVIV+T+IIA+L                     N +I+P DL WYWDP 
Sbjct:   179 RVSFGTALIASIVIVYTSIIALLSSKSEDDNRQRRRGRSYDSGFNFYINPVDLLWYWDPN 238

Query:   233 XXXXXXVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLV 276
                    + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW+++
Sbjct:   239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMI 281


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.138   0.407    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      276       249   0.00080  114 3  11 22  0.42    33
                                                     32  0.46    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  590 (63 KB)
  Total size of DFA:  170 KB (2100 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.16u 0.09s 20.25t   Elapsed:  00:00:00
  Total cpu time:  20.16u 0.09s 20.25t   Elapsed:  00:00:00
  Start:  Sat May 11 00:37:14 2013   End:  Sat May 11 00:37:14 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009536 "plastid" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	276
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.5
PRK13239	206	alkylmercury lyase; Provisional	95.05
COG3355	126	Predicted transcriptional regulator [Transcription	95.0
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	94.69
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.04
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.9
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	93.63
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	93.61
PRK06266	178	transcription initiation factor E subunit alpha; V	93.46
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	93.38
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	93.3
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	92.61
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	92.07
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	92.06
KOG3341	249	consensus RNA polymerase II transcription factor c	91.91
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	91.89
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.83
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	91.53
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	91.33
TIGR02844	80	spore_III_D sporulation transcriptional regulator	90.23
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	90.23
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	89.29
PRK15466	166	carboxysome structural protein EutK; Provisional	88.42
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	88.0
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	87.72
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	87.57
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	86.41
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	85.17
smart00753	88	PAM PCI/PINT associated module.	85.17
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	84.34
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	84.17
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	84.06
COG2512	258	Predicted membrane-associated trancriptional regul	83.89
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	83.2
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	82.56
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	82.48
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	82.4
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	82.15
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	82.12
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	81.51
PHA02943	165	hypothetical protein; Provisional	81.44
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	80.19

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

Probab=95.50  E-value=0.034  Score=41.47  Aligned_cols=46  Identities=15%  Similarity=0.252  Sum_probs=41.6

Q ss_pred             CchhhHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~-rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +..++.+|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+.
T Consensus         4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G   50 (68)
T smart00550        4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG   50 (68)
T ss_pred             chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            34677899999999988 69999999999999999999999998873

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

>PRK13239 alkylmercury lyase; Provisional

Probab=95.05  E-value=0.048  Score=49.67  Aligned_cols=53  Identities=19%  Similarity=0.297  Sum_probs=46.3

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY  139 (276)
                      ..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|.     ..+..++|+|+-
T Consensus        21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~   73 (206)
T PRK13239         21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG   73 (206)
T ss_pred             hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe
Confidence            457778899988 99999999999999999999999999985     347899999974

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.00  E-value=0.27  Score=41.96  Aligned_cols=86  Identities=19%  Similarity=0.162  Sum_probs=68.5

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEee-cCccEEEEc-CcchHHHhhhhhHHHhHHHH
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV  161 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~-~GhLeVS-esGDIlYvF-P~nfRs~L~~Ks~r~rl~~~  161 (276)
                      -.++.++-+.++..|+-|+|..-+++...|+++|+.|.... ==.-+++ +.|---|.+ |.++-.  -.+-.+..+++|
T Consensus        30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee--~k~~i~~~l~~w  107 (126)
T COG3355          30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEE--IKKKILKDLDEW  107 (126)
T ss_pred             HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHH--HHHHHHHHHHHH
Confidence            45677777789999999999999999999999999999875 1223344 789999999 888876  455567778888


Q ss_pred             HHHHhhhhhhH
Q 023862          162 IDKAKAAAEYS  172 (276)
Q Consensus       162 ~~k~w~v~~Yl  172 (276)
                      .+++...+..+
T Consensus       108 ~~~~~~~i~~~  118 (126)
T COG3355         108 YDKMKQLIEEF  118 (126)
T ss_pred             HHHHHHHHHHH
Confidence            88888776554

>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=94.69  E-value=0.043  Score=38.43  Aligned_cols=40  Identities=23%  Similarity=0.398  Sum_probs=35.9

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      -+|++++.+.+...|+.|+|.++|++...+.+-|..|.+.
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~   45 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE   45 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3689999999999999999999999999999999999864

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.

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

Probab=94.04  E-value=0.11  Score=39.13  Aligned_cols=53  Identities=23%  Similarity=0.394  Sum_probs=41.5

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--CccEEE
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY  139 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe--sGDIlY  139 (276)
                      ++|++.+++.+.-+|..|||...|++..+|+.=|..|..+  |.++-++  .|-..|
T Consensus         3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e--G~V~~~~~~rG~~~~   57 (62)
T PF04703_consen    3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE--GKVERSPVRRGKSTY   57 (62)
T ss_dssp             HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC--TSEEEES-SSSSS-E
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCCCccee
Confidence            6799999998889999999999999999999999999876  4555544  355443

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.90  E-value=0.48  Score=35.35  Aligned_cols=54  Identities=20%  Similarity=0.346  Sum_probs=43.1

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      .+|++.+.+.++.+|+.|+|...|++...+.+-|..|.+  .|-|+-...+. .|..
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~--~g~l~~~~~~~-~y~l   61 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE--LGYVEQDGQNG-RYRL   61 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH--CCCeeecCCCC-ceee
Confidence            467888888767899999999999999999999999976  47777654333 3555

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

Probab=93.63  E-value=0.13  Score=40.77  Aligned_cols=50  Identities=22%  Similarity=0.353  Sum_probs=36.3

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl  138 (276)
                      +--.+++.+.+ |.-||+.++|+++|.++++++++|.++.     ..|-.++|.||
T Consensus        25 L~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV   74 (77)
T PF12324_consen   25 LLRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV   74 (77)
T ss_dssp             HHHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred             HHHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence            33445666665 9999999999999999999999988875     47888888887

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

>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=93.61  E-value=0.21  Score=34.06  Aligned_cols=42  Identities=17%  Similarity=0.338  Sum_probs=35.0

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      +.+.+|++++.+.+ ++|+.|+|...|++...+.+.|..|..+
T Consensus         3 ~~~~~Il~~l~~~~-~~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    3 ETQRKILNYLRENP-RITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             HHHHHHHHHHHHCT-TS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            35678999999955 5999999999999999999999999765

...

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=93.46  E-value=0.58  Score=41.32  Aligned_cols=66  Identities=18%  Similarity=0.154  Sum_probs=52.2

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCc---eEeecCccEEEEcCcchHH
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF---LEVSDEGDVLYVFPNNYRA  147 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~Gh---LeVSesGDIlYvFP~nfRs  147 (276)
                      .+..-+|++++.+.| .+|..|+|...|++.+++++.|..|..+.=..   .+..++|-+.|.+==+...
T Consensus        21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~   89 (178)
T PRK06266         21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEK   89 (178)
T ss_pred             CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHH
Confidence            445578999999888 69999999999999999999999999987322   3333688899977444444

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=93.38  E-value=0.67  Score=39.99  Aligned_cols=78  Identities=24%  Similarity=0.261  Sum_probs=58.2

Q ss_pred             HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeecCccEEEEcCcchHHHhhhhhHHHhHHHHH
Q 023862           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI  162 (276)
Q Consensus        86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G---hLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~~~  162 (276)
                      .|++|+-..| .+|..|+|...|++++++++.|..|..+.=.   +.+-.++|-+.|.+=-|+..+...  .+.++....
T Consensus        18 ~Vl~aL~~~~-~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~--Ik~~~~~~~   94 (158)
T TIGR00373        18 LVLFSLGIKG-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDV--LKRKLEETA   94 (158)
T ss_pred             HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHH--HHHHHHHHH
Confidence            5677777666 6999999999999999999999999999854   666777899999974477764443  333334444


Q ss_pred             HHHh
Q 023862          163 DKAK  166 (276)
Q Consensus       163 ~k~w  166 (276)
                      +++.
T Consensus        95 ~~lk   98 (158)
T TIGR00373        95 KKLR   98 (158)
T ss_pred             HHHH
Confidence            4443

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.

>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=93.30  E-value=0.26  Score=35.39  Aligned_cols=53  Identities=26%  Similarity=0.439  Sum_probs=45.1

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG  135 (276)
                      ....|-+|++.+ ..+...|++++|...|++...+..-|..|..  .|-+++.++|
T Consensus         8 ~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~~~g   60 (61)
T PF12840_consen    8 SDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVEREG   60 (61)
T ss_dssp             TSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEEET
T ss_pred             CCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEeccC
Confidence            346788899999 7788899999999999999999999999987  5778887776

...

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

Probab=92.61  E-value=0.24  Score=42.49  Aligned_cols=51  Identities=25%  Similarity=0.377  Sum_probs=42.8

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes  134 (276)
                      +++..+|++.|++. +|+|++|++..+|++.+.+++-|..|++  .|+|..+..
T Consensus        11 ~eLk~rIvElVRe~-GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~   61 (127)
T PF06163_consen   11 EELKARIVELVREH-GRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGR   61 (127)
T ss_pred             HHHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCC
Confidence            56677888888765 5899999999999999999999999986  567776654

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

Probab=92.07  E-value=1.3  Score=30.24  Aligned_cols=60  Identities=25%  Similarity=0.424  Sum_probs=46.6

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc-cEEEEcC
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP  142 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG-DIlYvFP  142 (276)
                      +..+.+..|++++.+.+  ++..|+|...|++...+.+.|..|.+.  |.+....++ ...|.+.
T Consensus         4 ~~~~~~~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~--g~i~~~~~~~~~~~~~~   64 (78)
T cd00090           4 LSDPTRLRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEA--GLVESRREGRRVYYSLT   64 (78)
T ss_pred             ccChHHHHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHC--CCeEEEEeccEEEEEeC
Confidence            34456778899888866  999999999999999999999999775  567665544 4555554

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.

