Citrus Sinensis ID: 027008

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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-------23
Protein Sequence
MMLQLQCLSSQTLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEEcccccccccEEEEEccccccccccccccccccccccccccccccccEEEEEcEEEEccEEEEEEEccccEEEcccccEEEEEEcEEEEEEccccccccccccccEEEEEEHHHHHHHHHHcccccEEEEEcccccccccccEEEEEEEEEcccccccEEEEEEEEcccccccEEEEEEcHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEEccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccEEccEEEEcccEEEEEEEEccEEEEccccEEEEEEccEEEEEEEEEcccccEcHHHcEEEEEcHHHHHHHHcccccccEEEEEccccccccccccEEEEEEEEcccccEEEEEEEEEEHHHcEEEEEEEEEEHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mmlqlqclssqtlnpklcpfhslsnskgngfgsisvtestsikkkkLYVKCRqseyyeqksfsaspsnssyaptdvavgtlptrvyvghsiykgkaaltveprgpefvsldsgavklsrEGFVMlqfapaagvrqydwsrkqVFSLSVTEIGSLVALgaresceffhdpfkgkseegkvrkvlkveplpdgsghffnLSVQNKlinldesiyipvtrAEYTVLVSAFNV
Flexible Loop (DISEMBL)
MMLQLQCLSSQTLNPKLCPFHSLSNSKGNGFGSisvtestsikkkklyVKCRQSEYYEqksfsaspsnssyaPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDpfkgkseegkvrKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
Low Complexity Region (SEG)
MMLQLQCLSSQTLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYYEQKsfsaspsnssYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
Disordered region (IsUnstruct)
********************************************KKLYVKCRQ********************TDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFK*******VRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAF**
Disordered Region (DISOPRED)
*************************************************************************************YVGHSIYKGKAALTVEPRGPEFVS*****VKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFF********************PLPDGSGHFFNLSVQNK**NLDESIYIPVTRAEYTVLVSAFNV
Disordered Region (DISEMBL)
MMLQLQCLSSQTLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYY***************PTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
Disordered Region (DISPRO)
*********SQTLNPKLCPFHSLSNSKGNGFGSISVTES*S***KKLYVKC*QSEYYEQ**********************PTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMLQLQCLSSQTLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV
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	229	2.2.26 [Sep-21-2011]
Q9M9S3	263	Single-stranded DNA-bindi	yes	no	0.794	0.692	0.740	6e-78
Q66GR6	268	Single-stranded DNA-bindi	no	no	0.768	0.656	0.728	5e-74
Q9LL85	274	Single-stranded DNA-bindi	N/A	no	0.908	0.759	0.623	4e-73
B2LXS7	266	Single-stranded DNA-bindi	N/A	no	0.764	0.657	0.621	9e-62
D9J034	238	Single-stranded DNA-bindi	N/A	no	0.628	0.605	0.513	5e-40
Q8VYF7	238	Single-stranded DNA-bindi	no	no	0.633	0.609	0.489	4e-39

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

 Score =  290 bits (742), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 140/189 (74%), Positives = 164/189 (86%), Gaps = 7/189 (3%)

Query: 41  SIKKKKLY-VKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALT 99
           + K  KL+ VK RQ++Y+E++ F  S S+ S A        LP R YVGHSIYKGKAALT
Sbjct: 42  TTKTVKLFSVKSRQTDYFEKQRFGDSSSSPSPAEG------LPARFYVGHSIYKGKAALT 95

Query: 100 VEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGA 159
           V+PR PEFV+LDSGA KLS++GF++LQFAP+AGVRQYDWS+KQVFSLSVTEIG+LV+LG 
Sbjct: 96  VDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGP 155

Query: 160 RESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAE 219
           RESCEFFHDPFKGKS+EGKVRKVLKVEPLPDGSGHFFNLSVQNKL+N+DESIYIP+TRAE
Sbjct: 156 RESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAE 215

Query: 220 YTVLVSAFN 228
           + VL+SAFN
Sbjct: 216 FAVLISAFN 224

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

 Score =  277 bits (708), Expect = 5e-74,   Method: Compositional matrix adjust.
 Identities = 134/184 (72%), Positives = 158/184 (85%), Gaps = 8/184 (4%)

Query: 46  KLYVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGP 105
           KL VK RQS+Y+E++ F  S S+ +   +         R YVGHSIYKGKAALT+EPR P
Sbjct: 53  KLTVKSRQSDYFEKQRFGDSSSSQNAEVSS-------PRFYVGHSIYKGKAALTIEPRAP 105

Query: 106 EFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEF 165
           EFV+L+SGA KL++EGF++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+LV+LG RESCEF
Sbjct: 106 EFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEF 165

Query: 166 FHDPFKGK-SEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLV 224
           FHDPFKGK S+EGKVRKVLKVEPLPDGSG FFNLSVQNKL+N+DES+YIP+T+AE+ VL+
Sbjct: 166 FHDPFKGKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLI 225

Query: 225 SAFN 228
           SAFN
Sbjct: 226 SAFN 229

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)

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

 Score =  274 bits (700), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 139/223 (62%), Positives = 162/223 (72%), Gaps = 15/223 (6%)

Query: 14  NPKLCPFHSLSNSKGNGFGSISVTESTSIK--------KKKLYVKCRQSEYYEQKSFSAS 65
           NP    + S S+S    F  +S   + S           + L + CR S+Y+E +     
Sbjct: 20  NPTKTSYLSFSSSINTIFAPLSSNTTKSFSGLTHKAALPRNLSLTCRHSDYFEPQQ---- 75

Query: 66  PSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVML 125
                        G    +V+VG+SIYKGKAALTVEPR PEF  LDSGA KLSREG VML
Sbjct: 76  ---QQQQQQQQPQGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVML 132

Query: 126 QFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKV 185
           QFAPAAGVRQYDWSRKQVFSLSVTEIGS+++LGA++SCEFFHDP KG+S+EG+VRKVLKV
Sbjct: 133 QFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKV 192

Query: 186 EPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           EPLPDGSGHFFNLSVQNKLINLDE+IYIPVT+AE+ VLVSAFN
Sbjct: 193 EPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFN 235

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

 Score =  236 bits (602), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 110/177 (62%), Positives = 137/177 (77%), Gaps = 2/177 (1%)

