Citrus Sinensis ID: 028165

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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--
Protein Sequence
MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGPVD
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHcccccccccccccccEEEEccccccccccccccccccEEEcccEEEEccEEEEEEEccccEEEcccccEEEEEEcEEEEEEEcccccccccccccEEEEEcHHHHHHHHHcccccccEEEccccccccccccccEEEEEEEcccccEEEEEEEEcccccccEEEEEEcHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccccccccccccccccHcccccHHcccccccccccccccccccccccccEEccEEEEcccEEEEEEEEccEEEEccccEEEEEEccEEEEEEEEEcccccEcHHHcEEEEEcHHHHHHHHcccccccEEEEEccccccccccccEEEEEEEEccccEEEEEEEEcccccccccEEEEccHHHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mmklsrslLSSRSQLSEKLLAGEANYVRDGLKSHVLISqagmsttghdvsakgslggrifapyyvykgkaafsvdpvlptfmkldsgdlkvkrkGVILLTfapaigerkydwakkqhfalsptevgslltmgprdsseffhdpamlssnagqmRKSLSIKANADGFFISLNVANNilktnerfvvpvSTAEFAVMKTACICIasshglgpvd
Flexible Loop (DISEMBL)
mmklsrsllssRSQLSEKLLAGEANYVRDGLKSHVLISQAgmsttghdvsakgslGGRIFAPYYVYKGKAAFSVDPVLPTFMKLdsgdlkvkrkgVILLTfapaigerkydWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIAsshglgpvd
Low Complexity Region (SEG)
MMklsrsllssrsqlsekllAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGPVD
Disordered region (IsUnstruct)
**********************EANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVG*L******************************IKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIAS********
Disordered Region (DISOPRED)
***********************************************************FAPYYVYKGKAAFSVDPVLPTFMKL****LKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFF******************IKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGP**
Disordered Region (DISEMBL)
************SQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGPVD
Disordered Region (DISPRO)
****************************D*L************************GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGPVD
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMKLSRSLLSSRSQLSEKLLAGEANYVRDGLKSHVLISQAGMSTTGHDVSAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADGFFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLGPVD
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	212	2.2.26 [Sep-21-2011]
D9J034	238	Single-stranded DNA-bindi	N/A	no	0.966	0.861	0.617	5e-65
Q8VYF7	238	Single-stranded DNA-bindi	yes	no	0.957	0.852	0.601	4e-60
B2LXS7	266	Single-stranded DNA-bindi	N/A	no	0.707	0.563	0.473	3e-36
Q9LL85	274	Single-stranded DNA-bindi	N/A	no	0.688	0.532	0.459	2e-34
Q9M9S3	263	Single-stranded DNA-bindi	no	no	0.679	0.547	0.465	3e-34
Q66GR6	268	Single-stranded DNA-bindi	no	no	0.665	0.526	0.451	5e-32

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

 Score =  247 bits (630), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 131/212 (61%), Positives = 160/212 (75%), Gaps = 7/212 (3%)

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 KTNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           KTN+RF VPV+TAEFAVM+TA    A  H +G
Sbjct: 178 KTNDRFTVPVTTAEFAVMRTA-FSFALPHIMG 208

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 =  230 bits (587), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 127/211 (60%), Positives = 159/211 (75%), Gaps = 8/211 (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 TNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           TN+ FVVPV+ AEFAVMKTA    A  H +G
Sbjct: 176 TNDYFVVPVTKAEFAVMKTA-FSFALPHIMG 205

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 =  151 bits (381), 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|Q9LL85|WHY1_SOLTU Single-stranded DNA-bindig protein WHY1, chloroplastic OS=Solanum tuberosum GN=WHY1 PE=1 SV=1

 Score =  145 bits (365), 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|Q9M9S3|WHY1_ARATH Single-stranded DNA-binding protein WHY1, chloroplastic OS=Arabidopsis thaliana GN=WHY1 PE=1 SV=1

