Citrus Sinensis ID: 029662

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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
Protein Sequence
MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDEKISRTGPLDGGDHREGNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPESSNKERNYP
Secondary Structure (PSIPRED)
ccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHcHHHHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccHcccccHHHHHHHHccEEEccccccccccccHHHEccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccHHHHHHHccccHHHHHHHHEEccccccccccccccc
Coil and Loop (DISEMBL)
mgqafrrasgritssssttssssktknvvdrgprvvptdekisrtgpldggdhregnrpvntgnvleerdpQYDAMLNQMLGRVktkaggkaemgEAAVVErqtrplpklrnttpvssryeekpsppgtlnVAQLRRIMLLHqgkaddhngpldAKQIAEKFRLDVLQVQAILQClslppessnkernyp
Flexible Loop (DISEMBL)
mgqafrrasgritssssttssssktknvvdrgprvvptdekisrtgpldggdhregnrpvntgnvleeRDPQYDAMLNQMLGRVKTKaggkaemgeaavverqtrplpklrnttpvssryeekpsppgtlnVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILqclslppessnkernyp
Low Complexity Region (SEG)
MGQAFRRASGRItssssttssssktkNVVDRGPRVVPTDEKISRTGPLDGGDHREGNRPVNTGNVLEERDPQYDAMLNQMLGRVKTkaggkaemgeaavveRQTRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPESSNKERNYP
Disordered region (IsUnstruct)
***********************************************************************************************************************************VAQLRRIMLLHQ*********LDAKQIAEKFRLDVLQVQAILQCLS*************
Disordered Region (DISOPRED)
*****************************************************************LEERDPQYDAMLNQMLG****************VVERQ**************************LNVAQLRRIMLLHQ************KQIAEKFRLDVLQVQAILQCL**************
Disordered Region (DISEMBL)
*******************************GPRVVPTDEKISRTGPLDGGDHREGNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNT**************GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPP**********
Disordered Region (DISPRO)
*****************************************************************L*ERDPQYDAMLNQMLGRVKTKAG********A**ERQTRPLPKLRNT********EKPSPPGTLNVAQLRRIMLLHQGKAD***GPLDAKQIAEKFRLDVLQVQAILQCLSLPP**********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDEKISRTGPLDGGDHREGNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPESSNKERNYP
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

No hits with e-value below 0.001 by BLAST

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	190
255551715	190	conserved hypothetical protein [Ricinus	0.973	0.973	0.642	4e-58
225432280	192	PREDICTED: uncharacterized protein LOC10	0.989	0.979	0.613	2e-57
449530794	189	PREDICTED: uncharacterized protein LOC10	0.947	0.952	0.588	3e-55
351724023	195	uncharacterized protein LOC100527797 [Gl	0.989	0.964	0.596	1e-54
356529714	191	PREDICTED: uncharacterized protein LOC10	0.968	0.963	0.581	5e-52
224123106	187	predicted protein [Populus trichocarpa]	0.968	0.983	0.586	1e-50
297835110	189	hypothetical protein ARALYDRAFT_898585 [	0.942	0.947	0.564	3e-49
15232549	188	uncharacterized protein [Arabidopsis tha	0.942	0.952	0.552	8e-48
388515547	139	unknown [Medicago truncatula]	0.657	0.899	0.688	6e-45
449450902	144	PREDICTED: uncharacterized protein LOC10	0.668	0.881	0.645	3e-44

>gi|255551715|ref|XP_002516903.1| conserved hypothetical protein [Ricinus communis] gi|223543991|gb|EEF45517.1| conserved hypothetical protein [Ricinus communis]

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 124/193 (64%), Positives = 146/193 (75%), Gaps = 8/193 (4%)

Query: 1   MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDE-KISRT-GPLDGGDH--REG 56
           MGQAFRRASGRI     TT+ S   K V DR P +   D  +ISRT G  +  D+   +G
Sbjct: 1   MGQAFRRASGRI----GTTNPSPTPKTVSDRRPPLRTNDNVEISRTAGQYNNQDNLDSDG 56

Query: 57  NRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPV 116
              VN  NVLEERDPQ+DAML+QM+GR+KTK GGK EM EAAVVER  RP+PKLRNTT  
Sbjct: 57  GSRVNVDNVLEERDPQFDAMLSQMVGRIKTKPGGKDEMAEAAVVERYNRPMPKLRNTTLD 116

Query: 117 SSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL 176
           S+RYEE+P+PPGTLNVAQLR+IMLLHQGKAD  N P+D  QIAEKFRL+V QVQ IL+ +
Sbjct: 117 SARYEERPAPPGTLNVAQLRQIMLLHQGKADGQNAPIDIHQIAEKFRLEVAQVQQILEFV 176

Query: 177 SLPPESSNKERNY 189
           SLPPE SNK+++Y
Sbjct: 177 SLPPEESNKQKDY 189

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432280|ref|XP_002272645.1| PREDICTED: uncharacterized protein LOC100252927 [Vitis vinifera] gi|297736864|emb|CBI26065.3| unnamed protein product [Vitis vinifera]

 Score =  227 bits (579), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 116/189 (61%), Positives = 140/189 (74%), Gaps = 1/189 (0%)

Query: 1   MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDE-KISRTGPLDGGDHREGNRP 59
           MGQAFRRASG +  +    SSSS  KNV DR P  VP D+  +S+T    G    EG   
Sbjct: 1   MGQAFRRASGSVRRADLDPSSSSHLKNVGDRRPPAVPVDKVGVSKTRDDIGSGSSEGAPR 60

Query: 60  VNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSR 119
            N+ N LEERDPQYDAML+QM+GR+++K+GG+ EMGEA V  R  RP+PKLRNT P S R
Sbjct: 61  FNSENFLEERDPQYDAMLSQMVGRIRSKSGGRLEMGEALVGGRYNRPMPKLRNTKPESGR 120

Query: 120 YEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLP 179
           YEEKP+P GTLN AQLR I+LLHQGKADDH+GP++ KQIAEKFR+D   V++ILQ LSLP
Sbjct: 121 YEEKPAPSGTLNAAQLRHILLLHQGKADDHDGPMNVKQIAEKFRIDATMVKSILQFLSLP 180

Query: 180 PESSNKERN 188
           PE S K++N
Sbjct: 181 PEDSTKQKN 189

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449530794|ref|XP_004172377.1| PREDICTED: uncharacterized protein LOC101223829 isoform 1 [Cucumis sativus] gi|449530796|ref|XP_004172378.1| PREDICTED: uncharacterized protein LOC101223829 isoform 2 [Cucumis sativus]

 Score =  219 bits (559), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 113/192 (58%), Positives = 148/192 (77%), Gaps = 12/192 (6%)

Query: 1   MGQAFRRASGRI---TSSSSTTSSSSKTKNVVDRGP--RVVPTDEKISRTGPLDGGDHRE 55
           MGQAFRRA+GRI   +S  STT+SS K +++VDR P  RV    EK   +G LD GD   
Sbjct: 1   MGQAFRRAAGRIKPASSIDSTTASSLKMESIVDRKPPPRVA---EKARESGALDSGDVPA 57

Query: 56  GNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTP 115
            +    +GN+LEERDPQ+DAML+QM+GR+K+K GGK EMGEA+VVER  RP+PKLR+T  
Sbjct: 58  SD----SGNMLEERDPQFDAMLSQMVGRIKSKPGGKLEMGEASVVERYGRPMPKLRDTNI 113

Query: 116 VSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175
            SS+YE++P+PPGTLNVAQ+R+I+LLH+GKADDH+GP+   QIAE++ + V Q+Q ILQ 
Sbjct: 114 SSSKYEDRPAPPGTLNVAQMRQIILLHEGKADDHDGPMGLHQIAERYNVSVAQIQTILQF 173

Query: 176 LSLPPESSNKER 187
           LSLPPE S +++
Sbjct: 174 LSLPPEDSLRDK 185

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724023|ref|NP_001237555.1| uncharacterized protein LOC100527797 [Glycine max] gi|255633234|gb|ACU16973.1| unknown [Glycine max]

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 114/191 (59%), Positives = 142/191 (74%), Gaps = 3/191 (1%)

Query: 1   MGQAFRRASGRI-TSSSSTTSSSSKTKNVVDRGPRVVPTDEKISRTGPLDGGD--HREGN 57
           MGQAFRRASGRI  +S + TSS SK+K  VDR P      +K ++       D  H +  
Sbjct: 1   MGQAFRRASGRIRAASEADTSSFSKSKTAVDRQPPPNAAADKAAQIPKAAEQDVLHTDDR 60

