Citrus Sinensis ID: 047658

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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-------210-------220-------23
Protein Sequence
MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVFSTEVS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEEccccccEEEccccccHHHccccccHHccHHHHHHHHHHHHccccccccEEEEEcccccEEEEccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cccHHcccccccccccccccccccccccccccccccccccccccHHHHHHHcHHccccccccccccccccccccccccccEcccEcccEccHHHHccEEEEEEEEcccEEEEcccccEEEEccEEEEEEEccHHHHHHHHHHHcHHHccccEEEEEcccccEEEEEccccccccccccccccccEEcccHHHcccHHHHcccccccccHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
matqaglftpsiittktsklllnpwkptssfsftspkpltfSMAQRTVRAAAAeekteaptkeapvgftppqldpntpspifggstggllrkAQVEEFYVITwespkeqifemptggaaimrqgpnLLKLARKEQCLALGTRLRSKYKIKYQFYRvfpngevqylhpkdgvypekvnpgrqgvgvnyrsigknvspiehKTELKKFHKRWLHMEHLIKSLCSVFSTEVS
Flexible Loop (DISEMBL)
matqaglftpsiittktsklllnpwkptssfsftspkplTFSMAQRTVRAAAAeekteaptkeapvgftppqldpnTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKvnpgrqgvgvnyrsigknvspiehKTELKKFHKRWLHMEHLIKSlcsvfstevs
Low Complexity Region (SEG)
MATQAGLFTPSIITTKTSKLLLNPWkptssfsftspkpltfsMAQRTVRaaaaeekteaptkeapVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVFSTEVS
Disordered region (IsUnstruct)
*******FTPSIITTKTSKLLLNPW**********************************************************GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVF*****
Disordered Region (DISOPRED)
*******FTPSII*******************************************************TPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPE**********V*YRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVFSTEV*
Disordered Region (DISEMBL)
MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQ******************APVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVFSTEVS
Disordered Region (DISPRO)
******************************************************************GFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVF*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSVFSTEVS
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	229	2.2.26 [Sep-21-2011]
P32869	207	Photosystem I reaction ce	N/A	no	0.882	0.975	0.735	1e-82
Q9SA56	204	Photosystem I reaction ce	yes	no	0.842	0.946	0.742	2e-80
P12372	208	Photosystem I reaction ce	N/A	no	0.886	0.975	0.745	2e-79
Q9S7H1	208	Photosystem I reaction ce	no	no	0.829	0.913	0.732	3e-78
P29302	204	Photosystem I reaction ce	N/A	no	0.868	0.975	0.75	3e-76
P12353	212	Photosystem I reaction ce	N/A	no	0.868	0.938	0.747	4e-76
P36213	205	Photosystem I reaction ce	N/A	no	0.812	0.907	0.682	5e-70
Q39615	196	Photosystem I reaction ce	N/A	no	0.580	0.678	0.751	1e-54
Q9T4W8	220	Photosystem I reaction ce	N/A	no	0.598	0.622	0.666	5e-50
O78502	141	Photosystem I reaction ce	yes	no	0.585	0.950	0.674	9e-47

>sp|P32869|PSAD_CUCSA Photosystem I reaction center subunit II, chloroplastic OS=Cucumis sativus GN=psaD PE=1 SV=1

 Score =  305 bits (782), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 153/208 (73%), Positives = 175/208 (84%), Gaps = 6/208 (2%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKP-LTFSMAQRTVRAAAAEEKTEA 59
           MATQA LFTPS+ T K++ + + PWK +S+ SF + KP L  + + R+ + +A  E +  
Sbjct: 3   MATQATLFTPSLSTPKSTGISI-PWKQSSTLSFLTSKPHLKAASSSRSFKVSAEAETS-- 59

Query: 60  PTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
              EAP GF+PP+LDP+TPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA
Sbjct: 60  --VEAPAGFSPPELDPSTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 117

Query: 120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
           IMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG
Sbjct: 118 IMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 177

