Citrus Sinensis ID: 022049

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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-------280-------290-------300---
Protein Sequence
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMV
Secondary Structure (PSIPRED)
cccccccEEEccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEEHHHHccccHHHHHHHHHHHHHHccccEEEEccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEcccccccEEEEccccccccccccccccccccEEEEEEEEEcccccccccHHHHHHHHHHHHHHHcccEEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEccccEEEEEcccccEEEcccccccccccccccccccccccccccEEEEEEccccccccccccEEccccccHHHHHHHHHHHHHcccEEEHHHHHHHccccHHHHHHHHHHHHHHccccEEEcccccEEEEccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEEEccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHHHHHHHcccEEEEHHcccccccccccc
Coil and Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfpriqplpfprisgkipgsrvlvpvakastdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADtdgflevsdegdvlyvfpnnyraKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfnifispsdlfwywdpyyyrrrrvqtddddkkmNFIKSVFSFvfgegdpnqgieEKRWKLIGEYIAsnggvvtaeelapyldidrtmv
Flexible Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfPRIQPLPFPRISGKIPGSRVLVPVAKAStdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIlssksddddrgrrrrsfdsgfnifispsdlfwywdpYYYRRRRvqtddddkkMNFIKSVFsfvfgegdpnqGIEEKRWKLIGEYIasnggvvtaeelapyldidrtmv
Low Complexity Region (SEG)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfNIFISPSDLFWYWDPyyyrrrrVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMV
Disordered region (IsUnstruct)
******CFTTTPKSRFFFTPLR****************LPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL****************DSGFNIFISPSDLFWYWDPYYYRR*************FIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDI*****
Disordered Region (DISOPRED)
*****TCFTTTPKSRF**********************************************************************AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAII***********************NIFISPSDLFWYWDP*********************SVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTM*
Disordered Region (DISEMBL)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSS**********RRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMV
Disordered Region (DISPRO)
*TSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSK*************DSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDID****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDIDRTMV
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	303	2.2.26 [Sep-21-2011]
Q8GW20	523	Uncharacterized protein A	yes	no	0.973	0.564	0.611	4e-99

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

 Score =  361 bits (926), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 187/306 (61%), Positives = 235/306 (76%), Gaps = 11/306 (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 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEEL 292
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW++IG+YI S GGVV A+EL
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMIGQYITSRGGVVAADEL 297

Query: 293 APYLDI 298
           APYLD+
Sbjct: 298 APYLDV 303

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	303
255575701	514	conserved hypothetical protein [Ricinus	0.966	0.570	0.696	1e-107
449462964	516	PREDICTED: uncharacterized protein At5g0	0.963	0.565	0.675	1e-105
118488331	288	unknown [Populus trichocarpa]	0.933	0.982	0.681	1e-104
224077276	374	predicted protein [Populus trichocarpa]	0.798	0.647	0.764	1e-104
225440882	495	PREDICTED: uncharacterized protein At5g0	0.811	0.496	0.755	1e-100
357503799	507	hypothetical protein MTR_7g030010 [Medic	0.937	0.560	0.673	2e-99
7406400	757	putative protein [Arabidopsis thaliana]	0.973	0.389	0.611	1e-97
312283379	523	unnamed protein product [Thellungiella h	0.980	0.567	0.601	2e-97
26453262	523	unknown protein [Arabidopsis thaliana]	0.973	0.564	0.611	2e-97
18414392	523	Iron-sulfur assembly-like protein [Arabi	0.973	0.564	0.611	3e-97

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

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 211/303 (69%), Positives = 248/303 (81%), Gaps = 10/303 (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 VQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYLDI 298
           ++ DDDD KMNFI+SVFSFVFG+GDPNQGIEE+RWKLIG+YI+SNGGVV AEELAP+LD+
Sbjct: 234 IKKDDDD-KMNFIESVFSFVFGDGDPNQGIEEERWKLIGQYISSNGGVVAAEELAPFLDL 292

Query: 299 DRT 301
             T
Sbjct: 293 QTT 295

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 =  388 bits (996), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 204/302 (67%), Positives = 248/302 (82%), Gaps = 10/302 (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 RRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPYL 296
           RR+QT+D+  KMNFI+S+FSFVFG+GDPNQGIEE+RWKLIG+YI+SNGGVV AEELAPYL
Sbjct: 237 RRLQTEDN--KMNFIESIFSFVFGDGDPNQGIEEERWKLIGQYISSNGGVVAAEELAPYL 294

Query: 297 DI 298
           D+
Sbjct: 295 DV 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  384 bits (985), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 201/295 (68%), Positives = 238/295 (80%), Gaps = 12/295 (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 RRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAE 290
           RR+++TD  D KMNFI+SVFSFVFG+GDPNQGIEE+RWKLIG+YI+SNGGVV AE
Sbjct: 235 RRQLRTDGGD-KMNFIESVFSFVFGDGDPNQGIEEERWKLIGQYISSNGGVVAAE 288

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  383 bits (983), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 188/246 (76%), Positives = 218/246 (88%), Gaps = 4/246 (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 RRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPY 295
           RR+++TD  D KMNFI+SVFSFVFG+GDPNQGIEE+RWKLIG+YI+SNGGVV AEELAP+
Sbjct: 185 RRQLRTDGGD-KMNFIESVFSFVFGDGDPNQGIEEERWKLIGQYISSNGGVVAAEELAPF 243

Query: 296 LDIDRT 301
           LD+  T
Sbjct: 244 LDLKTT 249

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 =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 188/249 (75%), Positives = 224/249 (89%), Gaps = 3/249 (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 PYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAE 290
           PYYYRRRR+Q +DD   MNFI+SVFSFVFG+GDPNQGIE++RWKLIG+YI+SNGGVVTAE
Sbjct: 208 PYYYRRRRIQKEDDG--MNFIESVFSFVFGDGDPNQGIEDERWKLIGQYISSNGGVVTAE 265

Query: 291 ELAPYLDID 299
           ELAPYLD++
Sbjct: 266 ELAPYLDLE 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357503799|ref|XP_003622188.1| hypothetical protein MTR_7g030010 [Medicago truncatula] gi|355497203|gb|AES78406.1| hypothetical protein MTR_7g030010 [Medicago truncatula]

 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 206/306 (67%), Positives = 238/306 (77%), Gaps = 22/306 (7%)

Query: 1   MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFP---RISGKIPGSRVLVPV 57
           M +I TCF  TP SR         +    P   P  +P  FP   RI+ +  G  ++VP 
Sbjct: 1   MATIPTCFAITPTSRL--------LTFTAP---PFHKPFIFPQNRRINKR--GWALVVP- 46

Query: 58  AKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKA 117
            +A+ DV  G+ PG +VESDKL +DVR R MDAVD C  RVT+GDVA +AGLKLNEAQKA
Sbjct: 47  -RAAVDVGRGIRPGGVVESDKLSSDVRKRTMDAVDGCGGRVTVGDVASRAGLKLNEAQKA 105

Query: 118 LQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLF 177
           LQALAADTDGFLEVS+EGDVLYVFP NYR+KL AKSFR+K EP I+KAK A EY IRV F
Sbjct: 106 LQALAADTDGFLEVSEEGDVLYVFPKNYRSKLGAKSFRIKAEPFIEKAKGAGEYLIRVSF 165

Query: 178 GTALIASIVIVFTAIIAIL-SSKSDDDDRGRR-RRSFDSGFNIFISPSDLFWYWDPYYYR 235
           GTALIASIVIV+TAIIA++ SS+S+DD+RGRR  RS+DSGFN + +P DLFWYWDPYY R
Sbjct: 166 GTALIASIVIVYTAIIALVTSSRSEDDNRGRRGGRSYDSGFNFYFNPVDLFWYWDPYYNR 225

Query: 236 RRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAPY 295
           RRRVQ DD+  K NFI+SVFSFVFG+GDPNQGIEE+RWKLIG+YIASNGGVV AEELAPY
Sbjct: 226 RRRVQVDDN--KTNFIESVFSFVFGDGDPNQGIEEERWKLIGQYIASNGGVVAAEELAPY 283

