Citrus Sinensis ID: 033164

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120------
Protein Sequence
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Secondary Structure (PSIPRED)
ccccHHccccccccccccccccccccccccccccEEEEEEccEEEcccccccccccccccccccccccccccEEEEEccccccccccccccEEcccHHHHHHHHHHHHHHHHHcEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccccccccccccEEEEEcccEEEcccccccccccccccccccccccccccEEEEEEcccccccccccccEEccccHHHHHHHHHHHHHHHHHHHHHHcHHHHcc
Coil and Loop (DISEMBL)
MAASVMAsslslkpapftveksaarglpslakTSFKIVAkggkiktdkpygvnggmdlregldasgrkakgkGVYQFVDKyganvdgysgdvytggaTGLAIWAVTLAGLLAGGALLVYNTSALAQ
Flexible Loop (DISEMBL)
maasvmasslslkpapftVEKSaarglpslaktsfkivakggkiktdkpygvnggMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Low Complexity Region (SEG)
maasvmasslslKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTlagllaggallVYNTSALAQ
Disordered region (IsUnstruct)
*********************************SFKIVAKGGKIK****YGV*****************KGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNT*****
Disordered Region (DISOPRED)
************************************************************************GVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSA***
Disordered Region (DISEMBL)
**********SLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Disordered Region (DISPRO)
********************************TSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALA*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
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	126	2.2.26 [Sep-21-2011]
P27202	140	Photosystem II 10 kDa pol	yes	no	1.0	0.9	0.75	1e-48
P49108	141	Photosystem II 10 kDa pol	N/A	no	1.0	0.893	0.737	5e-48
Q40519	136	Photosystem II 10 kDa pol	N/A	no	0.968	0.897	0.692	2e-45
P06183	138	Photosystem II 10 kDa pol	N/A	no	0.984	0.898	0.707	8e-45
Q40163	138	Photosystem II 10 kDa pol	N/A	no	0.984	0.898	0.7	9e-44
P10690	140	Photosystem II 10 kDa pol	N/A	no	0.992	0.892	0.687	3e-34
Q40070	138	Photosystem II 10 kDa pol	N/A	no	0.976	0.891	0.589	2e-31

>sp|P27202|PSBR_ARATH Photosystem II 10 kDa polypeptide, chloroplastic OS=Arabidopsis thaliana GN=PSBR PE=1 SV=1

 Score =  191 bits (485), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 105/140 (75%), Positives = 116/140 (82%), Gaps = 14/140 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSL--AKTSFKIVAKG-GKIKTDKPYGVNGGMD 57
           MAASVM SS++LKPA FTVEK+AARGLPSL  A+ SFKIVA G  KIKTDKP+G+NG MD
Sbjct: 1   MAASVMLSSVTLKPAGFTVEKTAARGLPSLTRARPSFKIVASGVKKIKTDKPFGINGSMD 60

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+G+DASGRK KG GVY++VDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVT 120

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           LAG+LAGGALLVYNTSALAQ
Sbjct: 121 LAGILAGGALLVYNTSALAQ 140

Associated with the oxygen-evolving complex of photosystem II.
Arabidopsis thaliana (taxid: 3702)

>sp|P49108|PSBR_BRACM Photosystem II 10 kDa polypeptide, chloroplastic OS=Brassica campestris GN=PSBR PE=2 SV=1

 Score =  189 bits (480), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 104/141 (73%), Positives = 115/141 (81%), Gaps = 15/141 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAK---TSFKIVAKG-GKIKTDKPYGVNGGM 56
           MAASVM SS++LKPA FTVEK +ARGLPSL +   +SF+IVA G  KIKTDKP+GVNG M
Sbjct: 1   MAASVMLSSVTLKPAGFTVEKMSARGLPSLTRASPSSFRIVASGVKKIKTDKPFGVNGSM 60

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAV 105
           DLR+G+DASGRK KG GVY+FVDKYGANVDGY           SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAV 120

Query: 106 TLAGLLAGGALLVYNTSALAQ 126
           TLAG+LAGGALLVYNTSALAQ
Sbjct: 121 TLAGILAGGALLVYNTSALAQ 141

Associated with the oxygen-evolving complex of photosystem II.