Query: 180 RQGVGVNYRSIGKNVSPIEHKTELKKFH 207
           R+GVG N+RSIGKNVSPIE K   K+ +
Sbjct: 178 REGVGQNFRSIGKNVSPIEVKFTGKQVY 205

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.
Cucumis sativus (taxid: 3659)

>sp|Q9SA56|PSAD2_ARATH Photosystem I reaction center subunit II-2, chloroplastic OS=Arabidopsis thaliana GN=psaD2 PE=1 SV=1

 Score =  298 bits (764), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 150/202 (74%), Positives = 166/202 (82%), Gaps = 9/202 (4%)

Query: 1   MATQA-GLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEA 59
           MATQA G+F+P+I TT ++   L+ +        +S +P + S  +  +RA   E  + A
Sbjct: 1   MATQAAGIFSPAITTTTSAVKKLHLFS-------SSHRPKSLSFTKTAIRAEKTESSSAA 53

Query: 60  P-TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 118
           P  KEAPVGFTPPQLDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGA
Sbjct: 54  PAVKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGA 113

Query: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178
           AIMR+GPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NP
Sbjct: 114 AIMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANP 173

Query: 179 GRQGVGVNYRSIGKNVSPIEHK 200
           GR+GVG+N RSIGKNVSPIE K
Sbjct: 174 GREGVGLNMRSIGKNVSPIEVK 195

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P12372|PSAD_SOLLC Photosystem I reaction center subunit II, chloroplastic OS=Solanum lycopersicum GN=psaD PE=2 SV=1

 Score =  295 bits (754), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 155/208 (74%), Positives = 168/208 (80%), Gaps = 5/208 (2%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMA-QRTVRAAAAEEKTEA 59
           MATQA LFTP +   K++     PWK  S  SF++PK L  +++  R +RA A E     
Sbjct: 3   MATQASLFTPPLSVPKSTTA---PWK-QSLVSFSTPKQLKSTVSVTRPIRAMAEEAPAAT 58

Query: 60  PTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
             K AP GFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA
Sbjct: 59  EEKPAPAGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 118

Query: 120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
           IMRQGPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEKVNPG
Sbjct: 119 IMRQGPNLLKLARKEQCLALGTRLRSKYKINYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 178

Query: 180 RQGVGVNYRSIGKNVSPIEHKTELKKFH 207
           R+GVG N+RSIGKN S IE K   K+ +
Sbjct: 179 REGVGQNFRSIGKNKSAIEVKFTGKQVY 206

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Solanum lycopersicum (taxid: 4081)

>sp|Q9S7H1|PSAD1_ARATH Photosystem I reaction center subunit II-1, chloroplastic OS=Arabidopsis thaliana GN=psaD1 PE=1 SV=1

 Score =  291 bits (745), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 153/209 (73%), Positives = 166/209 (79%), Gaps = 19/209 (9%)

Query: 1   MATQA-GLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEA 59
           MATQA G+F  +I T  TS +     K    FS T+ +P + S  +  +RA    EKT++
Sbjct: 1   MATQAAGIFNSAITTAATSGV-----KKLHFFS-TTHRPKSLSFTKTAIRA----EKTDS 50

Query: 60  P--------TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIF 111
                    TKEAPVGFTPPQLDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIF
Sbjct: 51  SAAAAAAPATKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIF 110

Query: 112 EMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGV 171
           EMPTGGAAIMR+GPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGV
Sbjct: 111 EMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGV 170

Query: 172 YPEKVNPGRQGVGVNYRSIGKNVSPIEHK 200
           YPEK NPGR+GVG+N RSIGKNVSPIE K
Sbjct: 171 YPEKANPGREGVGLNMRSIGKNVSPIEVK 199

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P29302|PSAD_NICSY Photosystem I reaction center subunit II, chloroplastic OS=Nicotiana sylvestris GN=psaD PE=2 SV=1

 Score =  284 bits (727), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 156/208 (75%), Positives = 169/208 (81%), Gaps = 9/208 (4%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSM-AQRTVRAAAAEEKTEA 59
           MATQA LFTP++   K+S     PWK   S +  SPK L  ++ A R +RA A E  T+ 
Sbjct: 3   MATQASLFTPALSAPKSSA----PWK--QSLASFSPKQLKSTVSAPRPIRAMAEEAATK- 55