 Score =  144 bits (364), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 68/146 (46%), Positives = 101/146 (69%), Gaps = 2/146 (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 ANNILKTNERFVVPVSTAEFAVMKTA 198
            N ++  +E   +P++ AEFAV+ +A
Sbjct: 197 QNKLVNVDESIYIPITRAEFAVLISA 222

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 =  137 bits (345), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 65/144 (45%), Positives = 101/144 (70%), Gaps = 3/144 (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 NILKTNERFVVPVSTAEFAVMKTA 198
            +L  +E   +P++ AEFAV+ +A
Sbjct: 204 KLLNVDESVYIPITKAEFAVLISA 227

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	212
426021772	238	RecName: Full=Single-stranded DNA-bindig	0.966	0.861	0.617	3e-63
118484514	229	unknown [Populus trichocarpa]	0.929	0.860	0.601	3e-61
356573153	235	PREDICTED: uncharacterized protein LOC10	0.910	0.821	0.613	3e-59
255637711	235	unknown [Glycine max]	0.910	0.821	0.608	1e-58
449447529	241	PREDICTED: single-stranded DNA-bindig pr	0.929	0.817	0.566	2e-58
22330568	238	protein WHIRLY 2 [Arabidopsis thaliana]	0.957	0.852	0.601	2e-58
12323827	237	unknown protein; 79476-81015 [Arabidopsi	0.952	0.852	0.6	1e-57
357512363	226	hypothetical protein MTR_7g116270 [Medic	0.858	0.805	0.605	1e-57
297841891	242	ATWHY2 [Arabidopsis lyrata subsp. lyrata	0.948	0.830	0.571	1e-57
225459963	231	PREDICTED: uncharacterized protein LOC10	0.976	0.896	0.561	2e-57

>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 =  247 bits (630), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 131/212 (61%), Positives = 160/212 (75%), Gaps = 7/212 (3%)

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 KTNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           KTN+RF VPV+TAEFAVM+TA    A  H +G
Sbjct: 178 KTNDRFTVPVTTAEFAVMRTA-FSFALPHIMG 208

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 =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 127/211 (60%), Positives = 156/211 (73%), Gaps = 14/211 (6%)

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 TNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           T ERF VPV+TAEF V+KTAC   A  H +G
Sbjct: 170 TTERFTVPVTTAEFTVLKTAC-SFALPHIMG 199

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 =  233 bits (595), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 124/202 (61%), Positives = 152/202 (75%), Gaps = 9/202 (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 KTNERFVVPVSTAEFAVMKTAC 199
            TN+ F VPV+TAEFAVMKTAC
Sbjct: 175 NTNDYFSVPVTTAEFAVMKTAC 196

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 =  231 bits (590), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 123/202 (60%), Positives = 152/202 (75%), Gaps = 9/202 (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----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 KTNERFVVPVSTAEFAVMKTAC 199
            TN+ F VPV+TAEFAVMKTAC
Sbjct: 175 NTNDYFSVPVTTAEFAVMKTAC 196

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 115/203 (56%), Positives = 150/203 (73%), Gaps = 6/203 (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 LKTNERFVVPVSTAEFAVMKTAC 199
             TN+   VP +T EF+VMKTAC
Sbjct: 179 QNTNDYLSVPFTTGEFSVMKTAC 201

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  230 bits (587), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 127/211 (60%), Positives = 159/211 (75%), Gaps = 8/211 (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 TNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           TN+ FVVPV+ AEFAVMKTA    A  H +G
Sbjct: 176 TNDYFVVPVTKAEFAVMKTA-FSFALPHIMG 205

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  228 bits (582), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 126/210 (60%), Positives = 158/210 (75%), Gaps = 8/210 (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 NERFVVPVSTAEFAVMKTACICIASSHGLG 209
           N+ FVVPV+ AEFAVMKTA    A  H +G
Sbjct: 176 NDYFVVPVTKAEFAVMKTA-FSFALPHIMG 204

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

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 =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 121/200 (60%), Positives = 145/200 (72%), Gaps = 18/200 (9%)

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 NERFVVPVSTAEFAVMKTAC 199
            + F VPV+TAEFAVMKTAC
Sbjct: 168 KDNFSVPVTTAEFAVMKTAC 187