Query: 58  RPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVS 117
             VNT N+LEERDP++DAML QM+GR+ +K GGK EMGEA VVE+  RP+PKLRNT P  
Sbjct: 61  PRVNTDNILEERDPKFDAMLGQMVGRITSKPGGKPEMGEAFVVEKFNRPMPKLRNTKPDF 120

Query: 118 SRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177
            R EE+P P GTLNVAQLR I+LLH+GKADD+NG +DA QIAEKFR++V+Q+Q ILQ LS
Sbjct: 121 GRNEERPVPAGTLNVAQLRHIILLHEGKADDYNGRMDAHQIAEKFRVNVVQIQTILQFLS 180

Query: 178 LPPESSNKERN 188
           LPPE+S+K++N
Sbjct: 181 LPPENSSKDKN 191

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529714|ref|XP_003533433.1| PREDICTED: uncharacterized protein LOC100806944 [Glycine max]

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 111/191 (58%), Positives = 139/191 (72%), Gaps = 7/191 (3%)

Query: 1   MGQAFRRASGRI-TSSSSTTSSSSKTKNVVDRGPRVVPTDEKISRTGPLDGGD--HREGN 57
           MGQAFRRASGRI  +S + TSS SK KN VDR P      +K ++       D  H   +
Sbjct: 1   MGQAFRRASGRIRAASEADTSSFSKPKNAVDRRPPPNAAADKAAQIPKAAEHDVLHANDS 60

Query: 58  RPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVS 117
             VNT N+LEERDP++DAML QM+GR+ +K     EMGEA VV++  RP+PKLRNT P S
Sbjct: 61  PRVNTDNILEERDPKFDAMLGQMIGRITSKP----EMGEAFVVDKYNRPMPKLRNTKPDS 116

Query: 118 SRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS 177
            RY+E+P P GTLNVAQLR ++LLH+GKADD+NG +DA QIAEKFR+DV+Q+Q ILQ LS
Sbjct: 117 GRYDERPVPAGTLNVAQLRHVILLHEGKADDYNGRMDAHQIAEKFRVDVVQIQRILQFLS 176

Query: 178 LPPESSNKERN 188
            PPE S+K++N
Sbjct: 177 QPPEGSSKDKN 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123106|ref|XP_002330340.1| predicted protein [Populus trichocarpa] gi|118483035|gb|ABK93428.1| unknown [Populus trichocarpa] gi|222871544|gb|EEF08675.1| predicted protein [Populus trichocarpa]

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 112/191 (58%), Positives = 136/191 (71%), Gaps = 7/191 (3%)

Query: 1   MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDE-KISRTGPLDGGDHREGNRP 59
           MGQAFRRASGRI +      S      V DR P V  T++ +IS T   +         P
Sbjct: 1   MGQAFRRASGRIRAPPDPPPS-----RVTDRRPPVTSTEKVEISSTTTTNQNSPGSDGAP 55

Query: 60  -VNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSS 118
            +N  NVLEERD QYDAML+QM+GR+K+K GGK E GEA VVER  RP+PKLRNT P S 
Sbjct: 56  RINPDNVLEERDTQYDAMLSQMVGRIKSKPGGKLETGEAPVVERYDRPMPKLRNTKPDSG 115

Query: 119 RYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL 178
           RYEE+   PGTLNVAQLR I+L++QGKADDH GP++ +QIAEKFRL+V QVQ ILQ LSL
Sbjct: 116 RYEERAVAPGTLNVAQLRHIILMYQGKADDHEGPMNIQQIAEKFRLEVAQVQRILQFLSL 175

Query: 179 PPESSNKERNY 189
           PPE +NK++++
Sbjct: 176 PPEDNNKQKSH 186

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297835110|ref|XP_002885437.1| hypothetical protein ARALYDRAFT_898585 [Arabidopsis lyrata subsp. lyrata] gi|297331277|gb|EFH61696.1| hypothetical protein ARALYDRAFT_898585 [Arabidopsis lyrata subsp. lyrata]

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 109/193 (56%), Positives = 133/193 (68%), Gaps = 14/193 (7%)

Query: 1   MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDEKIS------RTGPLDGGDHR 54
           MGQ  RRA G+I         SS ++ VVDR  R +PT+E  +       T  +DG   +
Sbjct: 1   MGQQLRRAVGKIKE----VERSSPSRVVVDR--RSLPTEELSAANSSSPSTAAVDGVSDK 54

Query: 55  EGNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTT 114
              R  +  NVLEERDP+YD MLNQM+GR++ K GGKAEMGEA+VVE   RPLPKLRNTT
Sbjct: 55  --GRRTSEDNVLEERDPKYDTMLNQMVGRIRAKPGGKAEMGEASVVETSKRPLPKLRNTT 112

Query: 115 PVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ 174
           P S+RYEE P P GTLNVAQ+R IMLL QGKA DH+GP+   QIAEK+R+DV QVQ I Q
Sbjct: 113 PESTRYEENPVPQGTLNVAQVRHIMLLFQGKAQDHHGPMSVNQIAEKYRIDVSQVQKITQ 172

Query: 175 CLSLPPESSNKER 187
            LSLP E ++K++
Sbjct: 173 FLSLPTEVTDKQK 185

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232549|ref|NP_188777.1| uncharacterized protein [Arabidopsis thaliana] gi|9294687|dbj|BAB03053.1| unnamed protein product [Arabidopsis thaliana] gi|26453072|dbj|BAC43612.1| unknown protein [Arabidopsis thaliana] gi|28973457|gb|AAO64053.1| unknown protein [Arabidopsis thaliana] gi|332642984|gb|AEE76505.1| uncharacterized protein [Arabidopsis thaliana]

 Score =  195 bits (495), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 106/192 (55%), Positives = 132/192 (68%), Gaps = 13/192 (6%)

Query: 1   MGQAFRRASGRITSSSSTTSSSSKTKNVVDRGPRVVPTDEKIS-----RTGPLDGGDHRE 55
           MGQ  RRA G+I         SS ++  +DR  R +PT+E  +      T  +DG   + 
Sbjct: 1   MGQQLRRAVGKIKE----VERSSPSRVSIDR--RSLPTEELSAVKSSPSTAAVDGVSDK- 53

Query: 56  GNRPVNTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTP 115
             R  +  NVLEERDP+YD MLNQM+GR+K K GGKAEMGEA+VVE   RPLPKLRNTTP
Sbjct: 54  -GRRTSEDNVLEERDPKYDTMLNQMVGRIKAKPGGKAEMGEASVVETSKRPLPKLRNTTP 112

Query: 116 VSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175
            S+RYEE P P GTLNVAQ+R IMLL QGK+ DH+GP+   +IAEK+R+DV QVQ I Q 
Sbjct: 113 ESTRYEENPVPQGTLNVAQVRHIMLLFQGKSQDHHGPMGVNEIAEKYRIDVSQVQKITQF 172

Query: 176 LSLPPESSNKER 187
           LSLP E ++K++
Sbjct: 173 LSLPQEITDKQK 184

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388515547|gb|AFK45835.1| unknown [Medicago truncatula]

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 86/125 (68%), Positives = 104/125 (83%)

Query: 64  NVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRYEEK 123
           NVLEE+DP++DAML QMLGR+ +K GGK EMGEA+VVE+  RP+PKLRNT P S  YEE+
Sbjct: 11  NVLEEKDPKFDAMLGQMLGRITSKPGGKREMGEASVVEKYNRPMPKLRNTKPNSGHYEER 70

Query: 124 PSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPESS 183
           P P GTLNVAQLR I+LLH+GKADDHNGP+D  QIAEKFR+DV Q+Q ILQ LS PPE  
Sbjct: 71  PVPAGTLNVAQLRHIILLHEGKADDHNGPMDVHQIAEKFRVDVGQIQKILQFLSHPPEGR 130

Query: 184 NKERN 188
           ++++N
Sbjct: 131 SEDKN 135

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450902|ref|XP_004143201.1| PREDICTED: uncharacterized protein LOC101223121 [Cucumis sativus]

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 82/127 (64%), Positives = 110/127 (86%)

Query: 61  NTGNVLEERDPQYDAMLNQMLGRVKTKAGGKAEMGEAAVVERQTRPLPKLRNTTPVSSRY 120
           ++GN+LEERDPQ+DAML+QM+GR+K+K GGK EMGEA+VVER  RP+PKLR+T   SS+Y
Sbjct: 14  DSGNMLEERDPQFDAMLSQMVGRIKSKPGGKLEMGEASVVERYGRPMPKLRDTNISSSKY 73

