Citrus Sinensis ID: 026468

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------24
Protein Sequence
MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSVLGDSRSKSITEK
Secondary Structure (PSIPRED)
ccccccHHHccHHHHHHHHccccccccccccccccEEEEccccccccccccccccccEEEEccEEEEccEEEEEEEccccEEEcccccEEEEEEcEEEEEEEcccccccccccccEEEEEcHHHHHHHHHcccccccEEEcccccccccccccEEEEEEEEcccccEEEEEEEEcccccccEEEEEccHHHHHHHHHHHHHHHcccccccccccccEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHccccccccccccccccHcccccHHcccccccccccccccccccccccccEEccEEEEcccEEEEEEEEccEEEEccccEEEEEEccEEEEEEEEEcccccEcHHHcEEEEEcHHHHHHHHcccccccEEEEEccccccccccccEEEEEEEEcccccEEEEEEEcccccccccEEEEccHHHHHHHHHHHHHHHHHHHcHHHccccEEEEEcccccEcccccccccccc
Coil and Loop (DISEMBL)
mmklsrslLSSRSQLSEKLLAGEANYVRDGLKSHVLISqagmsttghdvsakgslggrifapyyvykgkaafsvdpvlptfmkldsgdlkvkrkGVILLTfapaigerkydwakkqhfalsptevgslltmgprdsseffhdpamlssnagqmRKSLSIKANADGFFISLNVANNilktnerfvvpvsTAEFAVMKTACSVCTneiasrsqlgspaviccsqvtsvlgdsrsksitek
Flexible Loop (DISEMBL)
mmklsrsllssRSQLSEKLLAGEANYVRDGLKSHVLISQAgmsttghdvsakgslGGRIFAPYYVYKGKAAFSVDPVLPTFMKLdsgdlkvkrkgVILLTfapaigerkydWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIAsrsqlgspavICCSqvtsvlgdsrsksitek
Low Complexity Region (SEG)
MMklsrsllssrsqlsekllAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSVLGDSRSKSITEK
Disordered region (IsUnstruct)
**********************EANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVG*L******************************IKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSVL***********
Disordered Region (DISOPRED)
***********************************************************FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEF*******************IKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICC******************
Disordered Region (DISEMBL)
************SQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSV************
Disordered Region (DISPRO)
*******************************************************GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVT**************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSPAVICCSQVTSVLGDSRSKSITEK
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	238	2.2.26 [Sep-21-2011]
D9J034	238	Single-stranded DNA-bindi	N/A	no	0.852	0.852	0.622	9e-66
Q8VYF7	238	Single-stranded DNA-bindi	yes	no	0.869	0.869	0.593	5e-61
B2LXS7	266	Single-stranded DNA-bindi	N/A	no	0.630	0.563	0.473	3e-36
Q9M9S3	263	Single-stranded DNA-bindi	no	no	0.621	0.562	0.453	2e-34
Q9LL85	274	Single-stranded DNA-bindi	N/A	no	0.613	0.532	0.459	2e-34
Q66GR6	268	Single-stranded DNA-bindi	no	no	0.609	0.541	0.439	4e-32

>sp|D9J034|WHY2_SOLTU Single-stranded DNA-bindig protein WHY2, mitochondrial OS=Solanum tuberosum GN=WHY2 PE=1 SV=1

 Score =  249 bits (637), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 130/209 (62%), Positives = 158/209 (75%), Gaps = 6/209 (2%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAK-GSLGGRI 59
           M+K+SR LL  R+QL  K L GE   V+  +  H + + AG ST   +V A  G   GR+
Sbjct: 1   MLKVSR-LLHPRNQLLHKKLPGEC--VKGSIWQHAINTFAGFSTVRQNVVADAGKREGRV 57

Query: 60  FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFA 119
           FAPY V+KGKAA S +P LPTF +LDSG +K+ R+GVI+LTF P++GERKYDW K+Q FA
Sbjct: 58  FAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFA 117

Query: 120 LSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNIL 177
           LS TEVGSL++MG RDSSEFFHDP+MLSSNAGQ+RKSLSIK NAD  G+FISL+V NN L
Sbjct: 118 LSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNL 177

Query: 178 KTNERFVVPVSTAEFAVMKTACSVCTNEI 206
           KTN+RF VPV+TAEFAVM+TA S     I
Sbjct: 178 KTNDRFTVPVTTAEFAVMRTAFSFALPHI 206

Single-stranded DNA-binding protein that may be involved in the maintenance of mitochondrial genome stability by preventing break-induced DNA rearrangements.
Solanum tuberosum (taxid: 4113)

>sp|Q8VYF7|WHY2_ARATH Single-stranded DNA-binding protein WHY2, mitochondrial OS=Arabidopsis thaliana GN=WHY2 PE=2 SV=1

 Score =  234 bits (596), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 127/214 (59%), Positives = 160/214 (74%), Gaps = 7/214 (3%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIF 60
           MMK +RSLLS RS   +     EA+ +R G  S    S  G    G D +AK S  GR+F
Sbjct: 1   MMKQARSLLS-RSLCDQSKSLFEASTLR-GFASWSNSSTPGRGFPGKD-AAKPS--GRLF 55

Query: 61  APYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFAL 120
           APY ++KGKAA SV+PVLP+F ++DSG+L++ R+G +++TF PAIGERKYDW KKQ FAL
Sbjct: 56  APYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFAL 115

Query: 121 SPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNILK 178
           SPTEVGSL++MG +DSSEFFHDP+M SSNAGQ+RKSLS+K +AD  G+FISL+V N+ILK
Sbjct: 116 SPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNSILK 175

Query: 179 TNERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
           TN+ FVVPV+ AEFAVMKTA S     I   ++L
Sbjct: 176 TNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRL 209

Single-stranded DNA-binding protein that associates with mitochondrial DNA and may play a role in the regulation of the gene expression machinery. Seems also to be required to prevent break-induced DNA rearrangements in the mitochondrial genome. Can bind to melt double-stranded DNA in vivo.

Arabidopsis thaliana (taxid: 3702)

>sp|B2LXS7|WHY1_MAIZE Single-stranded DNA-bindig protein WHY1, chloroplastic OS=Zea mays GN=WHY1 PE=2 SV=1

 Score =  152 bits (383), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 72/152 (47%), Positives = 99/152 (65%), Gaps = 2/152 (1%)

Query: 46  GHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAI 105
           G+     G+  GR+F  Y +YKGKAA S DP  P F+ LDSG  KV ++G +LL FAPA+
Sbjct: 73  GYGRPPNGAQDGRVFTSYSIYKGKAALSFDPRPPLFVPLDSGAYKVAKEGFVLLQFAPAV 132

Query: 106 GERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD- 164
             R+YDW +KQ F+LS  E+G+LLT+GP DS EFFHDP    S  G++RK L I+   D 
Sbjct: 133 ATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKVRKVLKIEPTPDG 192

Query: 165 -GFFISLNVANNILKTNERFVVPVSTAEFAVM 195
            G F +L+V N ++  +E   +P++  EFAV+
Sbjct: 193 NGRFFNLSVQNRLINVDESIYIPITKGEFAVI 224

Single-stranded DNA and RNA binding protein that maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. Functions in RNA metabolism and is involved in the maturation of the atpF and 23S ribosomal RNAs.