Query: 52  RQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLD 111
           R S+Y++ ++      +  Y       G    RV+  +SIYKGKAAL+ +PR P FV LD
Sbjct: 55  RHSDYFDPRAPPPPRGDGGYG--RPPNGAQDGRVFTSYSIYKGKAALSFDPRPPLFVPLD 112

Query: 112 SGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFK 171
           SGA K+++EGFV+LQFAPA   RQYDW+RKQVFSLSV EIG+L+ LG  +SCEFFHDPFK
Sbjct: 113 SGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPFK 172

Query: 172 GKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           G+SEEGKVRKVLK+EP PDG+G FFNLSVQN+LIN+DESIYIP+T+ E+ V+VS FN
Sbjct: 173 GRSEEGKVRKVLKIEPTPDGNGRFFNLSVQNRLINVDESIYIPITKGEFAVIVSTFN 229

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

 Score =  164 bits (415), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 74/144 (51%), Positives = 104/144 (72%)

Query: 84  RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
           RV+  +S++KGKAAL+ EPR P F  LDSG VKL+R G +ML F P+ G R+YDW ++Q+
Sbjct: 56  RVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQL 115

Query: 144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
           F+LS TE+GSL+++G R+S EFFHDP    S  G+VRK L ++P  DGSG+F +LSV N 
Sbjct: 116 FALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNN 175

Query: 204 LINLDESIYIPVTRAEYTVLVSAF 227
            +  ++   +PVT AE+ V+ +AF
Sbjct: 176 NLKTNDRFTVPVTTAEFAVMRTAF 199

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 =  161 bits (407), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 71/145 (48%), Positives = 106/145 (73%)

Query: 84  RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
           R++  +SI+KGKAAL+VEP  P F  +DSG +++ R G +M+ F PA G R+YDW +KQ 
Sbjct: 53  RLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQK 112

Query: 144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
           F+LS TE+GSL+++G+++S EFFHDP    S  G+VRK L V+P  DGSG+F +LSV N 
Sbjct: 113 FALSPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNS 172

Query: 204 LINLDESIYIPVTRAEYTVLVSAFN 228
           ++  ++   +PVT+AE+ V+ +AF+
Sbjct: 173 ILKTNDYFVVPVTKAEFAVMKTAFS 197

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)

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	229
302399111	276	WHY domain class transcription factor [M	0.991	0.822	0.675	3e-79
225424922	268	PREDICTED: uncharacterized protein LOC10	0.965	0.824	0.656	3e-78
449520335	276	PREDICTED: single-stranded DNA-binding p	0.978	0.811	0.645	1e-76
15223748	263	ssDNA-binding transcriptional regulator	0.794	0.692	0.740	3e-76
255558202	271	conserved hypothetical protein [Ricinus	0.943	0.797	0.641	6e-76
297849846	264	ATWHY1/PTAC1 [Arabidopsis lyrata subsp.	0.799	0.693	0.740	2e-74
145328252	267	ssDNA-binding transcriptional regulator	0.768	0.659	0.726	3e-73
224099743	265	predicted protein [Populus trichocarpa]	0.956	0.826	0.653	3e-73
388509172	261	unknown [Lotus japonicus]	0.768	0.674	0.715	7e-73
297814520	268	ATWHY3/PTAC11 [Arabidopsis lyrata subsp.	0.786	0.671	0.723	8e-73

>gi|302399111|gb|ADL36850.1| WHY domain class transcription factor [Malus x domestica]

 Score =  300 bits (768), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 160/237 (67%), Positives = 182/237 (76%), Gaps = 10/237 (4%)

Query: 2   MLQLQCLSS----QTLNPKLCPFHS---LSNSKGNGFGSISVTESTSIKKKKLYVKCRQS 54
           ML+L  LSS    Q  N     F S   LS ++     +     S  + +K+L +KCRQS
Sbjct: 1   MLRLHLLSSPATAQKPNQNPSQFLSSQLLSRARVFSTNTFGFAPSPILSRKRLSLKCRQS 60

Query: 55  EYYEQK--SFSASPSNSSYAPTDVAVGT-LPTRVYVGHSIYKGKAALTVEPRGPEFVSLD 111
           EY++Q+  S +ASP+  S AP   A  T +  R YVGHSIYKGKAALTVEP+ PEF  LD
Sbjct: 61  EYFDQQRTSTAASPNKPSPAPPTPAGATGMAPRFYVGHSIYKGKAALTVEPKAPEFTPLD 120

Query: 112 SGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFK 171
           SGA KLSREGFV+LQFAPAAGVR YDWSRKQVFSLSVTEIGSLV+LG++ES EFFHDPFK
Sbjct: 121 SGAFKLSREGFVLLQFAPAAGVRVYDWSRKQVFSLSVTEIGSLVSLGSKESLEFFHDPFK 180

Query: 172 GKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           GKS+EGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIP+TRAE+ VL SAFN
Sbjct: 181 GKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPITRAEFAVLKSAFN 237

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225424922|ref|XP_002277278.1| PREDICTED: uncharacterized protein LOC100253653 [Vitis vinifera] gi|296086421|emb|CBI32010.3| unnamed protein product [Vitis vinifera]

 Score =  297 bits (760), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 155/236 (65%), Positives = 186/236 (78%), Gaps = 15/236 (6%)

Query: 2   MLQLQCLSSQ--TLNPKLCPFHSLSNSKGNGFGSIS-----VTESTSIKKKKLYVKCRQS 54
           M  L  LSS     NP+LCP HSLS+   +   S +     +  +T   +KK  ++CRQS
Sbjct: 1   MHHLHLLSSSFTIQNPRLCPNHSLSSLHSSSPLSFTSRTPLLLSTTRHFRKKRSLQCRQS 60

Query: 55  EYYEQKSFSAS--PSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDS 112
           +Y++Q++ +    P++SS+       G L  RV+VGHSIYKGKAALTVEP+ PEF  LDS
Sbjct: 61  DYFQQQNITRRQPPNDSSFG------GALQPRVFVGHSIYKGKAALTVEPKAPEFTPLDS 114