Query: 296 LDIDRT 301
           LDID T
Sbjct: 284 LDIDST 289

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  362 bits (930), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 187/306 (61%), Positives = 235/306 (76%), Gaps = 11/306 (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 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEEL 292
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW++IG+YI S GGVV A+EL
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMIGQYITSRGGVVAADEL 297

Query: 293 APYLDI 298
           APYLD+
Sbjct: 298 APYLDV 303

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  361 bits (927), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 183/304 (60%), Positives = 228/304 (75%), Gaps = 7/304 (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 RRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEELAP 294
            RRR + +D+ K MNFI+SVFSFVFG+GDPN+G EE+RW++IG YI S GGVV A+ELAP
Sbjct: 241 SRRRAR-EDEGKGMNFIESVFSFVFGDGDPNEGTEEERWQMIGRYITSRGGVVAADELAP 299

Query: 295 YLDI 298
           YLD+
Sbjct: 300 YLDV 303

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  361 bits (927), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 187/306 (61%), Positives = 236/306 (77%), Gaps = 11/306 (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 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEEL 292
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW++IG+YI S GGVV A+EL
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMIGQYITSRGGVVAADEL 297

Query: 293 APYLDI 298
           APYLD+
Sbjct: 298 APYLDV 303

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 =  361 bits (926), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 187/306 (61%), Positives = 235/306 (76%), Gaps = 11/306 (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 YYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEEL 292
           YY RRR + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW++IG+YI S GGVV A+EL
Sbjct: 239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMIGQYITSRGGVVAADEL 297

Query: 293 APYLDI 298
           APYLD+
Sbjct: 298 APYLDV 303

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	303
TAIR|locus:2150560	523	AT5G03900 "AT5G03900" [Arabido	0.973	0.564	0.552	3e-78

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

 Score = 787 (282.1 bits), Expect = 3.0e-78, P = 3.0e-78
 Identities = 169/306 (55%), Positives = 211/306 (68%)

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 XXXXXXVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLIGEYIASNGGVVTAEEL 292
                    + +D+ K MNFI+SVFSFVFG+GDPNQGIEE+RW++IG+YI S GGVV A+EL
Sbjct:   239 YYNRRRAR-EDEGKGMNFIESVFSFVFGDGDPNQGIEEERWQMIGQYITSRGGVVAADEL 297

Query:   293 APYLDI 298
             APYLD+
Sbjct:   298 APYLDV 303


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        0.320   0.138   0.404    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      303       276   0.00079  115 3  11 22  0.48    33
                                                     33  0.41    37


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:  591 (63 KB)
  Total size of DFA:  179 KB (2104 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:  22.80u 0.17s 22.97t   Elapsed:  00:00:02
  Total cpu time:  22.80u 0.17s 22.97t   Elapsed:  00:00:02
  Start:  Sat May 11 03:02:24 2013   End:  Sat May 11 03:02:26 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	303
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.88
COG3355	126	Predicted transcriptional regulator [Transcription	94.5
PRK13239	206	alkylmercury lyase; Provisional	94.47
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	93.98
PRK06266	178	transcription initiation factor E subunit alpha; V	93.47
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	93.33
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.29
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	92.9
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	92.63
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.61
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	92.09
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	91.88
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	91.52
KOG3341	249	consensus RNA polymerase II transcription factor c	91.44
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	91.26
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	89.96
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.9
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.85
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	89.77
TIGR02844	80	spore_III_D sporulation transcriptional regulator	88.52
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	86.95
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	86.64
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	85.34
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	85.22
PRK15466	166	carboxysome structural protein EutK; Provisional	85.2
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	85.13
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	84.78
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	82.58
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	82.49
COG2512	258	Predicted membrane-associated trancriptional regul	81.26
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	80.68
COG2345	218	Predicted transcriptional regulator [Transcription	80.63

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

Probab=94.88  E-value=0.054  Score=40.99  Aligned_cols=46  Identities=15%  Similarity=0.252  Sum_probs=41.3

Q ss_pred             CchhhHHHHHHHHhcCC-ceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~-rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      +....++|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+.
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            34567899999999988 59999999999999999999999998873

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

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.50  E-value=0.29  Score=42.25  Aligned_cols=86  Identities=19%  Similarity=0.162  Sum_probs=68.6

Q ss_pred             HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc-CCceEee-ccccEEEEc-ChhhHHHHhhhhHHHhHHHH
Q 022049           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV  161 (303)
Q Consensus        85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~-~G~LeVs-esGdIlYvF-P~~fRs~l~~Ks~r~rlq~~  161 (303)
                      -.+++++-+.++..|+-|+|..-+++.+.|+++|+.|.... ==.-+++ +.|-..|.+ |.++-.  -.+-.+..+++|
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            45677777678889999999999999999999999999875 1222344 789999999 988887  356677788999


Q ss_pred             HHHHhhhhHHH
Q 022049          162 IDKAKAAAEYS  172 (303)
Q Consensus       162 ~~k~w~v~~yl  172 (303)
                      .+++...+...
T Consensus       108 ~~~~~~~i~~~  118 (126)
T COG3355         108 YDKMKQLIEEF  118 (126)
T ss_pred             HHHHHHHHHHH
Confidence            88887775543

>PRK13239 alkylmercury lyase; Provisional

Probab=94.47  E-value=0.066  Score=49.42  Aligned_cols=56  Identities=18%  Similarity=0.284  Sum_probs=47.5

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcCh
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPN  143 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~  143 (303)
                      ..+.-.|++.+. .|.-||+.|+|+.+|.+.+++++.|.+|.     ..+..++|+|+- ||-
T Consensus        21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~-~pl   76 (206)
T PRK13239         21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG-YGL   76 (206)
T ss_pred             hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe-ccc
Confidence            346677888888 99999999999999999999999999985     447889999875 544

>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=93.98  E-value=0.067  Score=37.99  Aligned_cols=39  Identities=23%  Similarity=0.434  Sum_probs=35.4

Q ss_pred             HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (303)
Q Consensus        86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad  124 (303)
                      +|++++.+.+...|+.|+|.++|++...+.+-|..|.+.
T Consensus         7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~   45 (52)
T PF09339_consen    7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE   45 (52)
T ss_dssp             HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            678999999999999999999999999999999999864

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.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=93.47  E-value=0.45  Score=42.58  Aligned_cols=84  Identities=18%  Similarity=0.141  Sum_probs=60.7

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCc---eEeeccccEEEEcChhhHHHHhhhhHHHh
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF---LEVSDEGDVLYVFPNNYRAKLAAKSFRLK  157 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~---LeVsesGdIlYvFP~~fRs~l~~Ks~r~r  157 (303)
                      .+..-+|++++.++| .+|..|+|...|++.+++++.|..|..+.=..   .+..+.|-+.|.+--+...+  ....+.+
T Consensus        21 ~~~~~~Vl~~L~~~g-~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i--~d~ik~~   97 (178)
T PRK06266         21 DEEGFEVLKALIKKG-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKL--PEIIKKK   97 (178)
T ss_pred             CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHH--HHHHHHH
Confidence            445678999999988 69999999999999999999999999987322   23335788999776555553  2333444


Q ss_pred             HHHHHHHHhh
Q 022049          158 VEPVIDKAKA  167 (303)
Q Consensus       158 lq~~~~k~w~  167 (303)
                      +....++++.
T Consensus        98 ~~~~~~klk~  107 (178)
T PRK06266         98 KMEELKKLKE  107 (178)
T ss_pred             HHHHHHHHHH
Confidence            4555555443

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=93.33  E-value=0.56  Score=41.09  Aligned_cols=80  Identities=23%  Similarity=0.230  Sum_probs=60.8

Q ss_pred             HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeeccccEEEEcChhhHHHHhhhhHHHhHHHHH
Q 022049           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI  162 (303)
Q Consensus        86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G---~LeVsesGdIlYvFP~~fRs~l~~Ks~r~rlq~~~  162 (303)
                      .||+|+-.+| -+|..|+|...|++++++++.|..|..+.=.   +.+-.++|-+.|.+=-++..+  -...+.++....
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-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKA--LDVLKRKLEETA   94 (158)
T ss_pred             HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHH--HHHHHHHHHHHH
Confidence            5788888777 5999999999999999999999999998854   555667888999985577774  334444555555