Query: 60  PTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
              EAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA
Sbjct: 56  -EAEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 114

Query: 120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
           IMR+G NLLKLARKEQCLALGTRLRSKYKI Y+FYRVFPNGEVQYLHPKDGVYPEKVN G
Sbjct: 115 IMREGANLLKLARKEQCLALGTRLRSKYKINYRFYRVFPNGEVQYLHPKDGVYPEKVNAG 174

Query: 180 RQGVGVNYRSIGKNVSPIEHKTELKKFH 207
           RQGVG N+RSIGKN SPIE K   K+ +
Sbjct: 175 RQGVGQNFRSIGKNKSPIEVKFTGKQVY 202

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Nicotiana sylvestris (taxid: 4096)

>sp|P12353|PSAD_SPIOL Photosystem I reaction center subunit II, chloroplastic OS=Spinacia oleracea GN=psaD PE=1 SV=2

 Score =  284 bits (726), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 151/202 (74%), Positives = 165/202 (81%), Gaps = 3/202 (1%)

Query: 1   MATQAGLFTPSIITTK--TSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTE 58
           MATQA LF+PS +++       L   +K  S+ +F S KP +   + R   AA  +    
Sbjct: 3   MATQATLFSPSSLSSAKPIDTRLTTSFKQPSAVTFAS-KPASRHHSIRAAAAAEGKAAAA 61

Query: 59  APTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 118
             TKEAP GFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA
Sbjct: 62  TETKEAPKGFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 121

Query: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178
           AIMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNP
Sbjct: 122 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNP 181

Query: 179 GRQGVGVNYRSIGKNVSPIEHK 200
           GRQGVG+N RSIGKNVSPIE K
Sbjct: 182 GRQGVGLNMRSIGKNVSPIEVK 203

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Spinacia oleracea (taxid: 3562)

>sp|P36213|PSAD_HORVU Photosystem I reaction center subunit II, chloroplastic OS=Hordeum vulgare GN=psaD PE=1 SV=1

 Score =  263 bits (673), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 142/208 (68%), Positives = 153/208 (73%), Gaps = 22/208 (10%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAA-------- 52
           MATQA   T  +IT          W P++      P+P T +M   + R  A        
Sbjct: 3   MATQASAATRHLITAA--------WSPSAK-----PRPATLAMPS-SARGPAPLFAAAPD 48

Query: 53  AEEKTEAPTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFE 112
                  P + AP GF PPQLDP+TPSPIFGGSTGGLLRKAQVEEFYVITW SPKEQ+FE
Sbjct: 49  TPAPAAPPAEPAPAGFVPPQLDPSTPSPIFGGSTGGLLRKAQVEEFYVITWTSPKEQVFE 108

Query: 113 MPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVY 172
           MPTGGAAIMR+GPNLLKLARKEQCLALG RLRSKYKI YQFYRVFPNGEVQYLHPKDGVY
Sbjct: 109 MPTGGAAIMREGPNLLKLARKEQCLALGNRLRSKYKIAYQFYRVFPNGEVQYLHPKDGVY 168

Query: 173 PEKVNPGRQGVGVNYRSIGKNVSPIEHK 200
           PEKVN GRQGVG N+RSIGKNVSPIE K
Sbjct: 169 PEKVNAGRQGVGQNFRSIGKNVSPIEVK 196

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Hordeum vulgare (taxid: 4513)

>sp|Q39615|PSAD_CHLRE Photosystem I reaction center subunit II, chloroplastic OS=Chlamydomonas reinhardtii GN=psaD PE=1 SV=1

 Score =  213 bits (541), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 100/133 (75%), Positives = 114/133 (85%)

Query: 68  FTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNL 127
           +T P L+P+TPSPIFGGSTGGLLRKAQ EEFYVITWE+ KEQIFEMPTGGAAIMRQGPNL
Sbjct: 53  WTVPTLNPDTPSPIFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNL 112