Query: 113 GAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKG 172
           GA K+S+EGFV+LQFAPAAGVRQYDW RKQVFSLSVTEIGSL++LGARESCEFFHDPFKG
Sbjct: 115 GAFKVSKEGFVLLQFAPAAGVRQYDWGRKQVFSLSVTEIGSLISLGARESCEFFHDPFKG 174

Query: 173 KSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           +SEEGKVRKVLKVEPLPDGSGHFFNLSVQNKL+N+DE+IYIPVTRAE+ VL+SAFN
Sbjct: 175 RSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLLNMDENIYIPVTRAEFAVLISAFN 230

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520335|ref|XP_004167189.1| PREDICTED: single-stranded DNA-binding protein WHY1, chloroplastic-like [Cucumis sativus]

 Score =  291 bits (746), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 153/237 (64%), Positives = 178/237 (75%), Gaps = 13/237 (5%)

Query: 2   MLQLQCLSSQ---TLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQS---E 55
           ML+LQ LSS    T NP+L P  +LSN +     + S    T    +K   KC+ S   +
Sbjct: 1   MLRLQWLSSSFLPTFNPELSP-ETLSNPRLCTL-NFSRPLPTLTTTRKPTPKCQYSWNTQ 58

Query: 56  YYEQKSFSASPSNSSYAPTD-----VAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSL 110
            ++Q +F  +P   S +P        A   LP R +VGHSIYKGKAALTVEPR PEF  L
Sbjct: 59  QHQQSAFEPAPHTDSLSPQSRAGAAAAAAALPPRFFVGHSIYKGKAALTVEPRPPEFTPL 118

Query: 111 DSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPF 170
           DSGA K+SREG VMLQFAPAAGVRQYDWSRKQVFSLSVTE+GSL+ALG RE+CEFFHDP+
Sbjct: 119 DSGAFKISREGLVMLQFAPAAGVRQYDWSRKQVFSLSVTELGSLIALGPREACEFFHDPY 178

Query: 171 KGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAF 227
           KGKS+EGKVRK+LKVEPLPDGSGHFFNL+VQNKLIN+DESIYIP+T+AEYTVLV AF
Sbjct: 179 KGKSDEGKVRKILKVEPLPDGSGHFFNLTVQNKLINVDESIYIPITKAEYTVLVEAF 235

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223748|ref|NP_172893.1| ssDNA-binding transcriptional regulator [Arabidopsis thaliana] gi|75191428|sp|Q9M9S3.1|WHY1_ARATH RecName: Full=Single-stranded DNA-binding protein WHY1, chloroplastic; AltName: Full=Protein PLASTID TRANSCRIPTIONALLY ACTIVE 1; AltName: Full=Protein WHIRLY 1; Short=AtWHY1; Flags: Precursor gi|7262683|gb|AAF43941.1|AC012188_18 Contains similarity to a hypothetical protein from Arabidopsis thaliana gb|AC002521.2. EST gb|AI995686 comes from this gene [Arabidopsis thaliana] gi|12083312|gb|AAG48815.1|AF332452_1 putative DNA-binding protein p24 [Arabidopsis thaliana] gi|13877787|gb|AAK43971.1|AF370156_1 putative DNA-binding protein p24 [Arabidopsis thaliana] gi|16323418|gb|AAL15203.1| putative DNA-binding protein p24 [Arabidopsis thaliana] gi|332191039|gb|AEE29160.1| ssDNA-binding transcriptional regulator [Arabidopsis thaliana]

 Score =  290 bits (742), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 140/189 (74%), Positives = 164/189 (86%), Gaps = 7/189 (3%)

Query: 41  SIKKKKLY-VKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALT 99
           + K  KL+ VK RQ++Y+E++ F  S S+ S A        LP R YVGHSIYKGKAALT
Sbjct: 42  TTKTVKLFSVKSRQTDYFEKQRFGDSSSSPSPAEG------LPARFYVGHSIYKGKAALT 95

Query: 100 VEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGA 159
           V+PR PEFV+LDSGA KLS++GF++LQFAP+AGVRQYDWS+KQVFSLSVTEIG+LV+LG 
Sbjct: 96  VDPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGP 155

Query: 160 RESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAE 219
           RESCEFFHDPFKGKS+EGKVRKVLKVEPLPDGSGHFFNLSVQNKL+N+DESIYIP+TRAE
Sbjct: 156 RESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAE 215

Query: 220 YTVLVSAFN 228
           + VL+SAFN
Sbjct: 216 FAVLISAFN 224

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558202|ref|XP_002520128.1| conserved hypothetical protein [Ricinus communis] gi|223540620|gb|EEF42183.1| conserved hypothetical protein [Ricinus communis]

 Score =  289 bits (740), Expect = 6e-76,   Method: Compositional matrix adjust.
 Identities = 147/229 (64%), Positives = 179/229 (78%), Gaps = 13/229 (5%)

Query: 10  SQTLNPKLCPFHSLSNSKGNGFGSISVTESTSIKKK-----KLYVKCRQSEYYEQKSFSA 64
           + T NPKL   ++ S+ +     S +   + S  ++        VKCRQSE+Y+Q+    
Sbjct: 7   TSTQNPKLWTPNTFSSLQSFRTTSTTFIHTISAPRRLSTNTNRAVKCRQSEFYDQQQQKY 66

Query: 65  SPS-----NSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSR 119
           +PS     +SS+A    A   +P RVYVGHSIYKGKAALTVEPR PEF +LDSGA K++R
Sbjct: 67  NPSRPSSNDSSFASQSPAA--VP-RVYVGHSIYKGKAALTVEPRAPEFAALDSGAFKVAR 123

Query: 120 EGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKV 179
           EGFV+LQFAPAAGVRQYDWSRKQVFSLSVTEIG++++LGAR+SCEFFHDP KGKS+EGK+
Sbjct: 124 EGFVLLQFAPAAGVRQYDWSRKQVFSLSVTEIGTIISLGARDSCEFFHDPNKGKSDEGKI 183

Query: 180 RKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           RKVLKVEPLPDGSGHFFNLSVQNK +N+DESIYIPVT+AE+ VL+SAFN
Sbjct: 184 RKVLKVEPLPDGSGHFFNLSVQNKPMNMDESIYIPVTKAEFAVLISAFN 232