Brassica campestris (taxid: 3711)

>sp|Q40519|PSBR_TOBAC Photosystem II 10 kDa polypeptide, chloroplastic OS=Nicotiana tabacum GN=PSBR PE=2 SV=1

 Score =  180 bits (457), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 97/140 (69%), Positives = 112/140 (80%), Gaps = 18/140 (12%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTS--FKIVAKG-GKIKTDKPYGVNGGMD 57
           MA++VM    SLKPAPF+VEK+A +GLPSLA++S  F++ A G  K+KTDKPYG+NG M 
Sbjct: 1   MASTVM----SLKPAPFSVEKTAVKGLPSLARSSSSFRVQASGVKKLKTDKPYGINGSMS 56

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+G+DASGRK KGKGVYQFVDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 57  LRDGVDASGRKQKGKGVYQFVDKYGANVDGYSPIYNTDDWSPSGDVYVGGTTGLAIWAVT 116

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           L G+LAGGALLV+NTSALAQ
Sbjct: 117 LVGILAGGALLVFNTSALAQ 136

Associated with the oxygen-evolving complex of photosystem II.

Nicotiana tabacum (taxid: 4097)

>sp|P06183|PSBR_SOLTU Photosystem II 10 kDa polypeptide, chloroplastic OS=Solanum tuberosum GN=PSBR PE=2 SV=1

 Score =  178 bits (452), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 99/140 (70%), Positives = 114/140 (81%), Gaps = 16/140 (11%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTS--FKIVAKG-GKIKTDKPYGVNGGMD 57
           MA++VM SSLSLKP  FT+EK++ +GLPSLA++S  FK+VA G  K+KTDKPYG+NG M 
Sbjct: 1   MASTVM-SSLSLKPT-FTLEKTSVKGLPSLARSSSSFKVVASGVKKLKTDKPYGINGSMA 58

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGGTTGLAIWAVT 118

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           L G+LAGGALLVYNTSALAQ
Sbjct: 119 LVGILAGGALLVYNTSALAQ 138

Associated with the oxygen-evolving complex of photosystem II.

Solanum tuberosum (taxid: 4113)

>sp|Q40163|PSBR_SOLLC Photosystem II 10 kDa polypeptide, chloroplastic OS=Solanum lycopersicum GN=PSBR PE=2 SV=1

 Score =  175 bits (443), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 98/140 (70%), Positives = 112/140 (80%), Gaps = 16/140 (11%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTS--FKIVAKG-GKIKTDKPYGVNGGMD 57
           MA++VM SSLSLKP  FT+EK + +GLPSL ++S  FK+VA G  K+KTDKPYG+NG M 
Sbjct: 1   MASTVM-SSLSLKPT-FTLEKISVKGLPSLTRSSSSFKVVASGVKKLKTDKPYGINGSMA 58

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGGTTGLAIWAVT 118

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           L G+LAGGALLVYNTSALAQ
Sbjct: 119 LLGILAGGALLVYNTSALAQ 138

Associated with the oxygen-evolving complex of photosystem II.

Solanum lycopersicum (taxid: 4081)

>sp|P10690|PSBR_SPIOL Photosystem II 10 kDa polypeptide, chloroplastic OS=Spinacia oleracea GN=PSBR PE=2 SV=1

 Score =  143 bits (361), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 97/141 (68%), Positives = 108/141 (76%), Gaps = 16/141 (11%)

Query: 1   MAASVMASSLSLKPAPFTVE-KSAARGLPSLAKTS--FKIVAKG-GKIKTDKPYGVNGGM 56
           MA SVM SSLSLKP+ F V+ KSA +GLPSL+++S  F + A G  KIK DKP G+ GGM
Sbjct: 1   MATSVM-SSLSLKPSSFGVDTKSAVKGLPSLSRSSASFTVRASGVKKIKVDKPLGIGGGM 59

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAV 105
            LR+G+D+SGRK  GKGVYQFVDKYGANVDGYS           GDVY GG TGL IWAV
Sbjct: 60  KLRDGVDSSGRKPTGKGVYQFVDKYGANVDGYSPIYNEEEWAPTGDVYAGGTTGLLIWAV 119

Query: 106 TLAGLLAGGALLVYNTSALAQ 126
           TLAGLLAGGALLVYNTSALAQ
Sbjct: 120 TLAGLLAGGALLVYNTSALAQ 140

Associated with the oxygen-evolving complex of photosystem II.