>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=92.06  E-value=0.43  Score=34.42  Aligned_cols=41  Identities=12%  Similarity=0.282  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +..|++.+++. +.+|+.|+|..-|+|...+++.|..|+...
T Consensus         2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~g   42 (57)
T PF08220_consen    2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQG   42 (57)
T ss_pred             HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            46789999876 689999999999999999999999998764

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

>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]

Probab=91.91  E-value=0.45  Score=44.56  Aligned_cols=84  Identities=17%  Similarity=0.313  Sum_probs=70.6

Q ss_pred             cCCCcccccCCCCchhh---HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcc
Q 023862           68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN  144 (276)
Q Consensus        68 ~~~~~~v~~~~l~~~~~---~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~n  144 (276)
                      ++.||.----++|-+++   ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|.++.=+-+--...+|-.|-||.+
T Consensus       159 ~~iggK~~vrSVP~ELn~Dht~ILela~~~gy-vt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~e~~YW~ps~  237 (249)
T KOG3341|consen  159 IKIGGKKLVRSVPTELNMDHTVILELAEILGY-VTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGDEAAYWFPSL  237 (249)
T ss_pred             EEecCEEeeecCcchhcccHHHHHHHHHhcCc-eeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCcceeeechhh
Confidence            44556655566776665   579999999999 99999999999999999999999999998888888899999999999


Q ss_pred             hHHHhhhh
Q 023862          145 YRAKLAAK  152 (276)
Q Consensus       145 fRs~L~~K  152 (276)
                      |-......
T Consensus       238 ~~~~~~q~  245 (249)
T KOG3341|consen  238 FTDQYAQR  245 (249)
T ss_pred             hhHHHhhh
Confidence            97755443

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=91.89  E-value=0.54  Score=31.50  Aligned_cols=50  Identities=20%  Similarity=0.376  Sum_probs=39.4

Q ss_pred             HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862           87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (276)
Q Consensus        87 im~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv  140 (276)
                      |+..+.  ...+|+.|++...|++...+.+.|..|.++  |-++....|.-.|.
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~~   51 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVYY   51 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEEE
Confidence            566776  667899999999999999999999999986  66666564544443

>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=91.83  E-value=0.8  Score=31.75  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=36.0

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE  130 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe  130 (276)
                      +.+|++.+.+.+..+|..++|.+.|+|...+++.|..|-+. +..++
T Consensus         2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~-~~~I~   47 (55)
T PF08279_consen    2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW-GIPIE   47 (55)
T ss_dssp             HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT-T-EEE
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeEE
Confidence            35788899666666999999999999999999999999444 44443

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 ....

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=91.53  E-value=0.85  Score=30.14  Aligned_cols=47  Identities=15%  Similarity=0.319  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe  133 (276)
                      +..+++.+.+.+ .+|+.|+|...|++...+.+.|..|..+  |.++-..
T Consensus         2 ~~~il~~l~~~~-~~s~~~l~~~l~~s~~tv~~~l~~L~~~--g~i~~~~   48 (53)
T smart00420        2 QQQILELLAQQG-KVSVEELAELLGVSEMTIRRDLNKLEEQ--GLLTRVH   48 (53)
T ss_pred             HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEee
Confidence            356788888765 5999999999999999999999999886  5555433

>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=91.33  E-value=0.5  Score=37.00  Aligned_cols=45  Identities=20%  Similarity=0.440  Sum_probs=38.2

Q ss_pred             chhhHHHHHHHHH---cCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        81 ~~~~~rim~Ave~---lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      ..++.+|+++++.   ..-.+.+.+||.+.|++.++++++|..|..+.
T Consensus        46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG   93 (102)
T PF08784_consen   46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG   93 (102)
T ss_dssp             -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence            4578899999998   56679999999999999999999999999863

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.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=90.23  E-value=0.4  Score=37.77  Aligned_cols=34  Identities=12%  Similarity=0.081  Sum_probs=31.0

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL  118 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL  118 (276)
                      -+.+|++.+.+  +.+|+.|||..+|+|...+.+.|
T Consensus         7 R~~~I~e~l~~--~~~ti~dvA~~~gvS~~TVsr~L   40 (80)
T TIGR02844         7 RVLEIGKYIVE--TKATVRETAKVFGVSKSTVHKDV   40 (80)
T ss_pred             HHHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHh
Confidence            45788999999  99999999999999999998877

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

>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms

Probab=90.23  E-value=0.75  Score=43.21  Aligned_cols=57  Identities=18%  Similarity=0.367  Sum_probs=49.6

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl  138 (276)
                      |..++.+|.+.+...|||+++.|++..-|+..+..|+.+..++.+-. +++.. .||++
T Consensus        53 ~~~L~~EI~~el~~~gGRv~~~dL~~~LnVd~~~ie~~~~~i~~~~~-~~~l~-~geli  109 (272)
T PF09743_consen   53 PEQLEKEIKDELYVHGGRVNLVDLAQALNVDLDHIERRAQEIVKSDK-SLQLV-QGELI  109 (272)
T ss_pred             HHHHHHHHHHHHHHcCCceEHHHHHHhcCcCHHHHHHHHHHHHhCCC-cEEEE-CCEEc
Confidence            45678899999999999999999999999999999999999998877 56544 68864

Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.

>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=89.29  E-value=1.5  Score=31.76  Aligned_cols=53  Identities=21%  Similarity=0.312  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY  139 (276)
                      ..++..++- ..+.+|+.|+|..+|++...+.+.|..|...  |-++..+...-+|
T Consensus        10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y   62 (68)
T PF01978_consen   10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY   62 (68)
T ss_dssp             HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred             HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence            345666665 5778999999999999999999999999886  6677776443333

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.

>PRK15466 carboxysome structural protein EutK; Provisional

Probab=88.42  E-value=1  Score=40.22  Aligned_cols=42  Identities=24%  Similarity=0.385  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      .+.++.-+-...+..|.|+||+.-|.++++++.+|..|-+|.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (166)
T PRK15466        111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAG  152 (166)
T ss_pred             HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhcc
Confidence            456677777888999999999999999999999999998863

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=88.00  E-value=1  Score=33.77  Aligned_cols=40  Identities=23%  Similarity=0.300  Sum_probs=32.1

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCC-HHHHHHHHHHHHhh
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAAD  124 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~-l~~Ae~aL~aLAsD  124 (276)
                      .-|.+.+++.|+-.|+.|+|...|++ .+.|++-|.+|..+
T Consensus        13 ~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k   53 (65)
T PF01726_consen   13 EFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK   53 (65)
T ss_dssp             HHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence            44556677899999999999999997 99999999999865

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.

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

Probab=87.72  E-value=0.78  Score=33.81  Aligned_cols=53  Identities=25%  Similarity=0.255  Sum_probs=35.9

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD  136 (276)
                      +..+.+.-.++|...|..+||...|+++++.++.|.....-..=++.+..+++
T Consensus         7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~   59 (78)
T PF04539_consen    7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDD   59 (78)
T ss_dssp             HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSS
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCC
Confidence            34445556688999999999999999999998888765544444555555433

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

>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=87.57  E-value=1.9  Score=30.02  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=37.3

Q ss_pred             hhHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           83 VRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        83 ~~~rim~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      .+-+++.++...+.. +|+.|+|...|++...+.+.+..|.++.
T Consensus         6 ~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G   49 (62)
T PF12802_consen    6 SQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG   49 (62)
T ss_dssp             HHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            356789999999887 9999999999999999999999998764

...

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

Probab=86.41  E-value=2  Score=31.82  Aligned_cols=38  Identities=21%  Similarity=0.366  Sum_probs=30.3

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA  123 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs  123 (276)
                      .+|.+.+-+.| +.|+.+++..++|+.++++++|..|.+
T Consensus        16 ~~V~~~Ll~~G-~ltl~~i~~~t~l~~~~Vk~~L~~LiQ   53 (62)
T PF08221_consen   16 AKVGEVLLSRG-RLTLREIVRRTGLSPKQVKKALVVLIQ   53 (62)
T ss_dssp             HHHHHHHHHC--SEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            46667776655 999999999999999999999999976

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

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=85.17  E-value=4.2  Score=30.39  Aligned_cols=68  Identities=13%  Similarity=0.155  Sum_probs=51.3

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA  147 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs  147 (276)
                      -...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.--...|.
T Consensus         7 ~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~   74 (88)
T smart00088        7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR   74 (88)
T ss_pred             HHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence            34455666666666678899999999999999999999999999874444567766677666555553

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=85.17  E-value=4.2  Score=30.39  Aligned_cols=68  Identities=13%  Similarity=0.155  Sum_probs=51.3

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA  147 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs  147 (276)
                      -...+.+.+..+-+--..+|..++|...+++.+++|..|..+..+..=+-.++.....++.--...|.
T Consensus         7 ~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~   74 (88)
T smart00753        7 QRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR   74 (88)
T ss_pred             HHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh
Confidence            34455666666666678899999999999999999999999999874444567766677666555553

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=84.34  E-value=6.8  Score=35.78  Aligned_cols=50  Identities=10%  Similarity=0.089  Sum_probs=41.2

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe  133 (276)
                      .+-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+..  |.|+-.-
T Consensus         4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~--g~l~r~~   53 (256)
T PRK10434          4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA--GTVIRTY   53 (256)
T ss_pred             HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEE
Confidence            456788899888855 6999999999999999999999999876  4444433

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=84.17  E-value=3.2  Score=38.30  Aligned_cols=54  Identities=15%  Similarity=0.244  Sum_probs=44.8

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD  136 (276)
                      ..+-+.+|++.+++.+. +|+.|+|..-|+|...+++.|..|.+.  |-++-..-|-
T Consensus        15 ~~eR~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~--G~l~r~~GGa   68 (269)
T PRK09802         15 TSERREQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQ--GIAVRAYGGA   68 (269)
T ss_pred             HHHHHHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhC--CCeEEEeCCE
Confidence            35677888999999776 999999999999999999999999664  6666555554

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

Probab=84.06  E-value=2.5  Score=29.10  Aligned_cols=49  Identities=20%  Similarity=0.365  Sum_probs=35.8

Q ss_pred             chhhHHHHHHHHHcC----Cc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862           81 ADVRNRAMDAVDACN----RR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (276)
Q Consensus        81 ~~~~~rim~Ave~lg----~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV  131 (276)
                      .++...+.+.+....    .. .|+.|+|...|++...+.++|..|++.  |-|+.
T Consensus         4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~--G~i~~   57 (66)
T cd07377           4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAE--GLVER   57 (66)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence            345566666655432    22 459999999999999999999999984  34543

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

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=83.89  E-value=2  Score=40.15  Aligned_cols=46  Identities=20%  Similarity=0.328  Sum_probs=40.0

Q ss_pred             CCCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           78 KLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        78 ~l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      .|+.+ ...||++++.+|+|+|+.|+..+.|+|...+=+.|+.|...
T Consensus       192 ~L~~~-e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~  237 (258)
T COG2512         192 DLNED-EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR  237 (258)
T ss_pred             CCCHH-HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC
Confidence            34433 35789999999999999999999999999999999999764

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

Probab=83.20  E-value=5.4  Score=31.24  Aligned_cols=59  Identities=12%  Similarity=0.129  Sum_probs=48.1

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      .|..|++++.+.+.-+|+.||..+.     ++++..+=+.|..|++..=-+=-..++|...|..
T Consensus         2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~   65 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYEL   65 (116)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEe
Confidence            4788999999999899999999887     6899999999999998765444344456677765

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.

