Citrus Sinensis ID: 029024

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
Protein Sequence
MAAAMATTAVLNAKCFSISSPKSSIKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE
Secondary Structure (PSIPRED)
cHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHccccccccccccccccccccccHccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHEHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MAAAMATTAVLNAKcfsisspkssikpgttkptsplsmqnlpkgltvsskptdssslaAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLgglaatglmsmpphasaAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE
Flexible Loop (DISEMBL)
MAAAMATTAVLNakcfsisspkssikpgttkptsplsmqnlPKGLTVSSKPTDSSSLAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQpalnqinrmrse
Low Complexity Region (SEG)
maaamattaVLNAKCFsisspkssikpgttkptspLSMQNLPKGLTVSSKPTDSSSLAAGTAIAGAIFSTLSSCDaafaaqqiaeiaeGDNRGlalllpiipaiaWVLFNILQPALNQINRMRSTKGVIIglglgglaatglMSMPPHasaaasevatiaeaasDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE
Disordered region (IsUnstruct)
**********L***C*******************************************AGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLM***********************RGQLLLIVVTPAILWVLYNILQPALN********
Disordered Region (DISOPRED)
***A*ATTAVLNA************************************************AIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPAL***************LGLGGLAATGLMS***************AEAASDSRGQLLLIVVTPAILWVLYNILQPALN*I******
Disordered Region (DISEMBL)
********AVLNAKCFSISSP*************PLSMQNLPKG************LAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMP*************AEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE
Disordered Region (DISPRO)
MAAAMAT*AVLNAKCFSIS***************PLSM*NLPKGLTVSS*PTDSSSLAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRS*
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAAMATTAVLNAKCFSISSPKSSIKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE
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	200	2.2.26 [Sep-21-2011]
P80470	199	Photosystem II core compl	N/A	no	0.915	0.919	0.568	4e-50
O49347	189	Photosystem II core compl	yes	no	0.81	0.857	0.577	3e-38

>sp|P80470|PSBY_SPIOL Photosystem II core complex proteins psbY, chloroplastic OS=Spinacia oleracea GN=PSBY PE=1 SV=2

 Score =  197 bits (500), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 112/197 (56%), Positives = 141/197 (71%), Gaps = 14/197 (7%)

Query: 10  VLNAKCFSISSPKSSIKPGTTKPTS-PLSMQNLPKGLTVSSKPTDSSSLAAGTAIAGAIF 68
           VLN KC ++++ K++    + KPTS P+S+   P GL+ S  P   S +    AIAGA+F
Sbjct: 11  VLNTKCLTLNTNKTTST--SPKPTSKPISLS--PLGLSNSKLPMGLSPIITAPAIAGAVF 66

Query: 69  STLSSCDAAFAAQQIAEIA----EGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRS 124
           +TL S D AFA QQ+A+IA      DNRGLALLLPIIPA+ WVLFNILQPALNQIN+MR+
Sbjct: 67  ATLGSVDPAFAVQQLADIAAEAGTSDNRGLALLLPIIPALGWVLFNILQPALNQINKMRN 126

Query: 125 -TKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
             K  I+GLGL GLA +GL+   P A AA+ E+A      SD+RG LLL+VV PAI WVL
Sbjct: 127 EKKAFIVGLGLSGLATSGLLLATPEAQAASEEIAR----GSDNRGTLLLLVVLPAIGWVL 182

Query: 184 YNILQPALNQINRMRSE 200
           +NILQPALNQ+N+MRS+
Sbjct: 183 FNILQPALNQLNKMRSQ 199

PSBY-1 and -2 are manganese-binding polypeptides with L-arginine metabolizing enzyme activity. They are a component of the core of photosystem II. They have also a minor catalase-like activity since they cause evolution of oxygen from hydrogen peroxide in a reaction stimulated by manganese.
Spinacia oleracea (taxid: 3562)

>sp|O49347|PSBY_ARATH Photosystem II core complex proteins psbY, chloroplastic OS=Arabidopsis thaliana GN=PSBY PE=2 SV=1

 Score =  157 bits (398), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 101/175 (57%), Positives = 126/175 (72%), Gaps = 13/175 (7%)

Query: 34  SPLSMQNLPKG---LTVSSKPTDSSSLAA-GTAIAGAIFSTLSSCDAAFAAQQIAEIA-- 87
           SP  +QN  K    +++ + P  + SLA   TA+AGA+FS+LS  + A A QQIA++A  
Sbjct: 17  SPPKLQNQTKSKPFISLPTPPKPNVSLAVTSTALAGAVFSSLSYSEPALAIQQIAQLAAA 76

Query: 88  --EGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTK-GVIIGLGLGGLAATGLMS 144
               DNRGLALLLPI+PAIAWVL+NILQPA+NQ+N+MR +K  V+     GGLAA+GL++
Sbjct: 77  NASSDNRGLALLLPIVPAIAWVLYNILQPAINQVNKMRESKGIVVGLGIGGGLAASGLLT 136

Query: 145 MPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRS 199
                   A   A  A A+SDSRGQLLLIVVTPA+LWVLYNILQPALNQIN+MRS
Sbjct: 137 ----PPPEAYAAAEAAAASSDSRGQLLLIVVTPALLWVLYNILQPALNQINKMRS 187

PSBY-1 and -2 are manganese-binding polypeptides with L-arginine metabolizing enzyme activity. They are a component of the core of photosystem II.

