Citrus Sinensis ID: 023574

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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
Protein Sequence
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLVILQH
Secondary Structure (PSIPRED)
ccccccccEEccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccHHHHHHHHHHHHHccccEEEEEHHHHccccHHHHHHHHHHHHHHccccEEEEccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccEEccccccccEEEccccccccccccccccccccEEEEEEEEEcccccccccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEccccEEEEEcccccEEEcccccccccccccccccccccccccccEEEEEEccccccccccccEEccccccHHHHHHHHHHHHHcccEEEHHHHHHHccccHHHHHHHHHHHHHHccccEEEcccccEEEEccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfpriqplpfprisgkipgsrvlvpvakastdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADtdgflevsdegdvlyvfpnnyraKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfnifispsdlfwywdpyyyrrrrvqtddddkkmNFIKSVFSFvfgegdpnqgieeKRWKLVILQH
Flexible Loop (DISEMBL)
mtsistcftttpksrffftplrpsinlkppdsfPRIQPLPFPRISGKIPGSRVLVPVAKAStdvavgvgpgrivesdklpadVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIlssksddddrgrrrrsfdsgfnifispsdlfwywdpYYYRRRRvqtddddkkMNFIKSVFSfvfgegdpnqgieekrwkLVILQH
Low Complexity Region (SEG)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILssksddddrgrrrrsfdsgfNIFISPSDLFWYWDPyyyrrrrVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLVILQH
Disordered region (IsUnstruct)
******CFTTTPKSRFFFTPLR****************LPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAIL****************DSGFNIFISPSDLFWYWDPYYYRR********************************************
Disordered Region (DISOPRED)
*****TCFTTTPKSRF*********************************************************************RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAII***********************NIFISPSDLFWYWDP********************KSVFSFVFGEGDPNQGIEEKRWKLVILQ*
Disordered Region (DISEMBL)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSS**********RRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLVILQH
Disordered Region (DISPRO)
*TSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSK************FDSGFNIFISPSDLFWYWDPYYYRRRRV******KKMNFIKSVFSFVFGEGDPNQGIEEKRWKLVILQH
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSISTCFTTTPKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLVPVAKASTDVAVGVGPGRIVESDKLPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVIDKAKAAAEYSIRVLFGTALIASIVIVFTAIIAILSSKSDDDDRGRRRRSFDSGFNIFISPSDLFWYWDPYYYRRRRVQTDDDDKKMNFIKSVFSFVFGEGDPNQGIEEKRWKLVILQH
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	280	2.2.26 [Sep-21-2011]
Q8GW20	523	Uncharacterized protein A	yes	no	0.975	0.521	0.598	1e-88

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

 Score =  326 bits (835), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

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

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

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

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

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

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	280
118488331	288	unknown [Populus trichocarpa]	0.960	0.934	0.672	5e-97
255575701	514	conserved hypothetical protein [Ricinus	0.957	0.521	0.690	3e-95
449462964	516	PREDICTED: uncharacterized protein At5g0	0.964	0.523	0.660	1e-93
224077276	374	predicted protein [Populus trichocarpa]	0.775	0.580	0.764	2e-92
225440882	495	PREDICTED: uncharacterized protein At5g0	0.796	0.450	0.743	7e-88
312283379	523	unnamed protein product [Thellungiella h	0.982	0.525	0.588	2e-87
7406400	757	putative protein [Arabidopsis thaliana]	0.975	0.360	0.598	3e-87
26453262	523	unknown protein [Arabidopsis thaliana]	0.975	0.521	0.598	3e-87
21536751	523	unknown [Arabidopsis thaliana]	0.975	0.521	0.598	7e-87
18414392	523	Iron-sulfur assembly-like protein [Arabi	0.975	0.521	0.598	9e-87

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

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

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

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

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

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

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

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  353 bits (907), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 192/278 (69%), Positives = 226/278 (81%), Gaps = 10/278 (3%)

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

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

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

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

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

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  348 bits (894), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 185/280 (66%), Positives = 227/280 (81%), Gaps = 10/280 (3%)

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

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

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

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

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

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

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

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

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

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

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

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  329 bits (844), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 168/226 (74%), Positives = 201/226 (88%), Gaps = 3/226 (1%)

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

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

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

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

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 166/282 (58%), Positives = 210/282 (74%), Gaps = 7/282 (2%)

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

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

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

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

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

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

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

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

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

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

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

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  327 bits (838), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 217/284 (76%), Gaps = 11/284 (3%)

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

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

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

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

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

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  326 bits (835), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

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

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

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

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

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

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  326 bits (835), Expect = 9e-87,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 216/284 (76%), Gaps = 11/284 (3%)

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

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

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

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

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

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

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	280
TAIR|locus:2150560	523	AT5G03900 "AT5G03900" [Arabido	0.975	0.521	0.535	1e-68

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

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

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

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

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

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

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


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.138   0.408    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      280       253   0.00083  114 3  11 22  0.42    33
                                                     32  0.47    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  590 (63 KB)
  Total size of DFA:  171 KB (2100 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  20.02u 0.09s 20.11t   Elapsed:  00:00:01
  Total cpu time:  20.02u 0.09s 20.11t   Elapsed:  00:00:01
  Start:  Fri May 10 09:23:48 2013   End:  Fri May 10 09:23:49 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	280
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.8
PRK13239	206	alkylmercury lyase; Provisional	94.68
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	93.63
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	93.46
PRK06266	178	transcription initiation factor E subunit alpha; V	92.82
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	92.46
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	92.45
COG3355	126	Predicted transcriptional regulator [Transcription	92.21
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	91.71
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	91.33
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	90.74
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	90.64
KOG3341	249	consensus RNA polymerase II transcription factor c	90.22
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	88.92
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	88.78
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	88.39
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	88.39
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	88.17
TIGR02844	80	spore_III_D sporulation transcriptional regulator	87.62
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	87.27
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	86.94
PRK15466	166	carboxysome structural protein EutK; Provisional	85.68
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	85.51
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	85.05
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	82.89
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	82.39
smart00753	88	PAM PCI/PINT associated module.	82.19
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	82.19
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	82.13

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

Probab=94.80  E-value=0.071  Score=39.87  Aligned_cols=45  Identities=16%  Similarity=0.266  Sum_probs=41.1

Q ss_pred             CchHHHHHHHHHHHcCC-ceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           80 PADVRNRAMDAVDACNR-RVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~-RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +..++.+|++++.+.|. .+|+.|+|.+.|++...+.+.|..|..+
T Consensus         4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~   49 (68)
T smart00550        4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK   49 (68)
T ss_pred             chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            44677899999999988 6999999999999999999999999876

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

>PRK13239 alkylmercury lyase; Provisional

Probab=94.68  E-value=0.068  Score=48.82  Aligned_cols=53  Identities=19%  Similarity=0.297  Sum_probs=46.2