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849846|ref|XP_002892804.1| ATWHY1/PTAC1 [Arabidopsis lyrata subsp. lyrata] gi|297338646|gb|EFH69063.1| ATWHY1/PTAC1 [Arabidopsis lyrata subsp. lyrata]

 Score =  284 bits (726), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 140/189 (74%), Positives = 166/189 (87%), Gaps = 6/189 (3%)

Query: 41  SIKKKKLY-VKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALT 99
           + K  KL+ VK RQ++Y+E++ F     +SS + +  A G LP R YVGHSIYKGKAALT
Sbjct: 42  TTKTVKLFSVKSRQTDYFEKQRFG----DSSSSSSQNAEG-LPARFYVGHSIYKGKAALT 96

Query: 100 VEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGA 159
           +EPR PEFV+LDSGA KLS++GF++LQFAP+AGVRQYDWS+KQVFSLSVTEIG+LV+LG 
Sbjct: 97  MEPRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGP 156

Query: 160 RESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAE 219
           RESCEFFHDPFKGKS+EGKVRKVLKVEPLPDGSGHFFNLSVQNKL+N+DESIYIP+TRAE
Sbjct: 157 RESCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAE 216

Query: 220 YTVLVSAFN 228
           + VL+SAFN
Sbjct: 217 FAVLISAFN 225

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145328252|ref|NP_001077872.1| ssDNA-binding transcriptional regulator [Arabidopsis thaliana] gi|330250525|gb|AEC05619.1| ssDNA-binding transcriptional regulator [Arabidopsis thaliana]

 Score =  280 bits (716), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 133/183 (72%), Positives = 157/183 (85%), Gaps = 7/183 (3%)

Query: 46  KLYVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGP 105
           KL VK RQS+Y+E++ F  S S+ +   +         R YVGHSIYKGKAALT+EPR P
Sbjct: 53  KLTVKSRQSDYFEKQRFGDSSSSQNAEVSS-------PRFYVGHSIYKGKAALTIEPRAP 105

Query: 106 EFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEF 165
           EFV+L+SGA KL++EGF++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+LV+LG RESCEF
Sbjct: 106 EFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRESCEF 165

Query: 166 FHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVS 225
           FHDPFKGK +EGKVRKVLKVEPLPDGSG FFNLSVQNKL+N+DES+YIP+T+AE+ VL+S
Sbjct: 166 FHDPFKGKGDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEFAVLIS 225

Query: 226 AFN 228
           AFN
Sbjct: 226 AFN 228

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099743|ref|XP_002311601.1| predicted protein [Populus trichocarpa] gi|118485247|gb|ABK94483.1| unknown [Populus trichocarpa] gi|222851421|gb|EEE88968.1| predicted protein [Populus trichocarpa]

 Score =  280 bits (716), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 153/234 (65%), Positives = 180/234 (76%), Gaps = 15/234 (6%)

Query: 2   MLQLQCLS---SQTLNPKLC--PFHSLSNSKGNGFGSISVTESTSI--KKKKLYVKCRQS 54
           MLQL  +S   S   NPKL    ++SL ++K     SIS+   TS   KKK L VKC   
Sbjct: 1   MLQLNSVSRVSSSPQNPKLWLPQYNSLCSTK-----SISLNSKTSSTEKKKTLGVKC--- 52

Query: 55  EYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGA 114
           +YY+Q+  + + S+ S   +   VG  P +V+VGHSIYKGKAALTVEPR PEF  LDSGA
Sbjct: 53  QYYDQQHKTFTTSSRSSPSSAPPVGESPPKVFVGHSIYKGKAALTVEPRSPEFSPLDSGA 112

Query: 115 VKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKS 174
            KL +EGFV+LQFAPAA VRQYDW+RKQVFSLSVTEIG LV+L A+ SCEFFHDP KGKS
Sbjct: 113 YKLVKEGFVLLQFAPAASVRQYDWTRKQVFSLSVTEIGHLVSLDAKGSCEFFHDPNKGKS 172

Query: 175 EEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           +EGKVRK+LKVEPLPDGSGHFFNLSVQNK++N+DE+IYIPVT+AEYTVL SAFN
Sbjct: 173 DEGKVRKLLKVEPLPDGSGHFFNLSVQNKVLNIDENIYIPVTKAEYTVLTSAFN 226

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388509172|gb|AFK42652.1| unknown [Lotus japonicus]

 Score =  279 bits (713), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 131/183 (71%), Positives = 155/183 (84%), Gaps = 7/183 (3%)

Query: 49  VKCRQSEYYEQKSFSAS---PSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGP 105
           ++CR S+ ++QK+FS+S   P+N    P  V+VG LP RVYVGHSIYKGKAALTV PR P
Sbjct: 44  IRCRHSDLFDQKTFSSSTPQPAN----PAAVSVGALPPRVYVGHSIYKGKAALTVTPRPP 99

Query: 106 EFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEF 165
           EF  LDSGA K+SREG+V+LQFAPA   RQYDW+RKQVFSLSV E+GS+++LG RESCEF
Sbjct: 100 EFAPLDSGAFKISREGYVLLQFAPAIASRQYDWNRKQVFSLSVVEMGSVISLGTRESCEF 159

Query: 166 FHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVS 225
           FHDP KGKS+EGKVRKVLK+EPLPDGSGHFFNLSVQNK++N+DE+IYIPVT+AE  VL S
Sbjct: 160 FHDPLKGKSDEGKVRKVLKLEPLPDGSGHFFNLSVQNKIVNIDENIYIPVTKAELAVLSS 219

Query: 226 AFN 228
            FN
Sbjct: 220 IFN 222

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814520|ref|XP_002875143.1| ATWHY3/PTAC11 [Arabidopsis lyrata subsp. lyrata] gi|297320981|gb|EFH51402.1| ATWHY3/PTAC11 [Arabidopsis lyrata subsp. lyrata]

 Score =  279 bits (713), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 136/188 (72%), Positives = 162/188 (86%), Gaps = 8/188 (4%)

Query: 42  IKKKKLYVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVE 101
           + + KL VK RQ +Y+E++ F  S S+ +      A G+ P R YVGHSIYKGKAALT+E
Sbjct: 49  MARLKLSVKSRQDDYFEKQRFGDSSSSQN------AEGSSP-RFYVGHSIYKGKAALTIE 101

