Psyllid ID: psy7155

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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-------17
Protein Sequence
MVQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTRVIALG
Secondary Structure (PSIPRED)
ccccccccccEEccccccEEEccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHcccccccccHHHHHHHHHcccccccccccccccEEEEEcccccccccccc
Secondary Structure Prediction (SSPRO)
ccEccccccEEEEccccEEEEEccccccccccEEEEEccccccccccHHHHHHccccccccccccccccccccccccccccccccHHcHHHHHHHEEEEEEEEEEHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mvqvsnapaqlignvnGTYLIQqtveptehaTIIAttasrdsphentevayivdepaqattatsntgdplspdnqaslshvtkiSPATVQWLIDNyetaegvslprsslfnhYIRHCAENKLDAVNAASFGKLIRSVFIGLRtrrlgtrrgwrfLSSSQSALTRVIALG
Flexible Loop (DISEMBL)
MVQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIattasrdspheNTEVAYIVDEPAQATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIglrtrrlgtrrgwrflsssqsaltrvialg
Low Complexity Region (SEG)
MVQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIglrtrrlgtrrgWRFLSSSQSALTRVIALG
Disordered region (IsUnstruct)
*********QLIGNVNGTYLIQQTVEPTEHATIIA*********************************************VTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLS*************
Disordered Region (DISOPRED)
****************************************************************************************VQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTRV****
Disordered Region (DISEMBL)
MVQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQA***********SPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTRVIALG
Disordered Region (DISPRO)
*****NAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASR*****NT****IVD*****************************ISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTRVIALG
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTRVIALG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	169	2.2.26 [Sep-21-2011]
B2GV50	692	DNA-binding protein RFX2	yes	N/A	0.431	0.105	0.808	3e-31
P22670	979	MHC class II regulatory f	no	N/A	0.461	0.079	0.743	1e-30
P48377	963	MHC class II regulatory f	no	N/A	0.461	0.080	0.743	2e-30
P48381	749	Transcription factor RFX3	no	N/A	0.739	0.166	0.486	3e-30
P48380	749	Transcription factor RFX3	no	N/A	0.739	0.166	0.486	3e-30
Q0V9K5	749	Transcription factor RFX3	no	N/A	0.739	0.166	0.486	3e-30
Q4R3I8	749	Transcription factor RFX3	N/A	N/A	0.751	0.169	0.486	9e-30
Q32NR3	694	DNA-binding protein RFX2	N/A	N/A	0.449	0.109	0.723	2e-28
B1WAV2	694	DNA-binding protein RFX2	no	N/A	0.449	0.109	0.723	2e-28
P48378	723	DNA-binding protein RFX2	yes	N/A	0.420	0.098	0.774	2e-28

>sp|B2GV50|RFX2_RAT DNA-binding protein RFX2 OS=Rattus norvegicus GN=Rfx2 PE=2 SV=1

 Score =  134 bits (337), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 59/73 (80%), Positives = 68/73 (93%)

Query: 77  SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
           SL+H  + SPAT+QWL+DNYETAEGVSLPRSSL+NHY+RHC E+KL+ VNAASFGKLIRS
Sbjct: 158 SLAHTARSSPATLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRS 217

Query: 137 VFIGLRTRRLGTR 149
           VF+GLRTRRLGTR
Sbjct: 218 VFMGLRTRRLGTR 230

Rattus norvegicus (taxid: 10116)

>sp|P22670|RFX1_HUMAN MHC class II regulatory factor RFX1 OS=Homo sapiens GN=RFX1 PE=1 SV=2

 Score =  132 bits (331), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 58/78 (74%), Positives = 67/78 (85%)

Query: 77  SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
           S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct: 427 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 486

Query: 137 VFIGLRTRRLGTRRGWRF 154
           VF+GLRTRRLGTR   ++
Sbjct: 487 VFMGLRTRRLGTRGNSKY 504

Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.

Homo sapiens (taxid: 9606)

>sp|P48377|RFX1_MOUSE MHC class II regulatory factor RFX1 OS=Mus musculus GN=Rfx1 PE=2 SV=2

 Score =  131 bits (330), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 58/78 (74%), Positives = 67/78 (85%)

Query: 77  SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
           S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct: 412 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 471

Query: 137 VFIGLRTRRLGTRRGWRF 154
           VF+GLRTRRLGTR   ++
Sbjct: 472 VFMGLRTRRLGTRGNSKY 489

Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes.

Mus musculus (taxid: 10090)

>sp|P48381|RFX3_MOUSE Transcription factor RFX3 OS=Mus musculus GN=Rfx3 PE=1 SV=2

 Score =  131 bits (329), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 73/150 (48%), Positives = 92/150 (61%), Gaps = 25/150 (16%)

Query: 2   VQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATT 61
           +Q+     QLI +  GTYLI  ++E + H+    T AS                PA    
Sbjct: 118 IQMGVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRAS----------------PATIEM 161

Query: 62  A--TSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAE 119
           A  T    D LS       +H + +  + +QWL+DNYETAEGVSLPRS+L+NHY+RHC E
Sbjct: 162 AIETLQKSDGLS-------THRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQE 214

Query: 120 NKLDAVNAASFGKLIRSVFIGLRTRRLGTR 149
           +KLD VNAASFGKLIRS+F+GLRTRRLGTR
Sbjct: 215 HKLDPVNAASFGKLIRSIFMGLRTRRLGTR 244

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells.

Mus musculus (taxid: 10090)

>sp|P48380|RFX3_HUMAN Transcription factor RFX3 OS=Homo sapiens GN=RFX3 PE=1 SV=2

 Score =  130 bits (328), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 73/150 (48%), Positives = 92/150 (61%), Gaps = 25/150 (16%)

Query: 2   VQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATT 61
           +Q+     QLI +  GTYLI  ++E + H+    T AS                PA    
Sbjct: 118 IQMGVTGGQLISSSGGTYLIGNSMENSGHSVTHTTRAS----------------PATIEM 161

Query: 62  A--TSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAE 119
           A  T    D LS       +H + +  + +QWL+DNYETAEGVSLPRS+L+NHY+RHC E
Sbjct: 162 AIETLQKSDGLS-------THRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQE 214

Query: 120 NKLDAVNAASFGKLIRSVFIGLRTRRLGTR 149
           +KLD VNAASFGKLIRS+F+GLRTRRLGTR
Sbjct: 215 HKLDPVNAASFGKLIRSIFMGLRTRRLGTR 244

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5) (By similarity). Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes. Acts as a transcription factor. Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells.