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY  139 (280)
                      ..+.-.|++.+. .|.-+|+.|+|+.+|.+.+++++.|.+|.     ..+.+++|+||-
T Consensus        21 ~~~~~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~-----~~~~d~~g~iv~   73 (206)
T PRK13239         21 ATLLVPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP-----DTEYDEDGRIIG   73 (206)
T ss_pred             hHHHHHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC-----CeEECCCCCEEe
Confidence            457778899988 99999999999999999999999999985     347888999974

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

Probab=93.63  E-value=0.12  Score=41.00  Aligned_cols=52  Identities=23%  Similarity=0.321  Sum_probs=37.4

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl  138 (280)
                      +.+-..+++.+.+ |.-||+.++|+.+|.++++++++|.+..     ..|-+++|.||
T Consensus        23 ~~L~r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p-----~tEyD~~GrIV   74 (77)
T PF12324_consen   23 AWLLRPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMP-----DTEYDDQGRIV   74 (77)
T ss_dssp             HHHHHHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-T-----TSEEETTSEEE
T ss_pred             HHHHHHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCC-----CceEcCCCCee
Confidence            3344456666666 9999999999999999999999988775     47778888886

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.

>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=93.46  E-value=0.11  Score=36.52  Aligned_cols=40  Identities=23%  Similarity=0.398  Sum_probs=35.8

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      -+|++++.+.+...|+.|+|.++|++...+.+-|..|...
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~   45 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE   45 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3689999999999999999999999999999999999865

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=92.82  E-value=0.79  Score=40.59  Aligned_cols=84  Identities=19%  Similarity=0.164  Sum_probs=59.6

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--C-CceEeccCCcEEEEcCcchHHHHhhhhHHHh
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--D-GFLEVSDEGDVLYVFPNNYRAKLAAKSFRLK  157 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~-GhLqVsesGEIlYvFP~~fRs~l~~Ks~r~r  157 (280)
                      .+..-+|++++.+.| .+|..|+|...|++.+++++.|..|..+.  . -..+..+.|-+.|.+=-+...+.  ...+.+
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-EVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLP--EIIKKK   97 (178)
T ss_pred             CccHhHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHH--HHHHHH
Confidence            445578999999888 69999999999999999999999999994  2 22333357999998754445433  333444


Q ss_pred             HHHHHHHhhh
Q 023574          158 VEPVIDKAKA  167 (280)
Q Consensus       158 l~~~~~k~w~  167 (280)
                      +....+++..
T Consensus        98 ~~~~~~klk~  107 (178)
T PRK06266         98 KMEELKKLKE  107 (178)
T ss_pred             HHHHHHHHHH
Confidence            4444444433

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=92.46  E-value=1.1  Score=33.43  Aligned_cols=77  Identities=21%  Similarity=0.379  Sum_probs=51.6

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc-CcchH---HHHhhhhHHHhHHH
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF-PNNYR---AKLAAKSFRLKVEP  160 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF-P~~fR---s~l~~Ks~r~rl~~  160 (280)
                      .+|++.+.+.++.+|+.|+|...|++...+.+-|..|.+.  |-|+-..++. .|.. |+.++   ..+.+..+.....+
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            4678888887678999999999999999999999999764  7777654333 3554 22222   22333344444555


Q ss_pred             HHHH
Q 023574          161 VIDK  164 (280)
Q Consensus       161 ~~~k  164 (280)
                      ..+.
T Consensus        85 ~l~~   88 (91)
T smart00346       85 VLEE   88 (91)
T ss_pred             HHHH
Confidence            5444

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=92.45  E-value=1.1  Score=38.86  Aligned_cols=79  Identities=24%  Similarity=0.256  Sum_probs=59.2

Q ss_pred             HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCC---ceEeccCCcEEEEcCcchHHHHhhhhHHHhHHHHH
Q 023574           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDG---FLEVSDEGDVLYVFPNNYRAKLAAKSFRLKVEPVI  162 (280)
Q Consensus        86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~G---hLqVsesGEIlYvFP~~fRs~l~~Ks~r~rl~~~~  162 (280)
                      .+++|+-..| -+|-.|+|...|++++++++.|..|..+.=.   +.+-.++|-+.|.+=-|+..+.  ...+.++....
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-EFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKAL--DVLKRKLEETA   94 (158)
T ss_pred             HHHHHHhccC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHH--HHHHHHHHHHH
Confidence            5677877666 6999999999999999999999999999532   5556667999999745777765  44444555555


Q ss_pred             HHhhh
Q 023574          163 DKAKA  167 (280)
Q Consensus       163 ~k~w~  167 (280)
                      +++..
T Consensus        95 ~~lk~   99 (158)
T TIGR00373        95 KKLRE   99 (158)
T ss_pred             HHHHH
Confidence            55443

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=92.21  E-value=1.5  Score=37.53  Aligned_cols=86  Identities=19%  Similarity=0.157  Sum_probs=66.5

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc-CCceEec-cCCcEEEEc-CcchHHHHhhhhHHHhHHHH
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT-DGFLEVS-DEGDVLYVF-PNNYRAKLAAKSFRLKVEPV  161 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~-~GhLqVs-esGEIlYvF-P~~fRs~l~~Ks~r~rl~~~  161 (280)
                      -.++.++-+.++..|+-|+|..-+++...|+++|+.|.... ==.-+++ +.|---|.+ |.++-.+  .+-....+++|
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 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEI--KKKILKDLDEW  107 (126)
T ss_pred             HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHH--HHHHHHHHHHH
Confidence            45666666688999999999999999999999999999874 1222344 679999999 8888763  35567778888


Q ss_pred             HHHhhhhhhhH
Q 023574          162 IDKAKAAAEYS  172 (280)
Q Consensus       162 ~~k~w~v~~yl  172 (280)
                      .+++...+..+
T Consensus       108 ~~~~~~~i~~~  118 (126)
T COG3355         108 YDKMKQLIEEF  118 (126)
T ss_pred             HHHHHHHHHHH
Confidence            88887766543

>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=91.71  E-value=0.52  Score=32.18  Aligned_cols=42  Identities=19%  Similarity=0.382  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +.+.+|++++.+ +++.|+.|+|...|++...+.+.|..|..+
T Consensus         3 ~~~~~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    3 ETQRKILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             HHHHHHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            356789999999 455999999999999999999999998765

...

>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=91.33  E-value=0.59  Score=33.58  Aligned_cols=53  Identities=26%  Similarity=0.439  Sum_probs=44.6

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG  135 (280)
                      ....|-+|++.+ ..+...|++++|...|++...+..-|..|..  .|-+++.++|
T Consensus         8 ~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~--aGli~~~~~g   60 (61)
T PF12840_consen    8 SDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKLEE--AGLIEVEREG   60 (61)
T ss_dssp             TSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH--TTSEEEEEET
T ss_pred             CCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH--CCCeEEeccC
Confidence            346788899999 7788899999999999999999999999977  5677777766

...

