Citrus Sinensis ID: 032633

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Secondary Structure (PSIPRED)
ccHHHHHHcccccccccHHHccccccccccccccEEEEEEccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccEEcccHHHHHHHHHHHHHHHHHcEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccccccccccccEEEEEcccEEEcccccccccccccccccccccccccccEEEEEEEccccccccccccccHHcccccccEEccccHHHHHHHHHHHHHHHHHHHHHHcHHHHcc
Coil and Loop (DISEMBL)
MAASVMAsslslkpapftveksaarglpslakTSFKIVAkggkiktdkpygvnggmdlregldasgrkakgkGVYQFVDkyganvdgyspiynendwspsgdvytggaTGLAIWAVTLAGLLAGGALLVYNTSALAQ
Flexible Loop (DISEMBL)
maasvmasslslkpapftVEKSaarglpslaktsfkivakggkiktdkpygvnggMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Low Complexity Region (SEG)
maasvmasslslKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTlagllaggallVYNTSALAQ
Disordered region (IsUnstruct)
*********************************SFKIVAKGGKIK****YGV******************GKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNT*****
Disordered Region (DISOPRED)
************************************************************************GVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSAL**
Disordered Region (DISEMBL)
**********SLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Disordered Region (DISPRO)
********************************TSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALA*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ
Positional Conservation
no confident homologs detected

---

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	137	2.2.26 [Sep-21-2011]
P27202	140	Photosystem II 10 kDa pol	yes	no	1.0	0.978	0.814	1e-57
P49108	141	Photosystem II 10 kDa pol	N/A	no	1.0	0.971	0.794	1e-56
Q40519	136	Photosystem II 10 kDa pol	N/A	no	0.970	0.977	0.757	1e-54
P06183	138	Photosystem II 10 kDa pol	N/A	no	0.985	0.978	0.764	2e-53
Q40163	138	Photosystem II 10 kDa pol	N/A	no	0.985	0.978	0.757	2e-52
P10690	140	Photosystem II 10 kDa pol	N/A	no	0.992	0.971	0.737	7e-43
Q40070	138	Photosystem II 10 kDa pol	N/A	no	0.978	0.971	0.640	1e-39

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

 Score =  221 bits (562), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 114/140 (81%), Positives = 126/140 (90%), Gaps = 3/140 (2%)

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

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVT 120

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  218 bits (554), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 112/141 (79%), Positives = 125/141 (88%), Gaps = 4/141 (2%)

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

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAV 116
           DLR+G+DASGRK KG GVY+FVDKYGANVDGYSPIYNE++WS SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAV 120

Query: 117 TLAGLLAGGALLVYNTSALAQ 137
           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 =  211 bits (536), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 106/140 (75%), Positives = 122/140 (87%), Gaps = 7/140 (5%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+G+DASGRK KGKGVYQFVDKYGANVDGYSPIYN +DWSPSGDVY GG TGLAIWAVT
Sbjct: 57  LRDGVDASGRKQKGKGVYQFVDKYGANVDGYSPIYNTDDWSPSGDVYVGGTTGLAIWAVT 116

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  207 bits (526), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 107/140 (76%), Positives = 124/140 (88%), Gaps = 5/140 (3%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG TGLAIWAVT
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGGTTGLAIWAVT 118

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  204 bits (518), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 106/140 (75%), Positives = 122/140 (87%), Gaps = 5/140 (3%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG TGLAIWAVT
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGGTTGLAIWAVT 118

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  172 bits (435), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 104/141 (73%), Positives = 118/141 (83%), Gaps = 5/141 (3%)

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  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAV 116
            LR+G+D+SGRK  GKGVYQFVDKYGANVDGYSPIYNE +W+P+GDVY GG TGL IWAV
Sbjct: 60  KLRDGVDSSGRKPTGKGVYQFVDKYGANVDGYSPIYNEEEWAPTGDVYAGGTTGLLIWAV 119

Query: 117 TLAGLLAGGALLVYNTSALAQ 137
           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 =  161 bits (407), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 89/139 (64%), Positives = 107/139 (76%), Gaps = 5/139 (3%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
            +EG+DASGR AKGKGVYQF DKYGANVDGYSPIY   +WSPSGDVY GG TGL +WAVT
Sbjct: 59  FKEGVDASGRVAKGKGVYQFADKYGANVDGYSPIYTPEEWSPSGDVYVGGKTGLFLWAVT 118