Homo sapiens (taxid: 9606)

>sp|Q0V9K5|RFX3_XENTR Transcription factor RFX3 OS=Xenopus tropicalis GN=rfx3 PE=2 SV=2

 Score =  130 bits (328), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 73/150 (48%), Positives = 91/150 (60%), Gaps = 25/150 (16%)

Query: 2   VQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATT 61
           +Q+     Q+I +  GTYLI   +E + H+    T AS                PA    
Sbjct: 118 IQMGVTGGQIISSTGGTYLIGNAMENSGHSVSHTTRAS----------------PATIEM 161

Query: 62  A--TSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAE 119
           A  T    D LS       SH + +  + +QWL+DNYETAEGVSLPRS+L+NHY+RHC E
Sbjct: 162 AIETLQKSDGLS-------SHRSSLLNSHLQWLLDNYETAEGVSLPRSTLYNHYLRHCQE 214

Query: 120 NKLDAVNAASFGKLIRSVFIGLRTRRLGTR 149
           +KLD VNAASFGKLIRS+F+GLRTRRLGTR
Sbjct: 215 HKLDPVNAASFGKLIRSIFMGLRTRRLGTR 244

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development.

Xenopus tropicalis (taxid: 8364)

>sp|Q4R3I8|RFX3_MACFA Transcription factor RFX3 OS=Macaca fascicularis GN=RFX3 PE=2 SV=1

 Score =  129 bits (324), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 72/148 (48%), Positives = 94/148 (63%), Gaps = 21/148 (14%)

Query: 2   VQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATT 61
           +Q+     QLI +  GTYLI  ++E + H+    T  +R SP    E+A           
Sbjct: 118 IQMGVTGGQLISSSGGTYLIGNSMENSGHS---VTHTTRASP-ATIEMA----------I 163

Query: 62  ATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENK 121
            T    D LS       +H + +  + +QWL+DNYETAEGVSLPRS+L++HY+RHC E+K
Sbjct: 164 ETLQKSDGLS-------THRSSLLNSHLQWLLDNYETAEGVSLPRSTLYDHYLRHCQEHK 216

Query: 122 LDAVNAASFGKLIRSVFIGLRTRRLGTR 149
           LD VNAASFGKLIRS+F+GLRTRRLGTR
Sbjct: 217 LDPVNAASFGKLIRSIFMGLRTRRLGTR 244

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells.

Macaca fascicularis (taxid: 9541)

>sp|Q32NR3|RFX2_XENLA DNA-binding protein RFX2 OS=Xenopus laevis GN=rfx2 PE=2 SV=1

 Score =  125 bits (313), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 74  NQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKL 133
           N+   SH + +  + +QWL+DNYETAEGVSLPRSSL+NHY+RHC ++KLD VNAASFGKL
Sbjct: 160 NEGITSHKSSLLNSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQDHKLDPVNAASFGKL 219

Query: 134 IRSVFIGLRTRRLGTR 149
           IRSVF+GLRTRRLGTR
Sbjct: 220 IRSVFMGLRTRRLGTR 235

Xenopus laevis (taxid: 8355)

>sp|B1WAV2|RFX2_XENTR DNA-binding protein RFX2 OS=Xenopus tropicalis GN=rfx2 PE=2 SV=1

 Score =  125 bits (313), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 55/76 (72%), Positives = 66/76 (86%)

Query: 74  NQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKL 133
           N+   SH + +  + +QWL+DNYETAEGVSLPRSSL+NHY+RHC ++KLD VNAASFGKL
Sbjct: 160 NEGITSHKSSLLNSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQDHKLDPVNAASFGKL 219

Query: 134 IRSVFIGLRTRRLGTR 149
           IRSVF+GLRTRRLGTR
Sbjct: 220 IRSVFMGLRTRRLGTR 235

Xenopus tropicalis (taxid: 8364)

>sp|P48378|RFX2_HUMAN DNA-binding protein RFX2 OS=Homo sapiens GN=RFX2 PE=2 SV=2

 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 55/71 (77%), Positives = 64/71 (90%)

Query: 79  SHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVF 138
           SH + +  + +QWL+DNYETAEGVSLPRSSL+NHY+RHC E+KLD VNAASFGKLIRSVF
Sbjct: 190 SHKSGLLNSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLDPVNAASFGKLIRSVF 249

Query: 139 IGLRTRRLGTR 149
           +GLRTRRLGTR
Sbjct: 250 MGLRTRRLGTR 260

Homo sapiens (taxid: 9606)

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	169
110758942	825	PREDICTED: transcription factor RFX3-lik	0.834	0.170	0.560	1e-37
380020466	825	PREDICTED: transcription factor RFX3-lik	0.834	0.170	0.547	7e-37
332016778	906	Transcription factor RFX3 [Acromyrmex ec	0.846	0.157	0.543	3e-36
156554603	806	PREDICTED: transcription factor RFX3-lik	0.852	0.178	0.533	5e-36
189241300	738	PREDICTED: similar to GA19507-PA [Tribol	0.828	0.189	0.545	1e-35
270013165	782	hypothetical protein TcasGA2_TC011734 [T	0.828	0.179	0.545	2e-35
383851469	868	PREDICTED: transcription factor RFX3-lik	0.834	0.162	0.541	2e-35
322800170	779	hypothetical protein SINV_04732 [Solenop	0.846	0.183	0.556	4e-35
328707501	763	PREDICTED: DNA-binding protein RFX2-like	0.828	0.183	0.551	4e-34
328707503	780	PREDICTED: DNA-binding protein RFX2-like	0.828	0.179	0.551	4e-34

>gi|110758942|ref|XP_395142.3| PREDICTED: transcription factor RFX3-like [Apis mellifera]

 Score =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 88/157 (56%), Positives = 110/157 (70%), Gaps = 16/157 (10%)

Query: 9   AQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPH-ENTEV-------AYIVDEPA 57
            QL+   NGTYLIQQ+V   +PT HA I A TA R SP  ENTE        AY++   +
Sbjct: 247 GQLLSQGNGTYLIQQSVVDGDPTAHALISAATA-RASPQTENTETVVSGGGGAYLISGNS 305

Query: 58  QATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHC 117
             TT T       +    A+++H T++S ATV WL++NYETA+GVSLPRS+L+NHY+RHC
Sbjct: 306 GNTTVTVEDAATAA----ANMTHATRVSQATVHWLLENYETADGVSLPRSTLYNHYLRHC 361

Query: 118 AENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           +ENKLD VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 362 SENKLDPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 398

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380020466|ref|XP_003694104.1| PREDICTED: transcription factor RFX3-like [Apis florea]

 Score =  158 bits (400), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 86/157 (54%), Positives = 109/157 (69%), Gaps = 16/157 (10%)

Query: 9   AQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPH-ENTEV-------AYIVDEPA 57
            QL+   NGTYLIQQ+V   +PT HA I A TA R SP  EN E        AY++   +
Sbjct: 247 GQLLSQGNGTYLIQQSVVDGDPTAHALISAATA-RASPQTENAETVVSGGGGAYLISGNS 305

Query: 58  QATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHC 117
            +T  T       +    A+++H T++S ATV WL++NYETA+GVSLPRS+L+NHY+RHC
Sbjct: 306 GSTAVTVEDAATAA----ANMTHATRVSQATVHWLLENYETADGVSLPRSTLYNHYLRHC 361