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

Probab=90.74  E-value=0.4  Score=36.20  Aligned_cols=53  Identities=23%  Similarity=0.394  Sum_probs=40.9

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEEE
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLY  139 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse--sGEIlY  139 (280)
                      ++|++.+++.+.-+|..|||...|++..+|+.=|..|..+  |.++-++  .|-..|
T Consensus         3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e--G~V~~~~~~rG~~~~   57 (62)
T PF04703_consen    3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE--GKVERSPVRRGKSTY   57 (62)
T ss_dssp             HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC--TSEEEES-SSSSS-E
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEecCCCCccee
Confidence            6789999998888999999999999999999999999876  4555544  355443

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

Probab=90.64  E-value=0.53  Score=40.53  Aligned_cols=51  Identities=25%  Similarity=0.377  Sum_probs=42.2

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses  134 (280)
                      +++..+|++.|++. +|+|++|++..+|++.+.+++-|..|++  .|+|..+..
T Consensus        11 ~eLk~rIvElVRe~-GRiTi~ql~~~TGasR~Tvk~~lreLVa--~G~l~~~G~   61 (127)
T PF06163_consen   11 EELKARIVELVREH-GRITIKQLVAKTGASRNTVKRYLRELVA--RGDLYRHGR   61 (127)
T ss_pred             HHHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHH--cCCeEeCCC
Confidence            56667888888765 5899999999999999999999999886  577777554

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

Probab=90.22  E-value=0.83  Score=42.93  Aligned_cols=83  Identities=17%  Similarity=0.306  Sum_probs=69.3

Q ss_pred             cCCCcccccCCCCchHH---HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcc
Q 023574           68 VGPGRIVESDKLPADVR---NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNN  144 (280)
Q Consensus        68 ~~~~~~v~~~~l~~~~~---~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~  144 (280)
                      ++.||.----++|-+++   ..|+++++.+|| ||+.-+-+.-|-.-.-|.++|..|..+.=+-+.-...+|-.|-||.+
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            44556655566676665   579999999999 99999988889999999999999999998888888889999999999


Q ss_pred             hHHHHhh
Q 023574          145 YRAKLAA  151 (280)
Q Consensus       145 fRs~l~~  151 (280)
                      |-.....
T Consensus       238 ~~~~~~q  244 (249)
T KOG3341|consen  238 FTDQYAQ  244 (249)
T ss_pred             hhHHHhh
Confidence            9775543

>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=88.92  E-value=1.2  Score=32.22  Aligned_cols=41  Identities=12%  Similarity=0.282  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      +..|++.+++. +.+|+.|+|..-|.|...+++.|..|+...
T Consensus         2 ~~~Il~~l~~~-~~~s~~ela~~~~VS~~TiRRDl~~L~~~g   42 (57)
T PF08220_consen    2 QQQILELLKEK-GKVSVKELAEEFGVSEMTIRRDLNKLEKQG   42 (57)
T ss_pred             HHHHHHHHHHc-CCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            46789999876 689999999999999999999999998763

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=88.78  E-value=3.7  Score=28.11  Aligned_cols=60  Identities=25%  Similarity=0.424  Sum_probs=46.2

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC-cEEEEcC
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG-DVLYVFP  142 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG-EIlYvFP  142 (280)
                      +..+.+..++.++.+.+  ++..|+|...|++...+.+.|..|.+.  |.+....++ ...|.+.
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            34456678888888765  999999999999999999999999765  566665543 4556554

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=88.39  E-value=2  Score=28.40  Aligned_cols=45  Identities=16%  Similarity=0.338  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV  131 (280)
                      +..+++.+.+.+ .+|+.|++..-|++...+.+.|..|..+  |.++-
T Consensus         2 ~~~il~~l~~~~-~~s~~~l~~~l~~s~~tv~~~l~~L~~~--g~i~~   46 (53)
T smart00420        2 QQQILELLAQQG-KVSVEELAELLGVSEMTIRRDLNKLEEQ--GLLTR   46 (53)
T ss_pred             HHHHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEE
Confidence            356788888765 5999999999999999999999999876  44543

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=88.39  E-value=1.6  Score=29.32  Aligned_cols=49  Identities=20%  Similarity=0.391  Sum_probs=38.4

Q ss_pred             HHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574           87 AMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (280)
Q Consensus        87 im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY  139 (280)
                      |+..+.  ....|+.|++...|++...+.+.|..|.++  |-++....|.-.|
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~--g~i~~~~~~~~~~   50 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREA--GLVESRREGKRVY   50 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHC--CCeeeeecCCEEE
Confidence            566666  667899999999999999999999999975  5666555444433

>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=88.17  E-value=2.2  Score=29.60  Aligned_cols=42  Identities=10%  Similarity=0.193  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      +.+|++.+.+.+..+|..++|.+-|+|...+++.|..|-+..
T Consensus         2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            357888896666669999999999999999999999994443

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 ....

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=87.62  E-value=0.81  Score=36.14  Aligned_cols=34  Identities=12%  Similarity=0.081  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHH
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKAL  118 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL  118 (280)
                      -+..|++.+.+  +.+|+.|||..+|++.+.+.+.|
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            45678999999  99999999999999999998876

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.

>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=87.27  E-value=1.5  Score=34.37  Aligned_cols=44  Identities=20%  Similarity=0.459  Sum_probs=37.6

Q ss_pred             chHHHHHHHHHHH---cCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           81 ADVRNRAMDAVDA---CNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        81 ~~~~~~im~Ave~---lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      ..++.+|+++++.   ..-.+.+.+|+.+-|++.++++++|..|..+
T Consensus        46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e   92 (102)
T PF08784_consen   46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE   92 (102)
T ss_dssp             -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence            4578899999998   5667999999999999999999999999876

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.

>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=86.94  E-value=1.6  Score=41.17  Aligned_cols=57  Identities=18%  Similarity=0.367  Sum_probs=48.9

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl  138 (280)
                      |..++..|.+.+...|+|+++.|++..-++.++..|+.+..++.+-. +++.. .||++
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            45677889999999999999999999999999999999999998876 55543 68873

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.