Query: 121 EEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPP 180
           E++P+PPGTLNVAQ+R+I+LLH+GKADDH+GP+   QIAE++ + V Q+Q ILQ LSLPP
Sbjct: 74  EDRPAPPGTLNVAQMRQIILLHEGKADDHDGPMGLHQIAERYNVSVAQIQTILQFLSLPP 133

Query: 181 ESSNKER 187
           E S +++
Sbjct: 134 EDSLRDK 140

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	190
TAIR|locus:2089463	188	AT3G21400 "AT3G21400" [Arabido	0.942	0.952	0.489	1.5e-37

TAIR|locus:2089463 AT3G21400 "AT3G21400" [Arabidopsis thaliana (taxid:3702)]

 Score = 403 (146.9 bits), Expect = 1.5e-37, P = 1.5e-37
 Identities = 94/192 (48%), Positives = 116/192 (60%)

Query:     1 MGQAFRRASGRIXXXXXXXXXXXXXXNVVDRGPRVVPTDE----KIS-RTGPLDGGDHRE 55
             MGQ  RRA G+I                +DR  R +PT+E    K S  T  +DG   + 
Sbjct:     1 MGQQLRRAVGKIKEVERSSPSRVS----IDR--RSLPTEELSAVKSSPSTAAVDGVSDK- 53

Query:    56 GNRPVNTGNVLEERDPQYDAMLNQMLGRVKTXXXXXXXXXXXXXXXRQTRPLPKLRNTTP 115
             G R  +  NVLEERDP+YD MLNQM+GR+K                   RPLPKLRNTTP
Sbjct:    54 GRR-TSEDNVLEERDPKYDTMLNQMVGRIKAKPGGKAEMGEASVVETSKRPLPKLRNTTP 112

Query:   116 VSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC 175
              S+RYEE P P GTLNVAQ+R IMLL QGK+ DH+GP+   +IAEK+R+DV QVQ I Q 
Sbjct:   113 ESTRYEENPVPQGTLNVAQVRHIMLLFQGKSQDHHGPMGVNEIAEKYRIDVSQVQKITQF 172

Query:   176 LSLPPESSNKER 187
             LSLP E ++K++
Sbjct:   173 LSLPQEITDKQK 184


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        0.315   0.135   0.390    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      190       161   0.00074  107 3  11 23  0.42    32
                                                     30  0.44    34


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:  526 (56 KB)
  Total size of DFA:  125 KB (2082 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:01
  No. of threads or processors used:  24
  Search cpu time:  14.72u 0.09s 14.81t   Elapsed:  00:00:03
  Total cpu time:  14.72u 0.09s 14.81t   Elapsed:  00:00:04
  Start:  Sat May 11 06:22:24 2013   End:  Sat May 11 06:22:28 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" 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	190
PF06784	179	UPF0240: Uncharacterised protein family (UPF0240);	97.73
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.5
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	94.83
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	94.25
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.15
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	94.03
PRK04217	110	hypothetical protein; Provisional	94.02
PHA00675	78	hypothetical protein	93.65
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.6
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.66
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	92.54
COG3355	126	Predicted transcriptional regulator [Transcription	92.49
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	92.48
PF08765	108	Mor: Mor transcription activator family; InterPro:	92.42
PF06413	225	Neugrin: Neugrin; InterPro: IPR010487 This family	92.06
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	92.0
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.74
PF13518	52	HTH_28: Helix-turn-helix domain	91.67
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	91.64
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	91.59
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.52
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	91.27
PF10668	60	Phage_terminase: Phage terminase small subunit; In	91.14
COG4367	97	Uncharacterized protein conserved in bacteria [Fun	90.98
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	90.48
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	90.38
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	90.16
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	90.01
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	89.62
TIGR00180	187	parB_part ParB-like partition proteins. This model	89.01
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	88.97
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	88.88
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	88.75
PF12298	172	Bot1p: Eukaryotic mitochondrial regulator protein	88.66
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	88.3
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	88.19
smart00351	125	PAX Paired Box domain.	87.76
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.35
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	87.34
PRK11014	141	transcriptional repressor NsrR; Provisional	87.34
PF04255	56	DUF433: Protein of unknown function (DUF433); Inte	86.93
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	86.54
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	86.33
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	85.93
cd00131	128	PAX Paired Box domain	85.85
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	85.65
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	85.25
PHA02943	165	hypothetical protein; Provisional	85.23
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	84.14
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	84.03
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	83.88
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	83.54
PF14502	48	HTH_41: Helix-turn-helix domain	83.48
PRK15431	78	ferrous iron transport protein FeoC; Provisional	83.47
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	83.46
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	82.93
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	82.45
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	81.68
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	81.57
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	81.35
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	81.03
PRK12542	185	RNA polymerase sigma factor; Provisional	81.01
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	80.82
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	80.67
PF04760	54	IF2_N: Translation initiation factor IF-2, N-termi	80.52
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	80.43
PF09286	143	Pro-kuma_activ: Pro-kumamolisin, activation domain	80.42
PRK12547	164	RNA polymerase sigma factor; Provisional	80.16
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	80.03

>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function

Probab=97.73  E-value=0.00013  Score=60.17  Aligned_cols=106  Identities=26%  Similarity=0.375  Sum_probs=77.4

Q ss_pred             ccccCchHHHHHHHhhcccccCC-CCccccchhhhhhhhcCCCCCCCCCCCC--CCCCCCCCCCCCcccHHHHHHHHHHh
Q 029662           66 LEERDPQYDAMLNQMLGRVKTKA-GGKAEMGEAAVVERQTRPLPKLRNTTPV--SSRYEEKPSPPGTLNVAQLRRIMLLH  142 (190)
Q Consensus        66 l~erDp~ydaMl~qmvGrI~tkp-GGk~Emgea~vv~~ynRP~Pk~R~t~~~--sg~~eer~~p~GTLNva~l~~ii~L~  142 (190)
                      +...|.+.+..|+++  .|+|+= =...+ =+.....+-.||+|-.|.+-++  -|-++..-||.|.|.+-|+-++|-.|
T Consensus        54 i~~Kd~~L~s~LK~V--yV~S~Dp~~~~~-~~~~~~~~~~r~l~l~r~~~~~~~fg~~ep~~vPkGkltl~qal~lL~~H  130 (179)
T PF06784_consen   54 ISRKDDKLLSRLKDV--YVTSKDPVPPQT-VKDAEPQQESRPLPLPRDTIPDFEFGFYEPEKVPKGKLTLRQALELLNNH  130 (179)
T ss_pred             HHhhhHHHHHhhcee--EeecCCCCcccc-cccccccccCCCccCCCCCcccccccccCcccCCCCceeHHHHHHHHHHh
Confidence            456788889999988  666652 11111 1222334567888876665433  35567789999999999999999988


Q ss_pred             hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662          143 QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL  178 (190)
Q Consensus       143 QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl  178 (190)
                      |-.-    --.++.-||++|.++...|.+||.|...
T Consensus       131 q~~P----~~WtaekIA~eY~L~~~dv~~iL~yF~~  162 (179)
T PF06784_consen  131 QLDP----ETWTAEKIAQEYKLDEKDVKNILKYFKP  162 (179)
T ss_pred             ccCc----cccCHHHHHHHhCCCHHHHHHHHHhcCC
Confidence            8332    2247999999999999999999999864

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=96.50  E-value=0.0035  Score=40.47  Aligned_cols=39  Identities=26%  Similarity=0.349  Sum_probs=30.5

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      .++-.++.+|+.||+      .| |++.+||+.|+|-.+-|.++|.
T Consensus         5 ~~~~~~~~~i~~l~~------~G-~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    5 KLSKEQIEEIKELYA------EG-MSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSHCCHHHHHHHHH------TT---HHHHHHHTTS-HHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH------CC-CCHHHHHHHHCcCHHHHHHHHh
Confidence            456667999999996      35 9999999999999999999873

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>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=94.83  E-value=0.036  Score=40.13  Aligned_cols=41  Identities=15%  Similarity=0.281  Sum_probs=30.3

Q ss_pred             HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      +.|+.+.+. ....+--|.|++||++|++....|..+|+||+
T Consensus        50 ~~Vl~~i~~-~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~   90 (102)
T PF08784_consen   50 DKVLNFIKQ-QPNSEEGVHVDEIAQQLGMSENEVRKALDFLS   90 (102)
T ss_dssp             HHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHh-cCCCCCcccHHHHHHHhCcCHHHHHHHHHHHH
Confidence            456666666 33333349999999999999999999999986

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.