Zea mays (taxid: 4577)

>sp|Q9M9S3|WHY1_ARATH Single-stranded DNA-binding protein WHY1, chloroplastic OS=Arabidopsis thaliana GN=WHY1 PE=1 SV=1

 Score =  145 bits (367), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/150 (45%), Positives = 102/150 (68%), Gaps = 2/150 (1%)

Query: 55  LGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAK 114
           L  R +  + +YKGKAA +VDP  P F+ LDSG  K+ + G +LL FAP+ G R+YDW+K
Sbjct: 77  LPARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSK 136

Query: 115 KQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNV 172
           KQ F+LS TE+G+L+++GPR+S EFFHDP    S+ G++RK L ++   D  G F +L+V
Sbjct: 137 KQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSV 196

Query: 173 ANNILKTNERFVVPVSTAEFAVMKTACSVC 202
            N ++  +E   +P++ AEFAV+ +A +  
Sbjct: 197 QNKLVNVDESIYIPITRAEFAVLISAFNFV 226

Single-stranded DNA-binding protein that functions in both chloroplasts and nucleus. In chloroplasts, maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. In nucleus, modulates telomere length homeostasis by inhibiting the action of the telomerase at the extreme termini of chromosomes. Is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Is required for full salicylic acid-dependent plant disease resistance responses. Can bind double-stranded DNA in vivo.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LL85|WHY1_SOLTU Single-stranded DNA-bindig protein WHY1, chloroplastic OS=Solanum tuberosum GN=WHY1 PE=1 SV=1

 Score =  145 bits (366), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 68/148 (45%), Positives = 103/148 (69%), Gaps = 2/148 (1%)

Query: 53  GSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDW 112
           G+   ++F  Y +YKGKAA +V+P  P F  LDSG  K+ R+G+++L FAPA G R+YDW
Sbjct: 86  GASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDW 145

Query: 113 AKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISL 170
           ++KQ F+LS TE+GS++++G +DS EFFHDP    S+ G++RK L ++   D  G F +L
Sbjct: 146 SRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNL 205

Query: 171 NVANNILKTNERFVVPVSTAEFAVMKTA 198
           +V N ++  +E   +PV+ AEFAV+ +A
Sbjct: 206 SVQNKLINLDENIYIPVTKAEFAVLVSA 233

Single-stranded DNA-binding protein that acts as a transcriptional activator of the pathogenesis-related gene PR-10a. Upon elicitation, binds a 30bp promoter sequence known as elicitor element response (ERE) and is required for PR-10a expression.

Solanum tuberosum (taxid: 4113)

>sp|Q66GR6|WHY3_ARATH Single-stranded DNA-binding protein WHY3, chloroplastic OS=Arabidopsis thaliana GN=WHY3 PE=1 SV=1

 Score =  138 bits (347), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 65/148 (43%), Positives = 102/148 (68%), Gaps = 3/148 (2%)

Query: 58  RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
           R +  + +YKGKAA +++P  P F+ L+SG  K+ ++G +LL FAPA G R+YDW++KQ 
Sbjct: 84  RFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQV 143

Query: 118 FALSPTEVGSLLTMGPRDSSEFFHDPAM-LSSNAGQMRKSLSIKANAD--GFFISLNVAN 174
           F+LS TE+G+L+++GPR+S EFFHDP     S+ G++RK L ++   D  G F +L+V N
Sbjct: 144 FSLSVTEIGNLVSLGPRESCEFFHDPFKGKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQN 203

Query: 175 NILKTNERFVVPVSTAEFAVMKTACSVC 202
            +L  +E   +P++ AEFAV+ +A +  
Sbjct: 204 KLLNVDESVYIPITKAEFAVLISAFNFV 231

Single-stranded DNA-binding protein that functions in both chloroplasts and nucleus. In chloroplasts, maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. In the nucleus, is recruited to a distal element upstream of the kinesin KP1 to mediate the transcriptional repression of KP1. Can bind double-stranded DNA in vivo.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	238
426021772	238	RecName: Full=Single-stranded DNA-bindig	0.852	0.852	0.622	5e-64
118484514	229	unknown [Populus trichocarpa]	0.857	0.890	0.589	7e-63
356573153	235	PREDICTED: uncharacterized protein LOC10	0.865	0.876	0.590	3e-60
255637711	235	unknown [Glycine max]	0.865	0.876	0.586	1e-59
22330568	238	protein WHIRLY 2 [Arabidopsis thaliana]	0.869	0.869	0.593	3e-59
449447529	241	PREDICTED: single-stranded DNA-bindig pr	0.894	0.883	0.534	4e-59
12323827	237	unknown protein; 79476-81015 [Arabidopsi	0.865	0.869	0.591	1e-58
297841891	242	ATWHY2 [Arabidopsis lyrata subsp. lyrata	0.861	0.847	0.563	2e-58
357512363	226	hypothetical protein MTR_7g116270 [Medic	0.819	0.862	0.582	2e-58
225459963	231	PREDICTED: uncharacterized protein LOC10	0.861	0.887	0.560	4e-58

>gi|426021772|sp|D9J034.1|WHY2_SOLTU RecName: Full=Single-stranded DNA-bindig protein WHY2, mitochondrial; AltName: Full=Protein WHIRLY 2; Short=StWHY2; Flags: Precursor gi|298359665|gb|ADI77438.1| Why2 protein [Solanum tuberosum]

 Score =  249 bits (637), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 130/209 (62%), Positives = 158/209 (75%), Gaps = 6/209 (2%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAK-GSLGGRI 59
           M+K+SR LL  R+QL  K L GE   V+  +  H + + AG ST   +V A  G   GR+
Sbjct: 1   MLKVSR-LLHPRNQLLHKKLPGEC--VKGSIWQHAINTFAGFSTVRQNVVADAGKREGRV 57

Query: 60  FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFA 119
           FAPY V+KGKAA S +P LPTF +LDSG +K+ R+GVI+LTF P++GERKYDW K+Q FA
Sbjct: 58  FAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFA 117

Query: 120 LSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNIL 177
           LS TEVGSL++MG RDSSEFFHDP+MLSSNAGQ+RKSLSIK NAD  G+FISL+V NN L
Sbjct: 118 LSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNL 177

Query: 178 KTNERFVVPVSTAEFAVMKTACSVCTNEI 206
           KTN+RF VPV+TAEFAVM+TA S     I
Sbjct: 178 KTNDRFTVPVTTAEFAVMRTAFSFALPHI 206

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118484514|gb|ABK94132.1| unknown [Populus trichocarpa]

 Score =  246 bits (627), Expect = 7e-63,   Method: Compositional matrix adjust.
 Identities = 128/217 (58%), Positives = 158/217 (72%), Gaps = 13/217 (5%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIF 60
           MMKLSR L  +R+ +      G+   VRDG   H L  QA +ST G     K S+  R+F
Sbjct: 1   MMKLSRFLNFNRNAV------GKPTDVRDGSALHALTFQASISTGG-----KSSIQDRVF 49

Query: 61  APYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFAL 120
           APY V+KGKAA SV+PVLPTF K  SG+L+V R+G ++LTF PAIGERKYD+ K+Q FAL
Sbjct: 50  APYSVFKGKAALSVEPVLPTFSKFGSGNLRVDRRGSMMLTFLPAIGERKYDYEKRQKFAL 109

