Citrus Sinensis ID: 033939

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK
Secondary Structure (PSIPRED)
ccHHHHHHccccccccccHHccccccccccccccEEEEEEccEEEEccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccccccccccccccccccccccccEEEEcccEEEcccccccccccccccccccccccccccEEEEEEcccccccccccccccHHcccccccEEEccc
Coil and Loop (DISEMBL)
MAASVMAsslslkpapftveksaarglpslakTSFKIVAkggkiktdkpygvnggmdlregldasgrkakgkGVYQFVDkyganvdgyspiynendwspsgdvytggk
Flexible Loop (DISEMBL)
maasvmasslslkpapftVEKSaarglpslaktsfkivakggkiktdkpygvnggMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSpiynendwspsgdvytggk
Low Complexity Region (SEG)
maasvmasslslKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK
Disordered region (IsUnstruct)
*********************************SFKIVAKGGKIK****YGV******************GKGVYQFVDKYGANVDGYSPIYNEND************
Disordered Region (DISOPRED)
******************************************************G*****************GVYQFVDKYGANVDGYSPIYNENDWSPSG**YT***
Disordered Region (DISEMBL)
**********SLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK
Disordered Region (DISPRO)
*********************************SFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVY****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK
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	108	2.2.26 [Sep-21-2011]
P27202	140	Photosystem II 10 kDa pol	yes	no	0.990	0.764	0.781	2e-41
P49108	141	Photosystem II 10 kDa pol	N/A	no	0.990	0.758	0.756	2e-40
Q40519	136	Photosystem II 10 kDa pol	N/A	no	0.953	0.757	0.727	4e-39
P06183	138	Photosystem II 10 kDa pol	N/A	no	0.972	0.760	0.727	9e-38
Q40163	138	Photosystem II 10 kDa pol	N/A	no	0.972	0.760	0.718	7e-37
P10690	140	Photosystem II 10 kDa pol	N/A	no	0.981	0.757	0.684	5e-34
Q40070	138	Photosystem II 10 kDa pol	N/A	no	0.981	0.768	0.603	3e-27

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

 Score =  167 bits (424), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 86/110 (78%), Positives = 97/110 (88%), Gaps = 3/110 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGG 110

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 =  164 bits (415), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 84/111 (75%), Positives = 96/111 (86%), Gaps = 4/111 (3%)

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

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           DLR+G+DASGRK KG GVY+FVDKYGANVDGYSPIYNE++WS SGDVY GG
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKGG 111

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 =  159 bits (403), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/110 (72%), Positives = 94/110 (85%), Gaps = 7/110 (6%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KGKGVYQFVDKYGANVDGYSPIYN +DWSPSGDVY GG
Sbjct: 57  LRDGVDASGRKQKGKGVYQFVDKYGANVDGYSPIYNTDDWSPSGDVYVGG 106

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 =  155 bits (391), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 80/110 (72%), Positives = 96/110 (87%), Gaps = 5/110 (4%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGG 108

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 =  152 bits (384), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 79/110 (71%), Positives = 94/110 (85%), Gaps = 5/110 (4%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GG
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGG 108

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 =  142 bits (358), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 76/111 (68%), Positives = 90/111 (81%), Gaps = 5/111 (4%)

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  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
            LR+G+D+SGRK  GKGVYQFVDKYGANVDGYSPIYNE +W+P+GDVY GG
Sbjct: 60  KLRDGVDSSGRKPTGKGVYQFVDKYGANVDGYSPIYNEEEWAPTGDVYAGG 110

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 =  120 bits (300), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 67/111 (60%), Positives = 82/111 (73%), Gaps = 5/111 (4%)

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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
            +EG+DASGR AKGKGVYQF DKYGANVDGYSPIY   +WSPSGDVY GGK
Sbjct: 59  FKEGVDASGRVAKGKGVYQFADKYGANVDGYSPIYTPEEWSPSGDVYVGGK 109

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	108
118489740	136	unknown [Populus trichocarpa x Populus d	0.990	0.786	0.777	3e-41
351722140	139	uncharacterized protein LOC100499745 [Gl	0.981	0.762	0.781	7e-41
351722402	138	uncharacterized protein LOC100305752 [Gl	0.981	0.768	0.770	1e-40
118488826	137	unknown [Populus trichocarpa x Populus d	0.990	0.781	0.788	2e-40
15219268	140	photosystem II subunit R [Arabidopsis th	0.990	0.764	0.781	6e-40
224115282	137	hypothetical protein POPTRDRAFT_674736 [	0.990	0.781	0.770	6e-40
297839767	133	hypothetical protein ARALYDRAFT_477073 [	0.990	0.804	0.781	1e-39
224115372	137	hypothetical protein POPTRDRAFT_569170 [	0.990	0.781	0.770	1e-39
224115278	141	predicted protein [Populus trichocarpa]	0.990	0.758	0.763	2e-39
449460036	138	PREDICTED: photosystem II 10 kDa polypep	0.972	0.760	0.8	2e-39

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

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 84/108 (77%), Positives = 96/108 (88%), Gaps = 1/108 (0%)