Query: 118 AENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           +ENKLD VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 362 SENKLDPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 398

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016778|gb|EGI57599.1| Transcription factor RFX3 [Acromyrmex echinatior]

 Score =  156 bits (394), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 82/151 (54%), Positives = 107/151 (70%), Gaps = 8/151 (5%)

Query: 9   AQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSN 65
            QL+   NGTYLIQQ+V   +PT   T+I+   +R SP   T  A +V     A   + N
Sbjct: 332 GQLLSQGNGTYLIQQSVVDADPTH--TLISAATTRTSPPTETAEA-VVSGGGGAYLISGN 388

Query: 66  TGDPLSPDNQ--ASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLD 123
           +GD      +  A+++H T++S ATV WL++NYETA+GVSLPRS+L+NHY+RHC+ENKLD
Sbjct: 389 SGDMTGAVEEVAANVTHATRVSQATVHWLLENYETADGVSLPRSTLYNHYLRHCSENKLD 448

Query: 124 AVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
            VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 449 PVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 479

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156554603|ref|XP_001604716.1| PREDICTED: transcription factor RFX3-like isoform 1 [Nasonia vitripennis]

 Score =  155 bits (392), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 88/165 (53%), Positives = 116/165 (70%), Gaps = 21/165 (12%)

Query: 5   SNAPAQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPH-ENTEV-------AYIV 53
           S    QL+   NGTYLIQQ+V   +P  HA I A  A+R SP  E+ E        AY++
Sbjct: 214 STTTGQLLSQGNGTYLIQQSVVDTDPATHALISAAAAARASPQTESAEAVVSGGGGAYLI 273

Query: 54  DEPAQATTATSNTGDPLSPDNQAS----LSHVTKISPATVQWLIDNYETAEGVSLPRSSL 109
                +TTAT+    P+S ++ A+    ++H T++S ATVQWL++NYETA+GVSLPRS+L
Sbjct: 274 S--GNSTTATA----PVSVEDAATAAANMTHATRVSQATVQWLLENYETADGVSLPRSTL 327

Query: 110 FNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           +NHY+RHC++NKLD VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 328 YNHYLRHCSDNKLDPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 372

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189241300|ref|XP_975182.2| PREDICTED: similar to GA19507-PA [Tribolium castaneum]

 Score =  154 bits (388), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 84/154 (54%), Positives = 110/154 (71%), Gaps = 14/154 (9%)

Query: 5   SNAPAQLIG--NVNGTYLIQQTVEPTEHATIIATTASRDSPHE-NTEVAYIVDEPAQATT 61
           S+A A  +G    +G Y++QQ V+P    T+IA+T  R+SP   N E +Y+      AT 
Sbjct: 161 SSATAGTVGYSTTSGHYVVQQAVDPD---TLIAST--RNSPQTTNAEPSYVATATVHATQ 215

Query: 62  ATSNTGDPLSPDNQAS-LSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAEN 120
           +     +P+S +   S L H T++SPATVQWL++NYETAEGVSLPRS+L+ HY+RHCAEN
Sbjct: 216 S-----NPVSNEEVGSALGHATRVSPATVQWLLENYETAEGVSLPRSTLYAHYLRHCAEN 270

Query: 121 KLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           KL+ VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 271 KLEPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 304

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270013165|gb|EFA09613.1| hypothetical protein TcasGA2_TC011734 [Tribolium castaneum]

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 84/154 (54%), Positives = 110/154 (71%), Gaps = 14/154 (9%)

Query: 5   SNAPAQLIG--NVNGTYLIQQTVEPTEHATIIATTASRDSPHE-NTEVAYIVDEPAQATT 61
           S+A A  +G    +G Y++QQ V+P    T+IA+T  R+SP   N E +Y+      AT 
Sbjct: 205 SSATAGTVGYSTTSGHYVVQQAVDPD---TLIAST--RNSPQTTNAEPSYVATATVHATQ 259

Query: 62  ATSNTGDPLSPDNQAS-LSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAEN 120
           +     +P+S +   S L H T++SPATVQWL++NYETAEGVSLPRS+L+ HY+RHCAEN
Sbjct: 260 S-----NPVSNEEVGSALGHATRVSPATVQWLLENYETAEGVSLPRSTLYAHYLRHCAEN 314

Query: 121 KLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           KL+ VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 315 KLEPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 348

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383851469|ref|XP_003701255.1| PREDICTED: transcription factor RFX3-like [Megachile rotundata]

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 85/157 (54%), Positives = 110/157 (70%), Gaps = 16/157 (10%)

Query: 9   AQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPH-ENTEV-------AYIVDEPA 57
            QL+   NGTYLIQQ+V   +PT HA +I+  A+R SP  EN E        AY++   +
Sbjct: 290 GQLLSQGNGTYLIQQSVVDGDPTTHA-LISAAAARASPQTENAETVVSGGGGAYLISGNS 348

Query: 58  QATTATSNTGDPLSPDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHC 117
             TT T       +    A+++H T++S ATV WL++NYETA+GVSLPRS+L+NHY+RHC
Sbjct: 349 GGTTVTVED----AAAAAANMTHATRVSQATVHWLLENYETADGVSLPRSTLYNHYLRHC 404

Query: 118 AENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           +ENKLD VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 405 SENKLDPVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 441

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322800170|gb|EFZ21255.1| hypothetical protein SINV_04732 [Solenopsis invicta]

 Score =  152 bits (384), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 84/151 (55%), Positives = 109/151 (72%), Gaps = 8/151 (5%)

Query: 9   AQLIGNVNGTYLIQQTV---EPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSN 65
            QL+   NGTYLIQQ+V   +PT HA +I+  A+R SP   T  A +V     A   + N
Sbjct: 226 GQLLSQGNGTYLIQQSVVDGDPT-HA-LISAAAARASPQTETAEA-VVSGGGGAYLISGN 282

Query: 66  TGDPLS--PDNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLD 123
           +G       +  A+++H T++S ATVQWL++NYETA+GVSLPRS+L+NHY+RHC+ENKLD
Sbjct: 283 SGGATVTVEETAANVTHATRVSQATVQWLLENYETADGVSLPRSTLYNHYLRHCSENKLD 342

Query: 124 AVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
            VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 343 PVNAASFGKLIRSVFLGLRTRRLGTRGNSKY 373

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328707501|ref|XP_001943107.2| PREDICTED: DNA-binding protein RFX2-like isoform 1 [Acyrthosiphon pisum]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 85/154 (55%), Positives = 111/154 (72%), Gaps = 14/154 (9%)

Query: 9   AQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHE--NTEVAYIVDEPAQATTATSNT 66
           AQ+IGN  GTY+IQQ V+  +H TIIAT A RDSP+   +++V+Y+    A  T +T+ +
Sbjct: 186 AQIIGN--GTYIIQQNVD-NDH-TIIAT-AQRDSPNSVISSDVSYLTVN-ATETGSTNPS 239