Arabidopsis thaliana (taxid: 3702)

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	200
225424556	201	PREDICTED: photosystem II core complex p	0.985	0.980	0.769	4e-71
118488993	196	unknown [Populus trichocarpa x Populus d	0.975	0.994	0.766	6e-71
118489498	196	unknown [Populus trichocarpa x Populus d	0.975	0.994	0.761	2e-70
255547954	195	photosystem II core complex proteins psb	0.97	0.994	0.776	2e-70
224110818	196	hypothetical protein POPTRDRAFT_726168 [	0.97	0.989	0.782	1e-64
224102363	192	predicted protein [Populus trichocarpa]	0.94	0.979	0.775	2e-62
118489582	192	unknown [Populus trichocarpa x Populus d	0.94	0.979	0.775	2e-62
118489584	192	unknown [Populus trichocarpa x Populus d	0.94	0.979	0.755	3e-59
356540203	197	PREDICTED: photosystem II core complex p	0.955	0.969	0.660	7e-57
359806150	187	uncharacterized protein LOC100779397 [Gl	0.935	1.0	0.64	2e-51

>gi|225424556|ref|XP_002285325.1| PREDICTED: photosystem II core complex proteins psbY, chloroplastic-like [Vitis vinifera]

 Score =  273 bits (697), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 157/204 (76%), Positives = 177/204 (86%), Gaps = 7/204 (3%)

Query: 1   MAAAMATTAVLNAKCFSISSPKS-SIKPGTTKPTSPLSMQNLPKGLTV--SSKPTDSSSL 57
           MAA +AT A+LNAKC SI+SPK+ ++   T KP S LS+QNLPKGLT   SS+  + S+ 
Sbjct: 1   MAATIATMAMLNAKCLSINSPKNLNLSKPTAKPISLLSIQNLPKGLTTLKSSENQNLSTS 60

Query: 58  AAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALN 117
            AGTAIAGAIFSTLSSCD A AAQQIAEIA+GDNRGLALLLPIIPAIAWVLFNILQPALN
Sbjct: 61  LAGTAIAGAIFSTLSSCDPALAAQQIAEIADGDNRGLALLLPIIPAIAWVLFNILQPALN 120

Query: 118 QINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAA-SDSRGQLLLIVVT 176
           Q+N+MRSTKGVIIGLGLGGLAA+G M + PHAS  ASE+AT+A+AA SD+RGQLLL VVT
Sbjct: 121 QLNKMRSTKGVIIGLGLGGLAASGFM-LTPHAS--ASEIATLADAASSDNRGQLLLFVVT 177

Query: 177 PAILWVLYNILQPALNQINRMRSE 200
           PAILWVLYNILQPALNQ+NRMRSE
Sbjct: 178 PAILWVLYNILQPALNQLNRMRSE 201

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488993|gb|ABK96304.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 154/201 (76%), Positives = 173/201 (86%), Gaps = 6/201 (2%)

Query: 1   MAAAMATTAVLNAKCFSISSPKSSIKPG-TTKPTSPLSMQNLPKGLTVSSKPTDSSSLAA 59
           MAA MAT A+LNAKC SI+S K+   P  +TKP S LSM NLPKGLT+S KP D++ L  
Sbjct: 1   MAATMATMAILNAKCLSINSIKNISPPKPSTKPVSLLSMLNLPKGLTIS-KPADNTVLT- 58

Query: 60  GTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQI 119
           GTAIAGAIF+TLSSC+ AFAAQQIAEIAEGDNRG+ALLLP+IPAIAWVLFNILQPALNQI
Sbjct: 59  GTAIAGAIFTTLSSCEPAFAAQQIAEIAEGDNRGIALLLPLIPAIAWVLFNILQPALNQI 118

Query: 120 NRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAI 179
           NRMR TKGVI+GLGLGGLAA+G +S P    A+ASE+A IAEAASD+RG LLLIVV PAI
Sbjct: 119 NRMRQTKGVIVGLGLGGLAASGFISTP---DASASEIAMIAEAASDNRGTLLLIVVAPAI 175

Query: 180 LWVLYNILQPALNQINRMRSE 200
           LWVLYNILQPALNQIN+MRS+
Sbjct: 176 LWVLYNILQPALNQINKMRSQ 196

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489498|gb|ABK96551.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 153/201 (76%), Positives = 172/201 (85%), Gaps = 6/201 (2%)