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=82.56  E-value=3.3  Score=28.58  Aligned_cols=39  Identities=13%  Similarity=0.313  Sum_probs=30.9

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL  121 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL  121 (276)
                      ++..+|++++.+. .|.+..++|.+.|++-.++.+-+..|
T Consensus         3 ~~D~~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen    3 ELDRKILRLLQED-GRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             HHHHHHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            3556788888776 88999999999999999999888776

...

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=82.48  E-value=2.5  Score=37.10  Aligned_cols=43  Identities=14%  Similarity=0.194  Sum_probs=37.7

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      .+-+.+|++.+.+ .+.+|+.|+|..-|.|...+++.|..|+.+
T Consensus         6 ~~R~~~Il~~l~~-~~~~~~~~La~~~~vS~~TiRRDl~~L~~~   48 (185)
T PRK04424          6 KERQKALQELIEE-NPFITDEELAEKFGVSIQTIRLDRMELGIP   48 (185)
T ss_pred             HHHHHHHHHHHHH-CCCEEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence            3566778888888 456999999999999999999999999887

>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=82.40  E-value=8.1  Score=26.96  Aligned_cols=38  Identities=21%  Similarity=0.391  Sum_probs=33.1

Q ss_pred             CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862           96 RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (276)
Q Consensus        96 ~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG  135 (276)
                      ..+|..|+|...|++...+.+.|..|.++  |-|+....|
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~--g~i~~~~~~   61 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEE--GLISRRGRG   61 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEecCCC
Confidence            57999999999999999999999999886  777766545

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=82.15  E-value=2.5  Score=28.57  Aligned_cols=38  Identities=18%  Similarity=0.359  Sum_probs=31.6

Q ss_pred             cCCce-ehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862           94 CNRRV-TIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (276)
Q Consensus        94 lg~rv-TvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe  133 (276)
                      .|.++ |..|+|...|++...++++|..|.++  |-|+...
T Consensus        16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~--g~i~~~~   54 (60)
T smart00345       16 PGDKLPSERELAAQLGVSRTTVREALSRLEAE--GLVQRRP   54 (60)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEec
Confidence            35667 89999999999999999999999986  4565443

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=82.12  E-value=4.2  Score=29.12  Aligned_cols=53  Identities=25%  Similarity=0.479  Sum_probs=39.2

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHH-HHHHHHHHhh-----cCCceEeecCcc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEA-QKALQALAAD-----TDGFLEVSDEGD  136 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~A-e~aL~aLAsD-----~~GhLeVSesGD  136 (276)
                      .++.+|-.+.. ..++...++..+.|.++.+. .+.|..+.++     .+++|.+|+.|-
T Consensus         7 ~~e~i~~~LR~-~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~   65 (66)
T PF06969_consen    7 LREYIMLGLRC-NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGGRLRLTEKGR   65 (66)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred             HHHHHHHHHHh-HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCCEEEECcccC
Confidence            45667777765 67899999999999997766 7779888886     378888888873

This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=81.51  E-value=2.8  Score=36.68  Aligned_cols=41  Identities=10%  Similarity=0.182  Sum_probs=37.8

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      .+.+|+..+.+.|. +|+.|+|...|++...+.+.|..|.++
T Consensus         2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~   42 (203)
T TIGR02702         2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETE   42 (203)
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            57899999998876 999999999999999999999999886

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.

>PHA02943 hypothetical protein; Provisional

Probab=81.44  E-value=11  Score=33.83  Aligned_cols=79  Identities=19%  Similarity=0.187  Sum_probs=55.8

Q ss_pred             hhhHHHHHHHHH-cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHhhhhhHHHhHHH
Q 023862           82 DVRNRAMDAVDA-CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEP  160 (276)
Q Consensus        82 ~~~~rim~Ave~-lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L~~Ks~r~rl~~  160 (276)
                      .+.+|+.+.+|- ..+-.|..+||-..|+|-.+||-.|..|..+  |.++--+-|-..|.+=.+      ..+... ..+
T Consensus         8 ~v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErE--G~VkrV~~G~~tyw~l~~------day~~~-v~~   78 (165)
T PHA02943          8 TVHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKE--GMVLKVEIGRAAIWCLDE------DAYTNL-VFE   78 (165)
T ss_pred             HHHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHc--CceEEEeecceEEEEECh------HHHHHH-HHH
Confidence            455666666665 5566789999999999999999999988765  556666799988888444      222222 566


Q ss_pred             HHHHHhhhh
Q 023862          161 VIDKAKAAA  169 (276)
Q Consensus       161 ~~~k~w~v~  169 (276)
                      +.+-+|+.+
T Consensus        79 ~~Relwrlv   87 (165)
T PHA02943         79 IKRELWRLV   87 (165)
T ss_pred             HHHHHHHHH
Confidence            666666643

>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=80.19  E-value=4.6  Score=27.70  Aligned_cols=41  Identities=20%  Similarity=0.323  Sum_probs=35.3

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      ..|-+|+.++.+  +..|+.|+|...|++...+.+-|..|-..
T Consensus         2 ~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L~~~   42 (47)
T PF01022_consen    2 PTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKLREA   42 (47)
T ss_dssp             HHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHHHHC
Confidence            357889999999  77999999999999999999999988654

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	276
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.0
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.83
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	95.75
3f2g_A	220	Alkylmercury lyase; MERB, organomercurial lyase, m	95.73
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	94.84
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	93.97
3r0a_A	123	Putative transcriptional regulator; structural gen	93.85
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	93.6
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.82
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	92.58
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	92.4
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	92.32
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	92.13
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	90.73
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	90.53
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	90.48
1y0u_A	96	Arsenical resistance operon repressor, putative; s	90.24
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	90.16
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	90.03
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	89.94
3jth_A	98	Transcription activator HLYU; transcription factor	89.38
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	89.0
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	88.87
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	88.7
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	88.61
2kko_A	108	Possible transcriptional regulatory protein (possi	88.36
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	88.34
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	85.65
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	85.39
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	84.5
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	84.38
1sfx_A	109	Conserved hypothetical protein AF2008; structural	84.27
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	84.15
2v9v_A	135	Selenocysteine-specific elongation factor; transcr	83.77
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	83.34
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	82.69
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	82.54
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	82.37
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	82.23
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	81.48
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	81.44
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	81.43
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	81.38
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	81.34
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	81.11
1p6r_A	82	Penicillinase repressor; transcription regulation,	80.42
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	80.16

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

Probab=96.00  E-value=0.019  Score=41.21  Aligned_cols=51  Identities=10%  Similarity=0.143  Sum_probs=44.3

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG  135 (276)
                      .+.+|++.+++.+..+|+.|+|.+.|++...+.+.|..|.++.-  ++.++.|
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~--I~~~~~G   61 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDR--VSSPSPK   61 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTS--EEEEETT
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCc--EecCCCc
Confidence            57899999999888899999999999999999999999987644  6656666

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

Probab=95.83  E-value=0.016  Score=43.66  Aligned_cols=49  Identities=24%  Similarity=0.339  Sum_probs=41.9

Q ss_pred             hhhHHHHHHHHHc-----CCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862           82 DVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS  132 (276)
Q Consensus        82 ~~~~rim~Ave~l-----g~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS  132 (276)
                      +-..+|++.+++.     ||.+|+.|+|...|+|...+++.|.+|..+  |.|+-.
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~k--G~I~R~   57 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDV--GVLEKV   57 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEE
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC--CcEEec
Confidence            3567899999888     999999999999999999999999999876  344443

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=95.75  E-value=0.015  Score=43.51  Aligned_cols=45  Identities=27%  Similarity=0.425  Sum_probs=39.3

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV  131 (276)
                      +.++.-+....+..|+|+||+.-|.++++|+.+|..|-+|  |.|+-
T Consensus         6 eaLLall~s~~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~--G~LRK   50 (68)
T 3i71_A            6 DELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA--GTLRK   50 (68)
T ss_dssp             HHHHHHHHHCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEE
T ss_pred             HHHHHHHHHHhccccHHHHHHHhCCcHHHHHHHHHHHHhc--chhhh
Confidence            5677888899999999999999999999999999999886  44443

>3f2g_A Alkylmercury lyase; MERB, organomercurial lyase, mercury resistance, mercuric resistance, plasmid; 1.78A {Escherichia coli} PDB: 3f2h_A 3fn8_A 1s6l_A 3f0o_A 3f0p_A 3f2f_A

Probab=95.73  E-value=0.011  Score=52.91  Aligned_cols=56  Identities=16%  Similarity=0.219  Sum_probs=48.7

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcC
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP  142 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP  142 (276)
                      ...+.-.+++.+. .|.-+|+.++|+.+|.+.+++++.|.+|.     .++.+++|+|+. ||
T Consensus        20 ~~~~~~~llr~la-~Grpv~~~~LA~~~g~~~~~v~~~L~~l~-----~~~~D~~G~Ivg-yp   75 (220)
T 3f2g_A           20 TADLLVPLLRELA-KGRPVSRTTLAGILDWPAERVAAVLEQAT-----STEYDKDGNIIG-YG   75 (220)
T ss_dssp             HHHHHHHHHHHHT-TTSCBCHHHHHHHHTCCHHHHHHHHHHCT-----TCEECTTSCEEE-SS
T ss_pred             chHHHHHHHHHHh-cCCCCCHHHHHHHhCcCHHHHHHHHHhCC-----cEEECCCCCEEE-ec
Confidence            3456667888888 99999999999999999999999999985     699999999977 63