>PRK15466 carboxysome structural protein EutK; Provisional

Probab=85.68  E-value=1.8  Score=38.79  Aligned_cols=41  Identities=24%  Similarity=0.404  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      .+.++.-+-...+..|.|+||+.-|.+|++++.+|..|-++
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (166)
T PRK15466        111 ADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA  151 (166)
T ss_pred             HHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhc
Confidence            46677778888999999999999999999999999999876

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

Probab=85.51  E-value=2.3  Score=31.51  Aligned_cols=39  Identities=21%  Similarity=0.360  Sum_probs=31.1

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      .+|.+.+-+.| +.|+.+++..++++.++++++|..|.+.
T Consensus        16 ~~V~~~Ll~~G-~ltl~~i~~~t~l~~~~Vk~~L~~LiQh   54 (62)
T PF08221_consen   16 AKVGEVLLSRG-RLTLREIVRRTGLSPKQVKKALVVLIQH   54 (62)
T ss_dssp             HHHHHHHHHC--SEEHHHHHHHHT--HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcC-CcCHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence            46677776665 9999999999999999999999999764

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.

>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=85.05  E-value=3.5  Score=29.93  Aligned_cols=53  Identities=21%  Similarity=0.312  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEE
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLY  139 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlY  139 (280)
                      ..++..++- ..+..|+.|||..+|++...+.+.|..|...  |-++..+...-+|
T Consensus        10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~--GlV~~~~~~~~~Y   62 (68)
T PF01978_consen   10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK--GLVEREEGRPKVY   62 (68)
T ss_dssp             HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT--TSEEEEEECCEEE
T ss_pred             HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEcCceEEE
Confidence            345666666 5678999999999999999999999999876  6667666443333

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.

>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=82.89  E-value=1.9  Score=31.86  Aligned_cols=53  Identities=23%  Similarity=0.245  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG  135 (280)
                      ++....+.-.++|...|..+||...|+++++.++.|.....-..=++.+..++
T Consensus         6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~   58 (78)
T PF04539_consen    6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDED   58 (78)
T ss_dssp             HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSS
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCC
Confidence            34445555668899999999999999999999888876544334444555443

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 ....

>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=82.39  E-value=2.8  Score=31.54  Aligned_cols=45  Identities=22%  Similarity=0.361  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCC-HHHHHHHHHHHHhhcCCceE
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLK-LNEAQKALQALAADTDGFLE  130 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~-L~~Ae~aL~aLAsD~~GhLq  130 (280)
                      -.-|.+.+++.|+-.|+.|+|..-|++ .+.+++-|.+|..+  |.|+
T Consensus        12 L~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k--G~I~   57 (65)
T PF01726_consen   12 LEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK--GYIR   57 (65)
T ss_dssp             HHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT--TSEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC--cCcc
Confidence            344566678899999999999999997 99999999999865  4444

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.

>smart00753 PAM PCI/PINT associated module

Probab=82.19  E-value=6.2  Score=29.55  Aligned_cols=68  Identities=15%  Similarity=0.178  Sum_probs=49.2

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR  146 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fR  146 (280)
                      |-...+.+.+..+-+.-..+|..++|...+++.+++|..|..+..+..=+-.++....+++.--..-|
T Consensus         6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r   73 (88)
T smart00753        6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR   73 (88)
T ss_pred             HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence            33455666666666677889999999999999999999999888885333345666566666544444

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

Probab=82.19  E-value=6.2  Score=29.55  Aligned_cols=68  Identities=15%  Similarity=0.178  Sum_probs=49.2

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcchH
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNYR  146 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~fR  146 (280)
                      |-...+.+.+..+-+.-..+|..++|...+++.+++|..|..+..+..=+-.++....+++.--..-|
T Consensus         6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r   73 (88)
T smart00088        6 LQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPR   73 (88)
T ss_pred             HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchh
Confidence            33455666666666677889999999999999999999999888885333345666566666544444

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

>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=82.13  E-value=4  Score=28.48  Aligned_cols=42  Identities=14%  Similarity=0.240  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           84 RNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        84 ~~~im~Ave~lg~R-vTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      +-+++.++...++. +|+.|+|...|++...+.+.+..|..+.
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            45678888888887 9999999999999999999999988763

...

---

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	280
3f2g_A	220	Alkylmercury lyase; MERB, organomercurial lyase, m	95.59
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	95.31
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.29
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.84
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	93.96
3r0a_A	123	Putative transcriptional regulator; structural gen	93.3
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	92.24
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	91.45
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	90.66
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	90.43
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	90.12
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	89.59
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	89.41
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	89.31
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	88.52
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	87.09
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	86.96
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	86.89
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	86.43
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.41
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	86.03
3jth_A	98	Transcription activator HLYU; transcription factor	85.33
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	84.85
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	84.25
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	83.87
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	83.71
2kko_A	108	Possible transcriptional regulatory protein (possi	83.3
1sfx_A	109	Conserved hypothetical protein AF2008; structural	82.43
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.15
2v9v_A	135	Selenocysteine-specific elongation factor; transcr	80.17

>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=95.59  E-value=0.013  Score=52.52  Aligned_cols=56  Identities=16%  Similarity=0.219  Sum_probs=49.0

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcC
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFP  142 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP  142 (280)
                      ...+.-.+++.+. .|.-+|+.++|+.+|.+.+++++.|..|.     .++.+++|+|+. ||
T Consensus        20 ~~~~~~~llr~la-~Grpv~~~~LA~~~g~~~~~v~~~L~~l~-----~~~~D~~G~Ivg-yp   75 (220)
T 3f2g_A           20 TADLLVPLLRELA-KGRPVSRTTLAGILDWPAERVAAVLEQAT-----STEYDKDGNIIG-YG   75 (220)
T ss_dssp             HHHHHHHHHHHHT-TTSCBCHHHHHHHHTCCHHHHHHHHHHCT-----TCEECTTSCEEE-SS
T ss_pred             chHHHHHHHHHHh-cCCCCCHHHHHHHhCcCHHHHHHHHHhCC-----cEEECCCCCEEE-ec
Confidence            3456677888888 99999999999999999999999999885     699999999977 64

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

Probab=95.31  E-value=0.027  Score=42.23  Aligned_cols=40  Identities=25%  Similarity=0.419  Sum_probs=37.1

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +.++.-+....+..|+|+||+.-|.+|++|+.+|..|-++
T Consensus         6 eaLLall~s~~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~   45 (68)
T 3i71_A            6 DELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSA   45 (68)
T ss_dssp             HHHHHHHHHCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhccccHHHHHHHhCCcHHHHHHHHHHHHhc
Confidence            5678888999999999999999999999999999999876

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

Probab=95.29  E-value=0.048  Score=39.21  Aligned_cols=51  Identities=10%  Similarity=0.143  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG  135 (280)
                      .+.+|++.+++.+..+|+.|+|.+.|++...+.+.|..|.++.-  ++.++.|
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            57899999999888899999999999999999999999987633  6555555

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

Probab=94.84  E-value=0.052  Score=40.91  Aligned_cols=43  Identities=21%  Similarity=0.296  Sum_probs=39.2