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

Query: 61  GLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
           GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY GGK
Sbjct: 60  GLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGK 107

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722140|ref|NP_001235442.1| uncharacterized protein LOC100499745 [Glycine max] gi|255626243|gb|ACU13466.1| unknown [Glycine max]

 Score =  171 bits (432), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 86/110 (78%), Positives = 99/110 (90%), Gaps = 4/110 (3%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAK--TSFKIVAKGGK-IKTDKPYGVNGGMD 57
           MA+SVMAS ++LKPAPFTVEKS+ RGLPSL++  +SF++VA GGK IKTDKPYG+NGGM 
Sbjct: 1   MASSVMAS-VALKPAPFTVEKSSVRGLPSLSRNSSSFRVVASGGKKIKTDKPYGINGGMA 59

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LREG+DASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY GG
Sbjct: 60  LREGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYAGG 109

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351722402|ref|NP_001236219.1| uncharacterized protein LOC100305752 [Glycine max] gi|255626523|gb|ACU13606.1| unknown [Glycine max]

 Score =  170 bits (431), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 97/109 (88%), Gaps = 3/109 (2%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAK--TSFKIVAKGGKIKTDKPYGVNGGMDL 58
           MA+SVMAS ++LKPAPFTVEKS+ RGLPSL++  +SF++VA G KIKTDKPYG+NGGM L
Sbjct: 1   MASSVMAS-VALKPAPFTVEKSSVRGLPSLSRNSSSFRVVASGKKIKTDKPYGINGGMAL 59

Query: 59  REGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           R+G DASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY GG
Sbjct: 60  RDGTDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYAGG 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  169 bits (428), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 86/109 (78%), Positives = 96/109 (88%), Gaps = 2/109 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GGK
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYAGGK 108

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  167 bits (424), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 86/110 (78%), Positives = 97/110 (88%), Gaps = 3/110 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGG 110

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  167 bits (424), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 96/109 (88%), Gaps = 2/109 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY GGK
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAGGK 108

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839767|ref|XP_002887765.1| hypothetical protein ARALYDRAFT_477073 [Arabidopsis lyrata subsp. lyrata] gi|297333606|gb|EFH64024.1| hypothetical protein ARALYDRAFT_477073 [Arabidopsis lyrata subsp. lyrata]

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 86/110 (78%), Positives = 97/110 (88%), Gaps = 3/110 (2%)

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

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGG 110

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

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 =  166 bits (421), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 95/109 (87%), Gaps = 2/109 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
            GLDASGRK +GKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY GGK
Sbjct: 60  NGLDASGRKPRGKGVYQYVDKYGANVDGYSPIYNADEWSPSGDVYAGGK 108

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115278|ref|XP_002332205.1| predicted protein [Populus trichocarpa] gi|222875312|gb|EEF12443.1| predicted protein [Populus trichocarpa]

 Score =  166 bits (419), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 84/110 (76%), Positives = 96/110 (87%), Gaps = 3/110 (2%)

Query: 2   AASVMASSLSLKPAPFTVEK-SAARGLPSLAK-TSFKIVA-KGGKIKTDKPYGVNGGMDL 58
            +SVMA S+SLKPAPFTV+K S+ RGLP+LA+ +SFK+ A +  K  TD+PYG+NGGMDL
Sbjct: 3   TSSVMAPSISLKPAPFTVKKPSSVRGLPTLARRSSFKVEASRTRKTNTDQPYGINGGMDL 62

Query: 59  REGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK 108
           REG+DASGRK KGKGVYQFVDKYGANVDGYSPIYN NDWSPSGDVY GGK
Sbjct: 63  REGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYNTNDWSPSGDVYVGGK 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460036|ref|XP_004147752.1| PREDICTED: photosystem II 10 kDa polypeptide, chloroplastic-like isoform 1 [Cucumis sativus] gi|449460038|ref|XP_004147753.1| PREDICTED: photosystem II 10 kDa polypeptide, chloroplastic-like isoform 2 [Cucumis sativus] gi|449502146|ref|XP_004161556.1| PREDICTED: photosystem II 10 kDa polypeptide, chloroplastic-like isoform 1 [Cucumis sativus] gi|449502150|ref|XP_004161557.1| PREDICTED: photosystem II 10 kDa polypeptide, chloroplastic-like isoform 2 [Cucumis sativus]

 Score =  166 bits (419), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 88/110 (80%), Positives = 98/110 (89%), Gaps = 5/110 (4%)

Query: 1   MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSF--KIVAKGGK-IKTDKPYGVNGGMD 57
           MAASVM +S+SLKPAPFTVEKSA+ GLPSLA+ SF  K+VA GGK IKTDKPYG+NG M+
Sbjct: 1   MAASVM-TSVSLKPAPFTVEKSAS-GLPSLARKSFSFKVVASGGKKIKTDKPYGINGSMN 58

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
           LR+GLDASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY GG
Sbjct: 59  LRDGLDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYVGG 108

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	108
TAIR|locus:2207320	140	PSBR "photosystem II subunit R	0.879	0.678	0.785	4.9e-37