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 124/217 (57%), Positives = 158/217 (72%), Gaps = 16/217 (7%)

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 ANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLG 209
            N ILKTN+ FVVPV+ AEFAVMKTA    A  H +G
Sbjct: 174 NNGILKTNDYFVVPVTKAEFAVMKTA-FSFALPHIMG 209

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  228 bits (580), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 118/210 (56%), Positives = 149/210 (70%), Gaps = 3/210 (1%)

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 NERFVVPVSTAEFAVMKTACICIASSHGLG 209
           NER  VP++ AEFAVM+TAC   A  H LG
Sbjct: 180 NERLAVPLTAAEFAVMQTAC-SFALPHILG 208

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	212
UNIPROTKB|D9J034	238	WHY2 "Single-stranded DNA-bind	0.858	0.764	0.634	6.8e-56
TAIR|locus:2032293	238	ATWHY2 "WHIRLY 2" [Arabidopsis	0.858	0.764	0.619	7e-54
UNIPROTKB|B2LXS7	266	WHY1 "Single-stranded DNA-bind	0.707	0.563	0.473	5.8e-34
UNIPROTKB|Q9LL85	274	WHY1 "Single-stranded DNA-bind	0.693	0.536	0.456	4.1e-33
TAIR|locus:2012542	263	WHY1 "WHIRLY 1" [Arabidopsis t	0.693	0.558	0.466	6.7e-33
TAIR|locus:2058822	268	WHY3 "AT2G02740" [Arabidopsis	0.665	0.526	0.451	5.4e-31

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

 Score = 576 (207.8 bits), Expect = 6.8e-56, P = 6.8e-56
 Identities = 118/186 (63%), Positives = 144/186 (77%)

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--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIA 203
             LSSNAGQ+RKSLSIK NADG  +FISL+V NN LKTN+RF VPV+TAEFAVM+TA    A
Sbjct:   144 LSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTA-FSFA 202

Query:   204 SSHGLG 209
               H +G
Sbjct:   203 LPHIMG 208

GO:0003677 "DNA binding" evidence=IDA

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

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 117/189 (61%), Positives = 147/189 (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--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACI 200
             P+M SSNAGQ+RKSLS+K +ADG  +FISL+V N+ILKTN+ FVVPV+ AEFAVMKTA  
Sbjct:   138 PSMKSSNAGQVRKSLSVKPHADGSGYFISLSVNNSILKTNDYFVVPVTKAEFAVMKTA-F 196

Query:   201 CIASSHGLG 209
               A  H +G
Sbjct:   197 SFALPHIMG 205

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        0.319   0.134   0.389    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      212       194   0.00076  111 3  11 22  0.45    32
                                                     31  0.43    35


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:  145 KB (2089 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:  16.25u 0.08s 16.33t   Elapsed:  00:00:00
  Total cpu time:  16.25u 0.08s 16.33t   Elapsed:  00:00:00
  Start:  Fri May 10 05:31:04 2013   End:  Fri May 10 05:31:04 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	0.6018	0.9575	0.8529	yes	no
D9J034	WHY2_SOLTU	No assigned EC number	0.6179	0.9669	0.8613	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

---

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	212
pfam08536	139	pfam08536, Whirly, Whirly transcription factor	6e-60

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

 Score =  183 bits (467), Expect = 6e-60
 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	212
PF08536	139	Whirly: Whirly transcription factor; InterPro: IPR	100.0
PF02035	174	Coagulin: Coagulin; InterPro: IPR000275 Coagulogen	85.44

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

Probab=100.00  E-value=5.4e-67  Score=427.37  Aligned_cols=137  Identities=59%  Similarity=1.002  Sum_probs=121.5

Q ss_pred             eeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhhhcCCCCcceeeeCc
Q 028165           64 YVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRDSSEFFHDP  143 (212)
Q Consensus        64 sVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Llslg~~~s~EffHDP  143 (212)
                      +||||||||+|+|++|+|++++||+++++|+|+||||||||+|+|||||+|||+|+|||+|+|+||+++++++|||||||
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             cCcCCCccccceeeEEeeCCCC--ceEEEEEeecccCCCceeeeccchhHHHHHHHHHH
Q 028165          144 AMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACI  200 (212)
Q Consensus       144 ~~g~S~~G~v~K~LkIep~~dG--~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~  200 (212)
                      +||+|++|+|+|+|||||+|||  |||||+|+|++.|++++|+||||+|||||||++||
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  99999999999999999999999999999999997