Q ss_pred             hHHHHHHHHHHHc-----CCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           82 DVRNRAMDAVDAC-----NRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        82 ~~~~~im~Ave~l-----g~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +-..+|++.+++.     |+.+|+.|+|..-|+|...+++.|.+|..+
T Consensus         4 ~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~k   51 (77)
T 2jt1_A            4 SIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDV   51 (77)
T ss_dssp             THHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            4567889999888     999999999999999999999999999876

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

Probab=93.96  E-value=0.095  Score=40.79  Aligned_cols=44  Identities=9%  Similarity=0.214  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      +..++|+++++..|.-+..||||..+|++..++.++|.+|-.+.
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            46899999999999999999999999999999999999998763

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

Probab=93.30  E-value=0.77  Score=35.92  Aligned_cols=84  Identities=14%  Similarity=0.200  Sum_probs=59.6

Q ss_pred             hHHHHHHHHHHHcCCc-eehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec----cCCcEEEEc-CcchHHHHhhhhHH
Q 023574           82 DVRNRAMDAVDACNRR-VTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS----DEGDVLYVF-PNNYRAKLAAKSFR  155 (280)
Q Consensus        82 ~~~~~im~Ave~lg~R-vTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs----esGEIlYvF-P~~fRs~l~~Ks~r  155 (280)
                      ..+.+|+.++.+.+.. +|+.|+|.+.|++...+.+.|..|....  -++-.    +.|-..|+| +.......  +-++
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--ILQRSQQNLDGGGYVYIYKIYSKNQIR--NIIQ  101 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTT--SEEEEEEECTTSCEEEEEEECCHHHHH--HHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEeeCCccCCCcceEEEecCCHHHHH--HHHH
Confidence            4467899999988877 9999999999999999999999998763  33322    234466666 33333322  4456


Q ss_pred             HhHHHHHHHhhhhh
Q 023574          156 LKVEPVIDKAKAAA  169 (280)
Q Consensus       156 ~rl~~~~~k~w~v~  169 (280)
                      ..+++|.+.+...+
T Consensus       102 ~~~~~~~~~~~~~l  115 (123)
T 3r0a_A          102 KIVQSWADRLGQEL  115 (123)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHH
Confidence            66777777766554

>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=92.24  E-value=0.39  Score=36.15  Aligned_cols=57  Identities=21%  Similarity=0.307  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEec-----cCCcEEEE
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVS-----DEGDVLYV  140 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVs-----esGEIlYv  140 (280)
                      +.+.+|+..+-+.|..+|+.|+|...|++...+.++|..|..+.  -++..     ..|-.+|.
T Consensus        18 ~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~G--lV~~~~~~~~~~g~~v~~   79 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQG--FVSYRKTRDKDSGWFIYY   79 (110)
T ss_dssp             STTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHT--SCEEEEEC---CCCCEEE
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC--CEEEEecccCCCceEEEE
Confidence            45678898887788789999999999999999999999999874  35544     45777773

>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=91.45  E-value=0.55  Score=41.39  Aligned_cols=69  Identities=20%  Similarity=0.251  Sum_probs=53.6

Q ss_pred             cccCCCC-chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcch
Q 023574           74 VESDKLP-ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (280)
Q Consensus        74 v~~~~l~-~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~f  145 (280)
                      |++..-. .....+|++.++.. +.+|+.++|..-|.+..-|+..|..+-.  .|-|=+++++|-+|.||.-|
T Consensus       145 vqs~~~~~~~~~~~il~~~~~~-g~vt~~~la~~l~ws~~~a~e~L~~~e~--~G~l~~D~~~eg~~y~pn~f  214 (218)
T 3cuq_B          145 IELQSHKEEEMVASALETVSEK-GSLTSEEFAKLVGMSVLLAKERLLLAEK--MGHLCRDDSVEGLRFYPNLF  214 (218)
T ss_dssp             EEETTCCGGGGHHHHHHHHHHT-SCBCHHHHHHHHTCCHHHHHHHHHHHHH--TTSEEEEESSSCEEEEECGG
T ss_pred             EEcCCCchHHHHHHHHHHHHHC-CCcCHHHHHHHhCCCHHHHHHHHHHHHH--cCCEEEECCCCceEEehhhc
Confidence            5554332 35678888888865 5699999999999999999999988555  67777777777788899655

>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=90.66  E-value=0.28  Score=37.06  Aligned_cols=45  Identities=24%  Similarity=0.353  Sum_probs=39.9

Q ss_pred             CchHHHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg--~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      ..+...+|++++++.+  .++|+.|+|.+-|++...+++.|..|..+
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~   54 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK   54 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3466788999999887  48999999999999999999999999865

>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=90.43  E-value=0.33  Score=36.86  Aligned_cols=58  Identities=12%  Similarity=0.184  Sum_probs=47.2

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHH-HHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLN-EAQKALQALAADTDGFLEVSDEGDVLYVF  141 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~-~Ae~aL~aLAsD~~GhLqVsesGEIlYvF  141 (280)
                      ++.+++|++.+++.| ..|+.|+|..-|++.. .+++.|..|..+  |-++-...|-.+|.-
T Consensus        10 ~~~~~~IL~~Lk~~g-~~ta~eiA~~Lgit~~~aVr~hL~~Le~e--GlV~~~~~gRP~w~L   68 (79)
T 1xmk_A           10 AEIKEKICDYLFNVS-DSSALNLAKNIGLTKARDINAVLIDMERQ--GDVYRQGTTPPIWHL   68 (79)
T ss_dssp             HHHHHHHHHHHHHTC-CEEHHHHHHHHCGGGHHHHHHHHHHHHHT--TSEEEECSSSCEEEE
T ss_pred             hhHHHHHHHHHHHcC-CcCHHHHHHHcCCCcHHHHHHHHHHHHHC--CCEEecCCCCCCeEe
Confidence            367899999999998 5899999999999999 999999999886  344434456666654

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

Probab=90.12  E-value=0.49  Score=34.19  Aligned_cols=45  Identities=16%  Similarity=0.218  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEe
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEV  131 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqV  131 (280)
                      +.+|++.+.+.+ .+|+.|+|...|++...+.+.|..|.++  |-++.
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            578899998764 6999999999999999999999999876  55663

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

Probab=89.59  E-value=0.81  Score=32.76  Aligned_cols=60  Identities=10%  Similarity=0.125  Sum_probs=46.1

Q ss_pred             chHHHHHHHHHHHcC-Cceehhhhhhhc-----CCCHHHHHHHHHHHHhhcCCceEeccCCcEEEE
Q 023574           81 ADVRNRAMDAVDACN-RRVTIGDVAGKA-----GLKLNEAQKALQALAADTDGFLEVSDEGDVLYV  140 (280)
Q Consensus        81 ~~~~~~im~Ave~lg-~RvTvGDVAa~a-----GL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYv  140 (280)
                      ...+..|++++.+.+ ..+|+.|++...     +++...+-+.|..|....-=+=...++|...|.
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            356788999998876 789999999998     999999999999998874332222234666664