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=94.25  E-value=0.076  Score=34.37  Aligned_cols=39  Identities=21%  Similarity=0.290  Sum_probs=22.6

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      .|+.++..+|..||+      .| |++.+||..|++..+-|-+.|+
T Consensus         4 ~Lt~~eR~~I~~l~~------~G-~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    4 HLTPEERNQIEALLE------QG-MSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             --------HHHHHHC------S----HHHHHHHTT--HHHHHHHHH
T ss_pred             chhhhHHHHHHHHHH------cC-CCHHHHHHHHCcCcHHHHHHHh
Confidence            367788888888876      33 9999999999999999988764

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=94.15  E-value=0.056  Score=36.39  Aligned_cols=39  Identities=23%  Similarity=0.379  Sum_probs=29.2

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      +|.+.+=.+||.+|+      +|+ ++.+||.+|+|..++|..|+.
T Consensus         6 ~LTl~eK~~iI~~~e------~g~-s~~~ia~~fgv~~sTv~~I~K   44 (53)
T PF04218_consen    6 SLTLEEKLEIIKRLE------EGE-SKRDIAREFGVSRSTVSTILK   44 (53)
T ss_dssp             S--HHHHHHHHHHHH------CTT--HHHHHHHHT--CCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH------cCC-CHHHHHHHhCCCHHHHHHHHH
Confidence            577888889999985      344 899999999999999999985

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

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

Probab=94.03  E-value=0.047  Score=37.54  Aligned_cols=36  Identities=22%  Similarity=0.383  Sum_probs=26.9

Q ss_pred             HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      +|+++|..        +|.+++.|||.+|+++...|+.+|.++-
T Consensus         4 ~i~~~l~~--------~~~~S~~eLa~~~~~s~~~ve~mL~~l~   39 (69)
T PF09012_consen    4 EIRDYLRE--------RGRVSLAELAREFGISPEAVEAMLEQLI   39 (69)
T ss_dssp             HHHHHHHH--------S-SEEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             HHHHHHHH--------cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45555543        4568999999999999999999999873

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

>PRK04217 hypothetical protein; Provisional

Probab=94.02  E-value=0.18  Score=39.28  Aligned_cols=59  Identities=17%  Similarity=0.252  Sum_probs=44.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          108 PKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       108 Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      |.+|.-+|. +.--.+++|+.-|..++. +|+.|+.-.-      |+++|||+.++|..+.|.++|.
T Consensus        22 ~~~~~~~~~-~~~~~~~~p~~~Lt~eer-eai~l~~~eG------lS~~EIAk~LGIS~sTV~r~L~   80 (110)
T PRK04217         22 PQVRHFYPA-IPPVGPPKPPIFMTYEEF-EALRLVDYEG------LTQEEAGKRMGVSRGTVWRALT   80 (110)
T ss_pred             CCcceEeCC-CCCccCCCCcccCCHHHH-HHHHHHHHcC------CCHHHHHHHHCcCHHHHHHHHH
Confidence            556666664 333457899999999995 6666554222      6999999999999999988875

>PHA00675 hypothetical protein

Probab=93.65  E-value=0.19  Score=38.05  Aligned_cols=45  Identities=27%  Similarity=0.324  Sum_probs=38.6

Q ss_pred             CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662          125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC  175 (190)
Q Consensus       125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf  175 (190)
                      -|.-+|+-+|+.+|..|+.      --.++..+||.+|.|--+-|++|.++
T Consensus        18 h~~AKLt~~qV~~IR~l~~------r~G~s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         18 HPNAKLTDAEVERIRELHE------VEGMSYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             CCCcccCHHHHHHHHHHHH------hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence            5677999999999999985      11258999999999999999999865

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=93.60  E-value=0.13  Score=33.19  Aligned_cols=41  Identities=29%  Similarity=0.460  Sum_probs=33.8

Q ss_pred             ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      ||..|+.=+..||+      +|+|++.+||++++++.+-+-++++-|
T Consensus         1 lt~~q~~iL~~l~~------~~~~~~~~la~~~~~~~~~~t~~i~~L   41 (59)
T PF01047_consen    1 LTPSQFRILRILYE------NGGITQSELAEKLGISRSTVTRIIKRL   41 (59)
T ss_dssp             STHHHHHHHHHHHH------HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH------cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            67788888888875      556999999999999999998888755

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=92.66  E-value=0.44  Score=30.12  Aligned_cols=27  Identities=30%  Similarity=0.378  Sum_probs=22.5

Q ss_pred             CCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          150 NGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      ++.|++.|||+++++...-|.++|+.|
T Consensus        15 ~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen   15 NPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            556999999999999999999999865

...

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=92.54  E-value=0.33  Score=33.25  Aligned_cols=40  Identities=18%  Similarity=0.230  Sum_probs=31.3

Q ss_pred             HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      +-...||.++..    +++++++.|||+.+++..+.|.++|+.|
T Consensus         5 ~r~~~Il~~l~~----~~~~~t~~~ia~~l~i~~~tv~r~l~~L   44 (91)
T smart00346        5 ERGLAVLRALAE----EPGGLTLAELAERLGLSKSTAHRLLNTL   44 (91)
T ss_pred             HHHHHHHHHHHh----CCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            344555655532    3468999999999999999999999877

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=92.49  E-value=0.14  Score=41.14  Aligned_cols=28  Identities=36%  Similarity=0.431  Sum_probs=26.2

Q ss_pred             CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          149 HNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      -+||++|++|||+.+++-+.||+.||=|
T Consensus        39 ~~~~~tvdelae~lnr~rStv~rsl~~L   66 (126)
T COG3355          39 ENGPLTVDELAEILNRSRSTVYRSLQNL   66 (126)
T ss_pred             hcCCcCHHHHHHHHCccHHHHHHHHHHH
Confidence            5899999999999999999999999865

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=92.48  E-value=0.49  Score=28.68  Aligned_cols=38  Identities=26%  Similarity=0.415  Sum_probs=29.1

Q ss_pred             CcccHHHHHHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          128 GTLNVAQLRRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       128 GTLNva~l~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      ..|+-.+.+ |+.++ +|        |+.++||+.++|....|.+.++
T Consensus         2 ~~l~~~e~~-i~~~~~~g--------~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421        2 ASLTPRERE-VLRLLAEG--------LTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             CCCCHHHHH-HHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHH
Confidence            457777776 66555 33        6899999999999998877655

lux regulon (activates the bioluminescence operon

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=92.42  E-value=0.2  Score=37.39  Aligned_cols=44  Identities=23%  Similarity=0.319  Sum_probs=27.4

Q ss_pred             CCCCCcccHHHH--HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662          124 PSPPGTLNVAQL--RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC  175 (190)
Q Consensus       124 ~~p~GTLNva~l--~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf  175 (190)
                      -+|-+.--...+  ++|+..|.|        |++.+||.||++-...|.+|+.-
T Consensus        50 yiP~~~~~~~~~R~~~I~~~f~G--------~n~~eLA~kyglS~r~I~~Ii~~   95 (108)
T PF08765_consen   50 YIPKCDRLLRALRNREIRREFNG--------MNVRELARKYGLSERQIYRIIKR   95 (108)
T ss_dssp             ----SHHHHHHHHHHHHHHH--S--------S-HHHHHHHHT--HHHHHHHHHH
T ss_pred             EeeCccHHHHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence            355565333444  478888885        77999999999999999999974

It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.