Query: 102 PRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARE 161
           PR PEFV+L+SGA KL++EGF++LQFAPAAGVRQYDWSRKQVFSLSVTEIG+LV+LG RE
Sbjct: 102 PRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSRKQVFSLSVTEIGNLVSLGPRE 161

Query: 162 SCEFFHDPFKGK-SEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEY 220
           SCEFFHDPFKGK S+EGKVRKVLKVEPLPDGSG FFNLSVQNKL+N+DES+YIP+T+AE+
Sbjct: 162 SCEFFHDPFKGKGSDEGKVRKVLKVEPLPDGSGRFFNLSVQNKLLNVDESVYIPITKAEF 221

Query: 221 TVLVSAFN 228
            VL+SAFN
Sbjct: 222 AVLISAFN 229

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	229
TAIR|locus:2012542	263	WHY1 "WHIRLY 1" [Arabidopsis t	0.786	0.684	0.737	1.8e-69
TAIR|locus:2058822	268	WHY3 "AT2G02740" [Arabidopsis	0.864	0.738	0.669	5.1e-67
UNIPROTKB|Q9LL85	274	WHY1 "Single-stranded DNA-bind	0.868	0.726	0.655	9.4e-66
UNIPROTKB|B2LXS7	266	WHY1 "Single-stranded DNA-bind	0.759	0.654	0.623	5.3e-56
UNIPROTKB|D9J034	238	WHY2 "Single-stranded DNA-bind	0.803	0.773	0.429	1.9e-37
TAIR|locus:2032293	238	ATWHY2 "WHIRLY 2" [Arabidopsis	0.633	0.609	0.489	1e-36

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

 Score = 704 (252.9 bits), Expect = 1.8e-69, P = 1.8e-69
 Identities = 138/187 (73%), Positives = 162/187 (86%)

Query:    43 KKKKLY-VKCRQSEYYEQKXXXXXXXXXXYAPTDVAVGTLPTRVYVGHSIYKGKAALTVE 101
             K  KL+ VK RQ++Y+E++           +P+  A G LP R YVGHSIYKGKAALTV+
Sbjct:    44 KTVKLFSVKSRQTDYFEKQRFGDSSS----SPSP-AEG-LPARFYVGHSIYKGKAALTVD 97

Query:   102 PRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARE 161
             PR PEFV+LDSGA KLS++GF++LQFAP+AGVRQYDWS+KQVFSLSVTEIG+LV+LG RE
Sbjct:    98 PRAPEFVALDSGAFKLSKDGFLLLQFAPSAGVRQYDWSKKQVFSLSVTEIGTLVSLGPRE 157

Query:   162 SCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYT 221
             SCEFFHDPFKGKS+EGKVRKVLKVEPLPDGSGHFFNLSVQNKL+N+DESIYIP+TRAE+ 
Sbjct:   158 SCEFFHDPFKGKSDEGKVRKVLKVEPLPDGSGHFFNLSVQNKLVNVDESIYIPITRAEFA 217

Query:   222 VLVSAFN 228
             VL+SAFN
Sbjct:   218 VLISAFN 224

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 = 681 (244.8 bits), Expect = 5.1e-67, P = 5.1e-67
 Identities = 140/209 (66%), Positives = 167/209 (79%)

Query:    21 HSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYYEQKXXXXXXXXXXYAPTDVAVGT 80
             HS+  S G   G I   + T+  + KL VK RQS+Y+E++              +  V +
Sbjct:    31 HSILTSGGFA-GKIIPLKPTA--RLKLTVKSRQSDYFEKQRFGDSSSSQ-----NAEVSS 82

Query:    81 LPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSR 140
              P R YVGHSIYKGKAALT+EPR PEFV+L+SGA KL++EGF++LQFAPAAGVRQYDWSR
Sbjct:    83 -P-RFYVGHSIYKGKAALTIEPRAPEFVALESGAFKLTKEGFLLLQFAPAAGVRQYDWSR 140

Query:   141 KQVFSLSVTEIGSLVALGARESCEFFHDPFKGK-SEEGKVRKVLKVEPLPDGSGHFFNLS 199
             KQVFSLSVTEIG+LV+LG RESCEFFHDPFKGK S+EGKVRKVLKVEPLPDGSG FFNLS
Sbjct:   141 KQVFSLSVTEIGNLVSLGPRESCEFFHDPFKGKGSDEGKVRKVLKVEPLPDGSGRFFNLS 200

Query:   200 VQNKLINLDESIYIPVTRAEYTVLVSAFN 228
             VQNKL+N+DES+YIP+T+AE+ VL+SAFN
Sbjct:   201 VQNKLLNVDESVYIPITKAEFAVLISAFN 229

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

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

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 137/209 (65%), Positives = 161/209 (77%)

Query:    20 FHSLSNSKGNGFGSISVTESTSIKKKKLYVKCRQSEYYEQKXXXXXXXXXXYAPTDVAVG 79
             F  LS++    F  +  T   ++ +  L + CR S+Y+E +            P     G
Sbjct:    37 FAPLSSNTTKSFSGL--THKAALPRN-LSLTCRHSDYFEPQQQQQQQQQQ---PQ----G 86

Query:    80 TLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWS 139
                 +V+VG+SIYKGKAALTVEPR PEF  LDSGA KLSREG VMLQFAPAAGVRQYDWS
Sbjct:    87 ASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWS 146

Query:   140 RKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLS 199
             RKQVFSLSVTEIGS+++LGA++SCEFFHDP KG+S+EG+VRKVLKVEPLPDGSGHFFNLS
Sbjct:   147 RKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLS 206

Query:   200 VQNKLINLDESIYIPVTRAEYTVLVSAFN 228
             VQNKLINLDE+IYIPVT+AE+ VLVSAFN
Sbjct:   207 VQNKLINLDENIYIPVTKAEFAVLVSAFN 235

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

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

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 111/178 (62%), Positives = 137/178 (76%)

Query:    52 RQSEYYEQKXXXXXXXXXXYA-PTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSL 110
             R S+Y++ +          Y  P +   G    RV+  +SIYKGKAAL+ +PR P FV L
Sbjct:    55 RHSDYFDPRAPPPPRGDGGYGRPPN---GAQDGRVFTSYSIYKGKAALSFDPRPPLFVPL 111