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=94.84  E-value=0.046  Score=42.49  Aligned_cols=44  Identities=9%  Similarity=0.214  Sum_probs=41.2

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +..++|+++++..|.-+..||||..+|++..++.++|.+|-.+.
T Consensus        19 d~eekVLe~LkeaG~PlkageIae~~GvdKKeVdKaik~LKkEg   62 (80)
T 2lnb_A           19 HLEQRILQVLTEAGSPVKLAQLVKECQAPKRELNQVLYRMKKEL   62 (80)
T ss_dssp             HHHHHHHHHHHHHTSCEEHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            46799999999999999999999999999999999999998764

>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=93.97  E-value=0.14  Score=38.92  Aligned_cols=58  Identities=12%  Similarity=0.184  Sum_probs=48.1

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHH-HHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLN-EAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~-~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      ++.+++|++.+++.| .+|+.|+|..-|++.. .+++.|..|..+  |-++-...|-.+|.-
T Consensus        10 ~~~~~~IL~~Lk~~g-~~ta~eiA~~Lgit~~~aVr~hL~~Le~e--GlV~~~~~gRP~w~L   68 (79)
T 1xmk_A           10 AEIKEKICDYLFNVS-DSSALNLAKNIGLTKARDINAVLIDMERQ--GDVYRQGTTPPIWHL   68 (79)
T ss_dssp             HHHHHHHHHHHHHTC-CEEHHHHHHHHCGGGHHHHHHHHHHHHHT--TSEEEECSSSCEEEE
T ss_pred             hhHHHHHHHHHHHcC-CcCHHHHHHHcCCCcHHHHHHHHHHHHHC--CCEEecCCCCCCeEe
Confidence            367899999999988 5899999999999999 999999999986  445545566666654

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

Probab=93.85  E-value=0.48  Score=36.98  Aligned_cols=85  Identities=14%  Similarity=0.214  Sum_probs=60.3

Q ss_pred             hhhHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee----cCccEEEEc-CcchHHHhhhhhHH
Q 023862           82 DVRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS----DEGDVLYVF-PNNYRAKLAAKSFR  155 (276)
Q Consensus        82 ~~~~rim~Ave~lg~r-vTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS----esGDIlYvF-P~nfRs~L~~Ks~r  155 (276)
                      ..+.+|+.++.+.++. +|+.|+|.+.|++...+.+.|..|....  -++-.    +.|-..|+| +.....  -.+.++
T Consensus        26 ~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~G--lV~r~~~~~d~~~~~~~y~~~~~~~--~~~~i~  101 (123)
T 3r0a_A           26 KADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKE--ILQRSQQNLDGGGYVYIYKIYSKNQ--IRNIIQ  101 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTT--SEEEEEEECTTSCEEEEEEECCHHH--HHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEeeCCccCCCcceEEEecCCHHH--HHHHHH
Confidence            4567899999988877 9999999999999999999999998764  44332    234466666 233332  124455


Q ss_pred             HhHHHHHHHHhhhhh
Q 023862          156 LKVEPVIDKAKAAAE  170 (276)
Q Consensus       156 ~rl~~~~~k~w~v~~  170 (276)
                      ..+++|.+.+...+.
T Consensus       102 ~~~~~~~~~~~~~l~  116 (123)
T 3r0a_A          102 KIVQSWADRLGQELK  116 (123)
T ss_dssp             HHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHH
Confidence            667777777765543

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=93.60  E-value=0.22  Score=37.45  Aligned_cols=57  Identities=21%  Similarity=0.307  Sum_probs=46.9

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-----cCccEEEE
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-----DEGDVLYV  140 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS-----esGDIlYv  140 (276)
                      +.+.+|+..+-+.|..+|+.|+|...|++...+.++|..|.++.  -++..     ..|-.+|.
T Consensus        18 ~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~G--lV~~~~~~~~~~g~~v~~   79 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQG--FVSYRKTRDKDSGWFIYY   79 (110)
T ss_dssp             STTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHT--SCEEEEEC---CCCCEEE
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEEEecccCCCceEEEE
Confidence            46778999887788789999999999999999999999999875  45554     56777773

>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=92.82  E-value=0.12  Score=39.02  Aligned_cols=50  Identities=26%  Similarity=0.367  Sum_probs=42.2

Q ss_pred             CchhhHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg--~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV  131 (276)
                      ..+...+|++++++.+  .++|+.|+|.+.|++...+++.|..|..+  |.++.
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~--G~I~~   59 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK--GKLQK   59 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEE
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEe
Confidence            3456788999999887  58999999999999999999999999865  44543

>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=92.58  E-value=0.35  Score=42.55  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=54.2

Q ss_pred             cccCCCC-chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcch
Q 023862           74 VESDKLP-ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (276)
Q Consensus        74 v~~~~l~-~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nf  145 (276)
                      |++..-. .....+|++.++.. +.||+.++|.+-|.+..-|+..|..+-.  .|.|=+.++++-+|.||.-|
T Consensus       145 vqs~~~~~~~~~~~il~~~~~~-g~vt~~~la~~l~ws~~~a~e~L~~~e~--~G~l~~D~~~eg~~y~pn~f  214 (218)
T 3cuq_B          145 IELQSHKEEEMVASALETVSEK-GSLTSEEFAKLVGMSVLLAKERLLLAEK--MGHLCRDDSVEGLRFYPNLF  214 (218)
T ss_dssp             EEETTCCGGGGHHHHHHHHHHT-SCBCHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEEESSSCEEEEECGG
T ss_pred             EEcCCCchHHHHHHHHHHHHHC-CCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCEEEECCCCceEEehhhc
Confidence            5554332 35778888888865 5699999999999999999999998655  67777777777788899655

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

Probab=92.40  E-value=0.3  Score=34.97  Aligned_cols=60  Identities=10%  Similarity=0.125  Sum_probs=47.2

Q ss_pred             chhhHHHHHHHHHcC-Cceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862           81 ADVRNRAMDAVDACN-RRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (276)
Q Consensus        81 ~~~~~rim~Ave~lg-~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv  140 (276)
                      ...|..|++++.+.+ ..+|+.|++...     +++...+-+.|..|.+..--+-...++|...|.
T Consensus        16 t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y~   81 (83)
T 2fu4_A           16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE   81 (83)
T ss_dssp             CHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEee
Confidence            456788999998876 789999999999     999999999999999875433222335666665

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

Probab=92.32  E-value=0.21  Score=36.05  Aligned_cols=45  Identities=13%  Similarity=0.192  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeV  131 (276)
                      +.+|++.+.+. +.+|+.|+|...|++...+.+.|..|.++  |-++.
T Consensus         2 r~~Il~~L~~~-~~~s~~eLa~~lgvs~~tv~r~L~~L~~~--GlI~~   46 (81)
T 2htj_A            2 KNEILEFLNRH-NGGKTAEIAEALAVTDYQARYYLLLLEKA--GMVQR   46 (81)
T ss_dssp             HHHHHHHHHHS-CCCCHHHHHHHHTSCHHHHHHHHHHHHHH--TSEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEE
Confidence            57899999876 46999999999999999999999999876  55663

>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=92.13  E-value=0.18  Score=37.34  Aligned_cols=46  Identities=24%  Similarity=0.338  Sum_probs=40.4

Q ss_pred             CchhhHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg--~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      ..+...+|++++++.+  .++|+.|+|.+.|++...+++.|..|..+.
T Consensus        12 ~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G   59 (77)
T 1qgp_A           12 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKG   59 (77)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            3456688999999988  589999999999999999999999998753

>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=90.73  E-value=0.45  Score=42.81  Aligned_cols=70  Identities=19%  Similarity=0.334  Sum_probs=52.3

Q ss_pred             ccccCC--CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--CccEEEEcCcchH
Q 023862           73 IVESDK--LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLYVFPNNYR  146 (276)
Q Consensus        73 ~v~~~~--l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe--sGDIlYvFP~nfR  146 (276)
                      .|+|..  |.++. .+|++.++. .+.||+.+++...|.+..-|+.+|..|.++  |.|=|.+  +||-.|-||.-|-
T Consensus       144 ~VqSvp~el~~D~-~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~--GllwvD~q~~ge~~Yw~P~lf~  217 (234)
T 3cuq_A          144 LIQSVPAELNMDH-TVVLQLAEK-NGYVTVSEIKASLKWETERARQVLEHLLKE--GLAWLDLQAPGEAHYWLPALFT  217 (234)
T ss_dssp             EEECSCCCCCHHH-HHHHHHHTT-TSEECHHHHHHHHTCCHHHHHHHHHHHHHH--TSCEEESSSSSSCEEECTTSSC
T ss_pred             EEEeCCCccchHH-HHHHHHHHh-cCcCcHHHHHHHhCCCHHHHHHHHHHHHhC--CCEEEeCCCCCcceeecchhhc
Confidence            344443  44443 447778875 467999999999999999999999998776  4555554  5899999996553

>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=90.53  E-value=0.26  Score=44.31  Aligned_cols=60  Identities=17%  Similarity=0.276  Sum_probs=47.9

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC--ccEEEEcCcchH
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE--GDVLYVFPNNYR  146 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes--GDIlYvFP~nfR  146 (276)
                      ..+|++.++. .+.||+.+++...|.+..-|+.+|..|.++  |.|=|.++  ||..|-||.-|-
T Consensus       169 ~~~vLe~a~~-~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~--G~lwvD~q~~~e~~Yw~P~lf~  230 (233)
T 1u5t_A          169 QTKILEICSI-LGYSSISLLKANLGWEAVRSKSALDEMVAN--GLLWIDYQGGAEALYWDPSWIT  230 (233)
T ss_dssp             HHHHHHTTTT-TSCCBHHHHHHHHCCCSHHHHHHHHHHHHT--TSSEEECSSSSSCEEECGGGGG
T ss_pred             HHHHHHHHHh-cCcCcHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEeCCCCCccceechhhhh
Confidence            4566777775 457999999999999999999999997665  66666653  588999996653

