Citrus Sinensis ID: 033928

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------11
Protein Sequence
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
Secondary Structure (PSIPRED)
ccHHHHHHccccccccccHHccccccccccccccEEEEEEccEEEEccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccEEEccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccccccccccccEEEEEcccEEEcccccccccccccccccccccccccccEEEEEEcccccccccccccccHccccccccEEEEcc
Coil and Loop (DISEMBL)
MAASVMAsslslkpapftveksaarglpslakTSFKIVAkggkiktdkpygvnggmdlregldasgrkakgkGVYQFVDkyganvdgyspiynendwspsgdvytgvl
Flexible Loop (DISEMBL)
maasvmasslslkpapftVEKSaarglpslaktsfkivakggkiktdkpygvnggMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSpiynendwspsgdvytgvl
Low Complexity Region (SEG)
maasvmasslslKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
Disordered region (IsUnstruct)
*********************************SFKIVAKGGKIK****YGV******************GKGVYQFVDKYGANVDGYSPIYNENDW***********
Disordered Region (DISOPRED)
******************************************************G*****************GVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
Disordered Region (DISEMBL)
**********SLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
Disordered Region (DISPRO)
********************************TSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
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)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGVL
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	108	2.2.26 [Sep-21-2011]
P27202	140	Photosystem II 10 kDa pol	yes	no	0.981	0.757	0.779	4e-41
P49108	141	Photosystem II 10 kDa pol	N/A	no	0.981	0.751	0.754	5e-40
Q40519	136	Photosystem II 10 kDa pol	N/A	no	0.944	0.75	0.724	1e-38
P06183	138	Photosystem II 10 kDa pol	N/A	no	0.962	0.753	0.724	3e-37
Q40163	138	Photosystem II 10 kDa pol	N/A	no	0.962	0.753	0.715	3e-36
P10690	140	Photosystem II 10 kDa pol	N/A	no	0.972	0.75	0.681	2e-33
Q40070	138	Photosystem II 10 kDa pol	N/A	no	0.962	0.753	0.596	3e-26

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

 Score =  166 bits (420), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 85/109 (77%), Positives = 96/109 (88%), Gaps = 3/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY G
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKG 109

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 =  162 bits (410), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 83/110 (75%), Positives = 95/110 (86%), Gaps = 4/110 (3%)

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

Query: 57  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           DLR+G+DASGRK KG GVY+FVDKYGANVDGYSPIYNE++WS SGDVY G
Sbjct: 61  DLRDGVDASGRKGKGYGVYKFVDKYGANVDGYSPIYNEDEWSASGDVYKG 110

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 =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 79/109 (72%), Positives = 93/109 (85%), Gaps = 7/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KGKGVYQFVDKYGANVDGYSPIYN +DWSPSGDVY G
Sbjct: 57  LRDGVDASGRKQKGKGVYQFVDKYGANVDGYSPIYNTDDWSPSGDVYVG 105

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 =  153 bits (386), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 79/109 (72%), Positives = 95/109 (87%), Gaps = 5/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY G
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVG 107

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 =  150 bits (378), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 78/109 (71%), Positives = 93/109 (85%), Gaps = 5/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY G
Sbjct: 59  LRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVG 107

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 =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 75/110 (68%), Positives = 89/110 (80%), Gaps = 5/110 (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  DLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
            LR+G+D+SGRK  GKGVYQFVDKYGANVDGYSPIYNE +W+P+GDVY G
Sbjct: 60  KLRDGVDSSGRKPTGKGVYQFVDKYGANVDGYSPIYNEEEWAPTGDVYAG 109

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 =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 65/109 (59%), Positives = 80/109 (73%), Gaps = 5/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
            +EG+DASGR AKGKGVYQF DKYGANVDGYSPIY   +WSPSGDVY G
Sbjct: 59  FKEGVDASGRVAKGKGVYQFADKYGANVDGYSPIYTPEEWSPSGDVYVG 107

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
351722140	139	uncharacterized protein LOC100499745 [Gl	0.972	0.755	0.779	2e-40
118489740	136	unknown [Populus trichocarpa x Populus d	0.972	0.772	0.773	3e-40
351722402	138	uncharacterized protein LOC100305752 [Gl	0.972	0.760	0.768	3e-40
15219268	140	photosystem II subunit R [Arabidopsis th	0.981	0.757	0.779	2e-39
118488826	137	unknown [Populus trichocarpa x Populus d	0.972	0.766	0.785	2e-39
297839767	133	hypothetical protein ARALYDRAFT_477073 [	0.981	0.796	0.779	3e-39
224115282	137	hypothetical protein POPTRDRAFT_674736 [	0.972	0.766	0.766	6e-39
449460036	138	PREDICTED: photosystem II 10 kDa polypep	0.962	0.753	0.798	7e-39
224115372	137	hypothetical protein POPTRDRAFT_569170 [	0.972	0.766	0.766	1e-38
224115278	141	predicted protein [Populus trichocarpa]	0.962	0.737	0.766	2e-38