Query: 67  GDPLSP------DNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAEN 120
            D L+          + L H  +ISPATV WL++NYE AEGVSLPRS+L+NHY+ HC+E 
Sbjct: 240 IDQLNGVESDGGMQNSGLMHANRISPATVNWLMENYEMAEGVSLPRSTLYNHYLTHCSET 299

Query: 121 KLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           K+D VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 300 KIDPVNAASFGKLIRSVFMGLRTRRLGTRGNSKY 333

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328707503|ref|XP_003243416.1| PREDICTED: DNA-binding protein RFX2-like isoform 2 [Acyrthosiphon pisum] gi|328707505|ref|XP_003243417.1| PREDICTED: DNA-binding protein RFX2-like isoform 3 [Acyrthosiphon pisum]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 85/154 (55%), Positives = 111/154 (72%), Gaps = 14/154 (9%)

Query: 9   AQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHE--NTEVAYIVDEPAQATTATSNT 66
           AQ+IGN  GTY+IQQ V+  +H TIIAT A RDSP+   +++V+Y+    A  T +T+ +
Sbjct: 203 AQIIGN--GTYIIQQNVD-NDH-TIIAT-AQRDSPNSVISSDVSYLTVN-ATETGSTNPS 256

Query: 67  GDPLSP------DNQASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAEN 120
            D L+          + L H  +ISPATV WL++NYE AEGVSLPRS+L+NHY+ HC+E 
Sbjct: 257 IDQLNGVESDGGMQNSGLMHANRISPATVNWLMENYEMAEGVSLPRSTLYNHYLTHCSET 316

Query: 121 KLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRF 154
           K+D VNAASFGKLIRSVF+GLRTRRLGTR   ++
Sbjct: 317 KIDPVNAASFGKLIRSVFMGLRTRRLGTRGNSKY 350

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

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	169
UNIPROTKB|F6UGA0	216	RFX3 "Transcription factor RFX	0.408	0.319	0.714	6.8e-24
FB|FBgn0020379	1079	Rfx "Rfx" [Drosophila melanoga	0.585	0.091	0.557	9.6e-24
RGD|1306574	964	Rfx1 "regulatory factor X, 1 (	0.372	0.065	0.761	8.6e-23
RGD|1588579	692	Rfx2 "regulatory factor X, 2 (	0.372	0.091	0.777	1.8e-22
MGI|MGI:105982	963	Rfx1 "regulatory factor X, 1 (	0.372	0.065	0.761	3.6e-22
UNIPROTKB|E2R585	966	RFX1 "Uncharacterized protein"	0.372	0.065	0.761	4.6e-22
UNIPROTKB|E2R2T9	973	RFX1 "Uncharacterized protein"	0.372	0.064	0.761	4.7e-22
UNIPROTKB|F1SD60	973	RFX1 "Uncharacterized protein"	0.372	0.064	0.761	4.7e-22
UNIPROTKB|P22670	979	RFX1 "MHC class II regulatory	0.372	0.064	0.761	4.8e-22
UNIPROTKB|P48378	723	RFX2 "DNA-binding protein RFX2	0.360	0.084	0.737	2.1e-21

UNIPROTKB|F6UGA0 RFX3 "Transcription factor RFX3" [Homo sapiens (taxid:9606)]

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 50/70 (71%), Positives = 62/70 (88%)

Query:    71 SPDNQA-SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAAS 129
             S +N   S++H T+ SPAT+QWL+DNYETAEGVSLPRS+L+NHY+RHC E+KLD VNAAS
Sbjct:   140 SMENSGHSVTHTTRASPATLQWLLDNYETAEGVSLPRSTLYNHYLRHCQEHKLDPVNAAS 199

Query:   130 FGKLIRSVFI 139
             FGKLIRS+F+
Sbjct:   200 FGKLIRSIFM 209

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

FB|FBgn0020379 Rfx "Rfx" [Drosophila melanogaster (taxid:7227)]

 Score = 285 (105.4 bits), Expect = 9.6e-24, P = 9.6e-24
 Identities = 63/113 (55%), Positives = 79/113 (69%)

Query:    40 RDSPHENTEVAYIVDE------PAQATTATSNTGDPL-------SPDN-QASLSHVTKIS 85
             RDSPH  TEVAYI +       P   TT  S +G  L       SPD+ Q++L    KI+
Sbjct:   491 RDSPHSLTEVAYIQEAQSTPQTPTSTTTTHSASGGSLGTGGGGASPDSDQSALGSSNKIA 550

Query:    86 PATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVF 138
              AT++WL  NYETA+GVSLPRS+L+NHY++HC+E+KL+ VNAASFGKLIRSVF
Sbjct:   551 SATIKWLSRNYETADGVSLPRSTLYNHYMQHCSEHKLEPVNAASFGKLIRSVF 603

GO:0005634 "nucleus" evidence=NAS

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0007605 "sensory perception of sound" evidence=IMP

GO:0007399 "nervous system development" evidence=IMP

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;TAS

GO:0048813 "dendrite morphogenesis" evidence=TAS

RGD|1306574 Rfx1 "regulatory factor X, 1 (influences HLA class II expression)" [Rattus norvegicus (taxid:10116)]

 Score = 257 (95.5 bits), Expect = 8.6e-23, Sum P(2) = 8.6e-23
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   413 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 472

Query:   137 VFI 139
             VF+
Sbjct:   473 VFM 475

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

RGD|1588579 Rfx2 "regulatory factor X, 2 (influences HLA class II expression)" [Rattus norvegicus (taxid:10116)]

 Score = 270 (100.1 bits), Expect = 1.8e-22, P = 1.8e-22
 Identities = 49/63 (77%), Positives = 58/63 (92%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             SL+H  + SPAT+QWL+DNYETAEGVSLPRSSL+NHY+RHC E+KL+ VNAASFGKLIRS
Sbjct:   158 SLAHTARSSPATLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLEPVNAASFGKLIRS 217

Query:   137 VFI 139
             VF+
Sbjct:   218 VFM 220

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

MGI|MGI:105982 Rfx1 "regulatory factor X, 1 (influences HLA class II expression)" [Mus musculus (taxid:10090)]

 Score = 257 (95.5 bits), Expect = 3.6e-22, Sum P(2) = 3.6e-22
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   412 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 471

Query:   137 VFI 139
             VF+
Sbjct:   472 VFM 474

GO:0003677 "DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E2R585 RFX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 257 (95.5 bits), Expect = 4.6e-22, Sum P(2) = 4.6e-22
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   421 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 480

Query:   137 VFI 139
             VF+
Sbjct:   481 VFM 483

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2R2T9 RFX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 257 (95.5 bits), Expect = 4.7e-22, Sum P(2) = 4.7e-22
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   421 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 480

Query:   137 VFI 139
             VF+
Sbjct:   481 VFM 483

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1SD60 RFX1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 257 (95.5 bits), Expect = 4.7e-22, Sum P(2) = 4.7e-22
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   421 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 480