Query: 1   MAAAMATTAVLNAKCFSISSPKSSIKPG-TTKPTSPLSMQNLPKGLTVSSKPTDSSSLAA 59
           MAA MAT A+LNAKC SI+S K+   P  +TKP S LSM NLPKGLT+S KP D++ L  
Sbjct: 1   MAATMATMAILNAKCLSINSIKNISPPKPSTKPVSLLSMLNLPKGLTIS-KPADNTVLT- 58

Query: 60  GTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQI 119
           GTAIAGAIF+TLSSC+ AFAAQQIAEIAEGDNRG+ALLLP+IPAIAWVLFNILQPALNQI
Sbjct: 59  GTAIAGAIFTTLSSCEPAFAAQQIAEIAEGDNRGIALLLPLIPAIAWVLFNILQPALNQI 118

Query: 120 NRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAI 179
           NRMR TKGVI+GLGLGGLAA+G +S P    A+ASE+A IAEA SD+RG LLLIVV PAI
Sbjct: 119 NRMRQTKGVIVGLGLGGLAASGFISTP---DASASEIAMIAEATSDNRGTLLLIVVAPAI 175

Query: 180 LWVLYNILQPALNQINRMRSE 200
           LWVLYNILQPALNQIN+MRS+
Sbjct: 176 LWVLYNILQPALNQINKMRSQ 196

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255547954|ref|XP_002515034.1| photosystem II core complex proteins psbY, chloroplast precursor [Ricinus communis] gi|223546085|gb|EEF47588.1| photosystem II core complex proteins psbY, chloroplast precursor [Ricinus communis]

 Score =  270 bits (691), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 153/197 (77%), Positives = 168/197 (85%), Gaps = 3/197 (1%)

Query: 5   MATTAVLNAKCFS-ISSPKSSIKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAI 63
           MAT A+LN KC S I+S K+  KP TTKP S LSMQ LPKGLT+S KPT+ + L AGTAI
Sbjct: 1   MATMAILNTKCLSNINSGKNINKPTTTKPISLLSMQELPKGLTIS-KPTNENKLLAGTAI 59

Query: 64  AGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMR 123
           AGAIFSTLSSCD AFAAQQIAEIAEGDNRGLALLLPIIPA+ WVLFNIL+PALNQINRMR
Sbjct: 60  AGAIFSTLSSCDPAFAAQQIAEIAEGDNRGLALLLPIIPALGWVLFNILRPALNQINRMR 119

Query: 124 STKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
            TKGVIIGLGLGGLAATG M+     ++A+  +A IA+AASD+RGQLLL VV PAILWVL
Sbjct: 120 ETKGVIIGLGLGGLAATGFMAA-APEASASENIAMIADAASDNRGQLLLFVVAPAILWVL 178

Query: 184 YNILQPALNQINRMRSE 200
           YNILQPALNQINRMRSE
Sbjct: 179 YNILQPALNQINRMRSE 195

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224110818|ref|XP_002315645.1| hypothetical protein POPTRDRAFT_726168 [Populus trichocarpa] gi|118489255|gb|ABK96433.1| unknown [Populus trichocarpa x Populus deltoides] gi|222864685|gb|EEF01816.1| hypothetical protein POPTRDRAFT_726168 [Populus trichocarpa]

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 158/202 (78%), Positives = 175/202 (86%), Gaps = 8/202 (3%)

Query: 1   MAAAMATTAVLNAKCFSISSPK--SSIKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLA 58
           MAA MAT A+LNAKC SI+S K  S  KP +TKP S LSMQNLPKGLT+S KP D++ L 
Sbjct: 1   MAATMATMAILNAKCLSINSNKNISPTKP-STKPVSLLSMQNLPKGLTIS-KPADNTVLT 58

Query: 59  AGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQ 118
            GTAIAGAIF+TLSSC+ AFAAQQIAEIAEGDNRGLALLLP+IPAIAWVLFNILQPALNQ
Sbjct: 59  -GTAIAGAIFTTLSSCEPAFAAQQIAEIAEGDNRGLALLLPLIPAIAWVLFNILQPALNQ 117

Query: 119 INRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPA 178
           INRMR TKGVI+GLGLGGLAA+G +S  PHAS  ASE+A IA+A SD+RG LLLIVV PA
Sbjct: 118 INRMRQTKGVIVGLGLGGLAASGFIST-PHAS--ASEIAMIADATSDNRGTLLLIVVAPA 174

Query: 179 ILWVLYNILQPALNQINRMRSE 200
           ILWVLYNILQPALNQIN+MRS+
Sbjct: 175 ILWVLYNILQPALNQINKMRSQ 196

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224102363|ref|XP_002312650.1| predicted protein [Populus trichocarpa] gi|222852470|gb|EEE90017.1| predicted protein [Populus trichocarpa]

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 152/196 (77%), Positives = 171/196 (87%), Gaps = 8/196 (4%)