Query: 118 LAGLLAGGALLVYNTSALA 136
           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	137
15219268	140	photosystem II subunit R [Arabidopsis th	1.0	0.978	0.814	9e-56
118489740	136	unknown [Populus trichocarpa x Populus d	0.992	1.0	0.795	4e-55
1346871	141	RecName: Full=Photosystem II 10 kDa poly	1.0	0.971	0.794	8e-55
119720780	140	photosystem II 10kDa polytpeptide [Brass	1.0	0.978	0.8	1e-54
118488826	137	unknown [Populus trichocarpa x Populus d	0.992	0.992	0.804	2e-54
83776786	129	chloroplast photosystem II 10 kDa protei	0.919	0.976	0.813	7e-54
224115282	137	hypothetical protein POPTRDRAFT_674736 [	0.992	0.992	0.789	7e-54
284520974	137	chloroplast photosystem II 10 kDa polype	0.992	0.992	0.775	7e-54
121483553	141	PSII 10Kd peptide [Brassica juncea]	1.0	0.971	0.780	1e-53
224115372	137	hypothetical protein POPTRDRAFT_569170 [	0.992	0.992	0.789	2e-53

>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 =  221 bits (562), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 114/140 (81%), Positives = 126/140 (90%), Gaps = 3/140 (2%)

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

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVT 120

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 109/137 (79%), Positives = 123/137 (89%), Gaps = 1/137 (0%)

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

Query: 61  GLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAG 120
           GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY GG TGL IWAVTLAG
Sbjct: 60  GLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGKTGLLIWAVTLAG 119

Query: 121 LLAGGALLVYNTSALAQ 137
           +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 =  218 bits (554), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 112/141 (79%), Positives = 125/141 (88%), Gaps = 4/141 (2%)

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

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAV 116
           DLR+G+DASGRK KG GVY+FVDKYGANVDGYSPIYNE++WS SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAV 120

Query: 117 TLAGLLAGGALLVYNTSALAQ 137
           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 =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 112/140 (80%), Positives = 124/140 (88%), Gaps = 3/140 (2%)

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

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVT 117
           LR+GLDASGRK KG GVY+FVDKYGANVDGYSPIYNE++WS SGDVY GG TGLAIWAVT
Sbjct: 61  LRDGLDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGGVTGLAIWAVT 120

Query: 118 LAGLLAGGALLVYNTSALAQ 137
           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 =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 111/138 (80%), Positives = 123/138 (89%), Gaps = 2/138 (1%)

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

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLA 119
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG TGL IWAVTLA
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYAGGKTGLLIWAVTLA 119

Query: 120 GLLAGGALLVYNTSALAQ 137
           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|83776786|gb|ABC46708.1| chloroplast photosystem II 10 kDa protein [Arachis hypogaea]

 Score =  214 bits (546), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 105/129 (81%), Positives = 119/129 (92%), Gaps = 3/129 (2%)

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

Query: 69  AKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALL 128
            KGKGVYQFVDKYGANVDGYSPIY++ DWSP+GDVYTGG TGLAIWAVTL GLLAGGALL
Sbjct: 61  GKGKGVYQFVDKYGANVDGYSPIYDQKDWSPTGDVYTGGTTGLAIWAVTLVGLLAGGALL 120

Query: 129 VYNTSALAQ 137
           VYNTSAL+Q
Sbjct: 121 VYNTSALSQ 129

Source: Arachis hypogaea

Species: Arachis hypogaea

Genus: Arachis

Family: Fabaceae

Order: Fabales

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 =  214 bits (546), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 109/138 (78%), Positives = 123/138 (89%), Gaps = 2/138 (1%)

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

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLA 119
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY GG TGL IWAVTLA
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGKTGLLIWAVTLA 119

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

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  214 bits (546), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 107/138 (77%), Positives = 123/138 (89%), Gaps = 2/138 (1%)

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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLA 119
            GLDASGRKA GKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY GG TGLAIWAVTL 
Sbjct: 60  NGLDASGRKATGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGTTGLAIWAVTLL 119

Query: 120 GLLAGGALLVYNTSALAQ 137
           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 =  213 bits (543), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 110/141 (78%), Positives = 123/141 (87%), Gaps = 4/141 (2%)

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

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAV 116
           DLR+G+DASGRK KG GVY+FVD+YGANVDGYSPIYNE +WS SGDVY GG TGLAIWAV
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDEYGANVDGYSPIYNEEEWSASGDVYKGGVTGLAIWAV 120

Query: 117 TLAGLLAGGALLVYNTSALAQ 137
           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 =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 109/138 (78%), Positives = 121/138 (87%), Gaps = 2/138 (1%)

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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLA 119
            GLDASGRK +GKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG TGL IWAVTLA
Sbjct: 60  NGLDASGRKPRGKGVYQYVDKYGANVDGYSPIYNADEWSPSGDVYAGGKTGLLIWAVTLA 119