Query: 121 SPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNILK 178
           S TEVGSL++ GP+DS EFFHDP+MLSSNAGQ+RK+LSIK +AD  G+F+SL+V NNILK
Sbjct: 110 SATEVGSLISTGPKDSCEFFHDPSMLSSNAGQVRKNLSIKPHADGSGYFVSLSVVNNILK 169

Query: 179 TNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSP 215
           T ERF VPV+TAEF V+KTACS     I    +L +P
Sbjct: 170 TTERFTVPVTTAEFTVLKTACSFALPHIMGWDRLTTP 206

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356573153|ref|XP_003554728.1| PREDICTED: uncharacterized protein LOC100817863 [Glycine max]

 Score =  237 bits (604), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 127/215 (59%), Positives = 156/215 (72%), Gaps = 9/215 (4%)

Query: 1   MMKLSRSL---LSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGG 57
           M KLSR L    +SR +L E +L+     V D L SH     AG+ST  ++ +AKG    
Sbjct: 1   MFKLSRMLPLTSTSRHRLLE-VLSSRKVEVGDRL-SH----SAGISTATNNYAAKGYASD 54

Query: 58  RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
           RIFAPY VYKGKAAFS+ P LPTF KL+SG + V R+G I++TF  +IGERKYDW K+Q 
Sbjct: 55  RIFAPYTVYKGKAAFSLIPCLPTFTKLNSGTVVVDRRGSIMMTFMHSIGERKYDWEKRQR 114

Query: 118 FALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNIL 177
           FALS TEVGSL+TMG +DS +FFHDP+MLSSNAGQ+RKSLSIK +A+G+F+SL V NN+L
Sbjct: 115 FALSATEVGSLITMGAQDSCDFFHDPSMLSSNAGQVRKSLSIKPHANGYFVSLTVVNNLL 174

Query: 178 KTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
            TN+ F VPV+TAEFAVMKTACS     I    Q+
Sbjct: 175 NTNDYFSVPVTTAEFAVMKTACSFALPHIMGWDQI 209

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255637711|gb|ACU19178.1| unknown [Glycine max]

 Score =  235 bits (599), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 126/215 (58%), Positives = 156/215 (72%), Gaps = 9/215 (4%)

Query: 1   MMKLSRSLL---SSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGG 57
           M KLSR L    +SR +L E +L+     V D L SH     AG+ST  ++ +AKG    
Sbjct: 1   MFKLSRMLPLTSTSRHRLLE-VLSSRKVEVGDRL-SH----SAGISTVTNNYAAKGYASD 54

Query: 58  RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
           RIFAPY VYKGKAAFS+ P LPTF KL+SG + V R+G I++TF  +IGERKYDW K+Q 
Sbjct: 55  RIFAPYTVYKGKAAFSLIPCLPTFTKLNSGTVVVDRRGSIMMTFMHSIGERKYDWEKRQR 114

Query: 118 FALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNIL 177
           FALS TEVGSL+TMG +DS +FFHDP+MLSSNAGQ+RKSLSIK +A+G+F+SL V +N+L
Sbjct: 115 FALSATEVGSLITMGAQDSCDFFHDPSMLSSNAGQVRKSLSIKPHANGYFVSLTVVDNLL 174

Query: 178 KTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
            TN+ F VPV+TAEFAVMKTACS     I    Q+
Sbjct: 175 NTNDYFSVPVTTAEFAVMKTACSFALPHIMGWDQI 209

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330568|ref|NP_177282.2| protein WHIRLY 2 [Arabidopsis thaliana] gi|75161474|sp|Q8VYF7.1|WHY2_ARATH RecName: Full=Single-stranded DNA-binding protein WHY2, mitochondrial; AltName: Full=Protein WHIRLY 2; Short=AtWHY2; Flags: Precursor gi|18175814|gb|AAL59932.1| unknown protein [Arabidopsis thaliana] gi|21689867|gb|AAM67494.1| unknown protein [Arabidopsis thaliana] gi|225898076|dbj|BAH30370.1| hypothetical protein [Arabidopsis thaliana] gi|332197060|gb|AEE35181.1| protein WHIRLY 2 [Arabidopsis thaliana]

 Score =  234 bits (596), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 127/214 (59%), Positives = 160/214 (74%), Gaps = 7/214 (3%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIF 60
           MMK +RSLLS RS   +     EA+ +R G  S    S  G    G D +AK S  GR+F
Sbjct: 1   MMKQARSLLS-RSLCDQSKSLFEASTLR-GFASWSNSSTPGRGFPGKD-AAKPS--GRLF 55

Query: 61  APYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFAL 120
           APY ++KGKAA SV+PVLP+F ++DSG+L++ R+G +++TF PAIGERKYDW KKQ FAL
Sbjct: 56  APYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFAL 115

Query: 121 SPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNILK 178
           SPTEVGSL++MG +DSSEFFHDP+M SSNAGQ+RKSLS+K +AD  G+FISL+V N+ILK
Sbjct: 116 SPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNSILK 175

Query: 179 TNERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
           TN+ FVVPV+ AEFAVMKTA S     I   ++L
Sbjct: 176 TNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRL 209

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447529|ref|XP_004141520.1| PREDICTED: single-stranded DNA-bindig protein WHY2, mitochondrial-like [Cucumis sativus]

 Score =  233 bits (595), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 117/219 (53%), Positives = 156/219 (71%), Gaps = 6/219 (2%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVS--AKGSLGGR 58
           MMKL+R  L SR+QL E+++  +A YV   L SH   S AG+S +  + +     + GGR
Sbjct: 1   MMKLTR--LFSRNQLFEQIVWKKAGYVGHPLGSHPFSSNAGISDSTQNFTRTVTKNAGGR 58

Query: 59  IFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHF 118
           +FA Y+VYKGKAA S++P +PTF K++SG+  + R+G I+LTFAPA+GERKYDW +KQ F
Sbjct: 59  VFASYHVYKGKAALSMEPCMPTFTKVESGNFIMDRRGSIMLTFAPAVGERKYDWTRKQLF 118

Query: 119 ALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNI 176
           ALS TE+GSL+++GPRDS EFFHDP MLSS AGQ+RKSL+IKA+ D  G+F SLNV N  
Sbjct: 119 ALSATEIGSLISLGPRDSCEFFHDPGMLSSTAGQVRKSLAIKAHTDGNGYFFSLNVVNKP 178

Query: 177 LKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLGSP 215
             TN+   VP +T EF+VMKTACS     +    ++ +P
Sbjct: 179 QNTNDYLSVPFTTGEFSVMKTACSFALPSLLGWDRVTNP 217

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12323827|gb|AAG51881.1|AC016162_2 unknown protein; 79476-81015 [Arabidopsis thaliana]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 126/213 (59%), Positives = 159/213 (74%), Gaps = 7/213 (3%)

Query: 2   MKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFA 61
           MK +RSLLS RS   +     EA+ +R G  S    S  G    G D +AK S  GR+FA
Sbjct: 1   MKQARSLLS-RSLCDQSKSLFEASTLR-GFASWSNSSTPGRGFPGKD-AAKPS--GRLFA 55