Query:   111 DSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPF 170
             DSGA K+++EGFV+LQFAPA   RQYDW+RKQVFSLSV EIG+L+ LG  +SCEFFHDPF
Sbjct:   112 DSGAYKVAKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEIGTLLTLGPTDSCEFFHDPF 171

Query:   171 KGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
             KG+SEEGKVRKVLK+EP PDG+G FFNLSVQN+LIN+DESIYIP+T+ E+ V+VS FN
Sbjct:   172 KGRSEEGKVRKVLKIEPTPDGNGRFFNLSVQNRLINVDESIYIPITKGEFAVIVSTFN 229

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

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 79/184 (42%), Positives = 114/184 (61%)

Query:    45 KKLYVKCRQSEYYEQKXXXXXXXXXXYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRG 104
             KKL  +C +   ++                    G    RV+  +S++KGKAAL+ EPR 
Sbjct:    17 KKLPGECVKGSIWQHAINTFAGFSTVRQNVVADAGKREGRVFAPYSVFKGKAALSAEPRL 76

Query:   105 PEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCE 164
             P F  LDSG VKL+R G +ML F P+ G R+YDW ++Q+F+LS TE+GSL+++G R+S E
Sbjct:    77 PTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLISMGTRDSSE 136

Query:   165 FFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLV 224
             FFHDP    S  G+VRK L ++P  DGSG+F +LSV N  +  ++   +PVT AE+ V+ 
Sbjct:   137 FFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMR 196

Query:   225 SAFN 228
             +AF+
Sbjct:   197 TAFS 200

GO:0003677 "DNA binding" evidence=IDA

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

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 71/145 (48%), Positives = 106/145 (73%)

Query:    84 RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
             R++  +SI+KGKAAL+VEP  P F  +DSG +++ R G +M+ F PA G R+YDW +KQ 
Sbjct:    53 RLFAPYSIFKGKAALSVEPVLPSFTEIDSGNLRIDRRGSLMMTFMPAIGERKYDWEKKQK 112

Query:   144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
             F+LS TE+GSL+++G+++S EFFHDP    S  G+VRK L V+P  DGSG+F +LSV N 
Sbjct:   113 FALSPTEVGSLISMGSKDSSEFFHDPSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNS 172

Query:   204 LINLDESIYIPVTRAEYTVLVSAFN 228
             ++  ++   +PVT+AE+ V+ +AF+
Sbjct:   173 ILKTNDYFVVPVTKAEFAVMKTAFS 197


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   0.133   0.385    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      229       219   0.00092  112 3  11 22  0.40    33
                                                     32  0.39    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:  589 (63 KB)
  Total size of DFA:  164 KB (2098 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:  17.53u 0.11s 17.64t   Elapsed:  00:00:01
  Total cpu time:  17.53u 0.11s 17.64t   Elapsed:  00:00:01
  Start:  Mon May 20 19:40:55 2013   End:  Mon May 20 19:40:56 2013

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

---

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)
Q9M9S3	WHY1_ARATH	No assigned EC number	0.7407	0.7947	0.6920	yes	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: GSVIVG00029003001 SubName- Full=Chromosome chr1 scaffold_46, whole genome shotgun sequence; (268 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	229
pfam08536	139	pfam08536, Whirly, Whirly transcription factor	5e-74

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

 Score =  220 bits (562), Expect = 5e-74
 Identities = 80/139 (57%), Positives = 103/139 (74%)

Query: 90  SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVT 149
           SIYKGKAAL V+P  P F +LDSG +++ R G ++L+FAPA G RQYDW +KQ F LS T
Sbjct: 1   SIYKGKAALKVKPVRPTFTALDSGNLRIDRRGGLLLEFAPATGPRQYDWEKKQSFMLSPT 60

Query: 150 EIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDE 209
           E G L ++G+ +SCEFFHDP  G S  G+VRK LKVEP+PDGSG+F NLSV N ++  ++
Sbjct: 61  EAGELASMGSNDSCEFFHDPSAGGSNAGQVRKALKVEPMPDGSGYFVNLSVTNSILKGND 120

Query: 210 SIYIPVTRAEYTVLVSAFN 228
           S  +PVT AE+ VL +AF 
Sbjct: 121 SFSVPVTYAEFAVLRTAFV 139

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	229
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=4.5e-71  Score=455.34  Aligned_cols=139  Identities=74%  Similarity=1.128  Sum_probs=123.9

Q ss_pred             eeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeecccccccccCccceEEeeehhhhhhhhhcCccccceeeecC
Q 027008           90 SIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDP  169 (229)
Q Consensus        90 sIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq~FsLS~tEvG~LisLg~~~s~efFHDP  169 (229)
                      +||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+|+++++|||||||
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             CCCCCCCCceeEEEEEEeCCCCCcceEEEEeeeccccCCcceeeeechhhHHHHhhhhc
Q 027008          170 FKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN  228 (229)
Q Consensus       170 ~~g~S~~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~de~~~iPVt~aEfaVl~S~f~  228 (229)
                      +||+|++|+|||+|||||+|||+|+||||+|+|++.|++++|+||||+|||||||++||
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            99999999999999999999999999999999999999999999999999999999996

; 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	229
1l3a_A	227	Structure Of The Plant Transcriptional Regulator Pb		4e-71
3n1h_A	178	Crystal Structure Of Stwhy2 Length = 178		3e-41
3r9y_A	178	Crystal Structure Of Stwhy2 K67a (Form I) Length =		1e-40

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

Iteration: 1
 Score =  264 bits (674), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 124/150 (82%), Positives = 138/150 (92%)
Query: 79  GTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDW 138
           G    +V+VG+SIYKGKAALTVEPR PEF  LDSGA KLSREG VMLQFAPAAGVRQYDW
Sbjct: 32  GASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDW 91
Query: 139 SRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNL 198
           SRKQVFSLSVTEIGS+++LG ++SCEFFHDP KG+S+EG+VRKVLKVEPLPDGSGHFFNL
Sbjct: 92  SRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNL 151
Query: 199 SVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           SVQNKLINLDE+IYIPVT+AE+ VLVSAFN
Sbjct: 152 SVQNKLINLDENIYIPVTKAEFAVLVSAFN 181

