Citrus Sinensis ID: 034359

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
Secondary Structure (PSIPRED)
ccccccccccccccccccEEccccccccccccccEEEEEcccEEEEccccccccccccccccccccccEEEEEEEccccccccEEEEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHccccccccccccccccccccccccEEEEEcccEEEcccccccccccEccccccccccccEEEEEEccccccccEEEEEEcccccccc
Coil and Loop (DISEMBL)
MAASVMAsslslkpapftveksaarglpslakTSFKIVAkggkiktdkpygvnggmdlreglDASGRKAKYKFlnqqplnsgelFVYIFgerclpic
Flexible Loop (DISEMBL)
maasvmasslslkpapftVEKSaarglpslaktsfkivakggkiktdkpygvnggMDLREGLDASGRKAKYKflnqqplnsgelFVYIFGERCLPIC
Low Complexity Region (SEG)
maasvmasslslKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
Disordered region (IsUnstruct)
*********************************SFKIVAKGGKIKT**PYGVNG**************AKYKFLNQQPLNSGELFVYIFGERCLPI*
Disordered Region (DISOPRED)
*************************************************YGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
Disordered Region (DISEMBL)
**********SLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
Disordered Region (DISPRO)
****************************SLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAASVMASSLSLKPAPFTVEKSAARGLPSLAKTSFKIVAKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELFVYIFGERCLPIC
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	97	2.2.26 [Sep-21-2011]
P27202	140	Photosystem II 10 kDa pol	yes	no	0.824	0.571	0.666	1e-22
P49108	141	Photosystem II 10 kDa pol	N/A	no	0.824	0.567	0.647	5e-22
Q40519	136	Photosystem II 10 kDa pol	N/A	no	0.783	0.558	0.563	7e-18
P06183	138	Photosystem II 10 kDa pol	N/A	no	0.804	0.565	0.574	4e-17
Q40163	138	Photosystem II 10 kDa pol	N/A	no	0.804	0.565	0.563	4e-16
P10690	140	Photosystem II 10 kDa pol	N/A	no	0.814	0.564	0.534	2e-13
Q40070	138	Photosystem II 10 kDa pol	N/A	no	0.762	0.536	0.468	2e-06

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

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 58/87 (66%), Positives = 70/87 (80%), Gaps = 7/87 (8%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    YK++++   N
Sbjct: 61 LRDGVDASGRKGKGYGVYKYVDKYGAN 87

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 =  103 bits (256), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 57/88 (64%), Positives = 69/88 (78%), Gaps = 8/88 (9%)

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

Query: 57 DLREGLDASGRKAK----YKFLNQQPLN 80
          DLR+G+DASGRK K    YKF+++   N
Sbjct: 61 DLRDGVDASGRKGKGYGVYKFVDKYGAN 88

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 = 89.4 bits (220), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 49/87 (56%), Positives = 66/87 (75%), Gaps = 11/87 (12%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    Y+F+++   N
Sbjct: 57 LRDGVDASGRKQKGKGVYQFVDKYGAN 83

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 = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 50/87 (57%), Positives = 68/87 (78%), Gaps = 9/87 (10%)

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 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    Y+++++   N
Sbjct: 59 LRDGVDASGRKPKGKGVYQYVDKYGAN 85

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 = 83.2 bits (204), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 49/87 (56%), Positives = 66/87 (75%), Gaps = 9/87 (10%)

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 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    Y+++++   N
Sbjct: 59 LRDGVDASGRKPKGKGVYQYVDKYGAN 85

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 = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 47/88 (53%), Positives = 62/88 (70%), Gaps = 9/88 (10%)

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 DLREGLDASGR----KAKYKFLNQQPLN 80
           LR+G+D+SGR    K  Y+F+++   N
Sbjct: 60 KLRDGVDSSGRKPTGKGVYQFVDKYGAN 87

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 = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/79 (46%), Positives = 52/79 (65%), Gaps = 5/79 (6%)

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 LREGLDASGRKAKYKFLNQ 76
           +EG+DASGR AK K + Q
Sbjct: 59 FKEGVDASGRVAKGKGVYQ 77

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	97
351722140	139	uncharacterized protein LOC100499745 [Gl	0.814	0.568	0.655	3e-21
15219268	140	photosystem II subunit R [Arabidopsis th	0.824	0.571	0.666	4e-21
351722402	138	uncharacterized protein LOC100305752 [Gl	0.814	0.572	0.639	5e-21
297839767	133	hypothetical protein ARALYDRAFT_477073 [	0.824	0.601	0.666	6e-21
118489740	136	unknown [Populus trichocarpa x Populus d	0.814	0.580	0.642	2e-20
1346871	141	RecName: Full=Photosystem II 10 kDa poly	0.824	0.567	0.647	2e-20
119720780	140	photosystem II 10kDa polytpeptide [Brass	0.824	0.571	0.655	3e-20
193872616	146	ST244 [Eutrema halophilum]	0.824	0.547	0.647	4e-20
227204419	77	AT1G79040 [Arabidopsis thaliana]	0.731	0.922	0.743	5e-20
8698891	82	polypeptide precursor of photosystem II	0.773	0.914	0.646	6e-20