>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins

Probab=92.06  E-value=0.36  Score=41.50  Aligned_cols=56  Identities=23%  Similarity=0.453  Sum_probs=46.8

Q ss_pred             CCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCCCCC
Q 029662          123 KPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLPPES  182 (190)
Q Consensus       123 r~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP~e~  182 (190)
                      .-.|+-+|.-+++..|=.||+-..+    -+++..|||.|+|....|.+||.-=-.|.++
T Consensus         4 ~~~p~k~Ls~~~~~~ir~L~~~~p~----~~t~~~Lae~F~vspe~irrILkskw~p~~~   59 (225)
T PF06413_consen    4 PGNPPKKLSREAMEQIRYLHKEDPE----EWTVERLAESFKVSPEAIRRILKSKWVPTEE   59 (225)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCcc----ccCHHHHHhhCCCCHHHHHHHHhcCCCCCHH
Confidence            3468889999999999999986543    3789999999999999999999876667553

Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=92.00  E-value=0.33  Score=34.16  Aligned_cols=40  Identities=30%  Similarity=0.471  Sum_probs=28.7

Q ss_pred             HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      |+-++.|.+.   ...+++++++||+++++....|.+|++.|.
T Consensus        11 l~~l~~la~~---~~~~~~s~~eiA~~~~i~~~~l~kil~~L~   50 (83)
T PF02082_consen   11 LRILLYLARH---PDGKPVSSKEIAERLGISPSYLRKILQKLK   50 (83)
T ss_dssp             HHHHHHHHCT---TTSC-BEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHhC---CCCCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence            4444555332   234569999999999999999999999874

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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=91.74  E-value=0.39  Score=30.70  Aligned_cols=38  Identities=26%  Similarity=0.340  Sum_probs=26.7

Q ss_pred             ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      |+-.+ ++||.++-.      ..|+..|||+.+++....|.++..
T Consensus         5 L~~~e-r~vi~~~y~------~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen    5 LPPRE-REVIRLRYF------EGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             S-HHH-HHHHHHHHT------ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHhc------CCCCHHHHHHHHCCcHHHHHHHHH
Confidence            44444 455655553      349999999999999999988864

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 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; 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: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.67  E-value=0.39  Score=29.99  Aligned_cols=33  Identities=21%  Similarity=0.275  Sum_probs=26.4

Q ss_pred             HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      +||++|..      | +++.+||++|+|..+.|.+.++-.
T Consensus         4 ~iv~~~~~------g-~s~~~~a~~~gis~~tv~~w~~~y   36 (52)
T PF13518_consen    4 QIVELYLE------G-ESVREIAREFGISRSTVYRWIKRY   36 (52)
T ss_pred             HHHHHHHc------C-CCHHHHHHHHCCCHhHHHHHHHHH
Confidence            56777762      2 389999999999999999888643

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=91.64  E-value=0.57  Score=27.63  Aligned_cols=39  Identities=26%  Similarity=0.292  Sum_probs=28.0

Q ss_pred             cccHHHHHHHHHHh-hccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662          129 TLNVAQLRRIMLLH-QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC  175 (190)
Q Consensus       129 TLNva~l~~ii~L~-QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf  175 (190)
                      +|+-.+.+-++++| +|        |+..+||+.+++....|.++++-
T Consensus        10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~   49 (55)
T cd06171          10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHR   49 (55)
T ss_pred             hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence            34445544444455 44        78999999999999999888753

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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=91.59  E-value=0.35  Score=30.97  Aligned_cols=35  Identities=26%  Similarity=0.309  Sum_probs=25.0

Q ss_pred             HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      .-++||.|+--.-      |+.+|||+.+++..+.|+..+.
T Consensus        14 ~~r~i~~l~~~~g------~s~~eIa~~l~~s~~~v~~~l~   48 (54)
T PF08281_consen   14 RQREIFLLRYFQG------MSYAEIAEILGISESTVKRRLR   48 (54)
T ss_dssp             HHHHHHHHHHTS---------HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHC------cCHHHHHHHHCcCHHHHHHHHH
Confidence            3477888865554      8999999999999999987664

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 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=91.52  E-value=0.22  Score=31.98  Aligned_cols=28  Identities=21%  Similarity=0.383  Sum_probs=23.7

Q ss_pred             CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          149 HNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      +++++++++||++|+|...-|++-++.|
T Consensus        12 ~~~~it~~eLa~~l~vS~rTi~~~i~~L   39 (55)
T PF08279_consen   12 SKEPITAKELAEELGVSRRTIRRDIKEL   39 (55)
T ss_dssp             TTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred             cCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3456999999999999999999988876

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 ....

>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=91.27  E-value=0.22  Score=32.41  Aligned_cols=29  Identities=34%  Similarity=0.525  Sum_probs=24.8

Q ss_pred             CCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          148 DHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      .+.++|++.|||++.++..+-+.++|+-|
T Consensus        14 ~~~~~~t~~eia~~~gl~~stv~r~L~tL   42 (52)
T PF09339_consen   14 ESGGPLTLSEIARALGLPKSTVHRLLQTL   42 (52)
T ss_dssp             CTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45667999999999999999999999865

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.

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=91.14  E-value=0.3  Score=34.89  Aligned_cols=31  Identities=23%  Similarity=0.410  Sum_probs=25.9

Q ss_pred             HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHH
Q 029662          137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQA  171 (190)
Q Consensus       137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~  171 (190)
                      ++..||+    +|+|-|..++||++++|..++|.+
T Consensus        11 kA~e~y~----~~~g~i~lkdIA~~Lgvs~~tIr~   41 (60)
T PF10668_consen   11 KAFEIYK----ESNGKIKLKDIAEKLGVSESTIRK   41 (60)
T ss_pred             HHHHHHH----HhCCCccHHHHHHHHCCCHHHHHH
Confidence            4666774    478889999999999999999864

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.98  E-value=0.51  Score=37.12  Aligned_cols=49  Identities=27%  Similarity=0.306  Sum_probs=42.0

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcCC
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSLP  179 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~SlP  179 (190)
                      +||-+|++.--+-+|-..  ..-|+++.+||++.++.-.-||+|||..+-|
T Consensus         2 SLn~eq~~~Tk~elqan~--el~~LS~~~iA~~Ln~t~~~lekil~~tqr~   50 (97)
T COG4367           2 SLNPEQKQRTKQELQANF--ELCPLSDEEIATALNWTEVKLEKILQVTQRP   50 (97)
T ss_pred             CCCHHHHHHHHHHHHHhh--hhccccHHHHHHHhCCCHHHHHHHHHHhhcc
Confidence            689999988777777544  4678999999999999999999999988776

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=90.48  E-value=0.8  Score=29.53  Aligned_cols=40  Identities=25%  Similarity=0.233  Sum_probs=30.5

Q ss_pred             HHHHhhcc--CCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          138 IMLLHQGK--ADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       138 ii~L~QGk--~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      ++.|++.-  ....+++|+..+||+.+++...-|.++++-|.
T Consensus         9 l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~   50 (67)
T cd00092           9 LLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELE   50 (67)
T ss_pred             HHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44455432  23467899999999999999999999987653

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=90.38  E-value=0.66  Score=34.15  Aligned_cols=30  Identities=30%  Similarity=0.496  Sum_probs=26.4

Q ss_pred             CCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          148 DHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      +..+|+++.+||+.+++....|.+||+-|.
T Consensus        21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~   50 (132)
T TIGR00738        21 PDEGPVSVKEIAERQGISRSYLEKILRTLR   50 (132)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            334699999999999999999999998764

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

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

Probab=90.16  E-value=0.22  Score=35.35  Aligned_cols=28  Identities=36%  Similarity=0.635  Sum_probs=24.6

Q ss_pred             CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          150 NGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      ++|++..|||+.|++...++..+|++|-
T Consensus        13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le   40 (62)
T PF04703_consen   13 NGPLKTREIADALGLSIYQARYYLEKLE   40 (62)
T ss_dssp             TS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            7899999999999999999999999984

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=90.01  E-value=0.47  Score=28.86  Aligned_cols=27  Identities=19%  Similarity=0.353  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          151 GPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      +++++.+||+.|.+...-|.++|+.|.
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~   39 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNKLE   39 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            679999999999999999999998873

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=89.62  E-value=0.79  Score=34.19  Aligned_cols=29  Identities=38%  Similarity=0.471  Sum_probs=26.2

Q ss_pred             CCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          149 HNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      .++++++++||+++++....|+++|+-|.
T Consensus        22 ~~~~~s~~eia~~l~is~~~v~~~l~~L~   50 (130)
T TIGR02944        22 DSQPYSAAEIAEQTGLNAPTVSKILKQLS   50 (130)
T ss_pred             CCCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence            35789999999999999999999998764

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>TIGR00180 parB_part ParB-like partition proteins

Probab=89.01  E-value=0.33  Score=38.86  Aligned_cols=29  Identities=24%  Similarity=0.461  Sum_probs=27.9

Q ss_pred             CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE  181 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e  181 (190)
                      |+.++||++|++..+.|.+.+.+..||++
T Consensus       121 ~s~~~iA~~lg~s~~~V~r~l~l~~lp~~  149 (187)
T TIGR00180       121 MTQEDLAKKIGKSRAHITNLLRLLKLPSE  149 (187)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHcCCHH
Confidence            78999999999999999999999999986