Query: 62  PYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALS 121
           PY ++KGKAA SV+PVLP+F ++DSG+L++ R+G +++TF PAIGERKYDW KKQ FALS
Sbjct: 56  PYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALS 115

Query: 122 PTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNILKT 179
           PTEVGSL++MG +DSSEFFHDP+M SSNAGQ+RKSLS+K +AD  G+FISL+V N+ILKT
Sbjct: 116 PTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNSILKT 175

Query: 180 NERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
           N+ FVVPV+ AEFAVMKTA S     I   ++L
Sbjct: 176 NDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRL 208

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297841891|ref|XP_002888827.1| ATWHY2 [Arabidopsis lyrata subsp. lyrata] gi|297334668|gb|EFH65086.1| ATWHY2 [Arabidopsis lyrata subsp. lyrata]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 124/220 (56%), Positives = 159/220 (72%), Gaps = 15/220 (6%)

Query: 1   MMKLSRSLLS------SRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGS 54
           MMK +R+LLS      S+S   E++   +A+ +R G  S    S  G   +G D      
Sbjct: 1   MMKQARTLLSRSLCDHSKSLFEERV---KASTLR-GFASWSSSSTPGRGFSGKDAPKPS- 55

Query: 55  LGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAK 114
             GR+FAPY ++KGKAA SV+PVLP+F ++DSG+L++ R+G +++TF PAIGERKYDW K
Sbjct: 56  --GRLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEK 113

Query: 115 KQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNV 172
           KQ FALSPTEVGSL++MG +DSSEFFHDP+M SSNAGQ+RKSLSIK +AD  G+FISL+V
Sbjct: 114 KQKFALSPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSIKPHADGSGYFISLSV 173

Query: 173 ANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
            N ILKTN+ FVVPV+ AEFAVMKTA S     I   ++L
Sbjct: 174 NNGILKTNDYFVVPVTKAEFAVMKTAFSFALPHIMGWNRL 213

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357512363|ref|XP_003626470.1| hypothetical protein MTR_7g116270 [Medicago truncatula] gi|355501485|gb|AES82688.1| hypothetical protein MTR_7g116270 [Medicago truncatula] gi|388497124|gb|AFK36628.1| unknown [Medicago truncatula]

 Score =  231 bits (589), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 124/213 (58%), Positives = 149/213 (69%), Gaps = 18/213 (8%)

Query: 1   MMKLSRSLLSS-RSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRI 59
           M+K SR L SS R+ L E L      Y RD        S A    T ++ SAKG    RI
Sbjct: 5   MLKFSRMLHSSSRNHLLEVL------YARD-------FSTA----TNNNYSAKGYTSDRI 47

Query: 60  FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFA 119
           FAPY VYKGKAAFS+ P LPTF KLDSG L V R G I+++F PAIGERKYDW K+Q FA
Sbjct: 48  FAPYSVYKGKAAFSLSPCLPTFTKLDSGALVVDRHGSIMMSFMPAIGERKYDWEKRQIFA 107

Query: 120 LSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKT 179
           LS TEVGSL+ +GP+DS EFFHDP+M SSNAGQ+RKSLSIK +++G+F+SL+V N++L T
Sbjct: 108 LSATEVGSLIAIGPQDSCEFFHDPSMKSSNAGQVRKSLSIKPHSNGYFVSLSVVNSVLNT 167

Query: 180 NERFVVPVSTAEFAVMKTACSVCTNEIASRSQL 212
            + F VPV+TAEFAVMKTACS     I    +L
Sbjct: 168 KDNFSVPVTTAEFAVMKTACSFALPHIMGWDRL 200

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459963|ref|XP_002267315.1| PREDICTED: uncharacterized protein LOC100258449 [Vitis vinifera] gi|297734756|emb|CBI16990.3| unnamed protein product [Vitis vinifera]

 Score =  230 bits (586), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 116/207 (56%), Positives = 147/207 (71%), Gaps = 2/207 (0%)

Query: 1   MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIF 60
           MMKL + LL SR+ LSE LL G+   +R+    H   S+  +ST     + KG+   R++
Sbjct: 1   MMKL-KQLLQSRTHLSENLLHGKPGDIRNPSWLHAFTSRVSLSTATDHFADKGNYPDRVY 59

Query: 61  APYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFAL 120
           APY VYKGKA+ +V PVLP F +LDSG LKV R GV++L F+PA+GERKYDW KKQ FAL
Sbjct: 60  APYCVYKGKASLTVYPVLPKFSRLDSGGLKVDRHGVMMLQFSPAVGERKYDWEKKQFFAL 119

Query: 121 SPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG-FFISLNVANNILKT 179
           S  EVGSLL++ P    EFFHDP+M +SNAGQ+RKSLS+K+   G +F+SL+V NNI KT
Sbjct: 120 SAVEVGSLLSLSPGGGCEFFHDPSMKTSNAGQVRKSLSVKSMDGGSYFLSLSVVNNIQKT 179

Query: 180 NERFVVPVSTAEFAVMKTACSVCTNEI 206
           NER  VP++ AEFAVM+TACS     I
Sbjct: 180 NERLAVPLTAAEFAVMQTACSFALPHI 206

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	238
UNIPROTKB|D9J034	238	WHY2 "Single-stranded DNA-bind	0.731	0.731	0.655	8.6e-56
TAIR|locus:2032293	238	ATWHY2 "WHIRLY 2" [Arabidopsis	0.781	0.781	0.609	5.5e-54
UNIPROTKB|B2LXS7	266	WHY1 "Single-stranded DNA-bind	0.630	0.563	0.473	5.8e-34
UNIPROTKB|Q9LL85	274	WHY1 "Single-stranded DNA-bind	0.617	0.536	0.456	4.1e-33
TAIR|locus:2012542	263	WHY1 "WHIRLY 1" [Arabidopsis t	0.617	0.558	0.466	6.7e-33
TAIR|locus:2058822	268	WHY3 "AT2G02740" [Arabidopsis	0.592	0.526	0.451	5.4e-31

UNIPROTKB|D9J034 WHY2 "Single-stranded DNA-bindig protein WHY2, mitochondrial" [Solanum tuberosum (taxid:4113)]

 Score = 575 (207.5 bits), Expect = 8.6e-56, P = 8.6e-56
 Identities = 116/177 (65%), Positives = 141/177 (79%)

Query:    27 VRDGLKSHVLISQAGMSTTGHDVSAK-GSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLD 85
             V+  +  H + + AG ST   +V A  G   GR+FAPY V+KGKAA S +P LPTF +LD
Sbjct:    24 VKGSIWQHAINTFAGFSTVRQNVVADAGKREGRVFAPYSVFKGKAALSAEPRLPTFNRLD 83

Query:    86 SGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAM 145
             SG +K+ R+GVI+LTF P++GERKYDW K+Q FALS TEVGSL++MG RDSSEFFHDP+M
Sbjct:    84 SGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSM 143

Query:   146 LSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200
             LSSNAGQ+RKSLSIK NADG  +FISL+V NN LKTN+RF VPV+TAEFAVM+TA S
Sbjct:   144 LSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFS 200

GO:0003677 "DNA binding" evidence=IDA

TAIR|locus:2032293 ATWHY2 "WHIRLY 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 558 (201.5 bits), Expect = 5.5e-54, P = 5.5e-54
 Identities = 117/192 (60%), Positives = 148/192 (77%)