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

Iteration: 1
 Score =  164 bits (416), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 74/145 (51%), Positives = 105/145 (72%)
Query: 84  RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
           RV+  +S++KGKAAL+ EPR P F  LDSG VKL+R G +ML F P+ G R+YDW ++Q+
Sbjct: 10  RVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQL 69
Query: 144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
           F+LS TE+GSL+++G R+S EFFHDP    S  G+VRK L ++P  DGSG+F +LSV N 
Sbjct: 70  FALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNN 129
Query: 204 LINLDESIYIPVTRAEYTVLVSAFN 228
            +  ++   +PVT AE+ V+ +AF+
Sbjct: 130 NLKTNDRFTVPVTTAEFAVMRTAFS 154

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

Iteration: 1
 Score =  162 bits (410), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 73/145 (50%), Positives = 104/145 (71%)
Query: 84  RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
           RV+  +S++KG AAL+ EPR P F  LDSG VKL+R G +ML F P+ G R+YDW ++Q+
Sbjct: 10  RVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQL 69
Query: 144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
           F+LS TE+GSL+++G R+S EFFHDP    S  G+VRK L ++P  DGSG+F +LSV N 
Sbjct: 70  FALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNN 129
Query: 204 LINLDESIYIPVTRAEYTVLVSAFN 228
            +  ++   +PVT AE+ V+ +AF+
Sbjct: 130 NLKTNDRFTVPVTTAEFAVMRTAFS 154

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
1l3a_A	227	PBF-2, P24: plant transcriptional regulator PBF-2;	4e-70
3r9z_A	178	WHY2 protein; stwhy2, single-stranded DNA binding	8e-68
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

>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 =  213 bits (542), Expect = 4e-70
 Identities = 128/177 (72%), Positives = 145/177 (81%), Gaps = 7/177 (3%)

Query: 52  RQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLD 111
           R S+Y+E +                  G    +V+VG+SIYKGKAALTVEPR PEF  LD
Sbjct: 12  RGSDYFEPQQQQQQQQQQP-------QGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLD 64

Query: 112 SGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFK 171
           SGA KLSREG VMLQFAPAAGVRQYDWSRKQVFSLSVTEIGS+++LG ++SCEFFHDP K
Sbjct: 65  SGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNK 124

Query: 172 GKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           G+S+EG+VRKVLKVEPLPDGSGHFFNLSVQNKLINLDE+IYIPVT+AE+ VLVSAFN
Sbjct: 125 GRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFN 181

>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 =  205 bits (523), Expect = 8e-68
 Identities = 74/152 (48%), Positives = 105/152 (69%)

Query: 77  AVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQY 136
             G    RV+  +S++KG AAL+ EPR P F  LDSG VKL+R G +ML F P+ G R+Y
Sbjct: 3   DAGKREGRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKY 62

Query: 137 DWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFF 196
           DW ++Q+F+LS TE+GSL+++G R+S EFFHDP    S  G+VRK L ++P  DGSG+F 
Sbjct: 63  DWEKRQLFALSATEVGSLISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFI 122

Query: 197 NLSVQNKLINLDESIYIPVTRAEYTVLVSAFN 228
           +LSV N  +  ++   +PVT AE+ V+ +AF+
Sbjct: 123 SLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFS 154

>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 = 39.8 bits (92), Expect = 5e-04
 Identities = 30/180 (16%), Positives = 60/180 (33%), Gaps = 51/180 (28%)

Query: 80  TLPTRVYVGH--SIYKGKAALT---VEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAG-- 132
           ++ TR+Y+     +Y          V  R   ++ L    ++L     V++     +G  
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNV-SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164

Query: 133 ------VRQYDWSRK---QVFSLSVTEIGS-------LVALGARESCEF-------FHDP 169
                    Y    K   ++F L++    S       L  L  +    +        +  
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224

Query: 170 FKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV 229
            +  S + ++R++LK +P              N L+ L       V  A+     +AFN+
Sbjct: 225 LRIHSIQAELRRLLKSKPYE------------NCLLVLLN-----VQNAK---AWNAFNL 264

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
1l3a_A	227	PBF-2, P24: plant transcriptional regulator PBF-2;	100.0
3r9z_A	178	WHY2 protein; stwhy2, single-stranded DNA binding	100.0

>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=4.8e-74  Score=501.60  Aligned_cols=175  Identities=73%  Similarity=1.148  Sum_probs=147.0

Q ss_pred             EEeeccccccccCCCCCCCCCCCCCCCCccCCCCCCeeeeeeeeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEe
Q 027008           48 YVKCRQSEYYEQKSFSASPSNSSYAPTDVAVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQF  127 (229)
Q Consensus        48 ~~~~~~s~~f~~~~~~~~~~~~~~~~~~~~~~~~~~RVy~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeF  127 (229)
                      ..+|||+||||+|++++++.+    +|   ++.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+|||||
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~----~~---a~~~~~Rvf~~ysVYkgkAALsv~pi~PtF~~l~sG~~kv~R~G~ILLEF   80 (227)
T 1l3a_A            8 QQMGRGSDYFEPQQQQQQQQQ----QP---QGASTPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQF   80 (227)
T ss_dssp             ----------------------------------CCCEECCEEEECSSEEEEEEEECCEEEECSTTEEEEEECCEEEEEE
T ss_pred             ccccchhhhccccCCCCCccC----CC---CCCCCCeeecceeEEccceEEEEEecCCcceEcCCCcEEEeeCCEEEEEE
Confidence            468999999999998654321    11   58889999999999999999999999999999999999999999999999