Spinacia oleracea (taxid: 3562)

>sp|Q40070|PSBR_HORVU Photosystem II 10 kDa polypeptide, chloroplastic OS=Hordeum vulgare GN=PSBR PE=3 SV=1

 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/139 (58%), Positives = 99/139 (71%), Gaps = 16/139 (11%)

Query: 1   MAASVMASSLSLKPA--PFTVEKSAARGLPSLAKTSFKIVAKGGK-IKTDKPYGVNGGMD 57
           M+A VMAS L+LKP+  P  +++S   G+   A+ S  IVAK  K ++T +PYG  GG+ 
Sbjct: 1   MSACVMAS-LALKPSSSPL-LQRSKLGGVRPSARPSLVIVAKKAKKVQTAQPYGPGGGVA 58

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
            +EG+DASGR AKGKGVYQF DKYGANVDGY           SGDVY GG TGL +WAVT
Sbjct: 59  FKEGVDASGRVAKGKGVYQFADKYGANVDGYSPIYTPEEWSPSGDVYVGGKTGLFLWAVT 118

Query: 107 LAGLLAGGALLVYNTSALA 125
           LAG+L GGALLVY+TSALA
Sbjct: 119 LAGILLGGALLVYSTSALA 137

Associated with the oxygen-evolving complex of photosystem II.

Hordeum vulgare (taxid: 4513)

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	126
15219268	140	photosystem II subunit R [Arabidopsis th	1.0	0.9	0.75	8e-47
118489740	136	unknown [Populus trichocarpa x Populus d	0.992	0.919	0.744	9e-47
1346871	141	RecName: Full=Photosystem II 10 kDa poly	1.0	0.893	0.737	3e-46
119720780	140	photosystem II 10kDa polytpeptide [Brass	1.0	0.9	0.75	5e-46
118488826	137	unknown [Populus trichocarpa x Populus d	0.992	0.912	0.746	6e-46
224115282	137	hypothetical protein POPTRDRAFT_674736 [	0.992	0.912	0.739	1e-45
83776786	129	chloroplast photosystem II 10 kDa protei	0.912	0.891	0.759	1e-45
284520974	137	chloroplast photosystem II 10 kDa polype	0.992	0.912	0.724	2e-45
121483553	141	PSII 10Kd peptide [Brassica juncea]	1.0	0.893	0.723	3e-45
224115372	137	hypothetical protein POPTRDRAFT_569170 [	0.992	0.912	0.731	5e-45

>gi|15219268|ref|NP_178025.1| photosystem II subunit R [Arabidopsis thaliana] gi|131398|sp|P27202.1|PSBR_ARATH RecName: Full=Photosystem II 10 kDa polypeptide, chloroplastic; Flags: Precursor gi|16447|emb|CAA39441.1| photosystem II 10 kDa polypeptide [Arabidopsis thaliana] gi|3152571|gb|AAC17052.1| Match to photosystem II 10kDa polypeptide gb|X55970. ESTs gb|Z17693, gb|N37616, gb|T41858, gb|T88021, gb|R37531, gb|T04679, gb|N37520, gb|N64965, gb|Z17592 and gb|N65338, gb|N37466 and gb|T45400 come from this gene [Arabidopsis thaliana] gi|17979203|gb|AAL49840.1| putative photosystem II polypeptide protein [Arabidopsis thaliana] gi|20465469|gb|AAM20194.1| putative photosystem II polypeptide [Arabidopsis thaliana] gi|21536748|gb|AAM61080.1| photosystem II polypeptide, putative [Arabidopsis thaliana] gi|110740828|dbj|BAE98511.1| PSII-R protein [Arabidopsis thaliana] gi|332198075|gb|AEE36196.1| photosystem II subunit R [Arabidopsis thaliana]

 Score =  191 bits (485), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 105/140 (75%), Positives = 116/140 (82%), Gaps = 14/140 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSL--AKTSFKIVAKG-GKIKTDKPYGVNGGMD 57
           MAASVM SS++LKPA FTVEK+AARGLPSL  A+ SFKIVA G  KIKTDKP+G+NG MD
Sbjct: 1   MAASVMLSSVTLKPAGFTVEKTAARGLPSLTRARPSFKIVASGVKKIKTDKPFGINGSMD 60