Query:    23 EANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFM 82
             EA+ +R G  S    S  G    G D +AK S  GR+FAPY ++KGKAA SV+PVLP+F 
Sbjct:    22 EASTLR-GFASWSNSSTPGRGFPGKD-AAKPS--GRLFAPYSIFKGKAALSVEPVLPSFT 77

Query:    83 KLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHD 142
             ++DSG+L++ R+G +++TF PAIGERKYDW KKQ FALSPTEVGSL++MG +DSSEFFHD
Sbjct:    78 EIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQKFALSPTEVGSLISMGSKDSSEFFHD 137

Query:   143 PAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200
             P+M SSNAGQ+RKSLS+K +ADG  +FISL+V N+ILKTN+ FVVPV+ AEFAVMKTA S
Sbjct:   138 PSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTAFS 197

Query:   201 VCTNEIASRSQL 212
                  I   ++L
Sbjct:   198 FALPHIMGWNRL 209

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

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

GO:0009507 "chloroplast" evidence=ISM

GO:0006952 "defense response" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006281 "DNA repair" evidence=IMP

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0009086 "methionine biosynthetic process" evidence=RCA

UNIPROTKB|B2LXS7 WHY1 "Single-stranded DNA-bindig protein WHY1, chloroplastic" [Zea mays (taxid:4577)]

 Score = 369 (135.0 bits), Expect = 5.8e-34, P = 5.8e-34
 Identities = 72/152 (47%), Positives = 99/152 (65%)

Query:    46 GHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAI 105
             G+     G+  GR+F  Y +YKGKAA S DP  P F+ LDSG  KV ++G +LL FAPA+
Sbjct:    73 GYGRPPNGAQDGRVFTSYSIYKGKAALSFDPRPPLFVPLDSGAYKVAKEGFVLLQFAPAV 132

Query:   106 GERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG 165
               R+YDW +KQ F+LS  E+G+LLT+GP DS EFFHDP    S  G++RK L I+   DG
Sbjct:   133 ATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFKGRSEEGKVRKVLKIEPTPDG 192

Query:   166 F--FISLNVANNILKTNERFVVPVSTAEFAVM 195
                F +L+V N ++  +E   +P++  EFAV+
Sbjct:   193 NGRFFNLSVQNRLINVDESIYIPITKGEFAVI 224

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0045910 "negative regulation of DNA recombination" evidence=IMP

UNIPROTKB|Q9LL85 WHY1 "Single-stranded DNA-bindig protein WHY1, chloroplastic" [Solanum tuberosum (taxid:4113)]

 Score = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 68/149 (45%), Positives = 104/149 (69%)

Query:    52 KGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYD 111
             +G+   ++F  Y +YKGKAA +V+P  P F  LDSG  K+ R+G+++L FAPA G R+YD
Sbjct:    85 QGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYD 144

Query:   112 WAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFIS 169
             W++KQ F+LS TE+GS++++G +DS EFFHDP    S+ G++RK L ++   DG   F +
Sbjct:   145 WSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFN 204

Query:   170 LNVANNILKTNERFVVPVSTAEFAVMKTA 198
             L+V N ++  +E   +PV+ AEFAV+ +A
Sbjct:   205 LSVQNKLINLDENIYIPVTKAEFAVLVSA 233

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0050832 "defense response to fungus" evidence=TAS

TAIR|locus:2012542 WHY1 "WHIRLY 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 359 (131.4 bits), Expect = 6.7e-33, P = 6.7e-33
 Identities = 70/150 (46%), Positives = 104/150 (69%)

Query:    51 AKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKY 110
             A+G L  R +  + +YKGKAA +VDP  P F+ LDSG  K+ + G +LL FAP+ G R+Y
Sbjct:    74 AEG-LPARFYVGHSIYKGKAALTVDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQY 132

Query:   111 DWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFI 168
             DW+KKQ F+LS TE+G+L+++GPR+S EFFHDP    S+ G++RK L ++   DG   F 
Sbjct:   133 DWSKKQVFSLSVTEIGTLVSLGPRESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFF 192

Query:   169 SLNVANNILKTNERFVVPVSTAEFAVMKTA 198
             +L+V N ++  +E   +P++ AEFAV+ +A
Sbjct:   193 NLSVQNKLVNVDESIYIPITRAEFAVLISA 222

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0006952 "defense response" evidence=TAS

GO:0003677 "DNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0032211 "negative regulation of telomere maintenance via telomerase" evidence=IMP

GO:0042162 "telomeric DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006281 "DNA repair" evidence=IMP

TAIR|locus:2058822 WHY3 "AT2G02740" [Arabidopsis thaliana (taxid:3702)]

 Score = 341 (125.1 bits), Expect = 5.4e-31, P = 5.4e-31
 Identities = 65/144 (45%), Positives = 101/144 (70%)

Query:    58 RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
             R +  + +YKGKAA +++P  P F+ L+SG  K+ ++G +LL FAPA G R+YDW++KQ 
Sbjct:    84 RFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQV 143

Query:   118 FALSPTEVGSLLTMGPRDSSEFFHDPAM-LSSNAGQMRKSLSIKANADGF--FISLNVAN 174
             F+LS TE+G+L+++GPR+S EFFHDP     S+ G++RK L ++   DG   F +L+V N
Sbjct:   144 FSLSVTEIGNLVSLGPRESCEFFHDPFKGKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQN 203

Query:   175 NILKTNERFVVPVSTAEFAVMKTA 198
              +L  +E   +P++ AEFAV+ +A
Sbjct:   204 KLLNVDESVYIPITKAEFAVLISA 227


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        0.317   0.131   0.373    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      238       220   0.00094  112 3  11 22  0.39    33
                                                     32  0.40    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  596 (63 KB)
  Total size of DFA:  155 KB (2093 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  16.44u 0.18s 16.62t   Elapsed:  00:00:01
  Total cpu time:  16.44u 0.18s 16.62t   Elapsed:  00:00:01
  Start:  Fri May 10 15:11:28 2013   End:  Fri May 10 15:11:29 2013

GO:0003677 "DNA binding" evidence=ISS;IDA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0006952 "defense response" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0006281 "DNA repair" evidence=IMP

---

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)
Q8VYF7	WHY2_ARATH	No assigned EC number	0.5934	0.8697	0.8697	yes	no
D9J034	WHY2_SOLTU	No assigned EC number	0.6220	0.8529	0.8529	N/A	no