>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=89.41  E-value=0.43  Score=35.29  Aligned_cols=45  Identities=24%  Similarity=0.353  Sum_probs=39.9

Q ss_pred             CchHHHHHHHHHHHcC--CceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           80 PADVRNRAMDAVDACN--RRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg--~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      ..+...+|++++++.+  .++|+.|+|.+-|++...+++.|..|..+
T Consensus        12 ~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~   58 (77)
T 1qgp_A           12 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3456788999999988  58999999999999999999999999765

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A

Probab=89.31  E-value=0.69  Score=41.72  Aligned_cols=69  Identities=19%  Similarity=0.340  Sum_probs=51.7

Q ss_pred             ccccCC--CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEEEEcCcch
Q 023574           73 IVESDK--LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLYVFPNNY  145 (280)
Q Consensus        73 ~v~~~~--l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse--sGEIlYvFP~~f  145 (280)
                      .|+|..  |.++. .+++++++. .+.||+.+++..-|.+..-|+.+|..|..+  |.|=|++  +||-.|-||.-|
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-TVVLQLAEK-NGYVTVSEIKASLKWETERARQVLEHLLKE--GLAWLDLQAPGEAHYWLPALF  216 (234)
T ss_dssp             EEECSCCCCCHHH-HHHHHHHTT-TSEECHHHHHHHHTCCHHHHHHHHHHHHHH--TSCEEESSSSSSCEEECTTSS
T ss_pred             EEEeCCCccchHH-HHHHHHHHh-cCcCcHHHHHHHhCCCHHHHHHHHHHHHhC--CCEEEeCCCCCcceeecchhh
Confidence            344443  44444 446777764 467999999999999999999999997766  4555554  589999999655

>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=88.52  E-value=0.47  Score=42.76  Aligned_cols=59  Identities=17%  Similarity=0.281  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC--CcEEEEcCcch
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE--GDVLYVFPNNY  145 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses--GEIlYvFP~~f  145 (280)
                      ..++++.++. .+.||+.+++..-|.+..-|+.+|..|..+  |.|=|+++  ||..|-||..|
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 QTKILEICSI-LGYSSISLLKANLGWEAVRSKSALDEMVAN--GLLWIDYQGGAEALYWDPSWI  229 (233)
T ss_dssp             HHHHHHTTTT-TSCCBHHHHHHHHCCCSHHHHHHHHHHHHT--TSSEEECSSSSSCEEECGGGG
T ss_pred             HHHHHHHHHh-cCcCcHHHHHHHhCCCHHHHHHHHHHHHHC--CCEEEeCCCCCccceechhhh
Confidence            3556677765 567999999999999999999999987655  66666664  58899999665

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

Probab=87.09  E-value=1.4  Score=31.65  Aligned_cols=59  Identities=14%  Similarity=0.330  Sum_probs=45.9

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-EEEEc
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGE-IlYvF  141 (280)
                      ....+.+|+.++.+ ++..|+.|+|...|++...+.+.|..|..  .|-++...+|. ..|..
T Consensus        22 ~~~~~~~il~~l~~-~~~~s~~ela~~l~is~~tvs~~l~~L~~--~glv~~~~~~r~~~y~l   81 (99)
T 3cuo_A           22 SHPKRLLILCMLSG-SPGTSAGELTRITGLSASATSQHLARMRD--EGLIDSQRDAQRILYSI   81 (99)
T ss_dssp             CSHHHHHHHHHHTT-CCSEEHHHHHHHHCCCHHHHHHHHHHHHH--TTSEEEEECSSCEEEEE
T ss_pred             CChHHHHHHHHHHh-CCCcCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEEE
Confidence            34667889998865 66899999999999999999999999963  56676666554 44544

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

Probab=86.96  E-value=6.3  Score=29.03  Aligned_cols=59  Identities=20%  Similarity=0.234  Sum_probs=44.8

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcE-EEEc
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDV-LYVF  141 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEI-lYvF  141 (280)
                      |....+.+|+..+ ..| ..|+.|+|...|++...+.+.|..|..  .|-++...+|.- .|..
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 489999999999999999999999964  466766655654 3443

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

Probab=86.89  E-value=4.4  Score=30.99  Aligned_cols=59  Identities=15%  Similarity=0.282  Sum_probs=46.9

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-EEEEc
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGE-IlYvF  141 (280)
                      |....|.+|+..+.  .+..|++|+|...|++...+-+-|..|..  .|-++...+|. +.|..
T Consensus        15 l~~~~R~~Il~~L~--~~~~~~~eLa~~l~is~~tvs~hL~~L~~--~GlV~~~~~gr~~~y~l   74 (118)
T 3f6o_A           15 LADPTRRAVLGRLS--RGPATVSELAKPFDMALPSFMKHIHFLED--SGWIRTHKQGRVRTCAI   74 (118)
T ss_dssp             HTSHHHHHHHHHHH--TCCEEHHHHHTTCCSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHhCcCHHHHHHHHHHHHH--CCCeEEEecCCEEEEEE
Confidence            34567889999997  46789999999999999999999999964  56777777765 44444

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

Probab=86.43  E-value=1.2  Score=32.80  Aligned_cols=46  Identities=17%  Similarity=0.138  Sum_probs=42.4

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      .|-....+++.++..|+-+-+.++|++-|++.+++-..|..|+++.
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            4666789999999999999999999999999999999999999873

>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=86.41  E-value=1.4  Score=32.51  Aligned_cols=54  Identities=15%  Similarity=0.198  Sum_probs=42.5

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF  141 (280)
                      ....+.+|++.+   .+..|++|+|.+.|++...+.+.|..|...  |-++... |  .|..
T Consensus        29 ~~~~r~~Il~~L---~~~~~~~eLa~~l~is~~tv~~~L~~L~~~--Glv~~~~-g--~y~l   82 (96)
T 1y0u_A           29 TNPVRRKILRML---DKGRSEEEIMQTLSLSKKQLDYHLKVLEAG--FCIERVG-E--RWVV   82 (96)
T ss_dssp             SCHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEET-T--EEEE
T ss_pred             CCHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC--CCEEEEC-C--EEEE
Confidence            345677889988   345999999999999999999999999765  5666555 5  4544

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

Probab=86.03  E-value=0.95  Score=34.83  Aligned_cols=42  Identities=19%  Similarity=0.270  Sum_probs=37.7