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

>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]

Probab=85.44  E-value=0.81  Score=38.92  Aligned_cols=51  Identities=25%  Similarity=0.541  Sum_probs=28.6

Q ss_pred             eeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCccccccccee
Q 028165           60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQH  117 (212)
Q Consensus        60 y~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~  117 (212)
                      |+||+-|+..+-.+.+..-|.|.-.-+|.++      |++| ||.+|-||--|+.|-.
T Consensus        76 f~pf~hf~secpvstrdcepvfgyt~a~efr------vivq-apragfrqcvwqhkcr  126 (174)
T PF02035_consen   76 FPPFHHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKCR  126 (174)
T ss_dssp             STT----SSB--EEEE----SEEE-TTS-EE------EE---BCCCTB-B---EEEET
T ss_pred             CCCcccccccCCcccccccccccceecceEE------EEEe-CchhhHHHHHHHhhhc
Confidence            6999999999999999999999988888765      4555 9999999999999864

The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	212
3n1h_A	178	Crystal Structure Of Stwhy2 Length = 178		3e-59
3r9y_A	178	Crystal Structure Of Stwhy2 K67a (Form I) Length =		1e-58
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 =  224 bits (571), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 110/159 (69%), Positives = 131/159 (82%), Gaps = 3/159 (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 NVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           +V NN LKTN+RF VPV+TAEFAVM+TA    A  H +G
Sbjct: 125 SVVNNNLKTNDRFTVPVTTAEFAVMRTA-FSFALPHIMG 162

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

Iteration: 1
 Score =  222 bits (565), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 109/159 (68%), Positives = 130/159 (81%), Gaps = 3/159 (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 NVANNILKTNERFVVPVSTAEFAVMKTACICIASSHGLG 209
           +V NN LKTN+RF VPV+TAEFAVM+TA    A  H +G
Sbjct: 125 SVVNNNLKTNDRFTVPVTTAEFAVMRTA-FSFALPHIMG 162

>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 = 67/143 (46%), Positives = 101/143 (70%), Gaps = 2/143 (1%)
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 ILKTNERFVVPVSTAEFAVMKTA 198
           ++  +E   +PV+ AEFAV+ +A
Sbjct: 157 LINLDENIYIPVTKAEFAVLVSA 179

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	212
3r9z_A	178	WHY2 protein; stwhy2, single-stranded DNA binding	9e-59
1l3a_A	227	PBF-2, P24: plant transcriptional regulator PBF-2;	2e-57
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-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 =  181 bits (461), Expect = 9e-59
 Identities = 106/153 (69%), Positives = 128/153 (83%), Gaps = 2/153 (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 FISLNVANNILKTNERFVVPVSTAEFAVMKTAC 199
           FISL+V NN LKTN+RF VPV+TAEFAVM+TA 
Sbjct: 121 FISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAF 153

>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 =  180 bits (457), Expect = 2e-57
 Identities = 67/152 (44%), Positives = 104/152 (68%), Gaps = 2/152 (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 ISLNVANNILKTNERFVVPVSTAEFAVMKTAC 199
            +L+V N ++  +E   +PV+ AEFAV+ +A 
Sbjct: 149 FNLSVQNKLINLDENIYIPVTKAEFAVLVSAF 180

>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 = 39.1 bits (90), Expect = 7e-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	212
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
1aoc_A	175	Coagulogen; coagulation factor, clottable protein,	84.91

>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=2.2e-69  Score=454.97  Aligned_cols=155  Identities=68%  Similarity=1.074  Sum_probs=140.6