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+G+DASGRK KG GVY++VDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVT 120

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           LAG+LAGGALLVYNTSALAQ
Sbjct: 121 LAGILAGGALLVYNTSALAQ 140

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489740|gb|ABK96671.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  191 bits (485), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 102/137 (74%), Positives = 113/137 (82%), Gaps = 12/137 (8%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLRE 60
           MAASVMAS LSLKP+PFTVEKS+ RGLP+L++ +FKI A G KIKTD PYG  GGM+LR+
Sbjct: 1   MAASVMAS-LSLKPSPFTVEKSSVRGLPTLSRRTFKIEASGVKIKTDTPYGTGGGMNLRD 59

Query: 61  GLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTLAG 109
           GLDASGRK KGKGVYQ+VDKYGANVDGYS           GDVY GG TGL IWAVTLAG
Sbjct: 60  GLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGKTGLLIWAVTLAG 119

Query: 110 LLAGGALLVYNTSALAQ 126
           +LAGGALLVY+TSALAQ
Sbjct: 120 ILAGGALLVYSTSALAQ 136

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1346871|sp|P49108.1|PSBR_BRACM RecName: Full=Photosystem II 10 kDa polypeptide, chloroplastic; Flags: Precursor gi|967968|gb|AAA74957.1| photosystem II 10kDa polypeptide [Brassica rapa subsp. campestris]

 Score =  189 bits (480), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 104/141 (73%), Positives = 115/141 (81%), Gaps = 15/141 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAK---TSFKIVAKG-GKIKTDKPYGVNGGM 56
           MAASVM SS++LKPA FTVEK +ARGLPSL +   +SF+IVA G  KIKTDKP+GVNG M
Sbjct: 1   MAASVMLSSVTLKPAGFTVEKMSARGLPSLTRASPSSFRIVASGVKKIKTDKPFGVNGSM 60

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAV 105
           DLR+G+DASGRK KG GVY+FVDKYGANVDGY           SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAV 120

Query: 106 TLAGLLAGGALLVYNTSALAQ 126
           TLAG+LAGGALLVYNTSALAQ
Sbjct: 121 TLAGILAGGALLVYNTSALAQ 141

Source: Brassica rapa subsp. campestris

Species: Brassica rapa

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|119720780|gb|ABL97960.1| photosystem II 10kDa polytpeptide [Brassica rapa]

 Score =  188 bits (478), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 105/140 (75%), Positives = 114/140 (81%), Gaps = 14/140 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSL--AKTSFKIVAKG-GKIKTDKPYGVNGGMD 57
           MAAS+M SS++LKPA FTVEK + RGLPSL  A +SFKIVA G  KIKTDKP+GVNG MD
Sbjct: 1   MAASLMLSSVTLKPAGFTVEKMSVRGLPSLTRAPSSFKIVASGVKKIKTDKPFGVNGSMD 60

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVT 106
           LR+GLDASGRK KG GVY+FVDKYGANVDGY           SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGLDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAVT 120

Query: 107 LAGLLAGGALLVYNTSALAQ 126
           LAG+LAGGALLVYNTSALAQ
Sbjct: 121 LAGILAGGALLVYNTSALAQ 140

Source: Brassica rapa

Species: Brassica rapa

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488826|gb|ABK96223.1| unknown [Populus trichocarpa x Populus deltoides] gi|118488997|gb|ABK96306.1| unknown [Populus trichocarpa x Populus deltoides] gi|118489823|gb|ABK96711.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  188 bits (477), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 103/138 (74%), Positives = 113/138 (81%), Gaps = 13/138 (9%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKG-GKIKTDKPYGVNGGMDLR 59
           MAASVMAS LSLKP+PFTVEKS+ RGLP+L++ SFKI A G  KIKTD PYG  GGM+LR
Sbjct: 1   MAASVMAS-LSLKPSPFTVEKSSVRGLPTLSRRSFKIEASGVKKIKTDTPYGTGGGMNLR 59

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVTLA 108
           +GLDASGRK KGKGVYQ+VDKYGANVDGY           SGDVY GG TGL IWAVTLA
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYAGGKTGLLIWAVTLA 119

Query: 109 GLLAGGALLVYNTSALAQ 126
           G+LAGGALLVY+TSALAQ
Sbjct: 120 GILAGGALLVYSTSALAQ 137

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115282|ref|XP_002332206.1| hypothetical protein POPTRDRAFT_674736 [Populus trichocarpa] gi|118487848|gb|ABK95747.1| unknown [Populus trichocarpa] gi|222875313|gb|EEF12444.1| hypothetical protein POPTRDRAFT_674736 [Populus trichocarpa]

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 102/138 (73%), Positives = 113/138 (81%), Gaps = 13/138 (9%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKG-GKIKTDKPYGVNGGMDLR 59
           MAASVMAS LSLKP+PFTVEKS+ RGLP+L++ +FKI A G  KIKTD PYG  GGM+LR
Sbjct: 1   MAASVMAS-LSLKPSPFTVEKSSVRGLPTLSRRTFKIEASGVKKIKTDTPYGTGGGMNLR 59

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTLA 108
           +GLDASGRK KGKGVYQ+VDKYGANVDGYS           GDVY GG TGL IWAVTLA
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGKTGLLIWAVTLA 119

Query: 109 GLLAGGALLVYNTSALAQ 126
           G+LAGGALLVY+TSALAQ
Sbjct: 120 GILAGGALLVYSTSALAQ 137

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|83776786|gb|ABC46708.1| chloroplast photosystem II 10 kDa protein [Arachis hypogaea]

 Score =  187 bits (474), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 98/129 (75%), Positives = 109/129 (84%), Gaps = 14/129 (10%)

Query: 12  LKPAPFTVEKSAARGLPSLAK--TSFKIVAKGGK-IKTDKPYGVNGGMDLREGLDASGRK 68
           LKPAPFT E+S+ RG+PSL++  +SFK+VA GGK IKTDKPYG+NGGM+LR+GLDASGRK
Sbjct: 1   LKPAPFTAERSSVRGIPSLSRASSSFKVVASGGKKIKTDKPYGINGGMNLRDGLDASGRK 60

Query: 69  AKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTLAGLLAGGALL 117
            KGKGVYQFVDKYGANVDGYS           GDVYTGG TGLAIWAVTL GLLAGGALL
Sbjct: 61  GKGKGVYQFVDKYGANVDGYSPIYDQKDWSPTGDVYTGGTTGLAIWAVTLVGLLAGGALL 120

Query: 118 VYNTSALAQ 126
           VYNTSAL+Q
Sbjct: 121 VYNTSALSQ 129

Source: Arachis hypogaea

Species: Arachis hypogaea

Genus: Arachis

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|284520974|gb|ADB93062.1| chloroplast photosystem II 10 kDa polypeptide [Jatropha curcas]

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 100/138 (72%), Positives = 113/138 (81%), Gaps = 13/138 (9%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGK-IKTDKPYGVNGGMDLR 59
           MA SVMAS +SLKP+PF+V+KS+ RGLP L++ +FK+ A GGK IKTDKPYG+ GGM+LR
Sbjct: 1   MATSVMAS-VSLKPSPFSVQKSSVRGLPKLSRRAFKVEAGGGKKIKTDKPYGIGGGMNLR 59

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTLA 108
            GLDASGRKA GKGVYQ+VDKYGANVDGYS           GDVY GG TGLAIWAVTL 
Sbjct: 60  NGLDASGRKATGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGTTGLAIWAVTLL 119

Query: 109 GLLAGGALLVYNTSALAQ 126
           G+LAGGALLVYNTSALAQ
Sbjct: 120 GILAGGALLVYNTSALAQ 137

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|121483553|gb|ABM54168.1| PSII 10Kd peptide [Brassica juncea]

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 102/141 (72%), Positives = 114/141 (80%), Gaps = 15/141 (10%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAK---TSFKIVAKG-GKIKTDKPYGVNGGM 56
           MAASVM S ++LKPA FTVEK +ARGLPSL +   +SF+IVA G  KIKTDKP+GVNG M
Sbjct: 1   MAASVMLSPVTLKPAGFTVEKMSARGLPSLTRASPSSFRIVASGVKKIKTDKPFGVNGSM 60

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAV 105
           DLR+G+DASGRK KG GVY+FVD+YGANVDGY           SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDEYGANVDGYSPIYNEEEWSASGDVYKGGVTGLAIWAV 120