Query: 120 GLLAGGALLVYNTSALAQ 137
           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	137
TAIR|locus:2207320	140	PSBR "photosystem II subunit R	0.912	0.892	0.742	1e-45

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

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 95/128 (74%), Positives = 104/128 (81%)

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

Query:    70 KGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTXXXXXXXXXXXV 129
             KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG TGLAIWAVT           V
Sbjct:    73 KGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGGVTGLAIWAVTLAGILAGGALLV 132

Query:   130 YNTSALAQ 137
             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        0.311   0.133   0.394    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      137       114   0.00091  102 3  11 23  0.42    31
                                                     29  0.44    32


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:  533 (57 KB)
  Total size of DFA:  116 KB (2077 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:  11.70u 0.11s 11.81t   Elapsed:  00:00:00
  Total cpu time:  11.70u 0.11s 11.81t   Elapsed:  00:00:00
  Start:  Mon May 20 19:19:34 2013   End:  Mon May 20 19:19:34 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	0.7571	0.9708	0.9779	N/A	no
Q40070	PSBR_HORVU	No assigned EC number	0.6402	0.9781	0.9710	N/A	no
P10690	PSBR_SPIOL	No assigned EC number	0.7375	0.9927	0.9714	N/A	no
P27202	PSBR_ARATH	No assigned EC number	0.8142	1.0	0.9785	yes	no
P49108	PSBR_BRACM	No assigned EC number	0.7943	1.0	0.9716	N/A	no
Q40163	PSBR_SOLLC	No assigned EC number	0.7571	0.9854	0.9782	N/A	no
P06183	PSBR_SOLTU	No assigned EC number	0.7642	0.9854	0.9782	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:
	PSBR	PSBR (photosystem II subunit R); Encodes for the 10 kDa PsbR subunit of photosystem II (PSII). This subunit appears to be involved in the stable assembly of PSII, particularly that of the oxygen-evolving complex subunit PsbP. Mutants defective in this gene have reduced amounts of subunits PsbP and PsbQ in PSII. In turn, assembly of PsbR is dependent on the presence of PsbJ. ; Associated with the oxygen-evolving complex of photosystem II (140 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
	PSBO1	PSBO1 (PS II OXYGEN-EVOLVING COMPLEX 1); oxygen evolving/ poly(U) binding; Encodes a protein wh [...] (332 aa)				•		•	•		0.977
	PSBQA	oxygen-evolving enhancer protein 3, chloroplast, putative (PSBQ1) (PSBQ); Encodes the PsbQ subu [...] (224 aa)				•		•	•		0.975
	PSAG	PSAG (PHOTOSYSTEM I SUBUNIT G); Encodes subunit G of photosystem I, an 11-kDa membrane protein [...] (160 aa)				•			•		0.973
	PSBP-1	PSBP-1 (PHOTOSYSTEM II SUBUNIT P-1); poly(U) binding; Encodes a 23 kD extrinsic protein that is [...] (263 aa)				•		•	•		0.962
	PSBO2	PSBO2 (PHOTOSYSTEM II SUBUNIT O-2); oxygen evolving/ poly(U) binding; Encodes a protein which i [...] (331 aa)				•		•	•		0.960
	PSAK	PSAK (photosystem I subunit K); Encodes subunit K of photosystem I reaction center. ; The exact [...] (130 aa)				•			•		0.960
	PSAF	PSAF (photosystem I subunit F); Encodes subunit F of photosystem I. ; Participates in efficienc [...] (221 aa)				•			•		0.958
	PSBQ-2	PSBQ-2; calcium ion binding; Encodes the PsbQ subunit of the oxygen evolving complex of photosy [...] (230 aa)				•		•	•		0.958
	LHCA3	LHCA3; chlorophyll binding; PSI type III chlorophyll a/b-binding protein (Lhca3*1) (273 aa)				•			•		0.953
	LHCB5	LHCB5 (LIGHT HARVESTING COMPLEX OF PHOTOSYSTEM II 5); chlorophyll binding; photosystem II encod [...] (280 aa)				•		•	•		0.940

---

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	137
PLN00053	117	PLN00053, PLN00053, photosystem II subunit R; Prov	1e-61
pfam04725	99	pfam04725, PsbR, Photosystem II 10 kDa polypeptide	3e-51
PLN00083	101	PLN00083, PLN00083, photosystem II subunit R; Prov	6e-06

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

 Score =  184 bits (468), Expect = 1e-61
 Identities = 92/117 (78%), Positives = 103/117 (88%), Gaps = 3/117 (2%)