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      .++..+|++.+++.|  .|+.|+|.+-|++...+++-|..|..+
T Consensus        16 ~~~~~~IL~lL~~~g--~sa~eLAk~LgiSk~aVr~~L~~Le~e   57 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEG--ATAAQLTRQLNMEKREVNKALYDLQRS   57 (82)
T ss_dssp             HHHHHHHHHHHSSST--EEHHHHHHHSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC--CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            357788999999766  999999999999999999999999776

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

Probab=85.33  E-value=1.3  Score=32.38  Aligned_cols=58  Identities=19%  Similarity=0.374  Sum_probs=46.7

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc-EEEEc
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD-VLYVF  141 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGE-IlYvF  141 (280)
                      ....+.+|+..+.+  +..|++|+|...|++...+.+.|..|..  .|-++...+|. +.|..
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  6899999999999999999999999965  56777777765 44544

>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=84.85  E-value=2.3  Score=31.88  Aligned_cols=59  Identities=15%  Similarity=0.259  Sum_probs=47.2

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF  141 (280)
                      |....+.+|+..+.  .+..|++|+|...|++...+.+.|..|.  ..|-++...+|.-+|..
T Consensus        23 l~~~~r~~IL~~L~--~~~~~~~ela~~l~is~stvs~~L~~L~--~~Glv~~~~~gr~~~y~   81 (106)
T 1r1u_A           23 LGDYNRIRIMELLS--VSEASVGHISHQLNLSQSNVSHQLKLLK--SVHLVKAKRQGQSMIYS   81 (106)
T ss_dssp             TCSHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHH--HTTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHHH--HCCCeEEEEeCCEEEEE
Confidence            44567788999997  3458999999999999999999999997  46777777777755544

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

Probab=84.25  E-value=2.8  Score=34.25  Aligned_cols=59  Identities=15%  Similarity=0.257  Sum_probs=47.7

Q ss_pred             CCchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574           79 LPADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (280)
Q Consensus        79 l~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF  141 (280)
                      |....|-+|+..+.  .+..|++|+|...|++...+-+-|..|..  -|-++...+|.-+|..
T Consensus        55 L~~p~R~~IL~~L~--~~~~t~~eLa~~lgls~stvs~hL~~L~~--aGlV~~~~~Gr~~~y~  113 (151)
T 3f6v_A           55 AAEPTRRRLVQLLT--SGEQTVNNLAAHFPASRSAISQHLRVLTE--AGLVTPRKDGRFRYYR  113 (151)
T ss_dssp             HTSHHHHHHHHHGG--GCCEEHHHHHTTSSSCHHHHHHHHHHHHH--TTSEEEEEETTEEEEE
T ss_pred             hCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHHHH--CCCEEEEecCCEEEEE
Confidence            34577899999997  35699999999999999999999999965  4677777777665554

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

Probab=83.87  E-value=1.6  Score=32.69  Aligned_cols=42  Identities=12%  Similarity=0.032  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      .-.+|++.+++. +++|+.|+|..-+++...+++.|..|....
T Consensus         3 ~L~~Il~~L~~~-g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G   44 (78)
T 1xn7_A            3 SLIQVRDLLALR-GRMEAAQISQTLNTPQPMINAMLQQLESMG   44 (78)
T ss_dssp             CHHHHHHHHHHS-CSBCHHHHHHHTTCCHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHc-CCCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            346788898775 579999999999999999999999999873

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

Probab=83.71  E-value=1.5  Score=33.76  Aligned_cols=42  Identities=10%  Similarity=0.014  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      .-.+|++.|++. +++|+.|+|..-|++...+++.|..|....
T Consensus         3 ~L~~Il~~L~~~-g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G   44 (87)
T 2k02_A            3 SLMEVRDMLALQ-GRMEAKQLSARLQTPQPLIDAMLERMEAMG   44 (87)
T ss_dssp             CTHHHHHHHHHS-CSEEHHHHHHHTTCCHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHc-CCCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            346788998775 689999999999999999999999998763

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

Probab=83.30  E-value=2.1  Score=32.43  Aligned_cols=57  Identities=26%  Similarity=0.390  Sum_probs=45.6

Q ss_pred             chHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEc
Q 023574           81 ADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVF  141 (280)
Q Consensus        81 ~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvF  141 (280)
                      ...+.+|+..+..  +..|++|+|...|++...+.+.|..|..  .|-++...+|.-+|..
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            4456789998864  6789999999999999999999999975  4677777777655543

>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=82.43  E-value=11  Score=26.75  Aligned_cols=57  Identities=18%  Similarity=0.241  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEecc--CCcEEEEc
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSD--EGDVLYVF  141 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVse--sGEIlYvF  141 (280)
                      ..+-+|+..+.+. +..|+.|+|...|++...+.+.|..|..+  |-++...  ++...|.+
T Consensus        20 ~~~~~il~~l~~~-~~~s~~ela~~l~is~~tv~~~l~~L~~~--glv~~~~~~~~r~~~~~   78 (109)
T 1sfx_A           20 PSDVRIYSLLLER-GGMRVSEIARELDLSARFVRDRLKVLLKR--GFVRREIVEKGWVGYIY   78 (109)
T ss_dssp             HHHHHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT--TSEEEEEEESSSEEEEE
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEeecCCceEEEE
Confidence            4567888998765 45999999999999999999999999776  4444433  45555544

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

Probab=81.15  E-value=1.4  Score=34.12  Aligned_cols=38  Identities=13%  Similarity=0.095  Sum_probs=32.7

Q ss_pred             CchHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHH
Q 023574           80 PADVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQ  119 (280)
Q Consensus        80 ~~~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~  119 (280)
                      +.+-+.+|++.+.+.+  +|+.|||..+|+|...+.+.|.
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            4456678899999887  9999999999999999988873

>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=80.17  E-value=14  Score=28.39  Aligned_cols=61  Identities=20%  Similarity=0.230  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcch
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~f  145 (280)
                      ....+...++..+..++..|++..+|++.++.++.|..|.+... -+.+..+++..| +..++
T Consensus         3 ~~~~l~~~L~~~~~~~~~~~l~~~~~l~~~~l~~~l~~l~~~~~-~~~~~~~~~~~~-~~~~~   63 (135)
T 2v9v_A            3 PEKILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQ-VTLLRVENDLYA-ISTER   63 (135)
T ss_dssp             HHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTC-EEEEEETTEEEE-EEHHH
T ss_pred             HHHHHHHHHHHcCcCCCHHHHHHHhCCCHHHHHHHHHHHHhCCc-EEEEecCCCeEE-ecHHH
Confidence            34567788888888887799999999999999988888875543 555544344334 53333

---

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	280
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	94.09
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	88.09
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	86.62
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	85.7
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	85.6
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	85.55
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	85.19
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	84.86
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	84.16
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	83.47
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	81.35