Query:   137 VFI 139
             VF+
Sbjct:   481 VFM 483

GO:0003677 "DNA binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|P22670 RFX1 "MHC class II regulatory factor RFX1" [Homo sapiens (taxid:9606)]

 Score = 257 (95.5 bits), Expect = 4.8e-22, Sum P(2) = 4.8e-22
 Identities = 48/63 (76%), Positives = 55/63 (87%)

Query:    77 SLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRS 136
             S SH T+ SPATVQWL+DNYETAEGVSLPRS+L+ HY+ HC E KL+ VNAASFGKLIRS
Sbjct:   427 SYSHTTRASPATVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRS 486

Query:   137 VFI 139
             VF+
Sbjct:   487 VFM 489

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0006955 "immune response" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|P48378 RFX2 "DNA-binding protein RFX2" [Homo sapiens (taxid:9606)]

 Score = 243 (90.6 bits), Expect = 2.1e-21, Sum P(2) = 2.1e-21
 Identities = 45/61 (73%), Positives = 54/61 (88%)

Query:    79 SHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVF 138
             SH + +  + +QWL+DNYETAEGVSLPRSSL+NHY+RHC E+KLD VNAASFGKLIRSVF
Sbjct:   190 SHKSGLLNSHLQWLLDNYETAEGVSLPRSSLYNHYLRHCQEHKLDPVNAASFGKLIRSVF 249

Query:   139 I 139
             +
Sbjct:   250 M 250

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P48378	RFX2_HUMAN	No assigned EC number	0.7746	0.4201	0.0982	yes	N/A
Q5EAP5	RFX2_DANRE	No assigned EC number	0.7605	0.4201	0.0967	yes	N/A
B2GV50	RFX2_RAT	No assigned EC number	0.8082	0.4319	0.1054	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	169
pfam02257	73	pfam02257, RFX_DNA_binding, RFX DNA-binding domain	1e-34

>gnl|CDD|190261 pfam02257, RFX_DNA_binding, RFX DNA-binding domain

 Score =  116 bits (292), Expect = 1e-34
 Identities = 40/62 (64%), Positives = 49/62 (79%)

Query: 88  TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLG 147
            +QWL DN E +EG SLPR+ ++ HY+ HCAE  L  ++AASFGKLIRSVF GL+TRRLG
Sbjct: 8   ALQWLRDNCEESEGSSLPRNRVYAHYVSHCAELGLKPLSAASFGKLIRSVFPGLKTRRLG 67

Query: 148 TR 149
           TR
Sbjct: 68  TR 69

RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. Length = 73

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
PF02257	85	RFX_DNA_binding: RFX DNA-binding domain; InterPro:	100.0
KOG3712|consensus	736		100.0
PF03288	86	Pox_D5: Poxvirus D5 protein-like; InterPro: IPR004	98.28
PRK07078	759	hypothetical protein; Validated	97.63
PRK14709	469	hypothetical protein; Provisional	97.27
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	96.84
PF09079	85	Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The	91.79
KOG3712|consensus	736		89.44
COG3378	517	Phage associated DNA primase [General function pre	89.02
cd08768	87	Cdc6_C Winged-helix domain of essential DNA replic	87.15

>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression

Probab=100.00  E-value=3.2e-39  Score=237.71  Aligned_cols=77  Identities=48%  Similarity=0.825  Sum_probs=64.6

Q ss_pred             HHHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeeccccccc
Q psy7155          87 ATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALT  163 (169)
Q Consensus        87 at~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir~~~  163 (169)
                      .|++||++|||.++++||||+.||++|+.+|++++++|||+|+|||+||.+||+++|||||+||+|||||+||+++.
T Consensus         7 ~a~~WL~~~~e~~~~~svpR~~lY~~Y~~~C~~~~~~pln~AsFGKlir~vFP~l~~RRLG~RG~SkYhY~Gir~k~   83 (85)
T PF02257_consen    7 FAMQWLRENYEESPGVSVPRSDLYAHYLSFCEKNGIKPLNAASFGKLIRQVFPNLKTRRLGTRGQSKYHYCGIRLKP   83 (85)
T ss_dssp             --HHHHHHHEEEEEEEEEEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHSTT-EEEEESSTT--EEEEEEEEE--
T ss_pred             HHHHHHHHHcccCCCCccchHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHcCCCcccccccCCCcceEEEeEEecC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999875

The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.

>KOG3712|consensus

Probab=100.00  E-value=1.9e-36  Score=286.59  Aligned_cols=136  Identities=43%  Similarity=0.705  Sum_probs=115.5

Q ss_pred             ceeecCCceeeeccCceeeeecccCCCCcceeeeecccCCCCCCccceeeeeeCCCccccccCCCCCCCCCCC-cccccc
Q psy7155           2 VQVSNAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDEPAQATTATSNTGDPLSPDN-QASLSH   80 (169)
Q Consensus         2 ~~~~~~~~q~~~~~~~~y~i~~~~~~~~~h~~~~t~~~r~sp~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~-~s~~~~   80 (169)
                      +.|.+++++.+++.++.|+|+.++...+| -.+++.  +.+|++.+-                       .+. ..+..+
T Consensus       141 ~~t~~~~~k~vs~~~~~~~~~~~~~~~~~-~~~~~~--~~~p~~~s~-----------------------~~~~~~~~~~  194 (736)
T KOG3712|consen  141 IGTRVTGSKAVSSAGKGYLIQGNMQFSRH-DKAHTS--SGSPQSPSS-----------------------LDKSSNNSTN  194 (736)
T ss_pred             ccccccchhhhhccccceeeccccccccc-cceeec--ccCCCCccc-----------------------cccccccccc
Confidence            46889999999988889999988887775 335534  555555211                       111 133446


Q ss_pred             ccCCCHHHHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeecccc
Q psy7155          81 VTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQS  160 (169)
Q Consensus        81 ~~r~spat~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir  160 (169)
                      .++..++|++||++|||..+|+||||+.+|+||++||++++++|||+|+||||||++||+|+|||||+||||||||+|||
T Consensus       195 ~~~~~~~tlqWL~~nyes~eg~~lPR~sly~hY~~~C~e~~l~PvsaAsfGKlIRsvFp~L~TRRLGtRGqSKYHYyGir  274 (736)
T KOG3712|consen  195 SNESSPATLQWLLDNYESAEGVSLPRSSLYDHYLKHCQEHNLDPVSAASFGKLIRSVFPDLKTRRLGTRGQSKYHYYGIR  274 (736)
T ss_pred             chhhhHHHHHHHHhccccccccccchHHHHHHHHHHHHhhCCCCcchHHHhHHHHHHcccchhhhcccCCCCceeeeeee
Confidence            68889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy7155         161 ALT  163 (169)
Q Consensus       161 ~~~  163 (169)
                      .+.
T Consensus       275 vk~  277 (736)
T KOG3712|consen  275 VKP  277 (736)
T ss_pred             cCC
Confidence            875