Query: 6   ATTAVLNAKCFSISSPKSS--IKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAI 63
           AT A+LNAKC SI++ K++  IKP  TKP   L+MQNLPKGLT+S KP D+++LA GTAI
Sbjct: 3   ATMAILNAKCLSINANKNTNPIKP-PTKPIYLLAMQNLPKGLTIS-KPADNTALA-GTAI 59

Query: 64  AGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMR 123
           AGAIF+TLSSC+ AFAAQQIAEIAEGDNRGLALLLP+IPAIAWVLFNILQPALNQ+NRMR
Sbjct: 60  AGAIFTTLSSCEPAFAAQQIAEIAEGDNRGLALLLPLIPAIAWVLFNILQPALNQVNRMR 119

Query: 124 STKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
            T+GVIIGLGLGGLAA+G MS P    A+ASE+A IAEA SDSRG LLL+VV PAILWVL
Sbjct: 120 ETRGVIIGLGLGGLAASGFMSTP---DASASEIAMIAEATSDSRGTLLLLVVAPAILWVL 176

Query: 184 YNILQPALNQINRMRS 199
           YNILQPALNQINRMRS
Sbjct: 177 YNILQPALNQINRMRS 192

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489582|gb|ABK96593.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  244 bits (622), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 152/196 (77%), Positives = 171/196 (87%), Gaps = 8/196 (4%)

Query: 6   ATTAVLNAKCFSISSPKSS--IKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAI 63
           AT A+LNAKC SI++ K++  IKP  TKP   L+MQNLPKGLT+S KP D+++LA GTAI
Sbjct: 3   ATMAILNAKCLSINANKNTNPIKP-PTKPIYLLAMQNLPKGLTIS-KPADNTALA-GTAI 59

Query: 64  AGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMR 123
           AGAIF+TLSSC+ AFAAQQIAEIAEGDNRGLALLLP+IPAIAWVLFNILQPALNQ+NRMR
Sbjct: 60  AGAIFTTLSSCEPAFAAQQIAEIAEGDNRGLALLLPLIPAIAWVLFNILQPALNQVNRMR 119

Query: 124 STKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
            T+GVIIGLGLGGLAA+G MS P    A+ASE+A IAEA SDSRG LLL+VV PAILWVL
Sbjct: 120 ETRGVIIGLGLGGLAASGFMSTP---DASASEIARIAEATSDSRGTLLLLVVAPAILWVL 176

Query: 184 YNILQPALNQINRMRS 199
           YNILQPALNQINRMRS
Sbjct: 177 YNILQPALNQINRMRS 192

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489584|gb|ABK96594.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 148/196 (75%), Positives = 167/196 (85%), Gaps = 8/196 (4%)

Query: 6   ATTAVLNAKCFSISSPKSS--IKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAI 63
           AT A+LNAKC SI++ K++  IKP  TKP   L+MQNL KGLT+S KP D+++LA GTAI
Sbjct: 3   ATMAILNAKCLSINANKNTNPIKP-PTKPIYLLAMQNLTKGLTIS-KPADNTALA-GTAI 59

Query: 64  AGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMR 123
           AGAIF+ LSS + AFAAQQIAEIAEGDNRGLALLLP+IPAIAWVLFNILQP LNQ+NRMR
Sbjct: 60  AGAIFTALSSSEPAFAAQQIAEIAEGDNRGLALLLPLIPAIAWVLFNILQPTLNQVNRMR 119

Query: 124 STKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
            T+GVIIGLGLGGLAA+G MS P    A+ASE+A IAEA SDSRG LLL+VV PAILWVL
Sbjct: 120 ETRGVIIGLGLGGLAASGFMSTP---DASASEIAMIAEATSDSRGTLLLLVVAPAILWVL 176

Query: 184 YNILQPALNQINRMRS 199
           YNILQPALNQINRMRS
Sbjct: 177 YNILQPALNQINRMRS 192

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356540203|ref|XP_003538579.1| PREDICTED: photosystem II core complex proteins psbY, chloroplastic-like [Glycine max]

 Score =  225 bits (574), Expect = 7e-57,   Method: Compositional matrix adjust.
 Identities = 136/206 (66%), Positives = 164/206 (79%), Gaps = 15/206 (7%)

Query: 1   MAAAMATT-AVLNAKCFSISSPKSSIKPGTTKPTSP----LSMQNLPKGLTVSSKPTDSS 55
           MAA +ATT A++N+KC + +     +      P+ P     S+QNLPKGLT     +  S
Sbjct: 1   MAATIATTMAMINSKCINTTGSSHKLHNPKLPPSKPTLSLFSLQNLPKGLT-----SHVS 55

Query: 56  SLAAGTAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPA 115
           +  AGTAIAGAIFS+L++CDAA AA QIAE+AEGDNRGLALLLP+IPAIAWVLFNILQPA
Sbjct: 56  TSTAGTAIAGAIFSSLANCDAALAASQIAELAEGDNRGLALLLPLIPAIAWVLFNILQPA 115