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

Your Input:
	ATWHY2	ATWHY2 (A. THALIANA WHIRLY 2); DNA binding; Encodes a homolog of the potato p24 protein. It shares the conserved KGKAAL domain, a putative DNA-binding domain, with potato p24 and is localized to mitochondria and not the nucleus. (238 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	AT1G80230	cytochrome c oxidase family protein; cytochrome c oxidase family protein; FUNCTIONS IN- cytochr [...] (171 aa)				•			•		0.833
	OSB1	OSB1 (Organellar Single-stranded); single-stranded DNA binding; Encodes an organellar single-st [...] (261 aa)							•		0.821
	CI51	CI51 (51 kDa subunit of complex I); 4 iron, 4 sulfur cluster binding / FMN binding / NAD or NAD [...] (486 aa)							•		0.819
	NRP1	NRP1 (NAP1-RELATED PROTEIN 1); DNA binding / chromatin binding / histone binding; Double nrp1-1 [...] (264 aa)				•					0.819
	DECOY	DECOY (DECOY); DECOY (DECOY); FUNCTIONS IN- molecular_function unknown; INVOLVED IN- biological [...] (233 aa)				•					0.817
	ROC2	ROC2 (ROTAMASE CYCLOPHILIN 2); cyclosporin A binding / peptidyl-prolyl cis-trans isomerase; rot [...] (176 aa)				•					0.808
	AT4G12600	ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein; ribosomal protein L7Ae/L30e/S12e/Gadd45 [...] (128 aa)				•					0.788
	AT1G52930	brix domain-containing protein; brix domain-containing protein; LOCATED IN- cellular_component [...] (320 aa)				•					0.736
	RPL13AA	60S ribosomal protein L13A (RPL13aA); 60S ribosomal protein L13A (RPL13aA); FUNCTIONS IN- struc [...] (207 aa)				•					0.722
	ORF262	unknown protein; hypothetical protein (262 aa)							•		0.716

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	238
pfam08536	139	pfam08536, Whirly, Whirly transcription factor	1e-59

>gnl|CDD|192059 pfam08536, Whirly, Whirly transcription factor

 Score =  184 bits (469), Expect = 1e-59
 Identities = 80/136 (58%), Positives = 102/136 (75%), Gaps = 2/136 (1%)

Query: 65  VYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTE 124
           +YKGKAA  V PV PTF  LDSG+L++ R+G +LL FAPA G R+YDW KKQ F LSPTE
Sbjct: 2   IYKGKAALKVKPVRPTFTALDSGNLRIDRRGGLLLEFAPATGPRQYDWEKKQSFMLSPTE 61

Query: 125 VGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANNILKTNER 182
            G L +MG  DS EFFHDP+   SNAGQ+RK+L ++   D  G+F++L+V N+ILK N+ 
Sbjct: 62  AGELASMGSNDSCEFFHDPSAGGSNAGQVRKALKVEPMPDGSGYFVNLSVTNSILKGNDS 121

Query: 183 FVVPVSTAEFAVMKTA 198
           F VPV+ AEFAV++TA
Sbjct: 122 FSVPVTYAEFAVLRTA 137

This family contains the plant whirly transcription factors. Length = 139

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	238
PF08536	139	Whirly: Whirly transcription factor; InterPro: IPR	100.0

>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors

Probab=100.00  E-value=2.2e-62  Score=406.00  Aligned_cols=137  Identities=59%  Similarity=1.011  Sum_probs=121.2

Q ss_pred             eEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhhhcCCCCceeeeeCc
Q 026468           64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP  143 (238)
Q Consensus        64 sVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~s~effHDP  143 (238)
                      +||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|||+||+++++++|||||||
T Consensus         1 sVYk~kaAl~v~p~~P~f~~~~sg~~kv~R~G~vlLefapa~g~r~YDW~kKq~FsLS~tEvG~ll~l~~~~s~effHdP   80 (139)
T PF08536_consen    1 SVYKGKAALSVRPIKPTFTSLDSGYFKVSREGSVLLEFAPAVGPRQYDWSKKQTFSLSPTEVGSLLSLGARESCEFFHDP   80 (139)
T ss_dssp             EEEESSEEEEEEEE--EEEE-TTSCEEEEC--EEEEEEEEBCSTTEB-GGG-EEEEE-HHHHHHHHT--TT--EEEEE-T
T ss_pred             CccccceeEEEEecCCccEECCCCcEEEeeccEEEEEEccccCCcccccccceEEEEcHHHhhhhhhhccCCceEEEecc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccCCCcccceeeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHH
Q 026468          144 AMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACS  200 (238)
Q Consensus       144 ~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~  200 (238)
                      +|++|++|+++|+|+|||+|||  |||||+|+|++.+++++|+||||+|||+|||++|+
T Consensus        81 ~~~~s~~G~v~K~Lkv~p~~dgsg~f~~Lsv~~~~~~~~~~~~ipVt~aEfavl~s~f~  139 (139)
T PF08536_consen   81 NMGSSNEGKVRKSLKVEPLPDGSGYFFNLSVQNKLLNGDENFSIPVTKAEFAVLRSAFN  139 (139)
T ss_dssp             TTTSTTTTSEEEEEEEEE-TTSSEEEEEEEEEECCCTEEEEEEEEEEHHHHHHHHHHHH
T ss_pred             ccCCCCCCceEEEEEeEECCCCCceEEEEEEecccccccceEEEechHHHHHHHHHhhC
Confidence            9999999999999999999996  99999999999999999999999999999999986

; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	238
3n1h_A	178	Crystal Structure Of Stwhy2 Length = 178		6e-60
3r9y_A	178	Crystal Structure Of Stwhy2 K67a (Form I) Length =		3e-59
1l3a_A	227	Structure Of The Plant Transcriptional Regulator Pb		2e-35

>pdb|3N1H|A Chain A, Crystal Structure Of Stwhy2 Length = 178

Iteration: 1
 Score =  226 bits (577), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 109/156 (69%), Positives = 129/156 (82%), Gaps = 2/156 (1%)
Query: 53  GSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDW 112
           G   GR+FAPY V+KGKAA S +P LPTF +LDSG +K+ R+GVI+LTF P++GERKYDW
Sbjct: 5   GKREGRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDW 64
Query: 113 AKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISL 170
            K+Q FALS TEVGSL++MG RDSSEFFHDP+MLSSNAGQ+RKSLSIK NAD  G+FISL
Sbjct: 65  EKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISL 124
Query: 171 NVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEI 206
           +V NN LKTN+RF VPV+TAEFAVM+TA S     I
Sbjct: 125 SVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHI 160

>pdb|3R9Y|A Chain A, Crystal Structure Of Stwhy2 K67a (Form I) Length = 178

Iteration: 1
 Score =  224 bits (571), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 108/156 (69%), Positives = 128/156 (82%), Gaps = 2/156 (1%)
Query: 53  GSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDW 112
           G   GR+FAPY V+KG AA S +P LPTF +LDSG +K+ R+GVI+LTF P++GERKYDW
Sbjct: 5   GKREGRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDW 64
Query: 113 AKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISL 170
            K+Q FALS TEVGSL++MG RDSSEFFHDP+MLSSNAGQ+RKSLSIK NAD  G+FISL
Sbjct: 65  EKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISL 124
Query: 171 NVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEI 206
           +V NN LKTN+RF VPV+TAEFAVM+TA S     I
Sbjct: 125 SVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHI 160

>pdb|1L3A|A Chain A, Structure Of The Plant Transcriptional Regulator Pbf-2 Length = 227

Iteration: 1
 Score =  145 bits (365), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 74/174 (42%), Positives = 109/174 (62%), Gaps = 16/174 (9%)
Query: 58  RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
           ++F  Y +YKGKAA +V+P  P F  LDSG  K+ R+G+++L FAPA G R+YDW++KQ 
Sbjct: 37  KVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQV 96
Query: 118 FALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GFFISLNVANN 175
           F+LS TE+GS++++G +DS EFFHDP    S+ G++RK L ++   D  G F +L+V N 
Sbjct: 97  FSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNK 156
Query: 176 ILKTNERFVVPVSTAEFAVM--------------KTACSVCTNEIASRSQLGSP 215
           ++  +E   +PV+ AEFAV+               TA +    E ASRS   +P
Sbjct: 157 LINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEDASRSNNANP 210