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases

Probab=88.97  E-value=0.64  Score=31.79  Aligned_cols=26  Identities=27%  Similarity=0.448  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhc----hhHHHHHHHHHhh
Q 029662          151 GPLDAKQIAEKFR----LDVLQVQAILQCL  176 (190)
Q Consensus       151 gPM~v~~iAeKFr----v~v~~vq~Ilqf~  176 (190)
                      +|+++.|||.+..    -+...+++|+.||
T Consensus        21 ~~ls~~eia~~l~~~~p~~~~~L~RimR~L   50 (51)
T PF08100_consen   21 GPLSLSEIAARLPTSNPSAPPMLDRIMRLL   50 (51)
T ss_dssp             S-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence            8999999999988    7788999999997

It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=88.88  E-value=1.1  Score=29.19  Aligned_cols=42  Identities=24%  Similarity=0.415  Sum_probs=27.6

Q ss_pred             ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      |+..|+.=+..|+     ..+++|+..+||+.++++...|-++++=|
T Consensus         1 lt~~q~~vL~~l~-----~~~~~~t~~~l~~~~~~~~~~vs~~i~~L   42 (68)
T PF13463_consen    1 LTRPQWQVLRALA-----HSDGPMTQSDLAERLGISKSTVSRIIKKL   42 (68)
T ss_dssp             --HHHHHHHHHHT-------TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-----ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4455665555565     56788999999999999999998888643

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=88.75  E-value=1.8  Score=22.50  Aligned_cols=36  Identities=14%  Similarity=0.110  Sum_probs=27.1

Q ss_pred             ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHH
Q 029662          130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAI  172 (190)
Q Consensus       130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~I  172 (190)
                      ++..+...|+.+|..       .+++.+||+.|++-...|-++
T Consensus         6 ~~~~~~~~i~~~~~~-------~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLAA-------GESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHHc-------CCCHHHHHHHHCCCHHHHHHh
Confidence            455667777777752       259999999999988877665

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes

Probab=88.66  E-value=1.7  Score=36.05  Aligned_cols=58  Identities=12%  Similarity=0.161  Sum_probs=44.4

Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhcC
Q 029662          104 TRPLPKLRNTTPVSSRYEEKPSPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLSL  178 (190)
Q Consensus       104 nRP~Pk~R~t~~~sg~~eer~~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~Sl  178 (190)
                      .+|.|-+...++.+-=.           =..=.+|+.+|+-      ++++|.+||.+|+|+..-|..||+...+
T Consensus         2 ~~PFP~Np~f~~~~~ls-----------e~~r~~Iy~~~~~------~~~sv~~vS~~ygi~~~RV~AIvrLkei   59 (172)
T PF12298_consen    2 LQPFPLNPSFRSNPVLS-----------EELREQIYEDVMQ------DGKSVREVSQKYGIKIQRVEAIVRLKEI   59 (172)
T ss_pred             CCCCCCCCCCCCCCcCC-----------HHHHHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            57888888887765433           3334567788864      3479999999999999999999987654

This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].

>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=88.30  E-value=0.25  Score=33.20  Aligned_cols=28  Identities=36%  Similarity=0.525  Sum_probs=25.5

Q ss_pred             CCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          149 HNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      .+|+|++.+||++.++.-+.|.++|+.|
T Consensus        19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L   46 (68)
T PF01978_consen   19 KNGPATAEEIAEELGISRSTVYRALKSL   46 (68)
T ss_dssp             HHCHEEHHHHHHHHTSSHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4577999999999999999999999876

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=88.19  E-value=1.3  Score=28.43  Aligned_cols=43  Identities=26%  Similarity=0.406  Sum_probs=32.0

Q ss_pred             ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          130 LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       130 LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      |+..|.+=++-|+.....    .|++.|||+.+.++.+.|.++|+-|
T Consensus         3 lt~~q~~vL~~l~~~~~~----~~t~~~la~~l~~~~~~vs~~v~~L   45 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGE----ELTQSELAERLGISKSTVSRIVKRL   45 (62)
T ss_dssp             STHHHHHHHHHHHHSTTS----GEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHCCCC----CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            566677666666553321    4999999999999999999998765

...

>smart00351 PAX Paired Box domain

Probab=87.76  E-value=1.6  Score=33.42  Aligned_cols=43  Identities=21%  Similarity=0.156  Sum_probs=35.3

Q ss_pred             CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      +++.-|..+.=..|++||.+-       ++..+||++|+|..+.|.++++
T Consensus        13 ~~~~~~s~~~R~riv~~~~~G-------~s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       13 VNGRPLPDEERQRIVELAQNG-------VRPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             cCCCCCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence            344447888888999998632       6899999999999999999887

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.35  E-value=2.3  Score=26.38  Aligned_cols=26  Identities=19%  Similarity=0.326  Sum_probs=23.4

Q ss_pred             CC-CHHHHHHHhchhHHHHHHHHHhhc
Q 029662          152 PL-DAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       152 PM-~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      .+ ++.+||+.|++...-|.+.|+.|.
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l~~L~   45 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREALSRLE   45 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46 899999999999999999998774

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=87.34  E-value=1.2  Score=33.82  Aligned_cols=28  Identities=18%  Similarity=0.404  Sum_probs=25.9

Q ss_pred             CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          150 NGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      .+++++++||+.+++....|.+||+-|.
T Consensus        23 ~~~~s~~~ia~~~~ip~~~l~kil~~L~   50 (135)
T TIGR02010        23 TGPVTLADISERQGISLSYLEQLFAKLR   50 (135)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4689999999999999999999999874

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

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=87.34  E-value=0.94  Score=34.63  Aligned_cols=27  Identities=15%  Similarity=0.199  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          151 GPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       151 gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      .++++.+||+.|+|....|.+|++-|.
T Consensus        24 ~~~s~~~ia~~~~is~~~vrk~l~~L~   50 (141)
T PRK11014         24 RMTSISEVTEVYGVSRNHMVKIINQLS   50 (141)
T ss_pred             CccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            489999999999999999999999774

>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins

Probab=86.93  E-value=1.4  Score=29.82  Aligned_cols=48  Identities=23%  Similarity=0.392  Sum_probs=27.9

Q ss_pred             CCCCCCCCCCCc-ccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhc-hhHHHHHHHHHh
Q 029662          118 SRYEEKPSPPGT-LNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFR-LDVLQVQAILQC  175 (190)
Q Consensus       118 g~~eer~~p~GT-LNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFr-v~v~~vq~Ilqf  175 (190)
                      +..+.+|+=.|| +-|..|-..+  .+|        +++++|++.|. ++..+|+..|.|
T Consensus         6 ~~~~G~P~i~GTRI~v~~i~~~~--~~G--------~s~eeI~~~yp~Lt~~~i~aAl~y   55 (56)
T PF04255_consen    6 DILGGQPVIRGTRIPVRDILDLL--AAG--------ESPEEIAEDYPSLTLEDIRAALAY   55 (56)
T ss_dssp             TSGGG--EETTSS-BHHHHHHHH--HTT----------HHHHHHHSTT--HHHHHHHHHH
T ss_pred             cccCCcceEcCceecHHHHHHHH--HcC--------CCHHHHHHHCCCCCHHHHHHHHHh
Confidence            333445555554 4455443333  334        78999999998 999999999987

; PDB: 2GA1_B.

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=86.54  E-value=2.2  Score=28.04  Aligned_cols=36  Identities=17%  Similarity=0.332  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          133 AQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       133 a~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      +.|+.+|.-+.      +|-|++.+.|.+|+|.-+-+.+.+.
T Consensus         3 e~l~~Ai~~v~------~g~~S~r~AA~~ygVp~sTL~~r~~   38 (45)
T PF05225_consen    3 EDLQKAIEAVK------NGKMSIRKAAKKYGVPRSTLRRRLR   38 (45)
T ss_dssp             HHHHHHHHHHH------TTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred             HHHHHHHHHHH------hCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            46777777776      4559999999999999998887653

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=86.33  E-value=2.4  Score=25.93  Aligned_cols=22  Identities=23%  Similarity=0.283  Sum_probs=19.5

Q ss_pred             CCHHHHHHHhchhHHHHHHHHH
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      |+.++||+.+++....|...+.
T Consensus        16 ~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          16 KTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Confidence            7999999999999998887654

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=85.93  E-value=1.5  Score=35.44  Aligned_cols=28  Identities=18%  Similarity=0.398  Sum_probs=25.7

Q ss_pred             CCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          150 NGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       150 ~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      .+|+++++||+++++....|.+||+-|.
T Consensus        23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~   50 (164)
T PRK10857         23 AGPVPLADISERQGISLSYLEQLFSRLR   50 (164)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4689999999999999999999999774