Query: 116 LNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAE-AASDSRGQLLLIV 174
           LNQ+NRMR++KGVI+GLGL GL A+G+MS P    A+ASE+A IA+ AASD+RGQLLL V
Sbjct: 116 LNQLNRMRNSKGVIVGLGL-GLCASGMMSGP---EASASEIAMIADAAASDNRGQLLLFV 171

Query: 175 VTPAILWVLYNILQPALNQINRMRSE 200
           VTPAI+WVLYNILQPALNQ+NRMRSE
Sbjct: 172 VTPAIVWVLYNILQPALNQLNRMRSE 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806150|ref|NP_001240940.1| uncharacterized protein LOC100779397 [Glycine max] gi|255646582|gb|ACU23765.1| unknown [Glycine max]

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 128/200 (64%), Positives = 147/200 (73%), Gaps = 13/200 (6%)

Query: 1   MAAAMATTAVLNAKCFSISSPKSSIKPGTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAG 60
           MA+ ++  A++NAKC +   P     P    P+ P    NLPKGL  S    +S+ L+  
Sbjct: 1   MASTISAMAMINAKCVNPKFPN----PTKLAPSKPSLQINLPKGLIASP---ESTKLSPA 53

Query: 61  TAIAGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQIN 120
           TAIAGAIF+TL +CDAAFA QQIA+IAEGDNRGLALLLPIIPAI WVLFNILQPALNQ+N
Sbjct: 54  TAIAGAIFTTLGTCDAAFAVQQIADIAEGDNRGLALLLPIIPAIGWVLFNILQPALNQLN 113

Query: 121 RMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAIL 180
           RMRSTKGVIIGLGLGGLA          A  A +  +  A AASD+RGQLLL VVTPAI 
Sbjct: 114 RMRSTKGVIIGLGLGGLAGLA------AAPHAWAAASEAAAAASDNRGQLLLFVVTPAIA 167

Query: 181 WVLYNILQPALNQINRMRSE 200
           WVLYNILQPALNQ+NRMRS+
Sbjct: 168 WVLYNILQPALNQLNRMRSQ 187

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	200
TAIR|locus:2008555	189	PSBY "photosystem II BY" [Arab	0.795	0.841	0.417	8.2e-28

TAIR|locus:2008555 PSBY "photosystem II BY" [Arabidopsis thaliana (taxid:3702)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 71/170 (41%), Positives = 92/170 (54%)

Query:    38 MQNLPKG---LTVSSKPTDSSSLAA-GTAIAGAIFSTLSSCDXXXX----XXXXXXXXXG 89
             +QN  K    +++ + P  + SLA   TA+AGA+FS+LS  +                  
Sbjct:    21 LQNQTKSKPFISLPTPPKPNVSLAVTSTALAGAVFSSLSYSEPALAIQQIAQLAAANASS 80

Query:    90 DNRGXXXXXXXXXXXXWVLFNILQPALNQINRMRSTKGVIIXXXXXXXXXXXXMSMPPHX 149
             DNRG            WVL+NILQPA+NQ+N+MR +KG+++            +  PP  
Sbjct:    81 DNRGLALLLPIVPAIAWVLYNILQPAINQVNKMRESKGIVVGLGIGGGLAASGLLTPPPE 140

Query:   150 XXXXXXXXXXXXXXXDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRS 199
                            DSRGQLLLIVVTPA+LWVLYNILQPALNQIN+MRS
Sbjct:   141 AYAAAEAAAASS---DSRGQLLLIVVTPALLWVLYNILQPALNQINKMRS 187


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        0.321   0.133   0.392    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      200       119   0.00091  102 3  11 22  0.46    30
                                                     29  0.47    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  502 (53 KB)
  Total size of DFA:  102 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:  8.51u 0.14s 8.65t   Elapsed:  00:00:00
  Total cpu time:  8.51u 0.14s 8.65t   Elapsed:  00:00:00
  Start:  Fri May 10 03:05:26 2013   End:  Fri May 10 03:05:26 2013

GO:0009507 "chloroplast" evidence=ISM

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

GO:0015979 "photosynthesis" evidence=IEA;ISS;TAS

GO:0016021 "integral to membrane" evidence=IEA

GO:0030095 "chloroplast photosystem II" evidence=ISS

GO:0030145 "manganese ion binding" evidence=IEA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0009533 "chloroplast stromal thylakoid" evidence=IDA

---

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)
O49347	PSBY_ARATH	No assigned EC number	0.5771	0.81	0.8571	yes	no
P80470	PSBY_SPIOL	No assigned EC number	0.5685	0.915	0.9195	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: estExt_Genewise1_v1.C_LG_X5024 photosystem II core complex proteins psbY (196 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	200
PLN00063	194	PLN00063, PLN00063, photosystem II core complex pr	2e-82
PRK13240	40	PRK13240, pbsY, photosystem II protein Y; Reviewed	4e-04
pfam06298	36	pfam06298, PsbY, Photosystem II protein Y (PsbY)	5e-04