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	238
3r9z_A	178	WHY2 protein; stwhy2, single-stranded DNA binding	2e-59
1l3a_A	227	PBF-2, P24: plant transcriptional regulator PBF-2;	9e-58
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>3r9z_A WHY2 protein; stwhy2, single-stranded DNA binding protein, plant, potato, mitochondria, DNA binding protein; 1.75A {Solanum tuberosum} PDB: 3r9y_A 3ra0_A* 3n1h_A 3n1i_A* 3n1j_A* 3n1k_A* 3n1l_A* Length = 178

 Score =  185 bits (469), Expect = 2e-59
 Identities = 107/154 (69%), Positives = 129/154 (83%), Gaps = 2/154 (1%)

Query: 49  VSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGER 108
           ++  G   GR+FAPY V+KG AA S +P LPTF +LDSG +K+ R+GVI+LTF P++GER
Sbjct: 1   MADAGKREGRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGER 60

Query: 109 KYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANAD--GF 166
           KYDW K+Q FALS TEVGSL++MG RDSSEFFHDP+MLSSNAGQ+RKSLSIK NAD  G+
Sbjct: 61  KYDWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGY 120

Query: 167 FISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200
           FISL+V NN LKTN+RF VPV+TAEFAVM+TA S
Sbjct: 121 FISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFS 154

>1l3a_A PBF-2, P24: plant transcriptional regulator PBF-2; single strand DNA binding protein, whirly, transcriptionnal activator, cyclic C4 symmetry; 2.30A {Solanum tuberosum} SCOP: d.18.1.2 Length = 227

 Score =  182 bits (461), Expect = 9e-58
 Identities = 67/153 (43%), Positives = 105/153 (68%), Gaps = 2/153 (1%)

Query: 50  SAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERK 109
             +G+   ++F  Y +YKGKAA +V+P  P F  LDSG  K+ R+G+++L FAPA G R+
Sbjct: 29  QPQGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQ 88

Query: 110 YDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIK--ANADGFF 167
           YDW++KQ F+LS TE+GS++++G +DS EFFHDP    S+ G++RK L ++   +  G F
Sbjct: 89  YDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHF 148

Query: 168 ISLNVANNILKTNERFVVPVSTAEFAVMKTACS 200
            +L+V N ++  +E   +PV+ AEFAV+ +A +
Sbjct: 149 FNLSVQNKLINLDENIYIPVTKAEFAVLVSAFN 181

>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 = 40.2 bits (93), Expect = 4e-04
 Identities = 28/174 (16%), Positives = 46/174 (26%), Gaps = 34/174 (19%)

Query: 6   RSLLSSRSQLSEKLLAGEANYVRD----------GLKSHVLISQAGMSTTGHDVSAKGSL 55
           R LL S+      LL      + +           L   +L+      TT         L
Sbjct: 235 RRLLKSK-PYENCLLV-----LLNVQNAKAWNAFNLSCKILL------TTR-FKQVTDFL 281

Query: 56  GGRIFAPYYVYKGKAAFSVDPVLPTFMK---LDSGDLKVKRKGVILLTFAPAIGERKYD- 111
                    +       + D V    +K       DL  +         +  I E   D 
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS-IIAESIRDG 340

Query: 112 ------WAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSI 159
                 W       L+     SL  + P +  + F   ++   +A      LS+
Sbjct: 341 LATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	238
3r9z_A	178	WHY2 protein; stwhy2, single-stranded DNA binding	100.0
1l3a_A	227	PBF-2, P24: plant transcriptional regulator PBF-2;	100.0

>3r9z_A WHY2 protein; stwhy2, single-stranded DNA binding protein, plant, potato, mitochondria, DNA binding protein; 1.75A {Solanum tuberosum} SCOP: d.18.1.0 PDB: 3r9y_A 3ra0_A* 3n1h_A 3n1i_A* 3n1j_A* 3n1k_A* 3n1l_A*

Probab=100.00  E-value=8.7e-73  Score=482.79  Aligned_cols=166  Identities=65%  Similarity=1.023  Sum_probs=150.3

Q ss_pred             ccCCCCCCeeeeceeEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhh
Q 026468           50 SAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLL  129 (238)
Q Consensus        50 ~~~~~~~~rvf~~ysVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LL  129 (238)
                      +++|.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+|||||||++|+|||||+|||+|+||++|||+||
T Consensus         2 ~~~~~~~~rvy~~~sVYkgkAAl~v~pi~Ptf~~~~sg~~~v~R~G~ilLefapa~g~rqYDW~kK~~FsLS~tEvG~Ll   81 (178)
T 3r9z_A            2 ADAGKREGRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLI   81 (178)
T ss_dssp             -----CTTCCCCCEEEECSSEEEEEEEECCCEEECTTSSEEECSCCEEEEEEEEEEETTEECGGGCEEEEECHHHHHHHH
T ss_pred             CCCCCCCCccccCeeEECCceEEEEEecCCcceEcCCCCEEEeeCCEEEEEEeecccccccccccCeEEEeCHHHHHHHH
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCCCceeeeeCcCccCCCcccceeeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHHhhhhhhc
Q 026468          130 TMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIA  207 (238)
Q Consensus       130 sl~~~~s~effHDP~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~y~lP~LL  207 (238)
                      +++++++|||||||+|++|++|+++|+|+|||+|||  +||||+|+|++++++++++||||+|||+|||++|+|+|||||
T Consensus        82 sl~~~~s~effHDP~~g~s~~g~v~K~Lkiep~~dgsG~f~~Lsv~n~~~~~~~~~~vpvt~gEfav~~~~~~~~lP~Ll  161 (178)
T 3r9z_A           82 SMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHIM  161 (178)
T ss_dssp             TCCTTCCEEEEECC--------CEEEEEEEEECTTSSEEEEEEEEEETTTTEEEEEEEEEEHHHHHHHHHHHHHHHHHHT
T ss_pred             HhcccCcceeEeCcccCCCccCCceeEEEEEECCCCcceEEEEEEecccccccccEEEEecHHHHHHHHHHHHHhhhhhh
Confidence            999999999999999999999999999999999998  999999999999999999999999999999999999999999


Q ss_pred             cccccCCC
Q 026468          208 SRSQLGSP  215 (238)
Q Consensus       208 GW~a~~np  215 (238)
                      |||+++|.
T Consensus       162 Gw~~~~~~  169 (178)
T 3r9z_A          162 GWDRFTNR  169 (178)
T ss_dssp             TGGGCCC-
T ss_pred             chHHHhCC
Confidence            99997664

>1l3a_A PBF-2, P24: plant transcriptional regulator PBF-2; single strand DNA binding protein, whirly, transcriptionnal activator, cyclic C4 symmetry; 2.30A {Solanum tuberosum} SCOP: d.18.1.2

Probab=100.00  E-value=4.1e-70  Score=480.31  Aligned_cols=172  Identities=40%  Similarity=0.706  Sum_probs=162.7

Q ss_pred             CCCCCCeeeeceeEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhhhc
Q 026468           52 KGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTM  131 (238)
Q Consensus        52 ~~~~~~rvf~~ysVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl  131 (238)
                      ++.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+|||||||++|+|||||+|||+|+||++|||+||++
T Consensus        31 a~~~~~Rvf~~ysVYkgkAALsv~pi~PtF~~l~sG~~kv~R~G~ILLEFAPa~g~RqYDW~kKq~FsLS~tEvG~LLsl  110 (227)
T 1l3a_A           31 QGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISL  110 (227)
T ss_dssp             ----CCCEECCEEEECSSEEEEEEEECCEEEECSTTEEEEEECCEEEEEEEEBCSTTCBCGGGCEEEEECHHHHHHHHTC
T ss_pred             CCCCCCeeecceeEEccceEEEEEecCCcceEcCCCcEEEeeCCEEEEEEeeccCccccccccceEEEeCHHHHhHHHhc
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCceeeeeCcCccCCCcccceeeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHHhhhhhhccc
Q 026468          132 GPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASR  209 (238)
Q Consensus       132 ~~~~s~effHDP~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~y~lP~LLGW  209 (238)
                      +++++|||||||+|++|++|+++|+|+|||+|||  +||||+|+|++++.+++|+||||+|||+|||++|+|+|||||||
T Consensus       111 ~~~~s~effHdP~~g~s~~g~v~K~LkIep~pdGsG~f~nLSV~nk~~~~de~~~VpVs~gEfaV~rsl~~f~LP~LlGw  190 (227)
T 1l3a_A          111 GTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGW  190 (227)
T ss_dssp             CTTCCEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTEEEEEEEEEEHHHHHHHHHHHHHHHHHHTTH
T ss_pred             ccccceEEEecCCcCCcccccceeEEEEeecCCCcccEEEEEeeecccCCcceEEEechHHHHHHHHHHHHhhchhhcch
Confidence            9999999999999999999999999999999997  99999999999999999999999999999999999999999999


Q ss_pred             cccCCCccccccee
Q 026468          210 SQLGSPAVICCSQV  223 (238)
Q Consensus       210 ~a~~np~~~~~~~~  223 (238)
                      |+++|+.+.||+.-
T Consensus       191 ~a~~~~~~~~~~~~  204 (227)
T 1l3a_A          191 HTAVNSFKPEDASR  204 (227)
T ss_dssp             HHHHTTCSCC----
T ss_pred             hhccccCChhhccc
Confidence            99999999999863

---

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	238
d1l3aa_	166	d.18.1.2 (A:) Plant transcriptional regulator PBF-	4e-61

>d1l3aa_ d.18.1.2 (A:) Plant transcriptional regulator PBF-2 {Potato (Solanum tuberosum) [TaxId: 4113]} Length = 166

class: Alpha and beta proteins (a+b)
fold: ssDNA-binding transcriptional regulator domain
superfamily: ssDNA-binding transcriptional regulator domain
family: Plant transcriptional regulator PBF-2
domain: Plant transcriptional regulator PBF-2
species: Potato (Solanum tuberosum) [TaxId: 4113]

 Score =  187 bits (476), Expect = 4e-61
 Identities = 67/145 (46%), Positives = 102/145 (70%), Gaps = 2/145 (1%)

Query: 58  RIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH 117
           ++F  Y +YKGKAA +V+P  P F  LDSG  K+ R+G+++L FAPA G R+YDW++KQ 
Sbjct: 3   KVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQV 62

Query: 118 FALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANN 175
           F+LS TE+GS++++G +DS EFFHDP    S+ G++RK L ++   DG   F +L+V N 
Sbjct: 63  FSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNK 122

Query: 176 ILKTNERFVVPVSTAEFAVMKTACS 200
           ++  +E   +PV+ AEFAV+ +A +
Sbjct: 123 LINLDENIYIPVTKAEFAVLVSAFN 147

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	238
d1l3aa_	166	Plant transcriptional regulator PBF-2 {Potato (Sol	100.0

>d1l3aa_ d.18.1.2 (A:) Plant transcriptional regulator PBF-2 {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a+b)
fold: ssDNA-binding transcriptional regulator domain
superfamily: ssDNA-binding transcriptional regulator domain
family: Plant transcriptional regulator PBF-2
domain: Plant transcriptional regulator PBF-2
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=100.00  E-value=2.4e-64  Score=425.32  Aligned_cols=164  Identities=41%  Similarity=0.734  Sum_probs=160.3

Q ss_pred             CCeeeeceeEeecceeEEEeecCCceeecCCCCeEEeeeceEEEEEeecccCcccccccceEEEeChhhhhhhhhcCCCC
Q 026468           56 GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRD  135 (238)
Q Consensus        56 ~~rvf~~ysVYkgKAALsv~pi~P~F~~~~sG~~kv~R~G~IlLeFAPavG~rqYDW~kKq~FsLS~tEvG~LLsl~~~~  135 (238)
                      ++|+|++|+||||||||+|+|++|+|..+++|+++|+|+|+|||||+|++|+|||||+|||+|+||++|||+||++++++
T Consensus         1 ~~r~y~~ysIyk~kaal~ikpi~P~f~~~~ng~~~v~k~G~illef~p~~g~r~YDw~~K~~f~Ls~~e~g~llsl~~~~   80 (166)
T d1l3aa_           1 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKD   80 (166)
T ss_dssp             CCCEECCEEEECSSEEEEEEEECCEEEECSTTEEEEEECCEEEEEEEEBCSTTCBCGGGCEEEEECHHHHHHHHTCCTTC
T ss_pred             CCccccceEEECCceEEEEEecCCceEEcCCCcEEEccCCEEEEEEccccCccccchhhCeeEEeCHHHHHHHHhhccCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeeeeCcCccCCCcccceeeEEEeeCCCC--ceEEEEEeecccCCCceEEEeecHHHHHHHHHHHHhhhhhhccccccC
Q 026468          136 SSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACSVCTNEIASRSQLG  213 (238)
Q Consensus       136 s~effHDP~~g~S~~g~v~K~Lkiep~pdG--~f~nLsV~n~~~~~~~~~~vpVT~gEf~v~rsl~~y~lP~LLGW~a~~  213 (238)
                      +|||||||.|+++++|+++|+|++||+|||  +|+|++|+|+..+.+++++||||+|||+|||++|+|+||||||||+++
T Consensus        81 s~~ffhdp~~~~s~~g~i~K~lk~~P~pdg~g~f~~l~v~~~~~~~~e~~~Vpvt~~Ef~v~~~~~~~~lP~LlGW~~~~  160 (166)
T d1l3aa_          81 SCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAV  160 (166)
T ss_dssp             CEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTEEEEEEEEEEHHHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             cceeecCcccccccCCceeEEEEeeecCCCCccEEEEEecccccCccceEEEeecHHHHHHHHHHHHHhhhHhhChHHHh
Confidence            999999999999999999999999999998  999999999999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 026468          214 SPAVIC  219 (238)
Q Consensus       214 np~~~~  219 (238)
                      +..+.|
T Consensus       161 ~~~~~~  166 (166)
T d1l3aa_         161 NSFKPE  166 (166)
T ss_dssp             TTCSCC
T ss_pred             hccCCC
Confidence            887654