Query: 106 TLAGLLAGGALLVYNTSALAQ 126
           TLAG+LAGGALLVYNTSALAQ
Sbjct: 121 TLAGILAGGALLVYNTSALAQ 141

Source: Brassica juncea

Species: Brassica juncea

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115372|ref|XP_002317015.1| hypothetical protein POPTRDRAFT_569170 [Populus trichocarpa] gi|118488264|gb|ABK95951.1| unknown [Populus trichocarpa] gi|222860080|gb|EEE97627.1| hypothetical protein POPTRDRAFT_569170 [Populus trichocarpa]

 Score =  185 bits (470), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 101/138 (73%), Positives = 111/138 (80%), Gaps = 13/138 (9%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKG-GKIKTDKPYGVNGGMDLR 59
           MAASVMAS L+LKP+PFTVEKS+ RGLP+L++ SFKI A G  KIKTD PYG  GGM+LR
Sbjct: 1   MAASVMAS-LNLKPSPFTVEKSSVRGLPTLSRRSFKIEASGVKKIKTDTPYGTGGGMNLR 59

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGY-----------SGDVYTGGATGLAIWAVTLA 108
            GLDASGRK +GKGVYQ+VDKYGANVDGY           SGDVY GG TGL IWAVTLA
Sbjct: 60  NGLDASGRKPRGKGVYQYVDKYGANVDGYSPIYNADEWSPSGDVYAGGKTGLLIWAVTLA 119

Query: 109 GLLAGGALLVYNTSALAQ 126
           G+LAGGALLVY TSALAQ
Sbjct: 120 GILAGGALLVYTTSALAQ 137

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	126
TAIR|locus:2207320	140	PSBR "photosystem II subunit R	0.904	0.814	0.671	8e-37

TAIR|locus:2207320 PSBR "photosystem II subunit R" [Arabidopsis thaliana (taxid:3702)]

 Score = 396 (144.5 bits), Expect = 8.0e-37, P = 8.0e-37
 Identities = 86/128 (67%), Positives = 94/128 (73%)

Query:    13 KPAPFTVEKSAARGLPSL--AKTSFKIVAKG-GKIKTDKPYGVNGGMDLREGLDASGRKA 69
             KPA FTVEK+AARGLPSL  A+ SFKIVA G  KIKTDKP+G+NG MDLR+G+DASGRK 
Sbjct:    13 KPAGFTVEKTAARGLPSLTRARPSFKIVASGVKKIKTDKPFGINGSMDLRDGVDASGRKG 72

Query:    70 KGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTXXXXXXXXXXXV 118
             KG GVY++VDKYGANVDGYS           GDVY GG TGLAIWAVT           V
Sbjct:    73 KGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVTLAGILAGGALLV 132

Query:   119 YNTSALAQ 126
             YNTSALAQ
Sbjct:   133 YNTSALAQ 140


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        0.312   0.133   0.386    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      126       103   0.00091  102 3  11 23  0.49    30
                                                     29  0.49    31


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  483 (51 KB)
  Total size of DFA:  95 KB (2070 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:  11.20u 0.12s 11.32t   Elapsed:  00:00:00
  Total cpu time:  11.20u 0.12s 11.32t   Elapsed:  00:00:00
  Start:  Fri May 10 16:30:23 2013   End:  Fri May 10 16:30:23 2013

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009523 "photosystem II" evidence=IEA;ISS

GO:0009654 "oxygen evolving complex" evidence=IEA

GO:0015979 "photosynthesis" evidence=IEA;ISS

GO:0042651 "thylakoid membrane" evidence=IEA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0010270 "photosystem II oxygen evolving complex assembly" evidence=IEP

GO:0009579 "thylakoid" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009637 "response to blue light" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0019344 "cysteine 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)
Q40519	PSBR_TOBAC	No assigned EC number	0.6928	0.9682	0.8970	N/A	no
Q40070	PSBR_HORVU	No assigned EC number	0.5899	0.9761	0.8913	N/A	no
P10690	PSBR_SPIOL	No assigned EC number	0.6879	0.9920	0.8928	N/A	no
P27202	PSBR_ARATH	No assigned EC number	0.75	1.0	0.9	yes	no
P49108	PSBR_BRACM	No assigned EC number	0.7375	1.0	0.8936	N/A	no
Q40163	PSBR_SOLLC	No assigned EC number	0.7	0.9841	0.8985	N/A	no
P06183	PSBR_SOLTU	No assigned EC number	0.7071	0.9841	0.8985	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	126
PLN00053	117	PLN00053, PLN00053, photosystem II subunit R; Prov	5e-49
pfam04725	99	pfam04725, PsbR, Photosystem II 10 kDa polypeptide	3e-40