>gnl|CDD|215044 PLN00063, PLN00063, photosystem II core complex proteins psbY; Provisional

 Score =  242 bits (619), Expect = 2e-82
 Identities = 144/197 (73%), Positives = 162/197 (82%), Gaps = 4/197 (2%)

Query: 5   MATTAVLNAKCFSISSPKSSIKPGT-TKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAI 63
           MAT A L  KC SI++ K+     T TKP   LSMQN PKGLT+S K  D++++A GTAI
Sbjct: 1   MATMAALATKCLSINARKNPNPSKTKTKPIILLSMQNKPKGLTIS-KSADNTNVA-GTAI 58

Query: 64  AGAIFSTLSSCDAAFAAQQIAEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMR 123
           AGAIFS LSS + A AAQQIAE+AEGDNRGLALLLPIIPAIAWVLFNILQPALNQ+N+MR
Sbjct: 59  AGAIFSALSSSEPALAAQQIAELAEGDNRGLALLLPIIPAIAWVLFNILQPALNQVNKMR 118

Query: 124 STKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVL 183
            TKGV+ GLGLGGLAA+G M+ PP ASAA  E+A IA AASDSRG LLLIVV PAILWVL
Sbjct: 119 ETKGVVAGLGLGGLAASGFMAAPPEASAAE-EIAMIAAAASDSRGLLLLIVVAPAILWVL 177

Query: 184 YNILQPALNQINRMRSE 200
           YNILQPALNQIN+MRS+
Sbjct: 178 YNILQPALNQINKMRSD 194

Length = 194

>gnl|CDD|183912 PRK13240, pbsY, photosystem II protein Y; Reviewed

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 14/33 (42%), Positives = 18/33 (54%)

Query: 90  DNRGLALLLPIIPAIAWVLFNILQPALNQINRM 122
           D R L +L PI+ A  W +FNI + A  Q  R 
Sbjct: 2   DLRLLIVLAPILAAAGWAVFNIGKAAREQFQRF 34

Length = 40

>gnl|CDD|148107 pfam06298, PsbY, Photosystem II protein Y (PsbY)

 Score = 36.2 bits (84), Expect = 5e-04
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 90  DNRGLALLLPIIPAIAWVLFNILQPALNQINRM 122
           D R L +L PI+ A  W +FNI + AL Q+ ++
Sbjct: 2   DWRLLVVLAPILLAAGWAVFNIGRAALGQLQKL 34

This family consists of several bacterial and plant photosystem II protein Y (PsbY) sequences. PsbY is a manganese-binding protein that has an L-arginine metabolising enzyme activity. Length = 36

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
PLN00063	194	photosystem II core complex proteins psbY; Provisi	100.0
PLN00063	194	photosystem II core complex proteins psbY; Provisi	99.82
PF06298	36	PsbY: Photosystem II protein Y (PsbY); InterPro: I	99.73
CHL00196	36	psbY photosystem II protein Y; Provisional	99.71
PRK13240	40	pbsY photosystem II protein Y; Reviewed	99.7
PF06298	36	PsbY: Photosystem II protein Y (PsbY); InterPro: I	99.46
CHL00196	36	psbY photosystem II protein Y; Provisional	99.38
PRK13240	40	pbsY photosystem II protein Y; Reviewed	99.22

>PLN00063 photosystem II core complex proteins psbY; Provisional

Probab=100.00  E-value=2.4e-73  Score=478.46  Aligned_cols=193  Identities=72%  Similarity=1.034  Sum_probs=179.4

Q ss_pred             hhHHHHhhhhhhccCCCCCCCCC-CCCCCCCccccccCCCcccccCCCCCcchhhHHHHHHHHHHHhhcCchHHHHHHHH
Q 029024            5 MATTAVLNAKCFSISSPKSSIKP-GTTKPTSPLSMQNLPKGLTVSSKPTDSSSLAAGTAIAGAIFSTLSSCDAAFAAQQI   83 (200)
Q Consensus         5 iatma~l~~k~~~~~~~~~~~~~-~~~~~~~~~s~~~~~k~l~~~s~~~~~~~~~a~~alAga~f~~L~~~~~A~Aaqqi   83 (200)
                      |+||+|+|+||+++|+||+++++ +++||.+.+|++++|||+++++.+.  +...++++++|++|++|+++|+++|+|||
T Consensus         1 ~atma~l~~k~~~~~~~~~~~~~~~~~~p~~~~~~~~~pk~~~~~~~~~--~~~v~~~~laga~~s~l~~~~~A~AAq~i   78 (194)
T PLN00063          1 MATMAALATKCLSINARKNPNPSKTKTKPIILLSMQNKPKGLTISKSAD--NTNVAGTAIAGAIFSALSSSEPALAAQQI   78 (194)
T ss_pred             CchHHHhhhHHhhcCCCCCCCCCCCCCCccccccccccccccccccccc--hhHHHHHHHHHHHHHhhcCCcHHHHHHHH
Confidence            67999999999999999999976 8899999999999999999885543  34688999999999999999999999999