>PF03288 Pox_D5: Poxvirus D5 protein-like; InterPro: IPR004968 This domain is found at the C terminus of phage P4 alpha protein and related proteins

Probab=98.28  E-value=7.5e-07  Score=62.86  Aligned_cols=54  Identities=22%  Similarity=0.481  Sum_probs=42.3

Q ss_pred             HHHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCc-CCchhhhHHHHHHcCC
Q psy7155          87 ATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDA-VNAASFGKLIRSVFIG  140 (169)
Q Consensus        87 at~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~P-lnaAsFGKLIR~vFP~  140 (169)
                      ...+|+.+.|+...+..+|+..||+.|..+|++++..| ++...|+|-|+..+|.
T Consensus         5 ~V~~F~~e~~~~~~~~~v~~~~lY~~Y~~wc~~ng~~~~ls~~~F~~~L~~~~~~   59 (86)
T PF03288_consen    5 PVLAFIEECCERDPGDFVPSKDLYDAYKEWCEENGYKPPLSKRKFGKELKQYFPE   59 (86)
T ss_dssp             HHHHHGGGEEE-S--S--TTTBHHHHHHHHHHHTT-S----HHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHhhhcCcccccHHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhhh
Confidence            45789999999999999999999999999999999998 9999999999999886

Phage P4 DNA replication depends on the product of the alpha gene, which has origin recognition ability, DNA helicase activity, and DNA primase activity. The structure of the protein can be summarised as follows: The N terminus provides the primase activity, the central region is the helicase/nucleoside triphosphatase domain and the ori DNA recognition resides in the C-terminal 1/3 of the protein []. The domain is also found at the C terminus of a number of proteins from orthopox viruses including vaccinia virus D5. D5 encodes a 90kDa protein that is transiently expressed at early times after infection. It has an nucleoside triphosphatase activity which is independent of common nucleic acid cofactors and it can hydrolyse all the common ribo- and deoxyribonucleoside triphosphates to diphosphates in the presence of a divalent cation [].; PDB: 1KA8_E.

>PRK07078 hypothetical protein; Validated

Probab=97.63  E-value=8.5e-05  Score=72.39  Aligned_cols=71  Identities=17%  Similarity=0.187  Sum_probs=60.2

Q ss_pred             HHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeeccccccce
Q psy7155          89 VQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALTR  164 (169)
Q Consensus        89 ~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir~~~r  164 (169)
                      .+||.+.|+..++..++...+|+.|..+|.+++..|++...|+|.|+..  ++..+|..   +.++.|.||+.+..
T Consensus       678 ~~Fl~e~c~~~~~~~~~~~~LY~~Y~~wc~~~G~~~~s~k~F~~~L~~~--Gf~~~r~~---~g~~~~~Gi~L~~~  748 (759)
T PRK07078        678 GQWIEERCERGANAKELTAELFNDWKEWAERAGEFVGSQKRFSDLLATR--GFEKWRLT---GGLRGFRGIGLKPK  748 (759)
T ss_pred             HHHHHHhceeCCCCceeHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhc--CCceeecc---CCcEEEeceEEecc
Confidence            5799999999999999999999999999999999999999999999987  55555532   33567999987753

>PRK14709 hypothetical protein; Provisional

Probab=97.27  E-value=0.00044  Score=63.72  Aligned_cols=69  Identities=19%  Similarity=0.249  Sum_probs=53.9

Q ss_pred             HHHHHhhcccCCCcccChhhhHHHHHHHHh---hcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeeccccccc
Q psy7155          89 VQWLIDNYETAEGVSLPRSSLFNHYIRHCA---ENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALT  163 (169)
Q Consensus        89 ~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~---~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir~~~  163 (169)
                      .+||.+.|+..++..++...+|+.|..+|+   +++.+|++...|+|.|+..  +.+.+|    .+....|.||+.+.
T Consensus       390 ~~Fl~e~c~~~~~~~~~~~~~~~~Y~~w~~~~~~~g~~~~s~~~F~~~L~~~--G~~~~r----~~~~~~~~Gi~L~~  461 (469)
T PRK14709        390 GQWLEERCIVDPGNPVCWDVLQDLYASWCEFARAEGEPAGTAKEFGERMEKL--GFKKDR----KNRGRGFRGIQLRP  461 (469)
T ss_pred             HHHHHhheEeCCCCccchHHHHHHHHHHHHHHHhcCCcCCcHHHHHHHHHHc--CCCcee----cCCCeEEeeeEEcc
Confidence            589999999999988998888777777666   7888999999999999985  334443    22344699998765

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=96.84  E-value=0.0011  Score=56.48  Aligned_cols=42  Identities=19%  Similarity=0.458  Sum_probs=39.8

Q ss_pred             HHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhh
Q psy7155          89 VQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASF  130 (169)
Q Consensus        89 ~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsF  130 (169)
                      .+||.++|+..++..+|+..+|+.|..+|++++..|++...|
T Consensus       263 ~~Fi~e~~~~~~~~~~~~~~ly~~y~~wc~~~g~~~~s~~~f  304 (304)
T TIGR01613       263 ARFLEECCDDSEGEKVPVRFVYEAYKEWCEEGGYPILSRNKF  304 (304)
T ss_pred             HHHHHhheEeCCCcEEEHHHHHHHHHHHHHHcCCCccccCCC
Confidence            689999999999999999999999999999999999998877

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8)

Probab=91.79  E-value=0.29  Score=34.48  Aligned_cols=46  Identities=13%  Similarity=0.335  Sum_probs=33.2

Q ss_pred             CcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHH-cCCCCcccC
Q psy7155         101 GVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSV-FIGLRTRRL  146 (169)
Q Consensus       101 g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~v-FP~l~TRRL  146 (169)
                      ...++=..+|+.|...|+..+.+|++...|-.+++.. +-++-..+-
T Consensus        13 ~~~~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~   59 (85)
T PF09079_consen   13 KEEVTTGEVYEVYEELCESLGVDPLSYRRFSDYLSELEMLGLIESER   59 (85)
T ss_dssp             SSSEEHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCceeHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence            4567778899999999999999999999999988764 555444443

It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.