Q ss_pred             HHHhhh
Q 022049          163 DKAKAA  168 (303)
Q Consensus       163 ~k~w~v  168 (303)
                      ++++.-
T Consensus        95 ~~lk~~  100 (158)
T TIGR00373        95 KKLREK  100 (158)
T ss_pred             HHHHHH
Confidence            555433

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.29  E-value=0.67  Score=35.09  Aligned_cols=78  Identities=19%  Similarity=0.335  Sum_probs=53.0

Q ss_pred             HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh-hH---HHHhhhhHHHhHHH
Q 022049           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN-YR---AKLAAKSFRLKVEP  160 (303)
Q Consensus        85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~-fR---s~l~~Ks~r~rlq~  160 (303)
                      -+|++.+.+.+..+|+.|+|...|++...+.+-|..|.+.  |-|+-..++. .|..-.. ++   ..+.+..+.....+
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~--g~l~~~~~~~-~y~l~~~~~~~~~~~~~~~~l~~~~~~   84 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL--GYVEQDGQNG-RYRLGPKVLELGQSYLSSLDLREVAKP   84 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC--CCeeecCCCC-ceeecHHHHHHHHHHHhcCCHHHHHHH
Confidence            4578888887668999999999999999999999999764  7777654332 3555332 22   22333445555555


Q ss_pred             HHHHH
Q 022049          161 VIDKA  165 (303)
Q Consensus       161 ~~~k~  165 (303)
                      +++.+
T Consensus        85 ~l~~l   89 (91)
T smart00346       85 VLEEL   89 (91)
T ss_pred             HHHHH
Confidence            55543

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

Probab=92.90  E-value=0.17  Score=38.66  Aligned_cols=54  Identities=20%  Similarity=0.356  Sum_probs=41.6

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--cccEEE
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY  139 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse--sGdIlY  139 (303)
                      .++|++.+++.+.-+|..|||...|++..+|+.=|..|..+.  .++-++  .|-..|
T Consensus         2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG--~V~~~~~~rG~~~~   57 (62)
T PF04703_consen    2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG--KVERSPVRRGKSTY   57 (62)
T ss_dssp             HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT--SEEEES-SSSSS-E
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC--CEEEecCCCCccee
Confidence            367999999988889999999999999999999999998764  556544  355433

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

Probab=92.63  E-value=0.19  Score=40.31  Aligned_cols=49  Identities=22%  Similarity=0.348  Sum_probs=35.9

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl  138 (303)
                      --.+++.+.+ |.-||+.++|+.+|.+.++++++|.++.     ..|-.++|.||
T Consensus        26 ~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV   74 (77)
T PF12324_consen   26 LRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV   74 (77)
T ss_dssp             HHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred             HHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence            3445666665 9999999999999999999999988775     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=92.61  E-value=0.27  Score=33.94  Aligned_cols=41  Identities=17%  Similarity=0.324  Sum_probs=34.6

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad  124 (303)
                      .+.+|++.+.+.+. .|+.|+|...|+|...+.+.|..|..+
T Consensus         4 ~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    4 TQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             HHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            46789999999655 999999999999999999999999865

...

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

Probab=92.09  E-value=0.25  Score=42.96  Aligned_cols=51  Identities=25%  Similarity=0.386  Sum_probs=43.2

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses  134 (303)
                      +++..+|++.|+++| |+|++|++..+|++.+.+++-|..|++  .|+|..+..
T Consensus        11 ~eLk~rIvElVRe~G-RiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~   61 (127)
T PF06163_consen   11 EELKARIVELVREHG-RITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGR   61 (127)
T ss_pred             HHHHHHHHHHHHHcC-CccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCC
Confidence            556778899998876 699999999999999999999999986  467776554

>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=91.88  E-value=0.38  Score=35.20  Aligned_cols=41  Identities=12%  Similarity=0.294  Sum_probs=36.9

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      +..|++.+++.| .+|+.|+|..-|+|...+++.|..|+...
T Consensus         2 ~~~Il~~l~~~~-~~s~~ela~~~~VS~~TiRRDl~~L~~~g   42 (57)
T PF08220_consen    2 QQQILELLKEKG-KVSVKELAEEFGVSEMTIRRDLNKLEKQG   42 (57)
T ss_pred             HHHHHHHHHHcC-CEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            467899998875 69999999999999999999999998864

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

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

Probab=91.52  E-value=1.4  Score=30.56  Aligned_cols=60  Identities=25%  Similarity=0.424  Sum_probs=47.1

Q ss_pred             CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc-cEEEEcC
Q 022049           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP  142 (303)
Q Consensus        79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG-dIlYvFP  142 (303)
                      +....+..|++++.+.+  ++..|+|...|++...+.+.|..|.+.  |.+....++ ...|.+.
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 4566665

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.

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

Probab=91.44  E-value=0.49  Score=44.86  Aligned_cols=84  Identities=17%  Similarity=0.313  Sum_probs=70.1

Q ss_pred             cCCCcccccCCCCchhh---HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049           68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN  144 (303)
Q Consensus        68 ~~~~~~~~~~~l~~~~~---~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~  144 (303)
                      ++.||.----++|.+++   ..|+++++.+|| ||+.-+-+.-|-.-.-|+++|..|.++.=+-+.-...+|..|-||..
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            44556555556666554   579999999999 99999999999999999999999999999999988999999999999


Q ss_pred             hHHHHhhh
Q 022049          145 YRAKLAAK  152 (303)
Q Consensus       145 fRs~l~~K  152 (303)
                      |-..+...
T Consensus       238 ~~~~~~q~  245 (249)
T KOG3341|consen  238 FTDQYAQR  245 (249)
T ss_pred             hhHHHhhh
Confidence            97754443

>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=91.26  E-value=0.53  Score=34.27  Aligned_cols=53  Identities=26%  Similarity=0.439  Sum_probs=44.2

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG  135 (303)
                      ....|-+|++.+ ..+...|++++|...|++...+..-|..|..  .|-+++.++|
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            345788899999 5677799999999999999999999999987  5778887776

...

>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=89.96  E-value=0.64  Score=36.98  Aligned_cols=45  Identities=20%  Similarity=0.440  Sum_probs=38.1

Q ss_pred             chhhHHHHHHHHh---cCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        81 ~~~~~~im~Ave~---~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ..++.+|++.++.   ..-.|.+.+|+.+.|++.++++++|..|..+.
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            4578999999998   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.

>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=89.90  E-value=1.2  Score=31.37  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=35.6

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE  130 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le  130 (303)
                      +.+|++.+.+.+..+|..++|.+.|+|...+++.|..|-+. +..++
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            35788889666666999999999999999999999999444 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=89.85  E-value=1.1  Score=29.97  Aligned_cols=47  Identities=15%  Similarity=0.319  Sum_probs=38.5

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD  133 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse  133 (303)
                      +..+++.+.+.+ .+|+.|+|...|++...+.+.|..|..+  |.++-..
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            356888888776 4999999999999999999999999886  5555433

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=89.77  E-value=0.92  Score=30.86  Aligned_cols=51  Identities=22%  Similarity=0.406  Sum_probs=39.6

Q ss_pred             HHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEc
Q 022049           87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (303)
Q Consensus        87 im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvF  141 (303)
                      |+..+.  ...+|+.|++...|++...+.+.|..|.++  |-++....|. ..|.+
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~~~~   53 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVYYSL   53 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEEEEE
Confidence            567776  566899999999999999999999999986  5666555454 44443

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=88.52  E-value=0.52  Score=37.63  Aligned_cols=34  Identities=12%  Similarity=0.081  Sum_probs=31.0

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHH
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL  118 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL  118 (303)
                      -+..|++.+.+  +.+|+.|||..+|+|...+.+.|
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            46788999999  88999999999999999999877

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=86.95  E-value=1.3  Score=42.17  Aligned_cols=57  Identities=18%  Similarity=0.367  Sum_probs=49.4

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl  138 (303)
                      |.-++..|.+.+..+|+|+++.|++..-|+..+..|+.+..++.+-. +++.. .||++
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            45677899999999999999999999999999999999999998877 55544 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.