Q ss_pred             HHHhccccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcccchhHHHhhhHHHHhhhcCCChhhhHHHHHHHHHHHHh
Q 029024           84 AEIAEGDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTKGVIIGLGLGGLAATGLMSMPPHASAAASEVATIAEAA  163 (200)
Q Consensus        84 a~lA~~D~RlliVl~Pil~A~gWalfNIg~pAl~Qlq~m~~kKgv~ag~gLgaaa~sgl~~~~p~Aa~aa~eia~~A~Aa  163 (200)
                      +|+|+.|+|+++|++|+++|+|||+|||++++++|+|||+++|||++|+|||+++.+|++. .|+.+++++|++++|+.+
T Consensus        79 a~~A~~D~R~liVl~Pil~AigWalfNIg~~Al~Qlq~m~s~kgv~aglGLgaaA~~g~l~-~~p~A~Aa~e~~~~A~~~  157 (194)
T PLN00063         79 AELAEGDNRGLALLLPIIPAIAWVLFNILQPALNQVNKMRETKGVVAGLGLGGLAASGFMA-APPEASAAEEIAMIAAAA  157 (194)
T ss_pred             HHHhccCcccchhHHHHHHHHHHHHHHhhHHHHHHHHHHhhccceeeecchHHHhhccccc-CCcchHHHHHHHHHHhhc
Confidence            9999999999999999999999999999999999999999999999999999999899887 345455569999999877


Q ss_pred             ccccchhhhHHHHHHHHHHHHHhhhHHHHHHHhhhcC
Q 029024          164 SDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE  200 (200)
Q Consensus       164 ~DnRg~~ll~v~~PaigWVlyNIl~PalnQlnrMr~~  200 (200)
                      +||||+++++||+|+||||+||||||+||||||||++
T Consensus       158 ~D~Rg~lll~v~~PaigWVlyNIL~PalnQin~Mrs~  194 (194)
T PLN00063        158 SDSRGLLLLIVVAPAILWVLYNILQPALNQINKMRSD  194 (194)
T ss_pred             CCccchhhHHHHHHHHHHHHHHHhhHHHHHHHHhhcC
Confidence            9999999999999999999999999999999999986

>PLN00063 photosystem II core complex proteins psbY; Provisional

Probab=99.82  E-value=1.9e-20  Score=158.62  Aligned_cols=68  Identities=46%  Similarity=0.774  Sum_probs=61.8

Q ss_pred             hHHHhhhHHHHhhhcCCChhhhHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhhhHHHHHHHhhhcC
Q 029024          129 IIGLGLGGLAATGLMSMPPHASAAASEVATIAEAASDSRGQLLLIVVTPAILWVLYNILQPALNQINRMRSE  200 (200)
Q Consensus       129 ~ag~gLgaaa~sgl~~~~p~Aa~aa~eia~~A~Aa~DnRg~~ll~v~~PaigWVlyNIl~PalnQlnrMr~~  200 (200)
                      ++|++++|+++++|.+  +++++++||++++|  ++|+|+++++++++|++|||+|||++|++||+|||+++
T Consensus        53 v~~~~laga~~s~l~~--~~~A~AAq~ia~~A--~~D~R~liVl~Pil~AigWalfNIg~~Al~Qlq~m~s~  120 (194)
T PLN00063         53 VAGTAIAGAIFSALSS--SEPALAAQQIAELA--EGDNRGLALLLPIIPAIAWVLFNILQPALNQVNKMRET  120 (194)
T ss_pred             HHHHHHHHHHHHhhcC--CcHHHHHHHHHHHh--ccCcccchhHHHHHHHHHHHHHHhhHHHHHHHHHHhhc
Confidence            8899999999999887  55567779999996  48999999999999999999999999999999999964

>PF06298 PsbY: Photosystem II protein Y (PsbY); InterPro: IPR009388 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=99.73  E-value=3.3e-18  Score=112.55  Aligned_cols=36  Identities=56%  Similarity=0.829  Sum_probs=34.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHhhc
Q 029024           89 GDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRS  124 (200)
Q Consensus        89 ~D~RlliVl~Pil~A~gWalfNIg~pAl~Qlq~m~~  124 (200)
                      ||+|+++|++|+++|+|||+|||+++|++|+|||.|
T Consensus         1 mD~R~liVl~Pil~A~gWa~fNIg~~Al~Q~~~~~~   36 (36)
T PF06298_consen    1 MDWRLLIVLLPILPAAGWALFNIGRAALNQLQRMLN   36 (36)
T ss_pred             CCchhHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhC
Confidence            799999999999999999999999999999999974