Q ss_pred             ccCCCCCceeeeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhh
Q 028165           50 SAKGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLL  129 (212)
Q Consensus        50 ~~~~~~~~rvy~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Ll  129 (212)
                      +++|.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+||||||||+|+|||||+|||+|+|||+|||+||
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             hcCCCCcceeeeCccCcCCCccccceeeEEeeCCCC--ceEEEEEeecccCCCceeeeccchhHHHHHHHHHHHHHc
Q 028165          130 TMGPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIAS  204 (212)
Q Consensus       130 slg~~~s~EffHDP~~g~S~~G~v~K~LkIep~~dG--~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~f~l~  204 (212)
                      +++++++|||||||+||+|++|+|+|+|||||++||  +||||||+|++++.+++++||||+|||+||+++|+|+|-
T Consensus        82 sl~~~~s~effHDP~~g~s~~g~v~K~Lkiep~~dgsG~f~~Lsv~n~~~~~~~~~~vpvt~gEfav~~~~~~~~lP  158 (178)
T 3r9z_A           82 SMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALP  158 (178)
T ss_dssp             TCCTTCCEEEEECC--------CEEEEEEEEECTTSSEEEEEEEEEETTTTEEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             HhcccCcceeEeCcccCCCccCCceeEEEEEECCCCcceEEEEEEecccccccccEEEEecHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999999999999998  999999999999999999999999999999999999984

>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=6.5e-65  Score=440.51  Aligned_cols=153  Identities=44%  Similarity=0.835  Sum_probs=147.1

Q ss_pred             CCCCCceeeeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhhhc
Q 028165           52 KGSLGGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTM  131 (212)
Q Consensus        52 ~~~~~~rvy~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Llsl  131 (212)
                      ++.+++|||++|+||||||||+|+|++|+|+.++||+++++|+|+|||||||++|+|||||+|||+|+||++|||+||++
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            58889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcceeeeCccCcCCCccccceeeEEeeCCCC--ceEEEEEeecccCCCceeeeccchhHHHHHHHHHHHHHc
Q 028165          132 GPRDSSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIAS  204 (212)
Q Consensus       132 g~~~s~EffHDP~~g~S~~G~v~K~LkIep~~dG--~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~f~l~  204 (212)
                      +++++|||||||+||+|++|+++|+|+|||+|||  +||||+|+|++.+.+++++||||+|||+|||++|+|+|-
T Consensus       111 ~~~~s~effHdP~~g~s~~g~v~K~LkIep~pdGsG~f~nLSV~nk~~~~de~~~VpVs~gEfaV~rsl~~f~LP  185 (227)
T 1l3a_A          111 GTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMP  185 (227)
T ss_dssp             CTTCCEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTEEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             ccccceEEEecCCcCCcccccceeEEEEeecCCCcccEEEEEeeecccCCcceEEEechHHHHHHHHHHHHhhch
Confidence            9999999999999999999999999999999997  999999999999999999999999999999999999984

>1aoc_A Coagulogen; coagulation factor, clottable protein, cystine knot superfamily; 2.00A {Tachypleus tridentatus} SCOP: g.17.1.5

Probab=84.91  E-value=0.45  Score=39.28  Aligned_cols=53  Identities=26%  Similarity=0.570  Sum_probs=46.7

Q ss_pred             eeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEe
Q 028165           60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFA  119 (212)
Q Consensus        60 y~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~Fs  119 (212)
                      |+||+-|++.+-.+.+..-|.|.-.-+|.++      |++| ||.+|-||--|+.|-.|.
T Consensus        78 f~pf~hf~secpvstrdcepvfgyt~a~efr------vivq-apragfrqcvwqhkcryg  130 (175)
T 1aoc_A           78 FPPFTHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKCRFG  130 (175)
T ss_dssp             STTCCCCSSBCCEEEECCCCSEEEBTTCCEE------EECC-BTTTTBCBCCCEEEETTS
T ss_pred             CCCcccccccCCcccccccccccceecceEE------EEEe-CchhhhHHHHHhhhcccc
Confidence            6999999999999999999999998888776      4455 999999999999997653