>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=86.64  E-value=1.1  Score=34.16  Aligned_cols=38  Identities=24%  Similarity=0.336  Sum_probs=30.6

Q ss_pred             HHHHHHhcCCceeehhhhhhcCCC-HHHHHHHHHHHHhh
Q 022049           87 AMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAAD  124 (303)
Q Consensus        87 im~Ave~~g~rvTvgDVAa~aGLs-l~eAe~aL~aLAad  124 (303)
                      |.+.+++.||-.|+.|+|...|++ .+.+++-|.+|..+
T Consensus        15 I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k   53 (65)
T PF01726_consen   15 IREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK   53 (65)
T ss_dssp             HHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence            445567799999999999999997 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.

>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=85.34  E-value=2.4  Score=31.15  Aligned_cols=52  Identities=21%  Similarity=0.316  Sum_probs=40.4

Q ss_pred             HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEE
Q 022049           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (303)
Q Consensus        85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlY  139 (303)
                      .+|..++- ..+.+|+.|+|..+|++...+.+.|..|...  |-++..+...-+|
T Consensus        11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y   62 (68)
T PF01978_consen   11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY   62 (68)
T ss_dssp             HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred             HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence            35566665 4567999999999999999999999999986  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.

>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=85.22  E-value=2.1  Score=30.27  Aligned_cols=42  Identities=14%  Similarity=0.240  Sum_probs=36.1

Q ss_pred             hHHHHHHHHhcCCc-eeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        84 ~~~im~Ave~~g~r-vTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      +-+++-++...+.. +|+.|+|...|++...+.+.+..|.++.
T Consensus         7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G   49 (62)
T PF12802_consen    7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG   49 (62)
T ss_dssp             HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            34678899888887 9999999999999999999999998764

...

>PRK15466 carboxysome structural protein EutK; Provisional

Probab=85.20  E-value=1.7  Score=39.42  Aligned_cols=42  Identities=24%  Similarity=0.385  Sum_probs=36.3

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      .+.++.-+-...+..|.|+||+.-|.++++++.+|..|-+|.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (166)
T PRK15466        111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAG  152 (166)
T ss_pred             HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhcc
Confidence            355566667778899999999999999999999999998874

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

Probab=85.13  E-value=1.7  Score=32.55  Aligned_cols=38  Identities=21%  Similarity=0.366  Sum_probs=30.6

Q ss_pred             HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHh
Q 022049           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAA  123 (303)
Q Consensus        85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAa  123 (303)
                      .+|.+.+-+.| |.|+.+++..++|+.++++++|..|.+
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            46677776666 899999999999999999999999975

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.

>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=84.78  E-value=1.1  Score=33.52  Aligned_cols=52  Identities=23%  Similarity=0.230  Sum_probs=34.8

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG  135 (303)
                      +..+.+.-.++|...|..+||...|+++++.++.|.....-..=++.+..++
T Consensus         7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~   58 (78)
T PF04539_consen    7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDED   58 (78)
T ss_dssp             HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSS
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCC
Confidence            3344455568899999999999999999999888876544334444454443

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 ....

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=82.58  E-value=7  Score=36.23  Aligned_cols=43  Identities=9%  Similarity=0.102  Sum_probs=38.5

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad  124 (303)
                      .+-+.+|++.+++.| ++|+.|+|..-|+|...+++.|..|+..
T Consensus         4 ~eR~~~Il~~L~~~~-~v~v~eLa~~l~VS~~TIRRDL~~Le~~   46 (256)
T PRK10434          4 RQRQAAILEYLQKQG-KTSVEELAQYFDTTGTTIRKDLVILEHA   46 (256)
T ss_pred             HHHHHHHHHHHHHcC-CEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            356788899998876 5999999999999999999999999876

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=82.49  E-value=8  Score=36.26  Aligned_cols=54  Identities=15%  Similarity=0.244  Sum_probs=44.4

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd  136 (303)
                      ..+-+.+|++.+++.|. +|+.|+|..-|+|...+++.|..|.+.  |-++-..-|-
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            34667888999999887 999999999999999999999999664  5665555443

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=81.26  E-value=2.3  Score=40.44  Aligned_cols=47  Identities=19%  Similarity=0.285  Sum_probs=40.4

Q ss_pred             CCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhh
Q 022049           77 DKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (303)
Q Consensus        77 ~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad  124 (303)
                      ..|+.+. ..||++++.+|+|+|+.|+..+.|+|...+=+.|+.|...
T Consensus       191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~  237 (258)
T COG2512         191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR  237 (258)
T ss_pred             CCCCHHH-HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC
Confidence            3444444 4689999999999999999999999999999999999764

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

Probab=80.68  E-value=3.1  Score=29.14  Aligned_cols=48  Identities=21%  Similarity=0.369  Sum_probs=35.0

Q ss_pred             hhhHHHHHHHHhc----CCc-eeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049           82 DVRNRAMDAVDAC----NRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (303)
Q Consensus        82 ~~~~~im~Ave~~----g~r-vTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV  131 (303)
                      ++.+.+.+.+...    |.. .|+.|+|...|+|...+.++|..|+..  |-|+.
T Consensus         5 ~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~--G~i~~   57 (66)
T cd07377           5 QIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAE--GLVER   57 (66)
T ss_pred             HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEe
Confidence            4456666665543    222 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

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=80.63  E-value=3.3  Score=38.76  Aligned_cols=50  Identities=16%  Similarity=0.281  Sum_probs=45.2

Q ss_pred             ccCCCCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           75 ESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        75 ~~~~l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ++.+.++..+.+|+..+++.|. +|++|+|.+-||+...|++-|..|.++.
T Consensus         4 ~~~~~~~~tr~~il~lL~~~g~-~sa~elA~~Lgis~~avR~HL~~Le~~G   53 (218)
T COG2345           4 MLADPSGSTRERILELLKKSGP-VSADELAEELGISPMAVRRHLDDLEAEG   53 (218)
T ss_pred             cccCCCccHHHHHHHHHhccCC-ccHHHHHHHhCCCHHHHHHHHHHHHhCc
Confidence            4567788899999999888876 8999999999999999999999999876

---

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	303
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.68
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.59
3f2g_A	220	Alkylmercury lyase; MERB, organomercurial lyase, m	95.13
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	95.13
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	94.05
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	93.17
3r0a_A	123	Putative transcriptional regulator; structural gen	93.07
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	92.66
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	91.87
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.74
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.61
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	91.56
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	90.98
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	90.86
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	90.08
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	89.69
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	89.61
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	89.54
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	87.88
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	87.84
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	86.87
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	86.77
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.65
3jth_A	98	Transcription activator HLYU; transcription factor	86.09
2kko_A	108	Possible transcriptional regulatory protein (possi	85.95
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	84.79
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	82.84
2v9v_A	135	Selenocysteine-specific elongation factor; transcr	82.72
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.97
1sfx_A	109	Conserved hypothetical protein AF2008; structural	80.9
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	80.82
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	80.52

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

Probab=95.68  E-value=0.016  Score=44.20  Aligned_cols=49  Identities=24%  Similarity=0.339  Sum_probs=42.0

Q ss_pred             hhhHHHHHHHHhc-----CCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee
Q 022049           82 DVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS  132 (303)
Q Consensus        82 ~~~~~im~Ave~~-----g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs  132 (303)
                      +...+|++.+++.     ||.+|+.|+|...|+|...+++.|.+|..+  |.|+-.
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            4567899999888     999999999999999999999999999876  344443

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

Probab=95.59  E-value=0.027  Score=41.02  Aligned_cols=51  Identities=10%  Similarity=0.143  Sum_probs=44.3

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG  135 (303)
                      .+++|++.+++.+..+|+.|+|...|++...+.+.|..|.++.-  ++.++.|
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