>KOG3712|consensus

Probab=89.44  E-value=0.061  Score=53.06  Aligned_cols=64  Identities=17%  Similarity=0.109  Sum_probs=53.8

Q ss_pred             HHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceee
Q psy7155          89 VQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLS  156 (169)
Q Consensus        89 ~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY  156 (169)
                      ..|++. |...+. -+=+...+.+|.+.|......|.|+++|  ..|.+|++++|||+|.++-++++|
T Consensus        93 ~~~~~~-y~~~e~-~~~~~~~~~s~~~~~gt~~~~~~~~~s~--~~~~~~~~~~t~~~~~k~vs~~~~  156 (736)
T KOG3712|consen   93 ASAIRN-YPYSES-QMYANNIPASYFEKTGTRAQVPGNEASE--EHRVLSISIGTRVTGSKAVSSAGK  156 (736)
T ss_pred             chhhhh-cccCcC-HHHhccCCcccccCCCCcCCCCcccccc--cceeecccccccccchhhhhcccc
Confidence            568887 433333 3677778899999999999999999999  677788899999999999999995

>COG3378 Phage associated DNA primase [General function prediction only]

Probab=89.02  E-value=0.32  Score=46.20  Aligned_cols=56  Identities=20%  Similarity=0.298  Sum_probs=45.8

Q ss_pred             HHHHHhhcccCCCcccChhh------hHHHHHHHHhhcC-CCcCCchhhhHHHHHHcCCCCcc
Q psy7155          89 VQWLIDNYETAEGVSLPRSS------LFNHYIRHCAENK-LDAVNAASFGKLIRSVFIGLRTR  144 (169)
Q Consensus        89 ~~WL~~nyE~~~g~sVPR~~------lY~~Y~~~C~~~~-l~PlnaAsFGKLIR~vFP~l~TR  144 (169)
                      .+|+.+-|+..+..-.|-..      +|+.|+.+|+.++ ..+++.+.|||.+..++-.-..+
T Consensus       416 ~~F~~d~~~~~~~~~~~~~~~~~~~~ly~~y~~w~e~~G~~~~~s~~~F~~~l~~~~v~~~r~  478 (517)
T COG3378         416 FQFCDDECVLGETDGTPTAFDNIVLELYEAYQEWCEANGYVVELSKTRFGKELPTKGVPKGRK  478 (517)
T ss_pred             HHHHHHHhhccccccccccchhhhHHHHHHHHHHHHhcCCcccchhhhhhcccccccccccce
Confidence            68999999998876666665      9999999999999 66999999999988655444433

>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding

Probab=87.15  E-value=1.6  Score=30.20  Aligned_cols=42  Identities=17%  Similarity=0.394  Sum_probs=34.2

Q ss_pred             cccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHH-cCCCCc
Q psy7155         102 VSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSV-FIGLRT  143 (169)
Q Consensus       102 ~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~v-FP~l~T  143 (169)
                      ..+.=..+|+.|...|+..+.+|++...|-.++... +-++-.
T Consensus        21 ~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~   63 (87)
T cd08768          21 EEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLE   63 (87)
T ss_pred             CCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeE
Confidence            346678899999999999999999999999888754 444433

This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	169
1dp7_P	76	Cocrystal Structure Of Rfx-Dbd In Complex With Its		5e-20

>pdb|1DP7|P Chain P, Cocrystal Structure Of Rfx-Dbd In Complex With Its Cognate X-Box Binding Site Length = 76

Iteration: 1
 Score = 93.6 bits (231), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 41/52 (78%), Positives = 47/52 (90%)
Query: 88  TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFI 139
           TVQWL+DNYETAEGVSLPRS+L+NHY+ H  E KL+ VNAASFGKLIRSVF+
Sbjct: 1   TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFM 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	169
1dp7_P	76	MHC class II transcription factor HRFX1; winged he	2e-28

>1dp7_P MHC class II transcription factor HRFX1; winged helix, protein- DNA conovel mode of DNA recognition, transcription/DNA complex; HET: DNA BRU; 1.50A {Synthetic} SCOP: a.4.5.20 Length = 76

 Score = 99.6 bits (248), Expect = 2e-28
 Identities = 51/62 (82%), Positives = 57/62 (91%)

Query: 88  TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLG 147
           TVQWL+DNYETAEGVSLPRS+L+NHY+ H  E KL+ VNAASFGKLIRSVF+GLRTRRLG
Sbjct: 1   TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFMGLRTRRLG 60

Query: 148 TR 149
           TR
Sbjct: 61  TR 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
1dp7_P	76	MHC class II transcription factor HRFX1; winged he	100.0
1ka8_A	100	Putative P4-specific DNA primase; winged helix, tr	96.41

>1dp7_P MHC class II transcription factor HRFX1; winged helix, protein- DNA conovel mode of DNA recognition, transcription/DNA complex; HET: DNA BRU; 1.50A {Synthetic} SCOP: a.4.5.20

Probab=100.00  E-value=1.3e-38  Score=229.03  Aligned_cols=75  Identities=68%  Similarity=1.046  Sum_probs=73.6

Q ss_pred             HHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeecccccc
Q psy7155          88 TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSAL  162 (169)
Q Consensus        88 t~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir~~  162 (169)
                      |++||++|||.++++||||++||++|+.+|++++++|||+|+|||+||.+||+|+|||||+||+|||||+|||++
T Consensus         1 t~~Wl~~~~e~~~~~svpR~~vY~~Y~~~C~~~~~~pl~~a~FGK~ir~~FP~l~trRLg~rG~skyhy~Girlk   75 (76)
T 1dp7_P            1 TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIK   75 (76)
T ss_dssp             CHHHHHHHEEEEEEEEEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHSTTCEEEEESSTTCCEEEEEEEEEC
T ss_pred             CceeHhhhcEECCCceechHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHCCCceeeeccccCCccEEEEeeEeC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999986

>1ka8_A Putative P4-specific DNA primase; winged helix, transferase; 2.95A {Enterobacteria phage P4} SCOP: a.4.5.20

Probab=96.41  E-value=0.0025  Score=47.82  Aligned_cols=37  Identities=16%  Similarity=0.219  Sum_probs=33.7

Q ss_pred             cChhhhHHHHHHHHhhcCCC-cCCchhhhHHHHHHcCC
Q psy7155         104 LPRSSLFNHYIRHCAENKLD-AVNAASFGKLIRSVFIG  140 (169)
Q Consensus       104 VPR~~lY~~Y~~~C~~~~l~-PlnaAsFGKLIR~vFP~  140 (169)
                      -||.-+|..|+.+|+.++++ ||+=.+|||-|+.++-.
T Consensus        32 ~pR~yLYhAYLaymea~g~~~pLsl~~Fg~~l~~alke   69 (100)
T 1ka8_A           32 NYRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVMLKE   69 (100)
T ss_dssp             CTTTBHHHHHHHHHHHTTCSCCCCHHHHHHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHHH
Confidence            47888999999999999999 99999999999988743

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	169
d1dp7p_	76	a.4.5.20 (P:) Class II MHC transcription factor RF	1e-27

>d1dp7p_ a.4.5.20 (P:) Class II MHC transcription factor RFX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: P4 origin-binding domain-like
domain: Class II MHC transcription factor RFX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.8 bits (241), Expect = 1e-27
 Identities = 51/62 (82%), Positives = 57/62 (91%)

Query: 88  TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLG 147
           TVQWL+DNYETAEGVSLPRS+L+NHY+ H  E KL+ VNAASFGKLIRSVF+GLRTRRLG
Sbjct: 1   TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFMGLRTRRLG 60