---

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	212
d1l3aa_	166	d.18.1.2 (A:) Plant transcriptional regulator PBF-	8e-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 =  185 bits (471), Expect = 8e-61
 Identities = 67/144 (46%), Positives = 101/144 (70%), Gaps = 2/144 (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 ILKTNERFVVPVSTAEFAVMKTAC 199
           ++  +E   +PV+ AEFAV+ +A 
Sbjct: 123 LINLDENIYIPVTKAEFAVLVSAF 146

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	212
d1l3aa_	166	Plant transcriptional regulator PBF-2 {Potato (Sol	100.0
d1aoca_	175	Coagulogen {Japanese horseshoe crab (Tachypleus tr	88.96

>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=1.7e-59  Score=388.99  Aligned_cols=149  Identities=45%  Similarity=0.841  Sum_probs=146.9

Q ss_pred             CceeeeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEeeChhhhhhhhhcCCCC
Q 028165           56 GGRIFAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFALSPTEVGSLLTMGPRD  135 (212)
Q Consensus        56 ~~rvy~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~FsLS~tEvG~Llslg~~~  135 (212)
                      ++|+|++|+|||+||||+++|++|+|..+++|+++++|+|.|||||||++|+|||||+|||+|+||++|+|+||++++++
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            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeeeCccCcCCCccccceeeEEeeCCCC--ceEEEEEeecccCCCceeeeccchhHHHHHHHHHHHHHc
Q 028165          136 SSEFFHDPAMLSSNAGQMRKSLSIKANADG--FFISLNVANNILKTNERFVVPVSTAEFAVMKTACICIAS  204 (212)
Q Consensus       136 s~EffHDP~~g~S~~G~v~K~LkIep~~dG--~F~nLsV~n~~~~~~~~~~vPVt~aEfavlrsl~~f~l~  204 (212)
                      +|||||||.|++|++|+++|+|++||+|||  +|+||+|+|++.+++++++||||+|||+|||++|||+|.
T Consensus        81 s~~ffhdp~~~~s~~g~i~K~lk~~P~pdg~g~f~~l~v~~~~~~~~e~~~Vpvt~~Ef~v~~~~~~~~lP  151 (166)
T d1l3aa_          81 SCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMP  151 (166)
T ss_dssp             CEEEEECSCCSSSCCCCCEEEEEEEECTTSSEEEEEEEEEEGGGTEEEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred             cceeecCcccccccCCceeEEEEeeecCCCCccEEEEEecccccCccceEEEeecHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999999998  999999999999999999999999999999999999985

>d1aoca_ g.17.1.5 (A:) Coagulogen {Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853]}

class: Small proteins
fold: Cystine-knot cytokines
superfamily: Cystine-knot cytokines
family: Coagulogen
domain: Coagulogen
species: Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853]

Probab=88.96  E-value=0.093  Score=41.32  Aligned_cols=53  Identities=26%  Similarity=0.570  Sum_probs=46.6

Q ss_pred             eeceeeeecceeEEEeecCCceeecCCCCeeEeeeceEEEEeeecccCcccccccceeEe
Q 028165           60 FAPYYVYKGKAAFSVDPVLPTFMKLDSGDLKVKRKGVILLTFAPAIGERKYDWAKKQHFA  119 (212)
Q Consensus        60 y~~ysVYkgKaAls~~p~~PtF~~~~sG~~kv~R~G~vlLeFAPavG~RqYDW~kKq~Fs  119 (212)
                      |.||+-|++.+-.+++..-|+|.-.-+|.++      |++| ||.+|-||--|+.|-.|.
T Consensus        78 f~pf~hf~secpvs~~~cep~fgyt~~~e~r------iivq-ap~agfrqcvwqhkcr~g  130 (175)
T d1aoca_          78 FPPFTHFKSECPVSTRDCEPVFGYTVAGEFR------VIVQ-APRAGFRQCVWQHKCRFG  130 (175)
T ss_dssp             STTCCCCSSBCCEEEECCCCSEEEBTTCCEE------EECC-BTTTTBCBCCCEEEETTS
T ss_pred             CCCcccCcccCCcccccccccccceecceEE------EEEe-CCchhhHHHHHhhhcccc
Confidence            5899999999999999999999988888765      4555 999999999999997763