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

Probab=90.48  E-value=0.62  Score=33.44  Aligned_cols=59  Identities=14%  Similarity=0.330  Sum_probs=46.2

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc-EEEEc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD-IlYvF  141 (276)
                      ....+.+|+.++.+ ++..|+.|+|...|++...+.+.|..|..  .|-++...+|. ..|..
T Consensus        22 ~~~~~~~il~~l~~-~~~~s~~ela~~l~is~~tvs~~l~~L~~--~glv~~~~~~r~~~y~l   81 (99)
T 3cuo_A           22 SHPKRLLILCMLSG-SPGTSAGELTRITGLSASATSQHLARMRD--EGLIDSQRDAQRILYSI   81 (99)
T ss_dssp             CSHHHHHHHHHHTT-CCSEEHHHHHHHHCCCHHHHHHHHHHHHH--TTSEEEEECSSCEEEEE
T ss_pred             CChHHHHHHHHHHh-CCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEEE
Confidence            34677889998855 66899999999999999999999999963  56776666665 44444

>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=90.24  E-value=0.57  Score=34.46  Aligned_cols=54  Identities=15%  Similarity=0.198  Sum_probs=43.3

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      ....+.+|++.+   .+..|++|+|.+.|++...+.+.|..|...  |-++... |  .|..
T Consensus        29 ~~~~r~~Il~~L---~~~~~~~eLa~~l~is~~tv~~~L~~L~~~--Glv~~~~-g--~y~l   82 (96)
T 1y0u_A           29 TNPVRRKILRML---DKGRSEEEIMQTLSLSKKQLDYHLKVLEAG--FCIERVG-E--RWVV   82 (96)
T ss_dssp             SCHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEET-T--EEEE
T ss_pred             CCHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEC-C--EEEE
Confidence            345677899998   355999999999999999999999999765  6676666 6  5554

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

Probab=90.16  E-value=0.36  Score=37.14  Aligned_cols=42  Identities=19%  Similarity=0.270  Sum_probs=37.9

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD  124 (276)
                      .++..+|++.+++.|  +|+.|+|.+-|++...+++-|..|..+
T Consensus        16 ~~~~~~IL~lL~~~g--~sa~eLAk~LgiSk~aVr~~L~~Le~e   57 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEG--ATAAQLTRQLNMEKREVNKALYDLQRS   57 (82)
T ss_dssp             HHHHHHHHHHHSSST--EEHHHHHHHSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC--CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            357789999999766  999999999999999999999999876

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

Probab=90.03  E-value=3.3  Score=30.51  Aligned_cols=57  Identities=19%  Similarity=0.239  Sum_probs=44.6

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY  139 (276)
                      |....+.+|+..+ .. +..|+.|+|...|++...+.+.|..|..  .|-++...+|.-.|
T Consensus        18 l~~~~r~~IL~~L-~~-~~~~~~ela~~l~is~~tv~~~l~~L~~--~gli~~~~~gr~~~   74 (114)
T 2oqg_A           18 LSDETRWEILTEL-GR-ADQSASSLATRLPVSRQAIAKHLNALQA--CGLVESVKVGREIR   74 (114)
T ss_dssp             TTCHHHHHHHHHH-HH-SCBCHHHHHHHSSSCHHHHHHHHHHHHH--TTSEEEEEETTEEE
T ss_pred             hCChHHHHHHHHH-Hc-CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeeEEecCCEEE
Confidence            3446678899999 43 4599999999999999999999999965  46676666666443

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

Probab=89.94  E-value=0.57  Score=34.55  Aligned_cols=46  Identities=17%  Similarity=0.138  Sum_probs=42.6

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      .|-....+++.++..|+-+-+.++|++-|++.+++-..|..|+++.
T Consensus         8 ~~~~e~~lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~KG   53 (59)
T 2xvc_A            8 HMITERELLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNKG   53 (59)
T ss_dssp             CCCCHHHHHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTT
T ss_pred             hhccHHHHHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            4666789999999999999999999999999999999999999874

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

Probab=89.38  E-value=0.59  Score=34.21  Aligned_cols=57  Identities=18%  Similarity=0.353  Sum_probs=46.6

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv  140 (276)
                      ....|.+|+..+.+  +..|++|+|...|++...+.+.|..|..  .|-++...+|.-+|.
T Consensus        21 ~~~~r~~Il~~L~~--~~~~~~ela~~l~is~~tvs~~L~~L~~--~Glv~~~~~g~~~~y   77 (98)
T 3jth_A           21 ANERRLQILCMLHN--QELSVGELCAKLQLSQSALSQHLAWLRR--DGLVTTRKEAQTVYY   77 (98)
T ss_dssp             CSHHHHHHHHHTTT--SCEEHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEECCTTCCEE
T ss_pred             CCHHHHHHHHHHhc--CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEEEeCCEEEE
Confidence            34567789998876  6899999999999999999999999965  577887787764443

>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=89.00  E-value=1  Score=33.70  Aligned_cols=59  Identities=15%  Similarity=0.259  Sum_probs=48.0

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      |....+.+|+..+.  .+..|++|+|...|++...+.+.|..|.  ..|-++...+|.-+|..
T Consensus        23 l~~~~r~~IL~~L~--~~~~~~~ela~~l~is~stvs~~L~~L~--~~Glv~~~~~gr~~~y~   81 (106)
T 1r1u_A           23 LGDYNRIRIMELLS--VSEASVGHISHQLNLSQSNVSHQLKLLK--SVHLVKAKRQGQSMIYS   81 (106)
T ss_dssp             TCSHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHH--HTTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEEEeCCEEEEE
Confidence            44567889999997  3558999999999999999999999997  46778777778765554

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

Probab=88.87  E-value=2.7  Score=32.09  Aligned_cols=59  Identities=17%  Similarity=0.280  Sum_probs=47.5

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      |....|-+|+..+.  .+..|++|+|...|++...+-+-|..|..  .|-++...+|.-+|..
T Consensus        15 l~~~~R~~Il~~L~--~~~~~~~eLa~~l~is~~tvs~hL~~L~~--~GlV~~~~~gr~~~y~   73 (118)
T 3f6o_A           15 LADPTRRAVLGRLS--RGPATVSELAKPFDMALPSFMKHIHFLED--SGWIRTHKQGRVRTCA   73 (118)
T ss_dssp             HTSHHHHHHHHHHH--TCCEEHHHHHTTCCSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCeEEEecCCEEEEE
Confidence            34567889999997  46789999999999999999999999964  5777777777644443

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

Probab=88.70  E-value=0.65  Score=35.80  Aligned_cols=42  Identities=10%  Similarity=0.014  Sum_probs=36.8

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      .-.+|++.+++. +++|+.|+|..-|+|...+++.|..|....
T Consensus         3 ~L~~Il~~L~~~-g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G   44 (87)
T 2k02_A            3 SLMEVRDMLALQ-GRMEAKQLSARLQTPQPLIDAMLERMEAMG   44 (87)
T ss_dssp             CTHHHHHHHHHS-CSEEHHHHHHHTTCCHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHc-CCCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            346789999775 689999999999999999999999998764

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

Probab=88.61  E-value=0.7  Score=34.62  Aligned_cols=42  Identities=12%  Similarity=0.032  Sum_probs=36.9

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      .-.+|++.+++. +++|+.|+|..-++|...+++.|..|.+..
T Consensus         3 ~L~~Il~~L~~~-g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G   44 (78)
T 1xn7_A            3 SLIQVRDLLALR-GRMEAAQISQTLNTPQPMINAMLQQLESMG   44 (78)
T ss_dssp             CHHHHHHHHHHS-CSBCHHHHHHHTTCCHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHc-CCCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            346789999775 589999999999999999999999999874

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

Probab=88.36  E-value=0.88  Score=34.51  Aligned_cols=57  Identities=26%  Similarity=0.390  Sum_probs=46.7

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      ...|.+|+..+.+  +..|++|+|...|++...+.+.|..|..  .|-++...+|.-+|..
T Consensus        24 ~~~r~~IL~~L~~--~~~s~~eLa~~lgis~stvs~~L~~L~~--~GlV~~~~~gr~~~y~   80 (108)
T 2kko_A           24 NGRRLQILDLLAQ--GERAVEAIATATGMNLTTASANLQALKS--GGLVEARREGTRQYYR   80 (108)
T ss_dssp             TSTTHHHHHHHTT--CCEEHHHHHHHHTCCHHHHHHHHHHHHH--HTSEEEEEETTEEEEE
T ss_pred             CHHHHHHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEEEeCCEEEEE
Confidence            4567889998864  6789999999999999999999999976  4677777788765544

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

Probab=88.34  E-value=1.3  Score=36.15  Aligned_cols=59  Identities=15%  Similarity=0.257  Sum_probs=48.7

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      |....|-+|+..+.  .+..|++|+|...|++...+-+-|..|..  .|-++...+|.-+|..
T Consensus        55 L~~p~R~~IL~~L~--~~~~t~~eLa~~lgls~stvs~hL~~L~~--aGlV~~~~~Gr~~~y~  113 (151)
T 3f6v_A           55 AAEPTRRRLVQLLT--SGEQTVNNLAAHFPASRSAISQHLRVLTE--AGLVTPRKDGRFRYYR  113 (151)
T ss_dssp             HTSHHHHHHHHHGG--GCCEEHHHHHTTSSSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEE
Confidence            34577899999997  45699999999999999999999999965  4678877888766554

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=85.65  E-value=0.73  Score=35.70  Aligned_cols=38  Identities=13%  Similarity=0.095  Sum_probs=33.0

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ  119 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~  119 (276)
                      +.+-+.+|++.+.+.+  +|+.|||..+|+|...+.+.|.
T Consensus         5 ~~~R~~~I~~~l~~~~--~ti~dlA~~~gVS~~TVsR~L~   42 (93)
T 2l0k_A            5 IKERTIKIGKYIVETK--KTVRVIAKEFGVSKSTVHKDLT   42 (93)
T ss_dssp             HHHHHHHHHHHHHHHC--CCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcC--CCHHHHHHHHCCCHHHHHHHHc
Confidence            4456678999999887  9999999999999999998874