Q ss_pred             ecccccccccCccceEEeeehhhhhhhhhcCccccceeeecCCCCCCCCCceeEEEEEEeCCCCCcceEEEEeeeccccC
Q 027008          128 APAAGVRQYDWSRKQVFSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINL  207 (229)
Q Consensus       128 APA~G~RqYDW~kKq~FsLS~tEvG~LisLg~~~s~efFHDP~~g~S~~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~  207 (229)
                      ||++|+|||||+|||+|+||++|||+||+|+++++|||||||+||+|++|+|+|+|+|||+|||+|+||||+|+|++.+.
T Consensus        81 APa~g~RqYDW~kKq~FsLS~tEvG~LLsl~~~~s~effHdP~~g~s~~g~v~K~LkIep~pdGsG~f~nLSV~nk~~~~  160 (227)
T 1l3a_A           81 APAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINL  160 (227)
T ss_dssp             EEBCSTTCBCGGGCEEEEECHHHHHHHHTCCTTCCEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTE
T ss_pred             eeccCccccccccceEEEeCHHHHhHHHhcccccceEEEecCCcCCcccccceeEEEEeecCCCcccEEEEEeeecccCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcceeeeechhhHHHHhhhhcC
Q 027008          208 DESIYIPVTRAEYTVLVSAFNV  229 (229)
Q Consensus       208 de~~~iPVt~aEfaVl~S~f~f  229 (229)
                      |++|+||||+|||+||+++|+|
T Consensus       161 de~~~VpVs~gEfaV~rsl~~f  182 (227)
T 1l3a_A          161 DENIYIPVTKAEFAVLVSAFNF  182 (227)
T ss_dssp             EEEEEEEEEHHHHHHHHHHHHH
T ss_pred             cceEEEechHHHHHHHHHHHHh
Confidence            9999999999999999999987

>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=2.8e-71  Score=470.26  Aligned_cols=153  Identities=48%  Similarity=0.845  Sum_probs=140.1

Q ss_pred             cCCCCCCeeeeeeeeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeecccccccccCccceEEeeehhhhhhhhh
Q 027008           77 AVGTLPTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVA  156 (229)
Q Consensus        77 ~~~~~~~RVy~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq~FsLS~tEvG~Lis  156 (229)
                      .+|.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+||||||||+|+|||||+|||+|+||++|||+||+
T Consensus         3 ~~~~~~~rvy~~~sVYkgkAAl~v~pi~Ptf~~~~sg~~~v~R~G~ilLefapa~g~rqYDW~kK~~FsLS~tEvG~Lls   82 (178)
T 3r9z_A            3 DAGKREGRVFAPYSVFKGAAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSLIS   82 (178)
T ss_dssp             ----CTTCCCCCEEEECSSEEEEEEEECCCEEECTTSSEEECSCCEEEEEEEEEEETTEECGGGCEEEEECHHHHHHHHT
T ss_pred             CCCCCCCccccCeeEECCceEEEEEecCCcceEcCCCCEEEeeCCEEEEEEeecccccccccccCeEEEeCHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCccccceeeecCCCCCCCCCceeEEEEEEeCCCCCcceEEEEeeeccccCCcceeeeechhhHHHHhhhhcC
Q 027008          157 LGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV  229 (229)
Q Consensus       157 Lg~~~s~efFHDP~~g~S~~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~de~~~iPVt~aEfaVl~S~f~f  229 (229)
                      |+++++|||||||+||+|++|+|+|+|||||++||||+||||||+|++.+++++++||||+|||+||+++|+|
T Consensus        83 l~~~~s~effHDP~~g~s~~g~v~K~Lkiep~~dgsG~f~~Lsv~n~~~~~~~~~~vpvt~gEfav~~~~~~~  155 (178)
T 3r9z_A           83 MGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSF  155 (178)
T ss_dssp             CCTTCCEEEEECC--------CEEEEEEEEECTTSSEEEEEEEEEETTTTEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             hcccCcceeEeCcccCCCccCCceeEEEEEECCCCcceEEEEEEecccccccccEEEEecHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999987

---

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	229
d1l3aa_	166	d.18.1.2 (A:) Plant transcriptional regulator PBF-	2e-70

>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 =  210 bits (537), Expect = 2e-70
 Identities = 123/145 (84%), Positives = 137/145 (94%)

Query: 84  RVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQV 143
           +V+VG+SIYKGKAALTVEPR PEF  LDSGA KLSREG VMLQFAPAAGVRQYDWSRKQV
Sbjct: 3   KVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQV 62

Query: 144 FSLSVTEIGSLVALGARESCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNK 203
           FSLSVTEIGS+++LG ++SCEFFHDP KG+S+EG+VRKVLKVEPLPDGSGHFFNLSVQNK
Sbjct: 63  FSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNK 122

Query: 204 LINLDESIYIPVTRAEYTVLVSAFN 228
           LINLDE+IYIPVT+AE+ VLVSAFN
Sbjct: 123 LINLDENIYIPVTKAEFAVLVSAFN 147

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	229
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=3.7e-61  Score=401.76  Aligned_cols=148  Identities=83%  Similarity=1.308  Sum_probs=146.2

Q ss_pred             CCeeeeeeeeeeCceeEEEeecCCceeecCCcceEEeeeceEEEEeecccccccccCccceEEeeehhhhhhhhhcCccc
Q 027008           82 PTRVYVGHSIYKGKAALTVEPRGPEFVSLDSGAVKLSREGFVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSLVALGARE  161 (229)
Q Consensus        82 ~~RVy~~ysIYKgKAAlsv~p~~P~F~~l~SG~~kv~R~G~vlLeFAPA~G~RqYDW~kKq~FsLS~tEvG~LisLg~~~  161 (229)
                      ++|+|++|+||||||||+|+|++|+|..+++|+++++|+|.|||||||++|+|||||+|||+|+||++|+|+||+|++++
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeeecCCCCCCCCCceeEEEEEEeCCCCCcceEEEEeeeccccCCcceeeeechhhHHHHhhhhcC
Q 027008          162 SCEFFHDPFKGKSEEGKVRKVLKVEPLPDGSGHFFNLSVQNKLINLDESIYIPVTRAEYTVLVSAFNV  229 (229)
Q Consensus       162 s~efFHDP~~g~S~~G~vrK~LkVeP~pDgSG~ffnLsV~n~~~n~de~~~iPVt~aEfaVl~S~f~f  229 (229)
                      ||||||||.|+++++|+|+|+|||||+|||+|+|+||+|+|++.|.+++++||||+|||+||+++|+|
T Consensus        81 s~~ffhdp~~~~s~~g~i~K~lk~~P~pdg~g~f~~l~v~~~~~~~~e~~~Vpvt~~Ef~v~~~~~~~  148 (166)
T d1l3aa_          81 SCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNF  148 (166)
T ss_dssp             CEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             cceeecCcccccccCCceeEEEEeeecCCCCccEEEEEecccccCccceEEEeecHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999986