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 transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants []. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea []. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.; GO: 0030145 manganese ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0016021 integral to membrane

>CHL00196 psbY photosystem II protein Y; Provisional

Probab=99.71  E-value=7.7e-18  Score=110.87  Aligned_cols=36  Identities=39%  Similarity=0.660  Sum_probs=34.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHhhc
Q 029024           89 GDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRS  124 (200)
Q Consensus        89 ~D~RlliVl~Pil~A~gWalfNIg~pAl~Qlq~m~~  124 (200)
                      ||+|+++|++|+++|+||++|||+++|++|+|+|++
T Consensus         1 mD~RlliVl~Pil~A~~Wa~fNIg~~Al~Q~q~~~~   36 (36)
T CHL00196          1 MDTRLLVIAAPVLAAASWALFNIGRLAIQQIQRLSR   36 (36)
T ss_pred             CChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhcC
Confidence            799999999999999999999999999999999974

>PRK13240 pbsY photosystem II protein Y; Reviewed

Probab=99.70  E-value=1.3e-17  Score=111.75  Aligned_cols=38  Identities=39%  Similarity=0.561  Sum_probs=36.3

Q ss_pred             cccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHhhccc
Q 029024           89 GDNRGLALLLPIIPAIAWVLFNILQPALNQINRMRSTK  126 (200)
Q Consensus        89 ~D~RlliVl~Pil~A~gWalfNIg~pAl~Qlq~m~~kK  126 (200)
                      ||+|+++|++|+++|+||++||||++|++|+|+|.+|+
T Consensus         1 mD~RlliVl~Pil~A~~Wa~fNIg~~Al~Q~q~~~~~~   38 (40)
T PRK13240          1 IDLRLLIVLAPILAAAGWAVFNIGKAAREQFQRFLNRK   38 (40)
T ss_pred             CchhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhc
Confidence            79999999999999999999999999999999998764

>PF06298 PsbY: Photosystem II protein Y (PsbY); InterPro: IPR009388 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=99.46  E-value=5.2e-14  Score=92.79  Aligned_cols=34  Identities=44%  Similarity=0.668  Sum_probs=33.0

Q ss_pred             cccchhhhHHHHHHHHHHHHHhhhHHHHHHHhhh
Q 029024          165 DSRGQLLLIVVTPAILWVLYNILQPALNQINRMR  198 (200)
Q Consensus       165 DnRg~~ll~v~~PaigWVlyNIl~PalnQlnrMr  198 (200)
                      |.|+++++++++|++|||+|||++|++||++||-
T Consensus         2 D~R~liVl~Pil~A~gWa~fNIg~~Al~Q~~~~~   35 (36)
T PF06298_consen    2 DWRLLIVLLPILPAAGWALFNIGRAALNQLQRML   35 (36)
T ss_pred             CchhHHHHHHHHHHHHHHHHHhHHHHHHHHHHhh
Confidence            8999999999999999999999999999999984

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 transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants []. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea []. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.; GO: 0030145 manganese ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0016021 integral to membrane

>CHL00196 psbY photosystem II protein Y; Provisional

Probab=99.38  E-value=4.2e-13  Score=88.56  Aligned_cols=35  Identities=34%  Similarity=0.515  Sum_probs=34.1

Q ss_pred             cccchhhhHHHHHHHHHHHHHhhhHHHHHHHhhhc
Q 029024          165 DSRGQLLLIVVTPAILWVLYNILQPALNQINRMRS  199 (200)
Q Consensus       165 DnRg~~ll~v~~PaigWVlyNIl~PalnQlnrMr~  199 (200)
                      |.|++++++++++++||++|||.+|+++|++||++
T Consensus         2 D~RlliVl~Pil~A~~Wa~fNIg~~Al~Q~q~~~~   36 (36)
T CHL00196          2 DTRLLVIAAPVLAAASWALFNIGRLAIQQIQRLSR   36 (36)
T ss_pred             ChhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhcC
Confidence            89999999999999999999999999999999985

>PRK13240 pbsY photosystem II protein Y; Reviewed

Probab=99.22  E-value=9.1e-12  Score=83.68  Aligned_cols=35  Identities=29%  Similarity=0.415  Sum_probs=33.7

Q ss_pred             cccchhhhHHHHHHHHHHHHHhhhHHHHHHHhhhc
Q 029024          165 DSRGQLLLIVVTPAILWVLYNILQPALNQINRMRS  199 (200)
Q Consensus       165 DnRg~~ll~v~~PaigWVlyNIl~PalnQlnrMr~  199 (200)
                      |-|.+++++++++++||++|||.+|+++|++||.+
T Consensus         2 D~RlliVl~Pil~A~~Wa~fNIg~~Al~Q~q~~~~   36 (40)
T PRK13240          2 DLRLLIVLAPILAAAGWAVFNIGKAAREQFQRFLN   36 (40)
T ss_pred             chhHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            78999999999999999999999999999999975

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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