>gnl|CDD|215041 PLN00053, PLN00053, photosystem II subunit R; Provisional

 Score =  152 bits (385), Expect = 5e-49
 Identities = 85/117 (72%), Positives = 94/117 (80%), Gaps = 14/117 (11%)

Query: 24  ARGLPSLAKT--SFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDK 80
            RGLP L++T  SFK+ A GG KIKTD+PYG +GGM+L++G+DASGRK KGKGVYQFVDK
Sbjct: 1   VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDK 60

Query: 81  YGANVDGYS-----------GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 126
           YGANVDGYS           GDVY GG TGL IWAVTLAGLLAGGALLVYNTSALAQ
Sbjct: 61  YGANVDGYSPIYTPDEWSPSGDVYVGGTTGLLIWAVTLAGLLAGGALLVYNTSALAQ 117

Length = 117

>gnl|CDD|147071 pfam04725, PsbR, Photosystem II 10 kDa polypeptide PsbR

 Score =  129 bits (326), Expect = 3e-40
 Identities = 74/99 (74%), Positives = 79/99 (79%), Gaps = 11/99 (11%)

Query: 39  AKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYS--------- 89
           + G K+KTDKPYG+ GGM L+ G+DASGRK KGKGVYQFVDKYGANVDGYS         
Sbjct: 1   SGGKKVKTDKPYGIGGGMALKNGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWS 60

Query: 90  --GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 126
             GDVY GG TGLAIWAVTLAGLL GGALLVYNTSALAQ
Sbjct: 61  PSGDVYVGGTTGLAIWAVTLAGLLGGGALLVYNTSALAQ 99

This protein is associated with the oxygen-evolving complex of photosystem II. Its function in photosynthesis is not known. The C-terminal hydrophobic region functions as a thylakoid transfer signal but is not removed. Length = 99

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	126
PLN00053	117	photosystem II subunit R; Provisional	100.0
PF04725	99	PsbR: Photosystem II 10 kDa polypeptide PsbR; Inte	100.0
PLN00083	101	photosystem II subunit R; Provisional	100.0

>PLN00053 photosystem II subunit R; Provisional

Probab=100.00  E-value=8.8e-57  Score=334.66  Aligned_cols=103  Identities=82%  Similarity=1.338  Sum_probs=100.8

Q ss_pred             ccCCCCCcc--ceeEEeecCc-eeecccccccCCCcccCCCcCCCCCCccCCeeEEecccccccccCCC-----------
Q 033164           24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------   89 (126)
Q Consensus        24 ~rglp~l~R--~~~~v~asgg-Kikt~kp~G~~ggm~~k~gvDasGRkgKg~gVYqf~~kyGANVDgYS-----------   89 (126)
                      +||||+++|  ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+|||||||||||           
T Consensus         1 ~~glp~l~r~~ss~~v~as~~kkikt~~p~G~~G~m~~k~gvDasGRk~kGkGVYqFvdKYGANVDgYSPIY~~~ews~~   80 (117)
T PLN00053          1 VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPS   80 (117)
T ss_pred             CCccCcccccccceEEEecCCceeeecCCcccCCCcccccccCCCCccCCCcceEEehhhcCccccccCCCcChhhcCCC
Confidence            589999999  6899999988 89999999999999999999999999999999999999999999999           


Q ss_pred             CceeccchhHHHHHHHHHHHHhhhceeeeeecccccC
Q 033164           90 GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ  126 (126)
Q Consensus        90 GD~Y~gG~~gL~~wA~tl~glL~~GallVy~TSaLa~  126 (126)
                      ||+|+|||+||+|||+||+|||++|||||||||||+|
T Consensus        81 Gd~Y~ggttgL~~wa~~l~gll~~gallvynTSaLa~  117 (117)
T PLN00053         81 GDVYVGGTTGLLIWAVTLAGLLAGGALLVYNTSALAQ  117 (117)
T ss_pred             CCeeeCChhhHHHHHHHHHHHHcccceeEEehhhhcC
Confidence            9999999999999999999999999999999999997