>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=95.13  E-value=0.019  Score=51.98  Aligned_cols=59  Identities=17%  Similarity=0.220  Sum_probs=50.4

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhH
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR  146 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fR  146 (303)
                      ..+.-.+++.+. .|.-+|+.++|+.+|.+.+++++.|.+|.     .++.+++|+|+. ||---|
T Consensus        21 ~~~~~~llr~la-~Grpv~~~~LA~~~g~~~~~v~~~L~~l~-----~~~~D~~G~Ivg-yp~S~~   79 (220)
T 3f2g_A           21 ADLLVPLLRELA-KGRPVSRTTLAGILDWPAERVAAVLEQAT-----STEYDKDGNIIG-YGLTLR   79 (220)
T ss_dssp             HHHHHHHHHHHT-TTSCBCHHHHHHHHTCCHHHHHHHHHHCT-----TCEECTTSCEEE-SSEESS
T ss_pred             hHHHHHHHHHHh-cCCCCCHHHHHHHhCcCHHHHHHHHHhCC-----cEEECCCCCEEE-ecCCCC
Confidence            445667788887 89999999999999999999999999985     699999999977 765544

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

Probab=95.13  E-value=0.027  Score=42.56  Aligned_cols=44  Identities=27%  Similarity=0.447  Sum_probs=38.3

Q ss_pred             HHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceE
Q 022049           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLE  130 (303)
Q Consensus        85 ~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~Le  130 (303)
                      +.++.-+....+..|+|+||+.-|.|+++|+.+|..|-+|  |.|+
T Consensus         6 eaLLall~s~~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~--G~LR   49 (68)
T 3i71_A            6 DELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA--GTLR   49 (68)
T ss_dssp             HHHHHHHHHCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEE
T ss_pred             HHHHHHHHHHhccccHHHHHHHhCCcHHHHHHHHHHHHhc--chhh
Confidence            4667778888999999999999999999999999999886  4444

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

Probab=94.05  E-value=0.07  Score=41.94  Aligned_cols=44  Identities=9%  Similarity=0.214  Sum_probs=41.0

Q ss_pred             hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      +..++|++++++.|.-+..||||..+|++..++.++|.+|-.+.
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            45789999999999999999999999999999999999998764

>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=93.17  E-value=0.23  Score=37.88  Aligned_cols=58  Identities=21%  Similarity=0.322  Sum_probs=47.0

Q ss_pred             hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee-----ccccEEEEc
Q 022049           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-----DEGDVLYVF  141 (303)
Q Consensus        82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs-----esGdIlYvF  141 (303)
                      +.+-+|+..+.+.|.++|+.|+|...|+|...+.++|..|.++.  -++..     ..|-.+|.+
T Consensus        18 ~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~G--lV~~~~~~~~~~g~~v~~~   80 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQG--FVSYRKTRDKDSGWFIYYW   80 (110)
T ss_dssp             STTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHT--SCEEEEEC---CCCCEEEE
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEEEecccCCCceEEEEe
Confidence            45678999887788789999999999999999999999999875  45554     467777733

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

Probab=93.07  E-value=0.58  Score=37.06  Aligned_cols=84  Identities=14%  Similarity=0.206  Sum_probs=59.2

Q ss_pred             hhhHHHHHHHHhcCCc-eeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEee----ccccEEEEc-ChhhHHHHhhhhHH
Q 022049           82 DVRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS----DEGDVLYVF-PNNYRAKLAAKSFR  155 (303)
Q Consensus        82 ~~~~~im~Ave~~g~r-vTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVs----esGdIlYvF-P~~fRs~l~~Ks~r  155 (303)
                      ..+-+|+.++.+.+.. +|+.|+|...|++...+.+.|..|....  -++-.    +.|-..|+| +......  ..-.+
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--ILQRSQQNLDGGGYVYIYKIYSKNQI--RNIIQ  101 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTT--SEEEEEEECTTSCEEEEEEECCHHHH--HHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEeeCCccCCCcceEEEecCCHHHH--HHHHH
Confidence            3467899999988877 9999999999999999999999998764  44332    234456665 3333332  23456


Q ss_pred             HhHHHHHHHHhhhh
Q 022049          156 LKVEPVIDKAKAAA  169 (303)
Q Consensus       156 ~rlq~~~~k~w~v~  169 (303)
                      ..++.|.+.+...+
T Consensus       102 ~~~~~~~~~~~~~l  115 (123)
T 3r0a_A          102 KIVQSWADRLGQEL  115 (123)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHH
Confidence            66777777765543

>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=92.66  E-value=0.14  Score=46.65  Aligned_cols=71  Identities=17%  Similarity=0.339  Sum_probs=53.5

Q ss_pred             ccccCC--CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhh
Q 022049           73 IVESDK--LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (303)
Q Consensus        73 ~~~~~~--l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~f  145 (303)
                      .|+|..  |.++. .+|++.++.+| .||+.+++...|.+..-|+.+|..|.++.-.-+.-..+||-.|-||.-|
T Consensus       144 ~VqSvp~el~~D~-~~vLela~~~g-~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD~q~~ge~~Yw~P~lf  216 (234)
T 3cuq_A          144 LIQSVPAELNMDH-TVVLQLAEKNG-YVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALF  216 (234)
T ss_dssp             EEECSCCCCCHHH-HHHHHHHTTTS-EECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEESSSSSSCEEECTTSS
T ss_pred             EEEeCCCccchHH-HHHHHHHHhcC-cCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEeCCCCCcceeecchhh
Confidence            344443  44443 45778888665 5999999999999999999999998887655555434689999999655

>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=91.87  E-value=0.38  Score=42.90  Aligned_cols=69  Identities=20%  Similarity=0.258  Sum_probs=53.6

Q ss_pred             cccCCCC-chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhh
Q 022049           74 VESDKLP-ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (303)
Q Consensus        74 ~~~~~l~-~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~f  145 (303)
                      |++..-. .....+|++.++.+| .||+.++|..-|.+..-|+..|..+..  .|.|=+.++++-+|.||.-|
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 IELQSHKEEEMVASALETVSEKG-SLTSEEFAKLVGMSVLLAKERLLLAEK--MGHLCRDDSVEGLRFYPNLF  214 (218)
T ss_dssp             EEETTCCGGGGHHHHHHHHHHTS-CBCHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEEESSSCEEEEECGG
T ss_pred             EEcCCCchHHHHHHHHHHHHHCC-CcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCEEEECCCCceEEehhhc
Confidence            5554332 356788899888766 499999999999999999999998666  56666666666688899655

>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=91.74  E-value=0.16  Score=39.08  Aligned_cols=61  Identities=11%  Similarity=0.192  Sum_probs=49.9

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHH-HHHHHHHHHHhhcCCceEeeccccEEEEcChh
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLN-EAQKALQALAADTDGFLEVSDEGDVLYVFPNN  144 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~-eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~  144 (303)
                      ++.+++|++.+++.|. +|+.|+|..-|++.. .+++.|..|..+  |-++-...|-.+|.-...
T Consensus        10 ~~~~~~IL~~Lk~~g~-~ta~eiA~~Lgit~~~aVr~hL~~Le~e--GlV~~~~~gRP~w~LT~~   71 (79)
T 1xmk_A           10 AEIKEKICDYLFNVSD-SSALNLAKNIGLTKARDINAVLIDMERQ--GDVYRQGTTPPIWHLTDK   71 (79)
T ss_dssp             HHHHHHHHHHHHHTCC-EEHHHHHHHHCGGGHHHHHHHHHHHHHT--TSEEEECSSSCEEEECHH
T ss_pred             hhHHHHHHHHHHHcCC-cCHHHHHHHcCCCcHHHHHHHHHHHHHC--CCEEecCCCCCCeEeCHh
Confidence            3578999999999984 999999999999999 999999999986  455545567677765443

>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=91.61  E-value=0.16  Score=38.90  Aligned_cols=50  Identities=26%  Similarity=0.367  Sum_probs=42.0