>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=84.50  E-value=3.5  Score=32.13  Aligned_cols=57  Identities=18%  Similarity=0.294  Sum_probs=46.4

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      ...+.+|+..+.+  +..|++|+|...|++...+-+.|..|-.  .|-++...+|.-+|..
T Consensus        45 ~~~rl~IL~~L~~--~~~s~~ela~~lgis~stvs~~L~~Le~--~Glv~~~~~gr~~~y~  101 (122)
T 1r1t_A           45 DPNRLRLLSLLAR--SELCVGDLAQAIGVSESAVSHQLRSLRN--LRLVSYRKQGRHVYYQ  101 (122)
T ss_dssp             CHHHHHHHHHHTT--CCBCHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEEEETTEEEEE
T ss_pred             CHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEEEeCCEEEEE
Confidence            3456788888863  5689999999999999999999999988  6777777778766655

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=84.38  E-value=2  Score=37.43  Aligned_cols=75  Identities=15%  Similarity=0.109  Sum_probs=47.6

Q ss_pred             HHcCCceehhhhhhhcCCCHHHHHHHHH--------------HHHhhcCC--------ceEeecCccEEEEcCcchHHHh
Q 023862           92 DACNRRVTIGDVAGKAGLKLNEAQKALQ--------------ALAADTDG--------FLEVSDEGDVLYVFPNNYRAKL  149 (276)
Q Consensus        92 e~lg~rvTvgDVAa~aGL~l~~Ae~aL~--------------aLAsD~~G--------hLeVSesGDIlYvFP~nfRs~L  149 (276)
                      .....++|+.|||.++|+|...+-++|+              +.|.+.|=        .|.-..++.|..++|.....-+
T Consensus         4 ~~~~~~~Ti~diA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~~lgY~~pn~~a~~l~~~~s~~Igvi~~~~~~~~~   83 (366)
T 3h5t_A            4 GRKQQYGTLASIAAKLGISRTTVSNAYNRPEQLSAELRQRILDTAEDMGYLGPDPVARSLRTRRAGAIGVLLTEDLTYAF   83 (366)
T ss_dssp             ---CCTTHHHHHHHHHTSCHHHHHHHHHCGGGSCHHHHHHHHHHHHHTTC--------------CCEEEEEESSCTTHHH
T ss_pred             CccCCCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHhhcCCCCEEEEEecCCccccc
Confidence            3456789999999999999999877774              34444432        2666678889999987655445


Q ss_pred             hhhhHHHhHHHHHHHHh
Q 023862          150 AAKSFRLKVEPVIDKAK  166 (276)
Q Consensus       150 ~~Ks~r~rl~~~~~k~w  166 (276)
                      .+.++..-++.+-+.+.
T Consensus        84 ~~~~~~~~~~gi~~~a~  100 (366)
T 3h5t_A           84 EDMASVDFLAGVAQAAG  100 (366)
T ss_dssp             HSHHHHHHHHHHHHHSS
T ss_pred             cCHHHHHHHHHHHHHHh
Confidence            66666665555555544

>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=84.27  E-value=9  Score=27.12  Aligned_cols=58  Identities=17%  Similarity=0.235  Sum_probs=44.4

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--CccEEEEc
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLYVF  141 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe--sGDIlYvF  141 (276)
                      ...+.+|+..+.+. +.+|+.|+|...|++...+.+.|..|.++  |-++...  ++...|.+
T Consensus        19 ~~~~~~il~~l~~~-~~~s~~ela~~l~is~~tv~~~l~~L~~~--glv~~~~~~~~r~~~~~   78 (109)
T 1sfx_A           19 KPSDVRIYSLLLER-GGMRVSEIARELDLSARFVRDRLKVLLKR--GFVRREIVEKGWVGYIY   78 (109)
T ss_dssp             CHHHHHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEEEEESSSEEEEE
T ss_pred             CHHHHHHHHHHHHc-CCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEeecCCceEEEE
Confidence            34567889999765 45999999999999999999999999776  4454433  45555554

>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=84.15  E-value=7.3  Score=27.64  Aligned_cols=59  Identities=12%  Similarity=0.102  Sum_probs=45.1

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec---CccEEEEc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD---EGDVLYVF  141 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe---sGDIlYvF  141 (276)
                      ....+-+|+..+.+.+ ..|+.|+|...|++...+-+.|..|..+  |-++...   +|.-.|+.
T Consensus        14 ~~~~~~~iL~~L~~~~-~~~~~ela~~l~is~~tvs~~l~~L~~~--gli~~~~~~~~~r~~~~~   75 (100)
T 1ub9_A           14 GNPVRLGIMIFLLPRR-KAPFSQIQKVLDLTPGNLDSHIRVLERN--GLVKTYKVIADRPRTVVE   75 (100)
T ss_dssp             HSHHHHHHHHHHHHHS-EEEHHHHHHHTTCCHHHHHHHHHHHHHT--TSEEEEEECSSSCEEEEE
T ss_pred             CChHHHHHHHHHHhcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEecCCCcceEEEE
Confidence            3456788899887654 6999999999999999999999999887  5565433   55544443

>2v9v_A Selenocysteine-specific elongation factor; transcription, protein conformational change, transcription elongation factor SELB; 1.10A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35

Probab=83.77  E-value=7.9  Score=29.69  Aligned_cols=62  Identities=19%  Similarity=0.225  Sum_probs=44.8

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHH
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRA  147 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs  147 (276)
                      ...+...++..+..++..|++..+|++.+++++.|.+|.+... -+.+..+++..| +..++-.
T Consensus         4 ~~~l~~~L~~~~~~~~~~~l~~~~~l~~~~l~~~l~~l~~~~~-~~~~~~~~~~~~-~~~~~~~   65 (135)
T 2v9v_A            4 EKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQ-VTLLRVENDLYA-ISTERYQ   65 (135)
T ss_dssp             HHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTC-EEEEEETTEEEE-EEHHHHH
T ss_pred             HHHHHHHHHHcCcCCCHHHHHHHhCCCHHHHHHHHHHHHhCCc-EEEEecCCCeEE-ecHHHHH
Confidence            4567788888888887799999999999999999999986544 555544344334 4344333

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

Probab=83.34  E-value=2.7  Score=33.32  Aligned_cols=63  Identities=16%  Similarity=0.263  Sum_probs=47.7

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhc--CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcchHHHh
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKL  149 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~a--GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nfRs~L  149 (276)
                      ..+.+|++.+.+.| +.|++++|...  |++...+.+-|..|..+  |-++....|  +|.-...=+..|
T Consensus        13 ~~d~~IL~~L~~~g-~~s~~eLA~~l~~giS~~aVs~rL~~Le~~--GLV~~~~rg--~Y~LT~~G~~~l   77 (111)
T 3b73_A           13 IWDDRILEIIHEEG-NGSPKELEDRDEIRISKSSVSRRLKKLADH--DLLQPLANG--VYVITEEGEAYL   77 (111)
T ss_dssp             HHHHHHHHHHHHHS-CBCHHHHHTSTTCCSCHHHHHHHHHHHHHT--TSEEECSTT--CEEECHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHhcCCCHHHHHHHHHHHHHC--CCEEecCCc--eEEECchHHHHH
Confidence            34688999998765 89999999999  99999999999999875  455554455  666543333333

>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=82.69  E-value=1.7  Score=32.08  Aligned_cols=59  Identities=17%  Similarity=0.302  Sum_probs=46.5

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc-EEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD-IlYvF  141 (276)
                      |....|-+|+..+.+  +..|++|+|...|++...+.+.|..|..  .|-++...+|. +.|.-
T Consensus        20 l~~~~r~~Il~~L~~--~~~~~~ela~~l~is~~tvs~~L~~L~~--~Glv~~~~~g~~~~y~l   79 (102)
T 3pqk_A           20 LSHPVRLMLVCTLVE--GEFSVGELEQQIGIGQPTLSQQLGVLRE--SGIVETRRNIKQIFYRL   79 (102)
T ss_dssp             HCSHHHHHHHHHHHT--CCBCHHHHHHHHTCCTTHHHHHHHHHHH--TTSEEEECSSSCCEEEE
T ss_pred             cCCHHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEEEeCCEEEEEE
Confidence            345678889999964  4599999999999999999999999964  46777777775 44544

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=82.54  E-value=3  Score=31.05  Aligned_cols=59  Identities=10%  Similarity=0.178  Sum_probs=46.7

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      |....|-+|+..+...| ..|++|+|...|++...+-+-|..|...   -++...+|.-+|..
T Consensus        24 L~~~~Rl~IL~~l~~~~-~~~~~ela~~l~is~stvs~hL~~L~~~---lv~~~~~gr~~~y~   82 (99)
T 2zkz_A           24 MAHPMRLKIVNELYKHK-ALNVTQIIQILKLPQSTVSQHLCKMRGK---VLKRNRQGLEIYYS   82 (99)
T ss_dssp             HCSHHHHHHHHHHHHHS-CEEHHHHHHHHTCCHHHHHHHHHHHBTT---TBEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHHHCC-CcCHHHHHHHHCcCHHHHHHHHHHHHHH---hhhheEeCcEEEEE
Confidence            34567788997766554 5999999999999999999999999765   66767777766554

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

Probab=82.37  E-value=12  Score=28.45  Aligned_cols=47  Identities=9%  Similarity=0.158  Sum_probs=38.1

Q ss_pred             HHHHHHHHH---cCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862           85 NRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (276)
Q Consensus        85 ~rim~Ave~---lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe  133 (276)
                      .++++++..   .++.+|+.|+|.+.|++...+.+.|..|..+  |-++...
T Consensus        16 ~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~--Gli~r~~   65 (139)
T 2x4h_A           16 FSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEK--GLVKKKE   65 (139)
T ss_dssp             HHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEET
T ss_pred             HHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHC--CCEEecC
Confidence            445555544   4788999999999999999999999999887  6776655

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

Probab=82.23  E-value=6.3  Score=29.52  Aligned_cols=58  Identities=14%  Similarity=0.176  Sum_probs=46.6