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

 Score =  169 bits (428), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 85/109 (77%), Positives = 98/109 (89%), Gaps = 4/109 (3%)

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

Query: 58  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LREG+DASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY G
Sbjct: 60  LREGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYAG 108

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  168 bits (426), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 82/106 (77%), Positives = 94/106 (88%), Gaps = 1/106 (0%)

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

Query: 61  GLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY G
Sbjct: 60  GLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAG 105

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  168 bits (426), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/108 (76%), Positives = 96/108 (88%), Gaps = 3/108 (2%)

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

Query: 59  REGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           R+G DASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY G
Sbjct: 60  RDGTDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYAG 107

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 85/109 (77%), Positives = 96/109 (88%), Gaps = 3/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY G
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKG 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

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 =  166 bits (420), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 84/107 (78%), Positives = 94/107 (87%), Gaps = 2/107 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY G
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYAG 106

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

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 =  165 bits (418), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 85/109 (77%), Positives = 96/109 (88%), Gaps = 3/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+G+DASGRK KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY G
Sbjct: 61  LRDGVDASGRKGKGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKG 109

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

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 =  164 bits (415), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 82/107 (76%), Positives = 94/107 (87%), Gaps = 2/107 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           +GLDASGRK KGKGVYQ+VDKYGANVDGYSPIYN ++WSP+GDVY G
Sbjct: 60  DGLDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPTGDVYAG 106

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 =  164 bits (415), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 87/109 (79%), Positives = 97/109 (88%), Gaps = 5/109 (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  LREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           LR+GLDASGRK KGKGVYQFVDKYGANVDGYSPIY+  DWSP+GDVY G
Sbjct: 59  LRDGLDASGRKGKGKGVYQFVDKYGANVDGYSPIYDTKDWSPTGDVYVG 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  163 bits (412), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 82/107 (76%), Positives = 93/107 (86%), Gaps = 2/107 (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  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
            GLDASGRK +GKGVYQ+VDKYGANVDGYSPIYN ++WSPSGDVY G
Sbjct: 60  NGLDASGRKPRGKGVYQYVDKYGANVDGYSPIYNADEWSPSGDVYAG 106

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 =  162 bits (411), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 82/107 (76%), Positives = 94/107 (87%), Gaps = 3/107 (2%)

Query: 3   ASVMASSLSLKPAPFTVEK-SAARGLPSLAK-TSFKIVA-KGGKIKTDKPYGVNGGMDLR 59
           +SVMA S+SLKPAPFTV+K S+ RGLP+LA+ +SFK+ A +  K  TD+PYG+NGGMDLR
Sbjct: 4   SSVMAPSISLKPAPFTVKKPSSVRGLPTLARRSSFKVEASRTRKTNTDQPYGINGGMDLR 63

Query: 60  EGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
           EG+DASGRK KGKGVYQFVDKYGANVDGYSPIYN NDWSPSGDVY G
Sbjct: 64  EGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYNTNDWSPSGDVYVG 110

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	108
TAIR|locus:2207320	140	PSBR "photosystem II subunit R	0.870	0.671	0.783	2.1e-36

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

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 76/97 (78%), Positives = 85/97 (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 KGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTG 106
             KG GVY++VDKYGANVDGYSPIYNEN+WS SGDVY G
Sbjct:    73 KGYGVYKYVDKYGANVDGYSPIYNENEWSASGDVYKG 109


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   0.135   0.400    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  0.48    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:  480 (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:  10.90u 0.09s 10.99t   Elapsed:  00:00:02
  Total cpu time:  10.90u 0.09s 10.99t   Elapsed:  00:00:02
  Start:  Fri May 10 08:39:31 2013   End:  Fri May 10 08:39:33 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	0.7247	0.9444	0.75	N/A	no
P27202	PSBR_ARATH	No assigned EC number	0.7798	0.9814	0.7571	yes	no
P49108	PSBR_BRACM	No assigned EC number	0.7545	0.9814	0.7517	N/A	no
Q40163	PSBR_SOLLC	No assigned EC number	0.7155	0.9629	0.7536	N/A	no
P06183	PSBR_SOLTU	No assigned EC number	0.7247	0.9629	0.7536	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	108
PLN00053	117	PLN00053, PLN00053, photosystem II subunit R; Prov	2e-42
pfam04725	99	pfam04725, PsbR, Photosystem II 10 kDa polypeptide	6e-34