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

 Score =  105 bits (262), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 57/87 (65%), Positives = 72/87 (82%), Gaps = 8/87 (9%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LREG+DASGRK K    Y+F+++   N
Sbjct: 60 LREGVDASGRKGKGKGVYQFVDKYGAN 86

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 =  105 bits (261), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 58/87 (66%), Positives = 70/87 (80%), Gaps = 7/87 (8%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    YK++++   N
Sbjct: 61 LRDGVDASGRKGKGYGVYKYVDKYGAN 87

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 55/86 (63%), Positives = 70/86 (81%), Gaps = 7/86 (8%)

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

Query: 59 REGLDASGRKAK----YKFLNQQPLN 80
          R+G DASGRK K    Y+F+++   N
Sbjct: 60 RDGTDASGRKGKGKGVYQFVDKYGAN 85

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  104 bits (260), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 58/87 (66%), Positives = 70/87 (80%), Gaps = 7/87 (8%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+G+DASGRK K    YK++++   N
Sbjct: 61 LRDGVDASGRKGKGYGVYKYVDKYGAN 87

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 54/84 (64%), Positives = 67/84 (79%), Gaps = 5/84 (5%)

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

Query: 61 GLDASGRKAK----YKFLNQQPLN 80
          GLDASGRK K    Y+++++   N
Sbjct: 60 GLDASGRKPKGKGVYQYVDKYGAN 83

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 =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 57/88 (64%), Positives = 69/88 (78%), Gaps = 8/88 (9%)

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

Query: 57 DLREGLDASGRKAK----YKFLNQQPLN 80
          DLR+G+DASGRK K    YKF+++   N
Sbjct: 61 DLRDGVDASGRKGKGYGVYKFVDKYGAN 88

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 =  102 bits (253), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 57/87 (65%), Positives = 68/87 (78%), Gaps = 7/87 (8%)

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

Query: 58 LREGLDASGRKAK----YKFLNQQPLN 80
          LR+GLDASGRK K    YKF+++   N
Sbjct: 61 LRDGLDASGRKGKGYGVYKFVDKYGAN 87

Source: Brassica rapa

Species: Brassica rapa

Genus: Brassica

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|193872616|gb|ACF23036.1| ST244 [Eutrema halophilum]

 Score =  102 bits (253), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 57/88 (64%), Positives = 69/88 (78%), Gaps = 8/88 (9%)

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

Query: 57 DLREGLDASGRKAK----YKFLNQQPLN 80
          DLR+G+DASGRK K    YKF+++   N
Sbjct: 61 DLRDGVDASGRKGKGYGVYKFVDKYGAN 88

Source: Eutrema halophilum

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|227204419|dbj|BAH57061.1| AT1G79040 [Arabidopsis thaliana]

 Score =  101 bits (252), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 55/74 (74%), Positives = 63/74 (85%), Gaps = 3/74 (4%)

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

Query: 58 LREGLDASGRKAKY 71
          LR+G+DASGRK K 
Sbjct: 61 LRDGVDASGRKGKV 74

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8698891|gb|AAF78511.1|AF195209_1 polypeptide precursor of photosystem II [Pyrus pyrifolia]

 Score =  101 bits (251), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 53/82 (64%), Positives = 67/82 (81%), Gaps = 7/82 (8%)

Query: 1  MAASVMASSLSLKPAPFTVEKSAARGLPSLAKT--SFKIVAKGG-KIKTDKPYGVNGGMD 57
          MAASVM SS+SLKP+PFTV+K A RGLPSL+++  SFK+ A GG KI+T  PYG+NGGMD
Sbjct: 1  MAASVMTSSVSLKPSPFTVDKPAVRGLPSLSRSSASFKVQASGGKKIRTATPYGINGGMD 60

Query: 58 LREGLDASGRKAK----YKFLN 75
          LR+G+DASGRK K    Y+F++
Sbjct: 61 LRDGVDASGRKGKGKGVYQFVD 82

Source: Pyrus pyrifolia

Species: Pyrus pyrifolia

Genus: Pyrus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	97
TAIR|locus:2207320	140	PSBR "photosystem II subunit R	0.701	0.485	0.653	1.4e-18

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

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 49/75 (65%), Positives = 59/75 (78%)

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

Query:    70 K----YKFLNQQPLN 80
             K    YK++++   N
Sbjct:    73 KGYGVYKYVDKYGAN 87


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        0.318   0.139   0.412    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       97        85   0.00091  102 3  11 22  0.48    29
                                                     29  0.46    30