>PF04725 PsbR: Photosystem II 10 kDa polypeptide PsbR; InterPro: IPR006814 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae

Probab=100.00  E-value=1.8e-50  Score=294.18  Aligned_cols=87  Identities=86%  Similarity=1.388  Sum_probs=85.1

Q ss_pred             cCc-eeecccccccCCCcccCCCcCCCCCCccCCeeEEecccccccccCCC-----------CceeccchhHHHHHHHHH
Q 033164           40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYS-----------GDVYTGGATGLAIWAVTL  107 (126)
Q Consensus        40 sgg-Kikt~kp~G~~ggm~~k~gvDasGRkgKg~gVYqf~~kyGANVDgYS-----------GD~Y~gG~~gL~~wA~tl  107 (126)
                      |++ ||||++|||++|+|++|+|+||+|||+||+|||||+|||||||||||           ||+|+|||+||+|||+||
T Consensus         1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gGt~gL~~WA~~l   80 (99)
T PF04725_consen    1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGGTTGLLIWAVTL   80 (99)
T ss_pred             CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCChhhHHHHHHHH
Confidence            455 99999999999999999999999999999999999999999999999           999999999999999999


Q ss_pred             HHHhhhceeeeeecccccC
Q 033164          108 AGLLAGGALLVYNTSALAQ  126 (126)
Q Consensus       108 ~glL~~GallVy~TSaLa~  126 (126)
                      +|||++||+||||||||+|
T Consensus        81 ~glL~~Gallvy~TSaL~q   99 (99)
T PF04725_consen   81 AGLLGGGALLVYNTSALAQ   99 (99)
T ss_pred             HHHHcccceeEEehhhhcC
Confidence            9999999999999999998

Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight intrinsic protein PsbR found in PSII, which is also known as the 10 kDa polypeptide. The PsbR gene is found only in the nucleus of green algae and higher plants. PsbR may provide a binding site for the extrinsic oxygen-evolving complex protein PsbP to the thylakoid membrane. PsbR has a transmembrane domain to anchor it to the thylakoid membrane, and a charged N-terminal domain capable of forming ion bridges with extrinsic proteins, allowing PsbR to act as a docking protein. PsbR may be a pH-dependent stabilising protein that functions at both donor and acceptor sides of PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0042651 thylakoid membrane

>PLN00083 photosystem II subunit R; Provisional

Probab=100.00  E-value=5.9e-35  Score=213.32  Aligned_cols=83  Identities=37%  Similarity=0.545  Sum_probs=78.3

Q ss_pred             ecCceeecccccccCCCcccCC----CcCCCCCCccCCeeEEeccccc-ccccCCC-----------CceeccchhHHHH
Q 033164           39 AKGGKIKTDKPYGVNGGMDLRE----GLDASGRKAKGKGVYQFVDKYG-ANVDGYS-----------GDVYTGGATGLAI  102 (126)
Q Consensus        39 asggKikt~kp~G~~ggm~~k~----gvDasGRkgKg~gVYqf~~kyG-ANVDgYS-----------GD~Y~gG~~gL~~  102 (126)
                      +|.++.+.+|.-+.+.++.+|+    |..|+|||+||+|||||+|||| |||||||           ||+|+|   ||+|
T Consensus         3 nssgpkrgtk~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~G---gL~~   79 (101)
T PLN00083          3 NSSGPKRGTKAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKL   79 (101)
T ss_pred             CCCCCCCccccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhc---cHHH
Confidence            4667788888899999999998    8889999999999999999999 9999999           999998   5999


Q ss_pred             HHHHHHHHhhhceeeeeecccc
Q 033164          103 WAVTLAGLLAGGALLVYNTSAL  124 (126)
Q Consensus       103 wA~tl~glL~~GallVy~TSaL  124 (126)
                      ||+||+|||++|||||||||||
T Consensus        80 WA~tlaglLg~GAllVy~TSaL  101 (101)
T PLN00083         80 AAAAVAGVIGTGALAILLTSAL  101 (101)
T ss_pred             HHHHHHHHHccceeEEEecccC
Confidence            9999999999999999999997

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00