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

 Score =  134 bits (339), Expect = 2e-42
 Identities = 63/86 (73%), Positives = 74/86 (86%), Gaps = 3/86 (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  YGANVDGYSPIYNENDWSPSGDVYTG 106
           YGANVDGYSPIY  ++WSPSGDVY G
Sbjct: 61  YGANVDGYSPIYTPDEWSPSGDVYVG 86

Length = 117

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

 Score =  112 bits (282), Expect = 6e-34
 Identities = 52/68 (76%), Positives = 59/68 (86%)

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

Query: 99  PSGDVYTG 106
           PSGDVY G
Sbjct: 61  PSGDVYVG 68

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=2.7e-50  Score=293.82  Aligned_cols=84  Identities=74%  Similarity=1.338  Sum_probs=81.8

Q ss_pred             ccCCCCCcc--ceeEEeecCc-eeeeccccccCCCcccCcCcCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCC
Q 033928           24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPS  100 (108)
Q Consensus        24 ~~glp~l~R--~s~~v~asgg-Kikt~kp~G~~ggm~~k~gvDasGRk~KgkgVYqf~~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             CCeeccC
Q 033928          101 GDVYTGV  107 (108)
Q Consensus       101 GD~Y~G~  107 (108)
                      ||+|+|+
T Consensus        81 Gd~Y~gg   87 (117)
T PLN00053         81 GDVYVGG   87 (117)
T ss_pred             CCeeeCC
Confidence            9999996

>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=8.9e-44  Score=253.90  Aligned_cols=68  Identities=79%  Similarity=1.411  Sum_probs=65.9

Q ss_pred             cCc-eeeeccccccCCCcccCcCcCCCCCCccCCeeEEeccccccCCCCccccccCCCCCCCCCeeccC
Q 033928           40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKGKGVYQFVDKYGANVDGYSPIYNENDWSPSGDVYTGV  107 (108)
Q Consensus        40 sgg-Kikt~kp~G~~ggm~~k~gvDasGRk~KgkgVYqf~~KyGANVDgYSPIY~p~eWs~~GD~Y~G~  107 (108)
                      |++ ||||++|+|++|+|++|+|+||+|||+||+|||||+||||||||||||||+||||||+||+|+|+
T Consensus         1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANVDgYSPIY~p~~Ws~~GD~Y~gG   69 (99)
T PF04725_consen    1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANVDGYSPIYTPDEWSPSGDVYVGG   69 (99)
T ss_pred             CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccccccCCCcChhhcCCCCCeecCC
Confidence            455 99999999999999999999999999999999999999999999999999999999999999996

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=2.7e-33  Score=200.48  Aligned_cols=71  Identities=34%  Similarity=0.565  Sum_probs=66.1

Q ss_pred             eecCceeeeccccccCCCcccCc----CcCCCCCCccCCeeEEeccccc-cCCCCccccccCCCCCCCCCeeccCC
Q 033928           38 VAKGGKIKTDKPYGVNGGMDLRE----GLDASGRKAKGKGVYQFVDKYG-ANVDGYSPIYNENDWSPSGDVYTGVL  108 (108)
Q Consensus        38 ~asggKikt~kp~G~~ggm~~k~----gvDasGRk~KgkgVYqf~~KyG-ANVDgYSPIY~p~eWs~~GD~Y~G~l  108 (108)
                      .+|.|+.+.+|.-+.+.++.+|+    |..++|||+||+|||||+|||| ||||||||||+||||+|+||+|+|+|
T Consensus         2 ~nssgpkrgtk~a~~q~~vgykgst~agsapkgRk~Kg~gVYqf~~KyGkANVDgYSPIY~p~eWs~sGD~Y~GgL   77 (101)
T PLN00083          2 ANSSGPKRGTKAAGGQAGVGYKGSTEAGSAPKTRSGKAGYVYKLGLRNGKANVDEYSPIYTPQEFKTDGDKYEGDL   77 (101)
T ss_pred             CCCCCCCCccccCccccccccccccccCCCCCCccCCCceEEEehhccCcccccccCCccChhhcCCCcchhhccH
Confidence            35677888889999999999998    8889999999999999999999 99999999999999999999999975

---

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