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:  474 (50 KB)
  Total size of DFA:  86 KB (2066 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:  9.88u 0.10s 9.98t   Elapsed:  00:00:01
  Total cpu time:  9.88u 0.10s 9.98t   Elapsed:  00:00:01
  Start:  Fri May 10 22:08:29 2013   End:  Fri May 10 22:08:30 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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	97
PLN00053	117	PLN00053, PLN00053, photosystem II subunit R; Prov	1e-16
pfam04725	99	pfam04725, PsbR, Photosystem II 10 kDa polypeptide	8e-11

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

 Score = 68.6 bits (168), Expect = 1e-16
 Identities = 34/60 (56%), Positives = 47/60 (78%), Gaps = 7/60 (11%)

Query: 24 ARGLPSLAKT--SFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAK----YKFLNQ 76
           RGLP L++T  SFK+ A GG KIKTD+PYG +GGM+L++G+DASGRK K    Y+F+++
Sbjct: 1  VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDK 60

Length = 117

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

 Score = 53.3 bits (128), Expect = 8e-11
 Identities = 22/34 (64%), Positives = 27/34 (79%)

Query: 39 AKGGKIKTDKPYGVNGGMDLREGLDASGRKAKYK 72
          + G K+KTDKPYG+ GGM L+ G+DASGRK K K
Sbjct: 1  SGGKKVKTDKPYGIGGGMALKNGVDASGRKGKGK 34

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	97
PLN00053	117	photosystem II subunit R; Provisional	100.0
PF04725	99	PsbR: Photosystem II 10 kDa polypeptide PsbR; Inte	99.91
PLN00083	101	photosystem II subunit R; Provisional	98.75

>PLN00053 photosystem II subunit R; Provisional

Probab=100.00  E-value=7.4e-34  Score=204.53  Aligned_cols=62  Identities=55%  Similarity=0.853  Sum_probs=59.9

Q ss_pred             ccCCCCCcc--ceeEEEEcCe-eeeeecccccCCCcccCCCcCcCCCcccceeeEecccccCcee
Q 034359           24 ARGLPSLAK--TSFKIVAKGG-KIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELF   85 (97)
Q Consensus        24 vrgLpslaR--ssf~VvAsg~-KIkt~kP~G~~ggm~~k~gvDAsGRk~KGkGVYqf~dKYGan~   85 (97)
                      +||||+++|  ++|+|+||++ ||||++|||++|+|++|+||||||||+||||||||+||||||.
T Consensus         1 ~~glp~l~r~~ss~~v~as~~kkikt~~p~G~~G~m~~k~gvDasGRk~kGkGVYqFvdKYGANV   65 (117)
T PLN00053          1 VRGLPPLSRTARSFKVTASGGKKIKTDQPYGPSGGMNLKDGVDASGRKGKGKGVYQFVDKYGANV   65 (117)
T ss_pred             CCccCcccccccceEEEecCCceeeecCCcccCCCcccccccCCCCccCCCcceEEehhhcCccc
Confidence            589999999  6899999988 9999999999999999999999999999999999999999996

>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=99.91  E-value=7.6e-26  Score=159.47  Aligned_cols=46  Identities=57%  Similarity=0.792  Sum_probs=44.2

Q ss_pred             cCe-eeeeecccccCCCcccCCCcCcCCCcccceeeEecccccCcee
Q 034359           40 KGG-KIKTDKPYGVNGGMDLREGLDASGRKAKYKFLNQQPLNSGELF   85 (97)
Q Consensus        40 sg~-KIkt~kP~G~~ggm~~k~gvDAsGRk~KGkGVYqf~dKYGan~   85 (97)
                      |++ |||||+|||++|+|++|+|+||||||+||||||||+||||||.
T Consensus         1 Sg~KKIkt~~p~G~~g~m~~k~gvDa~gRkgKg~gVYqf~~KyGANV   47 (99)
T PF04725_consen    1 SGGKKIKTDKPYGPSGGMTLKDGVDASGRKGKGKGVYQFVDKYGANV   47 (99)
T ss_pred             CCCccccccCCccCCCCccccCCccCCCCCCCCceeEEehhhcCccc
Confidence            455 9999999999999999999999999999999999999999996

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=98.75  E-value=3.6e-09  Score=75.31  Aligned_cols=25  Identities=20%  Similarity=0.287  Sum_probs=23.1

Q ss_pred             CcCcCCCcccceeeEecccccC-cee
Q 034359           61 GLDASGRKAKYKFLNQQPLNSG-ELF   85 (97)
Q Consensus        61 gvDAsGRk~KGkGVYqf~dKYG-an~   85 (97)
                      |--++|||+||||||||+|||| ||.
T Consensus        29 gsapkgRk~Kg~gVYqf~~KyGkANV   54 (101)
T PLN00083         29 GSAPKTRSGKAGYVYKLGLRNGKANV   54 (101)
T ss_pred             CCCCCCccCCCceEEEehhccCcccc
Confidence            6667999999999999999999 986

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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

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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