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN  143 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~  143 (276)
                      ..+.+|+.++.+  +..|+.|+|...|++...+-+.|..|-.  -|.++...+|.-+|..+.
T Consensus        32 ~~~~~il~~L~~--~~~s~~ela~~l~is~stvsr~l~~Le~--~Glv~~~~~~r~~~~~~~   89 (119)
T 2lkp_A           32 PSRLMILTQLRN--GPLPVTDLAEAIGMEQSAVSHQLRVLRN--LGLVVGDRAGRSIVYSLY   89 (119)
T ss_dssp             HHHHHHHHHHHH--CCCCHHHHHHHHSSCHHHHHHHHHHHHH--HCSEEEEEETTEEEEEES
T ss_pred             HHHHHHHHHHHH--CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEEEc
Confidence            467788999887  4689999999999999999999999988  566666666665555533

>2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, RNA_POL_RPC34 domain, RNA polymerase III C39 subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85

Probab=81.48  E-value=5.7  Score=30.46  Aligned_cols=60  Identities=17%  Similarity=0.305  Sum_probs=52.4

Q ss_pred             CchhhHHHHHHHHHcCCceehhhhhhhcC-CCHHHHHHHHHHHHhhcCCceEeecC-ccEEEEc
Q 023862           80 PADVRNRAMDAVDACNRRVTIGDVAGKAG-LKLNEAQKALQALAADTDGFLEVSDE-GDVLYVF  141 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg~rvTvgDVAa~aG-L~l~~Ae~aL~aLAsD~~GhLeVSes-GDIlYvF  141 (276)
                      +.++..+|++.+++....+|-.|++...+ ++.++--++++.|.+  .|.|++-.+ |.++|..
T Consensus        12 ~~~ie~~IL~l~~~~P~GItd~~L~~~~p~~~~~~r~~aIN~LL~--~gkiel~K~~~~liYr~   73 (81)
T 2dk8_A           12 PVEIENRIIELCHQFPHGITDQVIQNEMPHIEAQQRAVAINRLLS--MGQLDLLRSNTGLLYRI   73 (81)
T ss_dssp             HHHHHHHHHHHHHHCSSCEEHHHHHHHCTTSCHHHHHHHHHHHHH--HTSEEEEECSSSEEEEE
T ss_pred             HHHHHHHHHHHHHhCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHH--cCCeEEEecCCeEEEEe
Confidence            67888999999999999999999999877 699999999999998  467777775 5688865

>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=81.44  E-value=3.2  Score=29.66  Aligned_cols=47  Identities=13%  Similarity=0.134  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS  132 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVS  132 (276)
                      +-.++..+-+.++.+|+.|+|...|++...+.+.|..|.+.  |-++..
T Consensus        23 ~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~--g~v~~~   69 (109)
T 2d1h_A           23 DVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL--GLVVRT   69 (109)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCeEee
Confidence            44555555555678999999999999999999999999664  455544

>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=81.43  E-value=6.3  Score=26.33  Aligned_cols=53  Identities=13%  Similarity=0.224  Sum_probs=38.4

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeec-CccEEEE
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSD-EGDVLYV  140 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSe-sGDIlYv  140 (276)
                      .|..++..+-+.+..+|+.|++...     +++...+.+.|..+     |.+++.. +|...|.
T Consensus         5 ~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~l-----g~v~~~~~~~~~~Y~   63 (64)
T 2p5k_A            5 QRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKEL-----HLVKVPTNNGSYKYS   63 (64)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHHHH-----TCEEEEETTTEEEEE
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHHHc-----CCEEEecCCCceeee
Confidence            4555555554557789999999999     99999999999944     3456654 4555554

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

Probab=81.38  E-value=5.7  Score=31.08  Aligned_cols=61  Identities=13%  Similarity=0.142  Sum_probs=50.0

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~a-----GL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      ...|..|++++.+.+.-+|+.||..+.     ++++..+=+.|..|++..=-+=-...+|...|..
T Consensus        10 T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~~   75 (131)
T 2o03_A           10 TRQRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDTGESVYRR   75 (131)
T ss_dssp             HHHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTTSCEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCCCceEEEe
Confidence            356788999999988899999999988     8999999999999988765443334467788875

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=81.34  E-value=1.1  Score=35.25  Aligned_cols=36  Identities=19%  Similarity=0.199  Sum_probs=28.9

Q ss_pred             CCCCchhhHHHHHHH----HHcCC-ceehhhhhhhcCCCHH
Q 023862           77 DKLPADVRNRAMDAV----DACNR-RVTIGDVAGKAGLKLN  112 (276)
Q Consensus        77 ~~l~~~~~~rim~Av----e~lg~-rvTvgDVAa~aGL~l~  112 (276)
                      .+++.+.+.+|++|+    .+.|+ .+|+.|||.++|++..
T Consensus         7 ~~~~~~tr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~   47 (189)
T 3vp5_A            7 FSLSDEKRNRVYDACLNEFQTHSFHEAKIMHIVKALDIPRG   47 (189)
T ss_dssp             HTSCHHHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHH
T ss_pred             hhCCHHHHHHHHHHHHHHHHHCCcccccHHHHHHHhCCChH
Confidence            356778888887775    45687 8999999999999854

>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=81.11  E-value=2.5  Score=33.42  Aligned_cols=43  Identities=7%  Similarity=0.261  Sum_probs=37.3

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +.+.+|++++.+. ++.|..|+|.+.|++...+.+.|..|.+..
T Consensus         7 ~~~~~il~~L~~~-~~~s~~ela~~lg~s~~tv~~~l~~L~~~G   49 (151)
T 2cyy_A            7 EIDKKIIKILQND-GKAPLREISKITGLAESTIHERIRKLRESG   49 (151)
T ss_dssp             HHHHHHHHHHHHC-TTCCHHHHHHHHCSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            3466899988775 589999999999999999999999998764

>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=80.42  E-value=4.6  Score=28.66  Aligned_cols=56  Identities=20%  Similarity=0.232  Sum_probs=44.9

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcC----CCHHHHHHHHHHHHhhcCCceEeecCccEEEE
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAG----LKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aG----L~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYv  140 (276)
                      ..+..||+++.+ ++.+|+.|+|...+    ++...+-.-|..|..+  |.++...+|.-.+.
T Consensus         9 ~~e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~k--Glv~r~~~gr~~~y   68 (82)
T 1p6r_A            9 DAELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKK--GALNHHKEGRVFVY   68 (82)
T ss_dssp             HHHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHT--TSEEEEEETTEEEE
T ss_pred             HHHHHHHHHHHc-CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHC--CCeEEEecCCEEEE
Confidence            467889999988 56899999999986    7899999999999876  56776666764333

>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=80.16  E-value=3.5  Score=31.40  Aligned_cols=52  Identities=12%  Similarity=0.116  Sum_probs=43.0

Q ss_pred             CchhhHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 023862           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (276)
Q Consensus        80 ~~~~~~rim~Ave~lg--~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSe  133 (276)
                      .++.-+.+.+++..++  ...|.-++|.+-|++..++.+.|-.|..+  |-|.+..
T Consensus        10 ~~~~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kk--G~V~~~~   63 (75)
T 1sfu_A           10 DAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKE--DTVKMVP   63 (75)
T ss_dssp             SHHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHT--TSEEEEC
T ss_pred             hHHHHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHC--CCEecCC
Confidence            3588899999999985  44899999999999999999999999876  3444443

---

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	276
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	94.87
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	92.13
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	89.53
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	89.46
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	88.71
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	88.62
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	88.62
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	88.23
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	88.18
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	87.72
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	85.59
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	84.95
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	84.9
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	84.5
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	83.89
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	82.6
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.03
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	80.97
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	80.14

>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=94.87  E-value=0.015  Score=41.90  Aligned_cols=61  Identities=13%  Similarity=0.211  Sum_probs=50.4

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEcCcch
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvFP~nf  145 (276)
                      +..|+++++.. +.||+..+-.+.|-+.+-|+++|..|..+.=+=+---..||..|=||.-|
T Consensus         5 qt~vLe~a~~~-G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD~Q~~~e~~YWfPsl~   65 (68)
T d1u5ta2           5 QTKILEICSIL-GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWI   65 (68)
T ss_dssp             HHHHHHTTTTT-SCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEECGGGG
T ss_pred             HHHHHHHHHHc-CceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEecCCCCCceeeChHhh
Confidence            46788899888 58999999999999999999999999986544444333589999999765

>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=92.13  E-value=0.16  Score=34.63  Aligned_cols=52  Identities=8%  Similarity=0.059  Sum_probs=42.7

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCc
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesG  135 (276)
                      -..+|++.+.+..+.+|+.|+|..-|+|...+++.|.+|.+ .|..++.+..|
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~-~G~~I~~~~gG   59 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRS-LGYNIVATPRG   59 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHH-HTCCCEEETTE
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH-CCCeEEEeCCC
Confidence            34678889988888899999999999999999999999964 45556655444

>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=89.53  E-value=0.27  Score=34.18  Aligned_cols=49  Identities=18%  Similarity=0.303  Sum_probs=42.9

Q ss_pred             HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCcc
Q 023862           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (276)
Q Consensus        86 rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGD  136 (276)
                      +|++.+...+..+|+.|+|.++|++...+-+-|..|...  |.|+=+++|.
T Consensus         9 ~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~--g~l~~~~~g~   57 (75)
T d1mkma1           9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK--GFVLRKKDKR   57 (75)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT--TSEEECTTSC
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEECCCCC
Confidence            678899999999999999999999999999999888764  6777667775

>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=89.46  E-value=0.42  Score=32.76  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=41.5

Q ss_pred             hhhHHHHHHHHHcC-CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecC
Q 023862           82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (276)
Q Consensus        82 ~~~~rim~Ave~lg-~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSes  134 (276)
                      .+..+|.++.++.| .-.|+.|||...|++..++ +.+..++.+.|--.+|+++
T Consensus         7 ~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~-~~lL~~l~~~G~lvkI~~d   59 (64)
T d1lvaa3           7 KLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSEL-EELLHYLVREGVLVKINDE   59 (64)
T ss_dssp             HHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHH-HHHHHHHHHTTSEEESSSS
T ss_pred             HHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHH-HHHHHHHHHCCCEEEeccc
Confidence            56789999999988 5679999999999999999 5555566666666677553