>cd00131 PAX Paired Box domain

Probab=85.85  E-value=2.2  Score=33.01  Aligned_cols=43  Identities=23%  Similarity=0.211  Sum_probs=35.0

Q ss_pred             CCCCcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          125 SPPGTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       125 ~p~GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      +.+-.|....=..||++|+.-       |+..+||++|+|..+.|.++++
T Consensus        13 ~m~~~lS~d~R~rIv~~~~~G-------~s~~~iA~~~~Vs~~tV~r~i~   55 (128)
T cd00131          13 VNGRPLPDSIRQRIVELAQSG-------IRPCDISRQLRVSHGCVSKILN   55 (128)
T ss_pred             cCCCcCCHHHHHHHHHHHHcC-------CCHHHHHHHHCcCHHHHHHHHH
Confidence            344556677778899998632       8999999999999999999987

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=85.65  E-value=3.2  Score=34.90  Aligned_cols=45  Identities=16%  Similarity=0.226  Sum_probs=36.0

Q ss_pred             CcccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          128 GTLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       128 GTLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      |---++-.-.||.++.    .+++++++.|||+..++.-+-|.+||+=|
T Consensus        20 ~~~sl~r~l~IL~~~~----~~~~~~tl~eIa~~lglpkStv~RlL~tL   64 (271)
T PRK10163         20 GAQALERGIAILQYLE----KSGGSSSVSDISLNLDLPLSTTFRLLKVL   64 (271)
T ss_pred             cchHHHHHHHHHHHHH----hCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3334666777888873    46678999999999999999999999744

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=85.25  E-value=1.5  Score=27.59  Aligned_cols=22  Identities=14%  Similarity=0.252  Sum_probs=18.1

Q ss_pred             CCHHHHHHHhchhHHHHHHHHH
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      +++.+||+.|+|....|.++++
T Consensus        18 ~s~~~ia~~lgvs~~Tv~~w~k   39 (50)
T PF13384_consen   18 WSIREIAKRLGVSRSTVYRWIK   39 (50)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6799999999999999999986

>PHA02943 hypothetical protein; Provisional

Probab=85.23  E-value=1.4  Score=37.32  Aligned_cols=37  Identities=19%  Similarity=0.225  Sum_probs=32.0

Q ss_pred             HHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          134 QLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      -+.+|+.+.      +.|..+..|||+.+++..+++|.+|..|
T Consensus        12 R~~eILE~L------k~G~~TtseIAkaLGlS~~qa~~~LyvL   48 (165)
T PHA02943         12 RMIKTLRLL------ADGCKTTSRIANKLGVSHSMARNALYQL   48 (165)
T ss_pred             HHHHHHHHH------hcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence            456777776      5788999999999999999999999876

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=84.14  E-value=0.74  Score=33.19  Aligned_cols=29  Identities=28%  Similarity=0.318  Sum_probs=22.0

Q ss_pred             CCHHHHHHHhchhHHHHHHHHHhhcCCCC
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQCLSLPPE  181 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilqf~SlP~e  181 (190)
                      ++-.|||.+++..-+.|.+.|.++.||++
T Consensus         4 ~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~   32 (93)
T PF08535_consen    4 WTQEEIAKRLGKSRSWVSNHLALLDLPEE   32 (93)
T ss_dssp             --HHHHHHHTT--HHHHHHHHGGGS--HH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHcCCHH
Confidence            67899999999999999999999999975

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=84.03  E-value=1.5  Score=26.64  Aligned_cols=25  Identities=36%  Similarity=0.428  Sum_probs=22.9

Q ss_pred             CCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          152 PLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       152 PM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      ||++.+||+.+++...-|.++|+-|
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L   32 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRL   32 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHH
Confidence            6899999999999999999988765

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=83.88  E-value=1.1  Score=35.37  Aligned_cols=29  Identities=24%  Similarity=0.197  Sum_probs=26.1

Q ss_pred             CCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          149 HNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       149 h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      +.+++++++||++++|....|.+|++-|.
T Consensus        21 ~~~~~s~~eIA~~~~is~~~L~kIl~~L~   49 (153)
T PRK11920         21 DGKLSRIPEIARAYGVSELFLFKILQPLV   49 (153)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34689999999999999999999999875

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=83.54  E-value=1.5  Score=35.56  Aligned_cols=37  Identities=22%  Similarity=0.370  Sum_probs=33.3

Q ss_pred             HHHHHHHHhhccCCCCCCCCCHHHHHHHh--chhHHHHHHHHHhhc
Q 029662          134 QLRRIMLLHQGKADDHNGPLDAKQIAEKF--RLDVLQVQAILQCLS  177 (190)
Q Consensus       134 ~l~~ii~L~QGk~~~h~gPM~v~~iAeKF--rv~v~~vq~Ilqf~S  177 (190)
                      -|++++.|..|+.       |+.+||.++  .|.+.+|+..|+||-
T Consensus        28 ~ir~l~~l~~~~~-------d~~~iak~l~p~is~~ev~~sL~~L~   66 (171)
T PF14394_consen   28 AIRELLPLMPFAP-------DPEWIAKRLRPKISAEEVRDSLEFLE   66 (171)
T ss_pred             HHHHHhhcCCCCC-------CHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            4788999988876       899999999  999999999999983

>PF14502 HTH_41: Helix-turn-helix domain

Probab=83.48  E-value=1.2  Score=30.99  Aligned_cols=25  Identities=24%  Similarity=0.287  Sum_probs=23.2

Q ss_pred             CCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      ..|++++++|.|-+..||+-|+||.
T Consensus         7 ~tI~e~~~~~~vs~GtiQ~Alk~Le   31 (48)
T PF14502_consen    7 PTISEYSEKFGVSRGTIQNALKFLE   31 (48)
T ss_pred             CCHHHHHHHhCcchhHHHHHHHHHH
Confidence            5799999999999999999999984

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=83.47  E-value=2.4  Score=31.93  Aligned_cols=37  Identities=30%  Similarity=0.489  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          132 VAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       132 va~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      .-|||..|.++        |.|++.|||.+|+.....|+..|..+
T Consensus         4 L~qlRd~l~~~--------gr~s~~~Ls~~~~~p~~~VeaMLe~l   40 (78)
T PRK15431          4 LIQVRDLLALR--------GRMEAAQISQTLNTPQPMINAMLQQL   40 (78)
T ss_pred             HHHHHHHHHHc--------CcccHHHHHHHHCcCHHHHHHHHHHH
Confidence            34778888775        56999999999999999999999765

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=83.46  E-value=2  Score=29.69  Aligned_cols=23  Identities=35%  Similarity=0.343  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhchhHHHHHHHHHh
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQC  175 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilqf  175 (190)
                      ++..+||+++++....|.++++-
T Consensus       127 ~s~~eIA~~l~~s~~~v~~~~~~  149 (158)
T TIGR02937       127 LSYKEIAEILGISVGTVKRRLKR  149 (158)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Confidence            78999999999999999887753

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

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

Probab=82.93  E-value=2.8  Score=27.20  Aligned_cols=35  Identities=26%  Similarity=0.336  Sum_probs=25.8

Q ss_pred             HHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHh
Q 029662          136 RRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQC  175 (190)
Q Consensus       136 ~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf  175 (190)
                      +.||.+.|..     |.++..+||++.+|..+.|.+=++-
T Consensus         6 ~~Il~~Lq~d-----~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    6 RKILRLLQED-----GRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHH------TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHc-----CCccHHHHHHHHCcCHHHHHHHHHH
Confidence            4577777754     8899999999999999988775543

...