Q ss_pred             CchhhHHHHHHHHhcC--CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g--~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV  131 (303)
                      ..+...+|++++++.+  .++|+.|+|.+.|++...+++.|..|..+  |.|+.
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  58999999999999999999999999875  34543

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

Probab=91.56  E-value=0.23  Score=36.36  Aligned_cols=45  Identities=16%  Similarity=0.218  Sum_probs=39.1

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeV  131 (303)
                      +.+|++.+.+.| .+|+.|+|...|++...+.+.|..|.++  |-++.
T Consensus         2 r~~Il~~L~~~~-~~s~~eLa~~lgvs~~tv~r~L~~L~~~--GlI~~   46 (81)
T 2htj_A            2 KNEILEFLNRHN-GGKTAEIAEALAVTDYQARYYLLLLEKA--GMVQR   46 (81)
T ss_dssp             HHHHHHHHHHSC-CCCHHHHHHHHTSCHHHHHHHHHHHHHH--TSEEE
T ss_pred             HHHHHHHHHHcC-CCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEE
Confidence            578999998765 5999999999999999999999999876  55664

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

Probab=90.98  E-value=0.45  Score=34.59  Aligned_cols=60  Identities=10%  Similarity=0.125  Sum_probs=46.5

Q ss_pred             chhhHHHHHHHHhcC-Cceeehhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeeccccEEEE
Q 022049           81 ADVRNRAMDAVDACN-RRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (303)
Q Consensus        81 ~~~~~~im~Ave~~g-~rvTvgDVAa~a-----GLsl~eAe~aL~aLAad~~G~LeVsesGdIlYv  140 (303)
                      ...|..|++.+.+.+ ..+|+.|++...     +++...+-+.|..|....--+-...++|...|.
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 789999999998     999999999999999875433222235566665

>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=90.86  E-value=0.22  Score=45.43  Aligned_cols=61  Identities=13%  Similarity=0.218  Sum_probs=47.4

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhh
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~f  145 (303)
                      ..+|++.++..| .||+.+++...|.+..-|+.+|..|.++.-.-+.-..+|+..|-||..|
T Consensus       169 ~~~vLe~a~~~g-~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD~q~~~e~~Yw~P~lf  229 (233)
T 1u5t_A          169 QTKILEICSILG-YSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWI  229 (233)
T ss_dssp             HHHHHHTTTTTS-CCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEECGGGG
T ss_pred             HHHHHHHHHhcC-cCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCCCccceechhhh
Confidence            456678887665 4999999999999999999999998776544443323458899999665

>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=90.08  E-value=0.46  Score=35.57  Aligned_cols=46  Identities=24%  Similarity=0.338  Sum_probs=40.1

Q ss_pred             CchhhHHHHHHHHhcC--CceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g--~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ..+...+|++++++++  .++|+.|+|.+.|++...+++.|..|..+.
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            3455688999999988  589999999999999999999999998754

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

Probab=89.69  E-value=0.45  Score=36.19  Aligned_cols=43  Identities=12%  Similarity=0.040  Sum_probs=37.8

Q ss_pred             hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ..-.+|++.|++.| ++|+.|+|..-|+|...+++.|..|.+..
T Consensus         2 m~L~~Il~~L~~~g-~vsv~eLa~~l~VS~~TIRrdL~~Le~~G   44 (78)
T 1xn7_A            2 ASLIQVRDLLALRG-RMEAAQISQTLNTPQPMINAMLQQLESMG   44 (78)
T ss_dssp             CCHHHHHHHHHHSC-SBCHHHHHHHTTCCHHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            34467999998865 59999999999999999999999999874

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

Probab=89.61  E-value=0.38  Score=37.50  Aligned_cols=43  Identities=19%  Similarity=0.268  Sum_probs=38.5

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ..+..+|++.+++.|  .|+.|+|.+-|++...+++-|..|..+.
T Consensus        16 ~~~~~~IL~lL~~~g--~sa~eLAk~LgiSk~aVr~~L~~Le~eG   58 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEG--ATAAQLTRQLNMEKREVNKALYDLQRSA   58 (82)
T ss_dssp             HHHHHHHHHHHSSST--EEHHHHHHHSSSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcC--CCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            357789999999777  9999999999999999999999998763

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

Probab=89.54  E-value=0.45  Score=37.19  Aligned_cols=43  Identities=9%  Similarity=0.022  Sum_probs=37.7

Q ss_pred             hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ..-.+|++.|++.| ++|+.|+|..-|+|...+++.|..|....
T Consensus         2 m~L~~Il~~L~~~g-~vsv~eLA~~l~VS~~TIRrDL~~Le~~G   44 (87)
T 2k02_A            2 ASLMEVRDMLALQG-RMEAKQLSARLQTPQPLIDAMLERMEAMG   44 (87)
T ss_dssp             CCTHHHHHHHHHSC-SEEHHHHHHHTTCCHHHHHHHHHHHHTTC
T ss_pred             chHHHHHHHHHHcC-CCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            34468999998865 69999999999999999999999998764

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

Probab=87.88  E-value=5.5  Score=29.77  Aligned_cols=59  Identities=20%  Similarity=0.262  Sum_probs=45.4

Q ss_pred             CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEc
Q 022049           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (303)
Q Consensus        79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvF  141 (303)
                      |....|-+|+..+ ..| ..|+.|+|...|++...+.+.|..|..  .|-++...+|. ..|..
T Consensus        18 l~~~~r~~IL~~L-~~~-~~~~~ela~~l~is~~tv~~~l~~L~~--~gli~~~~~gr~~~y~l   77 (114)
T 2oqg_A           18 LSDETRWEILTEL-GRA-DQSASSLATRLPVSRQAIAKHLNALQA--CGLVESVKVGREIRYRA   77 (114)
T ss_dssp             TTCHHHHHHHHHH-HHS-CBCHHHHHHHSSSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEEE
T ss_pred             hCChHHHHHHHHH-HcC-CCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeeEEecCCEEEEEe
Confidence            3445678899999 444 489999999999999999999999965  46777666676 44444

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

Probab=87.84  E-value=1.1  Score=32.68  Aligned_cols=60  Identities=13%  Similarity=0.321  Sum_probs=46.9

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEcC
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVFP  142 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvFP  142 (303)
                      ....+-+|+.++.+ ++..|+.|+|...|++...+.+.|..|..  .|-++...+|. ..|...
T Consensus        22 ~~~~~~~il~~l~~-~~~~s~~ela~~l~is~~tvs~~l~~L~~--~glv~~~~~~r~~~y~l~   82 (99)
T 3cuo_A           22 SHPKRLLILCMLSG-SPGTSAGELTRITGLSASATSQHLARMRD--EGLIDSQRDAQRILYSIK   82 (99)
T ss_dssp             CSHHHHHHHHHHTT-CCSEEHHHHHHHHCCCHHHHHHHHHHHHH--TTSEEEEECSSCEEEEEC
T ss_pred             CChHHHHHHHHHHh-CCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEEEC
Confidence            34567889999865 56799999999999999999999999964  57777666665 445443

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

Probab=86.87  E-value=3.6  Score=31.89  Aligned_cols=61  Identities=15%  Similarity=0.274  Sum_probs=48.2

Q ss_pred             CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEcCh
Q 022049           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVFPN  143 (303)
Q Consensus        79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvFP~  143 (303)
                      |....|-+|+..+.  .+..|++|+|...|++...+-+-|..|..  .|-++...+|. ..|..-.
T Consensus        15 l~~~~R~~Il~~L~--~~~~~~~eLa~~l~is~~tvs~hL~~L~~--~GlV~~~~~gr~~~y~l~~   76 (118)
T 3f6o_A           15 LADPTRRAVLGRLS--RGPATVSELAKPFDMALPSFMKHIHFLED--SGWIRTHKQGRVRTCAIEK   76 (118)
T ss_dssp             HTSHHHHHHHHHHH--TCCEEHHHHHTTCCSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEEECS
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCeEEEecCCEEEEEECH
Confidence            34567888999997  35689999999999999999999999964  57787777776 4454433

>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=86.77  E-value=2.1  Score=32.50  Aligned_cols=59  Identities=15%  Similarity=0.272  Sum_probs=47.3