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

 Score = 398 (145.2 bits), Expect = 4.9e-37, P = 4.9e-37
 Identities = 77/98 (78%), Positives = 86/98 (87%)

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

Query:    70 KGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGG 107
             KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY GG
Sbjct:    73 KGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKGG 110


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        0.310   0.135   0.399    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      108        96   0.00091  102 3  11 23  0.49    30
                                                     29  0.43    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:  100 KB (2072 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:  11.19u 0.13s 11.32t   Elapsed:  00:00:00
  Total cpu time:  11.19u 0.13s 11.32t   Elapsed:  00:00:00
  Start:  Fri May 10 09:00:13 2013   End:  Fri May 10 09:00:13 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	0.7272	0.9537	0.7573	N/A	no
P27202	PSBR_ARATH	No assigned EC number	0.7818	0.9907	0.7642	yes	no
P49108	PSBR_BRACM	No assigned EC number	0.7567	0.9907	0.7588	N/A	no
Q40163	PSBR_SOLLC	No assigned EC number	0.7181	0.9722	0.7608	N/A	no
P06183	PSBR_SOLTU	No assigned EC number	0.7272	0.9722	0.7608	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: grail3.0202001702 SubName- Full=Putative uncharacterized protein; (138 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	108
PLN00053	117	PLN00053, PLN00053, photosystem II subunit R; Prov	6e-43
pfam04725	99	pfam04725, PsbR, Photosystem II 10 kDa polypeptide	3e-34

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

 Score =  136 bits (343), Expect = 6e-43
 Identities = 64/88 (72%), Positives = 75/88 (85%), Gaps = 3/88 (3%)

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  YGANVDGYSPIYNENDWSPSGDVYTGGK 108
           YGANVDGYSPIY  ++WSPSGDVY GG 
Sbjct: 61  YGANVDGYSPIYTPDEWSPSGDVYVGGT 88

Length = 117

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

 Score =  113 bits (284), Expect = 3e-34
 Identities = 53/70 (75%), Positives = 60/70 (85%)

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

Query: 99  PSGDVYTGGK 108
           PSGDVY GG 
Sbjct: 61  PSGDVYVGGT 70

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	108
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	99.97

>PLN00053 photosystem II subunit R; Provisional

Probab=100.00  E-value=5.1e-51  Score=297.65  Aligned_cols=85  Identities=74%  Similarity=1.361  Sum_probs=82.7

Q ss_pred             ccCCCCCcc--ceEEEeecCc-eeeeccccccCCCcccCcccCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCC
Q 033939           24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS  100 (108)
Q Consensus        24 ~rglp~l~R--~s~~v~asgg-Kikt~kp~G~~ggm~~k~gvDasgRk~Kg~gVYqf~~kyGANVDgYSPIY~p~ews~~  100 (108)
                      +||||+++|  ++|+|+||++ ||||++|||++|+|++|+|+||+|||+||||||||+||||||||||||||+||||||+
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 8999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccCCC
Q 033939          101 GDVYTGGK  108 (108)
Q Consensus       101 GD~Y~ggt  108 (108)
                      ||+|+|||
T Consensus        81 Gd~Y~ggt   88 (117)
T PLN00053         81 GDVYVGGT   88 (117)
T ss_pred             CCeeeCCh
Confidence            99999996

>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=1.4e-44  Score=258.07  Aligned_cols=69  Identities=80%  Similarity=1.438  Sum_probs=67.0

Q ss_pred             cCc-eeeeccccccCCCcccCcccCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCCCCcccCCC
Q 033939           40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGGK  108 (108)
Q Consensus        40 sgg-Kikt~kp~G~~ggm~~k~gvDasgRk~Kg~gVYqf~~kyGANVDgYSPIY~p~ews~~GD~Y~ggt  108 (108)
                      |++ ||||++|+|++|+|++|+|+||+|||+||+|||||+||||||||||||||+||||||+||+|+|||
T Consensus         1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gGt   70 (99)
T PF04725_consen    1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGGT   70 (99)
T ss_pred             CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCCh
Confidence            455 999999999999999999999999999999999999999999999999999999999999999986

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=99.97  E-value=1.1e-32  Score=197.33  Aligned_cols=70  Identities=33%  Similarity=0.568  Sum_probs=65.5

Q ss_pred             eecCceeeeccccccCCCcccCc----ccCCCCCCccCCeeEEeccccc-cCCCCccccccCCCCCCCCCcccCC
Q 033939           38 VAKGGKIKTDKPYGVNGGMDLRE----GLDASGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGG  107 (108)
Q Consensus        38 ~asggKikt~kp~G~~ggm~~k~----gvDasgRk~Kg~gVYqf~~kyG-ANVDgYSPIY~p~ews~~GD~Y~gg  107 (108)
                      .+|.|+.+.+|.-+.+.++.+|+    |..++||++||+|||||+|||| ||||||||||+||||+|+||+|+||
T Consensus         2 ~nssgpkrgtk~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~Gg   76 (101)
T PLN00083          2 ANSSGPKRGTKAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEGD   76 (101)
T ss_pred             CCCCCCCCccccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhcc
Confidence            35677888889999999999998    8889999999999999999999 9999999999999999999999986

---

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