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=82.45  E-value=2.5  Score=34.46  Aligned_cols=38  Identities=13%  Similarity=0.336  Sum_probs=29.7

Q ss_pred             HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      -++||.|+-|--  ...+|+.+|||+.++|....|.+|.+
T Consensus       181 er~vl~l~ygl~--~~~~~t~~EIA~~lgis~~~V~q~~~  218 (238)
T TIGR02393       181 ERKVLRMRYGLL--DGRPHTLEEVGKEFNVTRERIRQIES  218 (238)
T ss_pred             HHHHHHHHhCCC--CCCCccHHHHHHHHCCCHHHHHHHHH
Confidence            366788876652  24679999999999999999988753

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=81.68  E-value=4.2  Score=27.23  Aligned_cols=42  Identities=24%  Similarity=0.419  Sum_probs=33.0

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      -|+..++.-+..|++      +++|++++||+.+++....|-++|+-|
T Consensus         7 ~l~~~~~~il~~l~~------~~~~~~~~la~~~~~s~~~i~~~l~~L   48 (101)
T smart00347        7 GLTPTQFLVLRILYE------EGPLSVSELAKRLGVSPSTVTRVLDRL   48 (101)
T ss_pred             CCCHHHHHHHHHHHH------cCCcCHHHHHHHHCCCchhHHHHHHHH
Confidence            467777777777775      336999999999999988888877643

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=81.57  E-value=2.9  Score=29.77  Aligned_cols=35  Identities=20%  Similarity=0.241  Sum_probs=27.7

Q ss_pred             HHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          137 RIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       137 ~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      .|+.+.|-     +++++..+||+++++....|.+.++-|
T Consensus         7 ~il~~L~~-----~~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344        7 KILEELQK-----DARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             HHHHHHHH-----hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45555553     368999999999999999998887755

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

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=81.35  E-value=3  Score=31.56  Aligned_cols=31  Identities=26%  Similarity=0.363  Sum_probs=24.7

Q ss_pred             HHHHHHh--hccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          136 RRIMLLH--QGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       136 ~~ii~L~--QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      |+||.|+  +|        |+.+|||+.+++.+..|...+.
T Consensus       140 r~v~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~  172 (183)
T TIGR02999       140 AEVVELRFFAG--------LTVEEIAELLGVSVRTVERDWR  172 (183)
T ss_pred             HHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHH
Confidence            5666664  44        8899999999999999987664

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=81.03  E-value=2.3  Score=35.35  Aligned_cols=29  Identities=24%  Similarity=0.256  Sum_probs=26.1

Q ss_pred             CCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          148 DHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       148 ~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      +|++++++.|||+++++.-+-|.++|+-|
T Consensus        22 ~~~~~ls~~eia~~lgl~kstv~RlL~tL   50 (263)
T PRK09834         22 RLDGGATVGLLAELTGLHRTTVRRLLETL   50 (263)
T ss_pred             hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45677999999999999999999999865

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=81.01  E-value=2.5  Score=32.52  Aligned_cols=30  Identities=13%  Similarity=0.242  Sum_probs=23.9

Q ss_pred             HHHHHH--hhccCCCCCCCCCHHHHHHHhchhHHHHHHHH
Q 029662          136 RRIMLL--HQGKADDHNGPLDAKQIAEKFRLDVLQVQAIL  173 (190)
Q Consensus       136 ~~ii~L--~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Il  173 (190)
                      ++||.|  ++|        |+.+|||+.+++....|..-+
T Consensus       128 r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l  159 (185)
T PRK12542        128 RQVFKYKVFYN--------LTYQEISSVMGITEANVRKQF  159 (185)
T ss_pred             HHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHH
Confidence            556666  355        889999999999999887654

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=80.82  E-value=4.5  Score=29.62  Aligned_cols=46  Identities=22%  Similarity=0.360  Sum_probs=36.6

Q ss_pred             cccHHHHHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          129 TLNVAQLRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       129 TLNva~l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      -|+..|+.-+..|+  +-..++|+++.++||+.+.++.+-|-+++.-|
T Consensus        22 ~ls~~q~~vL~~l~--~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L   67 (109)
T TIGR01889        22 NLSLEELLILYYLG--KLENNEGKLTLKEIIKEILIKQSALVKIIKKL   67 (109)
T ss_pred             CCCHHHHHHHHHHH--hhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            37888888777777  22334588999999999999999999888754

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=80.67  E-value=1.8  Score=27.66  Aligned_cols=26  Identities=35%  Similarity=0.505  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHhchhHHHHHHHHHhh
Q 029662          151 GPLDAKQIAEKFRLDVLQVQAILQCL  176 (190)
Q Consensus       151 gPM~v~~iAeKFrv~v~~vq~Ilqf~  176 (190)
                      ||+++.|||+.|++..+.|..=|..|
T Consensus        14 ~~~~~~el~~~l~~s~~~vs~hL~~L   39 (47)
T PF01022_consen   14 GPLTVSELAEELGLSQSTVSHHLKKL   39 (47)
T ss_dssp             SSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCchhhHHHhccccchHHHHHHHHH
Confidence            77999999999999999988766654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2

Probab=80.52  E-value=0.99  Score=29.69  Aligned_cols=28  Identities=11%  Similarity=0.236  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhchhHHHHHHHH-HhhcC
Q 029662          151 GPLDAKQIAEKFRLDVLQVQAIL-QCLSL  178 (190)
Q Consensus       151 gPM~v~~iAeKFrv~v~~vq~Il-qf~Sl  178 (190)
                      .+|.|++||+++++.+..|-.+| +-+-+
T Consensus         2 ~~i~V~elAk~l~v~~~~ii~~l~~~~Gi   30 (54)
T PF04760_consen    2 EKIRVSELAKELGVPSKEIIKKLFKELGI   30 (54)
T ss_dssp             -EE-TTHHHHHHSSSHHHHHHHH-HHHTS
T ss_pred             CceEHHHHHHHHCcCHHHHHHHHHHhCCc
Confidence            46899999999999999999888 63443

It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=80.43  E-value=2.9  Score=35.03  Aligned_cols=36  Identities=17%  Similarity=0.281  Sum_probs=28.2

Q ss_pred             HHHHHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHH
Q 029662          135 LRRIMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       135 l~~ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      =|+||.|+=+.    ..+|+.+|||+.|+|....|.+|..
T Consensus       223 er~vl~l~y~~----~~~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       223 SRRIIEARWLD----DDKLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             HHHHHHHHhcC----CCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            36677775553    3479999999999999999987754

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=80.42  E-value=5.5  Score=30.22  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=32.9

Q ss_pred             cHHHHHH-HHHHhhccCCCCCCCCCHHHHHHHhchhHHHHHHHHHhhc
Q 029662          131 NVAQLRR-IMLLHQGKADDHNGPLDAKQIAEKFRLDVLQVQAILQCLS  177 (190)
Q Consensus       131 Nva~l~~-ii~L~QGk~~~h~gPM~v~~iAeKFrv~v~~vq~Ilqf~S  177 (190)
                      |.+.|.. +..+..=.+.+....|+-+||++.|.-....|+.|.+||.
T Consensus        25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~~~~v~~V~~wL~   72 (143)
T PF09286_consen   25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPSPEDVAAVKSWLK   72 (143)
T ss_dssp             THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS--HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            5666665 4445666677778889999999999999999999999985

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=80.16  E-value=2.9  Score=31.68  Aligned_cols=22  Identities=9%  Similarity=0.042  Sum_probs=19.2

Q ss_pred             CCHHHHHHHhchhHHHHHHHHH
Q 029662          153 LDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       153 M~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      |+++|||+.+++....|...|.
T Consensus       129 ~s~~eIA~~lgis~~tV~~~l~  150 (164)
T PRK12547        129 FSYEDAAAICGCAVGTIKSRVS  150 (164)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Confidence            7899999999999998876653

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=80.03  E-value=3  Score=30.80  Aligned_cols=23  Identities=22%  Similarity=0.182  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHhchhHHHHHHHHH
Q 029662          152 PLDAKQIAEKFRLDVLQVQAILQ  174 (190)
Q Consensus       152 PM~v~~iAeKFrv~v~~vq~Ilq  174 (190)
                      -|+.++||+++++.+..|...+.
T Consensus       144 ~~s~~eIA~~lgis~~tV~~~l~  166 (182)
T PRK09652        144 GLSYEEIAEIMGCPIGTVRSRIF  166 (182)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            38999999999999998876543

---

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

ID	Length	Definition	E-value
Query	190
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 38.3 bits (88), Expect = 9e-04
 Identities = 27/179 (15%), Positives = 52/179 (29%), Gaps = 47/179 (26%)

Query: 30  DRGPRVVPTDEKISRTGPLDGGDHREGNRPVNTG-------NVLEERDPQYDAMLNQMLG 82
            R P +  T   I +   L   +       V+           L E  P  + +++ +LG
Sbjct: 102 QRQPSM-MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160

Query: 83  --------------RVKTKAGGKA---EMGEAAVVERQTRPLPKL--RNTTPVSSRYEEK 123
                         +V+ K   K     +      E     L KL  +     +SR +  
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220

Query: 124 PSPPGTLNVAQ--LRRIMLLHQGKA-----DDHNGPLDAKQIAEKFRLDVLQVQAILQC 175
            +    ++  Q  LRR++     +       +    +   +    F  +       L C
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQNAKAWNAF--N-------LSC 266

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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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

No hit with probability above 80.00