Q ss_pred             CCchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (303)
Q Consensus        79 l~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF  141 (303)
                      |....|-+|+..+. . +..|++|+|...|++...+.+.|..|.  ..|-++...+|.-+|..
T Consensus        23 l~~~~r~~IL~~L~-~-~~~~~~ela~~l~is~stvs~~L~~L~--~~Glv~~~~~gr~~~y~   81 (106)
T 1r1u_A           23 LGDYNRIRIMELLS-V-SEASVGHISHQLNLSQSNVSHQLKLLK--SVHLVKAKRQGQSMIYS   81 (106)
T ss_dssp             TCSHHHHHHHHHHH-H-CCBCHHHHHHHHTCCHHHHHHHHHHHH--HTTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH-h-CCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEEEeCCEEEEE
Confidence            34556788999987 3 458999999999999999999999997  46778877778755543

>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=86.65  E-value=1.1  Score=33.43  Aligned_cols=54  Identities=15%  Similarity=0.183  Sum_probs=43.1

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF  141 (303)
                      ....|.+|++.+ .  +..|++|+|...|++...+.+.|..|...  |-++... |  .|..
T Consensus        29 ~~~~r~~Il~~L-~--~~~~~~eLa~~l~is~~tv~~~L~~L~~~--Glv~~~~-g--~y~l   82 (96)
T 1y0u_A           29 TNPVRRKILRML-D--KGRSEEEIMQTLSLSKKQLDYHLKVLEAG--FCIERVG-E--RWVV   82 (96)
T ss_dssp             SCHHHHHHHHHH-H--TTCCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEET-T--EEEE
T ss_pred             CCHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEC-C--EEEE
Confidence            345677889998 3  45999999999999999999999999765  6666666 6  5554

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

Probab=86.09  E-value=1.1  Score=33.31  Aligned_cols=58  Identities=19%  Similarity=0.374  Sum_probs=47.3

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc-EEEEc
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd-IlYvF  141 (303)
                      ....|-+|+..+.+  +..|++|+|...|++...+.+.|..|..  .|-++...+|. +.|..
T Consensus        21 ~~~~r~~Il~~L~~--~~~~~~ela~~l~is~~tvs~~L~~L~~--~Glv~~~~~g~~~~y~l   79 (98)
T 3jth_A           21 ANERRLQILCMLHN--QELSVGELCAKLQLSQSALSQHLAWLRR--DGLVTTRKEAQTVYYTL   79 (98)
T ss_dssp             CSHHHHHHHHHTTT--SCEEHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEECCTTCCEEEE
T ss_pred             CCHHHHHHHHHHhc--CCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCeEEEEeCCEEEEEE
Confidence            34567788998876  6799999999999999999999999975  57788888776 44544

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

Probab=85.95  E-value=1.7  Score=33.44  Aligned_cols=57  Identities=26%  Similarity=0.390  Sum_probs=46.3

Q ss_pred             chhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEc
Q 022049           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (303)
Q Consensus        81 ~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvF  141 (303)
                      ...|-+|+..+.+  +..|+.|+|...|++...+.+.|..|..  .|-++...+|.-+|..
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            4557789999874  5689999999999999999999999976  4678777788755543

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

Probab=84.79  E-value=2.1  Score=34.42  Aligned_cols=64  Identities=16%  Similarity=0.280  Sum_probs=50.6

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhc--CCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHHHhh
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKA--GLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAA  151 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~a--GLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~l~~  151 (303)
                      .+.+|++.+.+.| +.|++++|...  |++...+.+-|..|..+  |-++....|  +|.-...=+..|..
T Consensus        14 ~d~~IL~~L~~~g-~~s~~eLA~~l~~giS~~aVs~rL~~Le~~--GLV~~~~rg--~Y~LT~~G~~~l~~   79 (111)
T 3b73_A           14 WDDRILEIIHEEG-NGSPKELEDRDEIRISKSSVSRRLKKLADH--DLLQPLANG--VYVITEEGEAYLNG   79 (111)
T ss_dssp             HHHHHHHHHHHHS-CBCHHHHHTSTTCCSCHHHHHHHHHHHHHT--TSEEECSTT--CEEECHHHHHHHTT
T ss_pred             HHHHHHHHHHHcC-CCCHHHHHHHHhcCCCHHHHHHHHHHHHHC--CCEEecCCc--eEEECchHHHHHHH
Confidence            4688999998876 89999999999  99999999999999875  555555555  77776555555544

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

Probab=82.84  E-value=2  Score=32.00  Aligned_cols=46  Identities=17%  Similarity=0.138  Sum_probs=42.1

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      .|-.-..+++-++..|+-+-+.++|++-|++.+++-..|..|+++.
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            4556688999999999999999999999999999999999999874

>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=82.72  E-value=8.1  Score=30.12  Aligned_cols=63  Identities=19%  Similarity=0.220  Sum_probs=45.0

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhhHHH
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAK  148 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~fRs~  148 (303)
                      .+.+...++..+..++..|++..+|++.++.++.|.+|.+... -+.+..+++..| +..++-..
T Consensus         4 ~~~l~~~L~~~~~~~~~~~l~~~~~l~~~~l~~~l~~l~~~~~-~~~~~~~~~~~~-~~~~~~~~   66 (135)
T 2v9v_A            4 EKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQ-VTLLRVENDLYA-ISTERYQA   66 (135)
T ss_dssp             HHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTC-EEEEEETTEEEE-EEHHHHHH
T ss_pred             HHHHHHHHHHcCcCCCHHHHHHHhCCCHHHHHHHHHHHHhCCc-EEEEecCCCeEE-ecHHHHHH
Confidence            4567777888888887799999999999999999999986544 555543344334 54444443

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

Probab=81.97  E-value=0.99  Score=35.44  Aligned_cols=38  Identities=13%  Similarity=0.095  Sum_probs=32.8

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHH
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ  119 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~  119 (303)
                      +.+-+.+|++.+.+.+  +|+.|||..+|+|...+.+.|.
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            3456678899999887  9999999999999999988873

>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=80.90  E-value=13  Score=26.79  Aligned_cols=57  Identities=18%  Similarity=0.249  Sum_probs=43.5

Q ss_pred             hhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec--cccEEEEc
Q 022049           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLYVF  141 (303)
Q Consensus        82 ~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse--sGdIlYvF  141 (303)
                      ..+-+|+..+.+.+ .+|+.|+|...|++...+.+.|..|.++  |-++...  ++...|.+
T Consensus        20 ~~~~~il~~l~~~~-~~s~~ela~~l~is~~tv~~~l~~L~~~--glv~~~~~~~~r~~~~~   78 (109)
T 1sfx_A           20 PSDVRIYSLLLERG-GMRVSEIARELDLSARFVRDRLKVLLKR--GFVRREIVEKGWVGYIY   78 (109)
T ss_dssp             HHHHHHHHHHHHHC-CBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEEEEESSSEEEEE
T ss_pred             HHHHHHHHHHHHcC-CCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEeecCCceEEEE
Confidence            45677899997754 5999999999999999999999999776  4455433  45455544

>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=80.52  E-value=13  Score=26.77  Aligned_cols=63  Identities=10%  Similarity=0.085  Sum_probs=46.6

Q ss_pred             CchhhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeec---cccE-EEEcChhh
Q 022049           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD---EGDV-LYVFPNNY  145 (303)
Q Consensus        80 ~~~~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVse---sGdI-lYvFP~~f  145 (303)
                      ....+-+|+..+.+.+ ..|+.|+|...|++...+.+.|..|..+  |-++...   +|.- .|.-...-
T Consensus        14 ~~~~~~~iL~~L~~~~-~~~~~ela~~l~is~~tvs~~l~~L~~~--gli~~~~~~~~~r~~~~~lt~~g   80 (100)
T 1ub9_A           14 GNPVRLGIMIFLLPRR-KAPFSQIQKVLDLTPGNLDSHIRVLERN--GLVKTYKVIADRPRTVVEITDFG   80 (100)
T ss_dssp             HSHHHHHHHHHHHHHS-EEEHHHHHHHTTCCHHHHHHHHHHHHHT--TSEEEEEECSSSCEEEEEECHHH
T ss_pred             CChHHHHHHHHHHhcC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEecCCCcceEEEEECHHH
Confidence            3445778898887655 6999999999999999999999999887  5665433   5554 44444433