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  YGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 137
           YGANVDGYSPIY  ++WSPSGDVY GG TGL IWAVTLAGLLAGGALLVYNTSALAQ
Sbjct: 61  YGANVDGYSPIYTPDEWSPSGDVYVGGTTGLLIWAVTLAGLLAGGALLVYNTSALAQ 117

Length = 117

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

 Score =  157 bits (399), Expect = 3e-51
 Identities = 81/99 (81%), Positives = 88/99 (88%)

Query: 39  AKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWS 98
           + G K+KTDKPYG+ GGM L+ G+DASGRK KGKGVYQFVDKYGANVDGYSPIY  ++WS
Sbjct: 1   SGGKKVKTDKPYGIGGGMALKNGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWS 60

Query: 99  PSGDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ 137
           PSGDVY 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

>gnl|CDD|177706 PLN00083, PLN00083, photosystem II subunit R; Provisional

 Score = 42.0 bits (98), Expect = 6e-06
 Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 67  RKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLLAGG 125
           R  K   VY+   + G ANVD YSPIY   ++   GD Y G    L + A  +AG++  G
Sbjct: 35  RSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKLAAAAVAGVIGTG 91

Query: 126 ALLVYNTSAL 135
           AL +  TSAL
Sbjct: 92  ALAILLTSAL 101

Length = 101

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
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=1.4e-68  Score=402.19  Aligned_cols=114  Identities=80%  Similarity=1.357  Sum_probs=111.8

Q ss_pred             ccCCCCCCc--ceeEEEEccc-eeeeccccccCCCcccCccccCCCCCccCCcceeeehhcccCCCCccccccCCCCCCC
Q 032633           24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS  100 (137)
Q Consensus        24 ~rglp~l~R--~s~~v~as~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGvYqfv~KyGANVDgYSPIY~p~eWs~~  100 (137)
                      +||||+++|  ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+||||||||||||||+||||||+
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 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeccChhHHHHHHHHHHHHhhhceeeeeecccccC
Q 032633          101 GDVYTGGATGLAIWAVTLAGLLAGGALLVYNTSALAQ  137 (137)
Q Consensus       101 GD~Y~gG~~gL~~WA~tl~glL~~Gallvy~TSaLa~  137 (137)
                      ||+|+|||+||+|||+||+|||++|||||||||||+|
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=3e-62  Score=359.75  Aligned_cols=98  Identities=84%  Similarity=1.404  Sum_probs=96.1

Q ss_pred             ccc-eeeeccccccCCCcccCccccCCCCCccCCcceeeehhcccCCCCccccccCCCCCCCCCeeccChhHHHHHHHHH
Q 032633           40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTL  118 (137)
Q Consensus        40 s~~-Kikt~kp~G~~g~m~~k~~vDa~gRk~kgkGvYqfv~KyGANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl  118 (137)
                      |++ |||||+|||++|+|++|+|+||+|||+||+|||||+||||||||||||||+||||||+||+|+|||+||+|||+||
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            445 9999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhceeeeeecccccC
Q 032633          119 AGLLAGGALLVYNTSALAQ  137 (137)
Q Consensus       119 ~glL~~Gallvy~TSaLa~  137 (137)
                      +|||++|||||||||||+|
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=1.6e-44  Score=266.31  Aligned_cols=85  Identities=39%  Similarity=0.615  Sum_probs=80.5

Q ss_pred             cccccCCCcccCccccC----CCCCccCCcceeeehhcc-cCCCCccccccCCCCCCCCCeeccChhHHHHHHHHHHHHh
Q 032633           48 KPYGVNGGMDLREGLDA----SGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGGATGLAIWAVTLAGLL  122 (137)
Q Consensus        48 kp~G~~g~m~~k~~vDa----~gRk~kgkGvYqfv~KyG-ANVDgYSPIY~p~eWs~~GD~Y~gG~~gL~~WA~tl~glL  122 (137)
                      |.-+.+.++.+|+.+||    +|||+||+|||||+|||| ||||||||||+||||+|+||+|+|   ||+|||+||+|||
T Consensus        12 k~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~G---gL~~WA~tlaglL   88 (101)
T PLN00083         12 KAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEG---DLKLAAAAVAGVI   88 (101)
T ss_pred             ccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhc---cHHHHHHHHHHHH
Confidence            45577889999999997    589999999999999999 999999999999999999999998   6999999999999


Q ss_pred             hhceeeeeecccc
Q 032633          123 AGGALLVYNTSAL  135 (137)
Q Consensus       123 ~~Gallvy~TSaL  135 (137)
                      ++|||||||||||
T Consensus        89 g~GAllVy~TSaL  101 (101)
T PLN00083         89 GTGALAILLTSAL  101 (101)
T ss_pred             ccceeEEEecccC
Confidence            9999999999997

---

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