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.09  E-value=0.032  Score=40.25  Aligned_cols=61  Identities=13%  Similarity=0.211  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEEEEcCcch
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVLYVFPNNY  145 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIlYvFP~~f  145 (280)
                      +..|+++++.. +.||+..+-..-|-+.+-|+.+|..|..+.=+=+.--..||..|=||.-|
T Consensus         5 qt~vLe~a~~~-G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD~Q~~~e~~YWfPsl~   65 (68)
T d1u5ta2           5 QTKILEICSIL-GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWI   65 (68)
T ss_dssp             HHHHHHTTTTT-SCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEECGGGG
T ss_pred             HHHHHHHHHHc-CceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEecCCCCCceeeChHhh
Confidence            35788888887 58999999999999999999999999886555554444589999999765

>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=88.09  E-value=0.52  Score=31.99  Aligned_cols=52  Identities=8%  Similarity=0.059  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCC
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEG  135 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesG  135 (280)
                      -..+|++.+.+..+.+|+.|+|..-|+|...+.+.|.+|.+ .|..++.+..|
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            34678888888888899999999999999999999999964 45556554433

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

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

Probab=86.62  E-value=0.099  Score=37.01  Aligned_cols=41  Identities=20%  Similarity=0.269  Sum_probs=34.3

Q ss_pred             HcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCcEE
Q 023574           93 ACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGDVL  138 (280)
Q Consensus        93 ~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGEIl  138 (280)
                      ..|.-||+.++|...|-+.++++.+|.++.     .-|-+++|.||
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            468889999999999999999999998776     45666777765

>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=85.70  E-value=0.61  Score=32.40  Aligned_cols=49  Identities=18%  Similarity=0.303  Sum_probs=42.4

Q ss_pred             HHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccCCc
Q 023574           86 RAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDEGD  136 (280)
Q Consensus        86 ~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVsesGE  136 (280)
                      +|++++...+..+|+.|+|.+.|++...+-+-|..|...  |.|+=+++|.
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            578889999999999999999999999998888888764  6777667775

>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=85.60  E-value=3.6  Score=29.61  Aligned_cols=66  Identities=11%  Similarity=-0.020  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC-CcEEEEcCcchHHHH
Q 023574           83 VRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE-GDVLYVFPNNYRAKL  149 (280)
Q Consensus        83 ~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses-GEIlYvFP~~fRs~l  149 (280)
                      .+-+++.++-+. +..|+.|||..+|++...+-..|..|..+.=-.=+.+++ |...+..|..-...+
T Consensus        21 ~e~~v~~~L~~~-g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l   87 (109)
T d1sfxa_          21 SDVRIYSLLLER-GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVL   87 (109)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHH
T ss_pred             HHHHHHHHHHhc-CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHH
Confidence            345677777655 578999999999999999999999998875433334444 444445566655544

>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=85.55  E-value=1  Score=30.79  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHHcC-CceehhhhhhhcCCCHHHHHHHHHHHHhhcCCceEeccC
Q 023574           82 DVRNRAMDAVDACN-RRVTIGDVAGKAGLKLNEAQKALQALAADTDGFLEVSDE  134 (280)
Q Consensus        82 ~~~~~im~Ave~lg-~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~~GhLqVses  134 (280)
                      .+..+|.++.++.| .--|+-|||...|++..++ +.+..++.+.|=-.+|+++
T Consensus         7 ~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~-~~lL~~l~~~G~lvkI~~d   59 (64)
T d1lvaa3           7 KLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSEL-EELLHYLVREGVLVKINDE   59 (64)
T ss_dssp             HHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHH-HHHHHHHHHTTSEEESSSS
T ss_pred             HHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHH-HHHHHHHHHCCCEEEeccc
Confidence            56789999999988 5679999999999999999 4555555566666666553

>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=85.19  E-value=0.59  Score=31.36  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=28.8

Q ss_pred             HHHHHHcCCceehhhhhhhcCCCHHHHHHHHHH
Q 023574           88 MDAVDACNRRVTIGDVAGKAGLKLNEAQKALQA  120 (280)
Q Consensus        88 m~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~a  120 (280)
                      -+...++|...|..+||...|++.+++..+|.+
T Consensus        22 ~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          22 DELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344567899999999999999999999998875

>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=84.86  E-value=0.69  Score=31.46  Aligned_cols=41  Identities=15%  Similarity=0.157  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc
Q 023574           84 RNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT  125 (280)
Q Consensus        84 ~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~  125 (280)
                      +.+|++.+.+.| .+|..|+|...||+...+.+-|..|.++.
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            457899998765 69999999999999999999999998763

>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=84.16  E-value=0.95  Score=30.60  Aligned_cols=42  Identities=10%  Similarity=0.237  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +...+|++++++ +.|.|..|+|...|++..++.+-+..|-.+
T Consensus         5 ~~D~~IL~~L~~-n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~   46 (63)
T d2cfxa1           5 QIDLNIIEELKK-DSRLSMRELGRKIKLSPPSVTERVRQLESF   46 (63)
T ss_dssp             HHHHHHHHHHHH-CSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            356788999987 579999999999999999999999999776

>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=83.47  E-value=0.71  Score=34.44  Aligned_cols=57  Identities=18%  Similarity=0.221  Sum_probs=44.4

Q ss_pred             HHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhhc--CCceEe-ccCCcEEEEc
Q 023574           85 NRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAADT--DGFLEV-SDEGDVLYVF  141 (280)
Q Consensus        85 ~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD~--~GhLqV-sesGEIlYvF  141 (280)
                      -++++++-..+.-+|=-++|.++|++++++++.|..|....  ...=+- .++|=.+|..
T Consensus        21 ~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd~~~gw~~Y~W   80 (88)
T d1q1ha_          21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYW   80 (88)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEE
T ss_pred             HHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEEEeecCCCCcEEEEE
Confidence            35788887788999999999999999999999999998874  222222 3358888865

>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=81.35  E-value=1.3  Score=29.73  Aligned_cols=42  Identities=10%  Similarity=0.218  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHHcCCceehhhhhhhcCCCHHHHHHHHHHHHhh
Q 023574           82 DVRNRAMDAVDACNRRVTIGDVAGKAGLKLNEAQKALQALAAD  124 (280)
Q Consensus        82 ~~~~~im~Ave~lg~RvTvGDVAa~aGL~L~~Ae~aL~aLAsD  124 (280)
                      +...+|++.+++. .|.|..|+|.+.|+|...+..-+..|-++
T Consensus         5 ~~D~~IL~~L~~~-~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~   46 (63)
T d2cg4a1           5 NLDRGILEALMGN-ARTAYAELAKQFGVSPETIHVRVEKMKQA   46 (63)
T ss_dssp             HHHHHHHHHHHHC-TTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4567888888865 88999999999999999999999999876