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=88.71  E-value=0.29  Score=32.93  Aligned_cols=34  Identities=18%  Similarity=0.250  Sum_probs=29.2

Q ss_pred             HHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHH
Q 023862           88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQAL  121 (276)
Q Consensus        88 m~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aL  121 (276)
                      -+...++|...|..+||...|++.+++..+|.+.
T Consensus        22 ~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          22 DELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            3445678999999999999999999999988763

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MerB N-terminal domain-like
domain: Alkylmercury lyase MerB
species: Escherichia coli [TaxId: 562]

Probab=88.62  E-value=0.068  Score=37.85  Aligned_cols=41  Identities=20%  Similarity=0.269  Sum_probs=34.7

Q ss_pred             HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEE
Q 023862           93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (276)
Q Consensus        93 ~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIl  138 (276)
                      ..|.-||+.++|..+|-+.+|++++|.++.     .-|-.++|.||
T Consensus        12 A~G~PVs~~~LA~alg~~~~eV~~aL~~~p-----~tEyD~~G~iv   52 (60)
T d1s6la1          12 AKGRPVSRTTLAGILDWPAERVAAVLEQAT-----STEYDKDGNII   52 (60)
T ss_dssp             HTTCCBCHHHHHHHHTCCHHHHHHHHTTCC-----SSCEETTTEEC
T ss_pred             hCCCCcCHHHHHHHhCCCHHHHHHHHHhCC-----CceecCCCCEE
Confidence            468899999999999999999999988776     45667777765

>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=88.62  E-value=1.6  Score=31.53  Aligned_cols=66  Identities=15%  Similarity=0.076  Sum_probs=47.7

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEE-EcCcchHHHh
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY-VFPNNYRAKL  149 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlY-vFP~nfRs~L  149 (276)
                      .+-+|+.++-++ +..|+.|||..+|++...+-..|..|.++.=-.=+..++|.--| ..|..-...+
T Consensus        21 ~e~~v~~~L~~~-g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l   87 (109)
T d1sfxa_          21 SDVRIYSLLLER-GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVL   87 (109)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHH
T ss_pred             HHHHHHHHHHhc-CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHH
Confidence            456677777655 57899999999999999999999999987654434455444444 4466555444

>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=88.23  E-value=0.37  Score=32.80  Aligned_cols=41  Identities=15%  Similarity=0.157  Sum_probs=36.4

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +.+|++.+.+.| .+|..|+|..+||+...+.+-|..|.++.
T Consensus         8 ~~~Il~~l~~~g-~~sr~eLa~~~glS~~Tv~~~l~~L~~~G   48 (71)
T d1z05a1           8 AGRVYKLIDQKG-PISRIDLSKESELAPASITKITRELIDAH   48 (71)
T ss_dssp             HHHHHHHHHHHC-SBCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            457899998865 69999999999999999999999998764

>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=88.18  E-value=0.3  Score=36.51  Aligned_cols=57  Identities=18%  Similarity=0.198  Sum_probs=44.3

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeecCccEEEEc
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVF  141 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~G---hLeVSesGDIlYvF  141 (276)
                      -+|++++-+.+..+|=.++|.++|++++++++.|..|....=+   .-+=.++|=.+|..
T Consensus        21 ~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd~~~gw~~Y~W   80 (88)
T d1q1ha_          21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYW   80 (88)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEE
T ss_pred             HHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeecCCCCcEEEEE
Confidence            3578888778899999999999999999999999999877633   22234577777765

>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=87.72  E-value=0.51  Score=31.97  Aligned_cols=43  Identities=9%  Similarity=0.223  Sum_probs=37.5

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +...+|++++++ +.|.|..|+|.+.|++..++.+-++.|-.+.
T Consensus         5 ~~D~~IL~~L~~-n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~g   47 (63)
T d2cfxa1           5 QIDLNIIEELKK-DSRLSMRELGRKIKLSPPSVTERVRQLESFG   47 (63)
T ss_dssp             HHHHHHHHHHHH-CSCCCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            356788999987 5789999999999999999999999997653

>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=85.59  E-value=0.71  Score=31.07  Aligned_cols=43  Identities=9%  Similarity=0.204  Sum_probs=37.5

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +...+|++.+++. .|.|..|+|.+.|+|..++..-+..|-++.
T Consensus         5 ~~D~~IL~~L~~~-~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~G   47 (63)
T d2cg4a1           5 NLDRGILEALMGN-ARTAYAELAKQFGVSPETIHVRVEKMKQAG   47 (63)
T ss_dssp             HHHHHHHHHHHHC-TTSCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            3567889988865 889999999999999999999999998764

>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=84.95  E-value=3.6  Score=29.27  Aligned_cols=46  Identities=13%  Similarity=0.140  Sum_probs=39.2

Q ss_pred             hhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 023862           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE  130 (276)
Q Consensus        83 ~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLe  130 (276)
                      .+-.|+.++-+.++.+|+.|+|...|++...+.+.|..|..+  |-++
T Consensus        22 ~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~--GlV~   67 (109)
T d2d1ha1          22 TDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL--GLVV   67 (109)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT--TSEE
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHC--CCEE
Confidence            456788888777788999999999999999999999999974  5554

>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=84.90  E-value=0.59  Score=32.48  Aligned_cols=40  Identities=25%  Similarity=0.322  Sum_probs=35.5

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCC-CHHHHHHHHHHHHhh
Q 023862           85 NRAMDAVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAAD  124 (276)
Q Consensus        85 ~rim~Ave~lg~rvTvgDVAa~aGL-~l~~Ae~aL~aLAsD  124 (276)
                      .-|.+..++.|+-.|+.|+|...|+ |.+.++.-|.+|...
T Consensus        12 ~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1          12 DLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            3456777889999999999999999 799999999999875

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.50  E-value=0.74  Score=31.75  Aligned_cols=39  Identities=21%  Similarity=0.231  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHH
Q 023862           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALA  122 (276)
Q Consensus        84 ~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLA  122 (276)
                      +..+-+.-.++|...|..+||...|+++++.++.|.+..
T Consensus        13 ~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~   51 (77)
T d1rp3a1          13 KEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKIN   51 (77)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence            334444455669999999999999999999998876544

>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=83.89  E-value=1  Score=29.82  Aligned_cols=43  Identities=7%  Similarity=0.303  Sum_probs=37.2

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +...+|++.+++ +.|.|+.|+|.+.|++...+..-+..|-.+.
T Consensus         3 ~~D~~Il~~L~~-n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~g   45 (60)
T d2cyya1           3 EIDKKIIKILQN-DGKAPLREISKITGLAESTIHERIRKLRESG   45 (60)
T ss_dssp             HHHHHHHHHHHH-CTTCCHHHHHHHHCSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            345788999888 4888999999999999999999999997653

>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=82.60  E-value=2.9  Score=30.20  Aligned_cols=59  Identities=19%  Similarity=0.313  Sum_probs=49.8

Q ss_pred             CCchhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecCccEEEEc
Q 023862           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (276)
Q Consensus        79 l~~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~~GhLeVSesGDIlYvF  141 (276)
                      |....|-+|+..+.  .+..|++|+|...|++...+-+-|..|-..  |-+....+|.-+|..
T Consensus        20 L~~p~Rl~Il~~L~--~~~~~v~ela~~l~is~stvS~HL~~L~~a--glV~~~r~G~~~~Y~   78 (98)
T d1r1ta_          20 LADPNRLRLLSLLA--RSELCVGDLAQAIGVSESAVSHQLRSLRNL--RLVSYRKQGRHVYYQ   78 (98)
T ss_dssp             HCCHHHHHHHHHHT--TCCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC--CceEEEEECCEEEEE
Confidence            34567889999885  456999999999999999999999988754  788888999988876

>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=82.03  E-value=1.2  Score=29.78  Aligned_cols=43  Identities=16%  Similarity=0.332  Sum_probs=37.3

Q ss_pred             hhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023862           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (276)
Q Consensus        82 ~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAsD~  125 (276)
                      +...+|++.+++ +.|.|+.++|.+.|++...+..-+..|-.+.
T Consensus         3 ~~D~kIl~~L~~-n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~g   45 (60)
T d1i1ga1           3 ERDKIILEILEK-DARTPFTEIAKKLGISETAVRKRVKALEEKG   45 (60)
T ss_dssp             SHHHHHHHHHHH-CTTCCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            345789999986 5799999999999999999999999987653

>d1t33a1 a.4.1.9 (A:1-88) Putative transcriptional repressor YbiH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional repressor YbiH
species: Salmonella typhimurium [TaxId: 90371]

Probab=80.97  E-value=0.4  Score=33.64  Aligned_cols=33  Identities=18%  Similarity=0.279  Sum_probs=26.9

Q ss_pred             hhhHHHHHH----HHHcCCceehhhhhhhcCCCHHHH
Q 023862           82 DVRNRAMDA----VDACNRRVTIGDVAGKAGLKLNEA  114 (276)
Q Consensus        82 ~~~~rim~A----ve~lg~rvTvgDVAa~aGL~l~~A  114 (276)
                      +.+.+|++|    +.+.|+..|+.|||.++|++....
T Consensus        12 ~tr~~Il~aa~~l~~~~G~~~t~~~Ia~~agvs~~~~   48 (88)
T d1t33a1          12 QAKSQLIAAALAQFGEYGLHATTRDIAALAGQNIAAI   48 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHGGGSCHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccccCHHHHHHHhCCChhhh
Confidence            456777776    778899999999999999987654

>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=80.14  E-value=1.5  Score=29.48  Aligned_cols=42  Identities=12%  Similarity=0.105  Sum_probs=36.9

Q ss_pred             chhhHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHh
Q 023862           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA  123 (276)
Q Consensus        81 ~~~~~rim~Ave~lg~rvTvgDVAa~aGL~l~~Ae~aL~aLAs  123 (276)
                      .+.+.+|++.+. .+..+|..|+|.+-|+|...+.+.+..|-+
T Consensus         4 ~~~~~~iL~~L~-~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALLA-NGEFHSGEQLGETLGMSRAAINKHIQTLRD   45 (63)
T ss_dssp             CHHHHHHHHHHT-TSSCBCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH-HCCcCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356678898884 588899999999999999999999999976