---

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	303
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	95.47
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	90.43
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	87.89
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	87.56
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	87.26
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	87.13
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	86.88
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	86.3
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	85.99
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	84.36
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	83.31
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	82.47
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	81.76

>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=95.47  E-value=0.0074  Score=44.18  Aligned_cols=61  Identities=13%  Similarity=0.218  Sum_probs=52.6

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEEEEcChhh
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIlYvFP~~f  145 (303)
                      +..|+++++..| .||+..+-...|-+..-|+.+|..|..+.=+=+.--..||..|=||.-|
T Consensus         5 qt~vLe~a~~~G-~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD~Q~~~e~~YWfPsl~   65 (68)
T d1u5ta2           5 QTKILEICSILG-YSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWI   65 (68)
T ss_dssp             HHHHHHTTTTTS-CCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEECGGGG
T ss_pred             HHHHHHHHHHcC-ceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEecCCCCCceeeChHhh
Confidence            467899999886 5999999999999999999999999997766666555689999999866

>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=90.43  E-value=0.24  Score=34.19  Aligned_cols=52  Identities=8%  Similarity=0.059  Sum_probs=42.6

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG  135 (303)
                      -+.+|++.+.+..+.+|+.|+|..-|+|...+++.|.+|.+ .|..++.+..|
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            34678888888888899999999999999999999999965 45557655444

>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=87.89  E-value=0.32  Score=33.65  Aligned_cols=41  Identities=15%  Similarity=0.157  Sum_probs=36.9

Q ss_pred             hHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        84 ~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      +.+|++.+.+.| .+|..|+|..+|||...+.+-|..|.++.
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            457899998876 59999999999999999999999998875

>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=87.56  E-value=0.36  Score=34.02  Aligned_cols=49  Identities=18%  Similarity=0.303  Sum_probs=42.5

Q ss_pred             HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecccc
Q 022049           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (303)
Q Consensus        86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGd  136 (303)
                      +|++.+...+..+|+.|+|.++|++...+-+-|..|...  |.|+=+++|.
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            578888899999999999999999999999999888764  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=87.26  E-value=0.54  Score=32.64  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=40.9

Q ss_pred             hhhHHHHHHHHhcC-CceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeecc
Q 022049           82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (303)
Q Consensus        82 ~~~~~im~Ave~~g-~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVses  134 (303)
                      .++.+|.++.++.| .--|+.|||...|++..++ +.+..++.+.|=-.+|+++
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            56789999999888 5579999999999999999 4555555666666677553

>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=87.13  E-value=0.082  Score=37.80  Aligned_cols=41  Identities=20%  Similarity=0.269  Sum_probs=34.5

Q ss_pred             hcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccccEE
Q 022049           93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (303)
Q Consensus        93 ~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesGdIl  138 (303)
                      ..|.-||+.++|..+|-+.+|++++|.++.     .-|-.++|.||
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            458889999999999999999999988776     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=86.88  E-value=1.4  Score=32.45  Aligned_cols=67  Identities=12%  Similarity=0.038  Sum_probs=48.0

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCceEeeccc-cEEEEcChhhHHHHh
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFPNNYRAKLA  150 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~LeVsesG-dIlYvFP~~fRs~l~  150 (303)
                      ..-+|+.++-++| ..|+.|+|..+|++...+...|..|.++.=-.=+..++| ...+..|..-...+.
T Consensus        21 ~e~~v~~~L~~~g-~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l~   88 (109)
T d1sfxa_          21 SDVRIYSLLLERG-GMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLK   88 (109)
T ss_dssp             HHHHHHHHHHHHC-CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHH
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHHH
Confidence            3456778887665 699999999999999999999999998764433344444 444445666555443

>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=86.30  E-value=0.38  Score=32.74  Aligned_cols=31  Identities=19%  Similarity=0.258  Sum_probs=28.1

Q ss_pred             HHHhcCCceeehhhhhhcCCCHHHHHHHHHH
Q 022049           90 AVDACNRRVTIGDVAGKAGLKLNEAQKALQA  120 (303)
Q Consensus        90 Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~a  120 (303)
                      ...++|...|+.++|...|++.+++..+|.+
T Consensus        24 l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          24 LSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3567999999999999999999999988876

>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=85.99  E-value=0.39  Score=36.28  Aligned_cols=60  Identities=18%  Similarity=0.215  Sum_probs=45.7

Q ss_pred             HHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhcCCc---eEeeccccEEEEcChhh
Q 022049           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGF---LEVSDEGDVLYVFPNNY  145 (303)
Q Consensus        86 ~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~~G~---LeVsesGdIlYvFP~~f  145 (303)
                      +|++++-+.+..+|=-++|.++|++++++++.|..|....=..   -+=.++|=.+|..--+.
T Consensus        22 ~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd~~~gw~~Y~W~~~~   84 (88)
T d1q1ha_          22 DVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYWKPNI   84 (88)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEEECTH
T ss_pred             HHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeecCCCCcEEEEEEech
Confidence            5788887788899999999999999999999999998776332   22235777888654443

>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=84.36  E-value=0.74  Score=31.55  Aligned_cols=42  Identities=10%  Similarity=0.178  Sum_probs=36.8

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ...+|++++++. .|.|..|+|...|+|..++.+-++.|-...
T Consensus         6 ~D~~IL~~L~~n-~r~s~~~iA~~lgis~~tv~~Ri~~L~~~g   47 (63)
T d2cfxa1           6 IDLNIIEELKKD-SRLSMRELGRKIKLSPPSVTERVRQLESFG   47 (63)
T ss_dssp             HHHHHHHHHHHC-SCCCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            457889999875 689999999999999999999999997653

>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=83.31  E-value=0.62  Score=32.81  Aligned_cols=39  Identities=26%  Similarity=0.312  Sum_probs=34.6

Q ss_pred             HHHHHHHhcCCceeehhhhhhcCC-CHHHHHHHHHHHHhh
Q 022049           86 RAMDAVDACNRRVTIGDVAGKAGL-KLNEAQKALQALAAD  124 (303)
Q Consensus        86 ~im~Ave~~g~rvTvgDVAa~aGL-sl~eAe~aL~aLAad  124 (303)
                      -|.+.++++|+-.|+.|+|...|+ |.+.+..-|.+|..+
T Consensus        13 ~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1          13 LIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             HHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            345667889999999999999999 799999999999876

>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=82.47  E-value=0.89  Score=30.97  Aligned_cols=42  Identities=10%  Similarity=0.192  Sum_probs=36.8

Q ss_pred             hhHHHHHHHHhcCCceeehhhhhhcCCCHHHHHHHHHHHHhhc
Q 022049           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (303)
Q Consensus        83 ~~~~im~Ave~~g~rvTvgDVAa~aGLsl~eAe~aL~aLAad~  125 (303)
                      ...+|++.+++. .|.|..|+|.+.|+|..++..-+..|-++.
T Consensus         6 ~D~~IL~~L~~~-~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~G   47 (63)
T d2cg4a1           6 LDRGILEALMGN-ARTAYAELAKQFGVSPETIHVRVEKMKQAG   47 (63)
T ss_dssp             HHHHHHHHHHHC-TTSCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            456788888866 788999999999999999999999998764

>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=81.76  E-value=0.28  Score=34.99  Aligned_cols=33  Identities=18%  Similarity=0.279  Sum_probs=27.1

Q ss_pred             hhhHHHHHH----HHhcCCceeehhhhhhcCCCHHHH
Q 022049           82 DVRNRAMDA----VDACNRRVTIGDVAGKAGLKLNEA  114 (303)
Q Consensus        82 ~~~~~im~A----ve~~g~rvTvgDVAa~aGLsl~eA  114 (303)
                      ..|++|++|    +.+.|+..|+.|||.++|++....
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            356777776    778899999999999999987654