Query: 148 TR 149
           TR
Sbjct: 61  TR 62

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	169
d1dp7p_	76	Class II MHC transcription factor RFX1 {Human (Hom	100.0
d1fnna1	112	CDC6, C-terminal domain {Archaeon Pyrobaculum aero	95.06
d2ezia_	75	Transposase {Bacteriophage mu [TaxId: 10677]}	90.15
d1ka8a_	100	P4 origin-binding domain {Bacteriophage P4 [TaxId:	89.27
d1w5sa1	110	CDC6-like protein APE0152, C-terminal domain {Aero	85.97

>d1dp7p_ a.4.5.20 (P:) Class II MHC transcription factor RFX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: P4 origin-binding domain-like
domain: Class II MHC transcription factor RFX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.3e-39  Score=229.83  Aligned_cols=76  Identities=67%  Similarity=1.035  Sum_probs=74.4

Q ss_pred             HHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcccCCCCCCcceeeccccccc
Q psy7155          88 TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRRGWRFLSSSQSALT  163 (169)
Q Consensus        88 t~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TRRLGtRG~SKYHY~Gir~~~  163 (169)
                      |++||++|||.+++++|||++||++|+++|++++++|||+|+|||+||.+||++++||||+||+|||||+|||+++
T Consensus         1 T~~WL~~~~e~~~~~svpR~~lY~~Y~~~C~~~~~~~l~~a~FgKliR~vFP~~~~RRLg~rG~skYhY~Gir~ka   76 (76)
T d1dp7p_           1 TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA   76 (76)
T ss_dssp             CHHHHHHHEEEEEEEEEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHSTTCEEEEESSTTCCEEEEEEEEECC
T ss_pred             ChhHHHhhcccCCCccccHHHHHHHHHHHHHHcCCcccCHHHHHHHHHHHCCCceeeecCCCCCceEEEeeeEecC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999885

>d1fnna1 a.4.5.11 (A:277-388) CDC6, C-terminal domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6, C-terminal domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=95.06  E-value=0.012  Score=41.71  Aligned_cols=51  Identities=10%  Similarity=0.058  Sum_probs=39.9

Q ss_pred             cccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHH-cCCCCcccC
Q psy7155          96 YETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSV-FIGLRTRRL  146 (169)
Q Consensus        96 yE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~v-FP~l~TRRL  146 (169)
                      .+......+.=..+|+.|...|++.+.+|++...|-++|+.. |-|+-.-|.
T Consensus        24 ~~~~~~~~ittgevy~~Y~~lc~~~~~~pls~rr~~~~l~~Le~lGiI~~r~   75 (112)
T d1fnna1          24 LKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQ   75 (112)
T ss_dssp             HHHHCSSCEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred             HhcCCCCCccHHHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHhCCCeeeee
Confidence            333334456667899999999999999999999999999864 777665544

>d2ezia_ a.4.1.2 (A:) Transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=90.15  E-value=0.43  Score=31.23  Aligned_cols=63  Identities=14%  Similarity=0.156  Sum_probs=53.6

Q ss_pred             cccCCCHHHHHHHHhhcccCCCcccChhhhHHHHHHHHhhcCCCcCCchhhhHHHHHHcCCCCcc
Q psy7155          80 HVTKISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTR  144 (169)
Q Consensus        80 ~~~r~spat~~WL~~nyE~~~g~sVPR~~lY~~Y~~~C~~~~l~PlnaAsFGKLIR~vFP~l~TR  144 (169)
                      +...++|.+..-|.+.|...+.-++  ..+|..+...|.+.++.|-+-.+|-+.|..+=|...++
T Consensus         4 ~k~~~~~~~we~i~~~YL~~~~ps~--~~~y~~i~~~c~~~gl~~PS~~T~~rri~~l~~~~~~~   66 (75)
T d2ezia_           4 HKSEFDEDAWQFLIADYLRPEKPAF--RKCYERLELAAREHGWSIPSRATAFRRIQQLDEAMVVA   66 (75)
T ss_dssp             TTCCSCHHHHHHHHHHHTSTTCCCH--HHHHHHHHHHHHHHTCCCCCHHHHHHHHHHHCTHHHHH
T ss_pred             ccccCCHHHHHHHHHHHhCccCCCH--HHHHHHHHHHHHHcCCCCCCHHHHHHHHHhCCHHHHHH
Confidence            3467899999999999999988776  56799999999999999999999999999875554443

>d1ka8a_ a.4.5.20 (A:) P4 origin-binding domain {Bacteriophage P4 [TaxId: 10680]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: P4 origin-binding domain-like
domain: P4 origin-binding domain
species: Bacteriophage P4 [TaxId: 10680]

Probab=89.27  E-value=0.17  Score=36.28  Aligned_cols=34  Identities=18%  Similarity=0.296  Sum_probs=31.6

Q ss_pred             ChhhhHHHHHHHHhhcCCC-cCCchhhhHHHHHHc
Q psy7155         105 PRSSLFNHYIRHCAENKLD-AVNAASFGKLIRSVF  138 (169)
Q Consensus       105 PR~~lY~~Y~~~C~~~~l~-PlnaAsFGKLIR~vF  138 (169)
                      ||--+|-.|+.+-+.++.+ ||+=+.|||-|..+.
T Consensus        33 pR~yLYhAYLaymea~G~~~pLsLt~Fg~~ip~~l   67 (100)
T d1ka8a_          33 YRKYLYHAYLAYMEANGYRNVLSLKMFGLGLPVML   67 (100)
T ss_dssp             TTTBHHHHHHHHHHHTTCSCCCCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCCccHHHHHHhhHHHH
Confidence            8888999999999999997 999999999998775

>d1w5sa1 a.4.5.11 (A:300-409) CDC6-like protein APE0152, C-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6-like protein APE0152, C-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=85.97  E-value=0.62  Score=33.03  Aligned_cols=63  Identities=10%  Similarity=0.099  Sum_probs=41.4

Q ss_pred             ccCCCcccChhhhHHHHHH-HHhhcCCCcCCchhhhHHHHHH-cCCC---CcccCCCCCCcceeeccc
Q psy7155          97 ETAEGVSLPRSSLFNHYIR-HCAENKLDAVNAASFGKLIRSV-FIGL---RTRRLGTRRGWRFLSSSQ  159 (169)
Q Consensus        97 E~~~g~sVPR~~lY~~Y~~-~C~~~~l~PlnaAsFGKLIR~v-FP~l---~TRRLGtRG~SKYHY~Gi  159 (169)
                      +....-.+.=.++|+.|.+ .|.....+|++-+.|-++|... +-++   ++.--|.||.+|+-...+
T Consensus        22 ~~~~~~~~~tGei~~~Y~ev~c~~~~~~P~~~t~~~~~l~~Le~lGiI~~r~~~~G~rGrt~~isl~~   89 (110)
T d1w5sa1          22 TLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAP   89 (110)
T ss_dssp             HHTTCSSBCHHHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEECC-------CCEEEECT
T ss_pred             HhcCCCCCchHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHcCCeEEEeccCCCCCCeeEEeeCC
Confidence            3333445566889999987 5999999999999999999875 3343   344566788888766543