Query: 128 LKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNY 187
           LK  +KEQCLAL T+LR+K+K+   FYRVFP+G+VQYLHP DGVYPEKVN GR G   N 
Sbjct: 113 LKFGKKEQCLALTTQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNM 172

Query: 188 RSIGKNVSPIEHK 200
           R IG+NV+PI+ K
Sbjct: 173 RRIGQNVNPIKVK 185

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Chlamydomonas reinhardtii (taxid: 3055)

>sp|Q9T4W8|PSAD_CYAPA Photosystem I reaction center subunit II, cyanelle OS=Cyanophora paradoxa GN=psaD PE=2 SV=1

 Score =  197 bits (501), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 92/138 (66%), Positives = 110/138 (79%), Gaps = 1/138 (0%)

Query: 64  APVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQ 123
           AP  F+ P L+ N P+PIFGGSTGGLLRKA+VEEFY ITW    E +FE+PTGGAAIMR 
Sbjct: 70  APKPFSVPTLNLNAPTPIFGGSTGGLLRKAEVEEFYSITWTGKSETVFELPTGGAAIMRA 129

Query: 124 GPNLLKLARKEQCLALGTRLRSKYKI-KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQG 182
           G NLL+LARKEQC+ALG +L+ K+KI  Y+ YRV+P+GEVQ+LHPKDGV+PEKVNPGR  
Sbjct: 130 GENLLRLARKEQCIALGAQLKDKFKITDYKIYRVYPSGEVQFLHPKDGVFPEKVNPGRVA 189

Query: 183 VGVNYRSIGKNVSPIEHK 200
           VG N R IG+N  P + K
Sbjct: 190 VGSNKRRIGQNPDPAKLK 207

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. PSAD may encode the ferredoxin-docking protein.

Cyanophora paradoxa (taxid: 2762)

>sp|O78502|PSAD_GUITH Photosystem I reaction center subunit II OS=Guillardia theta GN=psaD PE=3 SV=1

 Score =  186 bits (473), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 91/135 (67%), Positives = 107/135 (79%), Gaps = 1/135 (0%)

Query: 73  LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLAR 132
           L+   PSP F GSTGG LR A+ EE Y ITW SPKEQ+FEMPTGGAAIMR+G NLL LAR
Sbjct: 5   LNLQIPSPTFEGSTGGWLRAAETEEKYAITWTSPKEQVFEMPTGGAAIMRKGENLLYLAR 64

Query: 133 KEQCLALGTRLRSKYKI-KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIG 191
           KEQCLALGT++++ +KI  Y+ YR+FP+GEVQYLHPKDGV+PEKVNPGR GVG    SIG
Sbjct: 65  KEQCLALGTQVKTSFKITDYKIYRIFPSGEVQYLHPKDGVFPEKVNPGRIGVGNVSHSIG 124

Query: 192 KNVSPIEHKTELKKF 206
           KN++P + K   K F
Sbjct: 125 KNLNPAQIKFTNKSF 139

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center.

Guillardia theta (taxid: 55529)

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	229
157678732	209	PSI reaction center subunit II [Citrus s	0.903	0.990	0.966	1e-111
157678962	209	PSI reaction center subunit II [Citrus s	0.903	0.990	0.937	1e-107
255559414	209	Photosystem I reaction center subunit II	0.895	0.980	0.846	3e-89
255551453	208	Photosystem I reaction center subunit II	0.886	0.975	0.783	2e-87
225432620	204	PREDICTED: photosystem I reaction center	0.842	0.946	0.82	4e-87
356575833	203	PREDICTED: photosystem I reaction center	0.838	0.945	0.8	1e-85
157678954	207	PSI reaction center subunit II [Citrus s	0.868	0.961	0.780	4e-84
157678730	207	PSI reaction center subunit II [Citrus s	0.868	0.961	0.780	5e-84
351727030	210	photosystem I subunit PsaD [Glycine max]	0.860	0.938	0.826	6e-84
357480841	209	Photosystem I reaction center subunit II	0.834	0.913	0.782	2e-83

>gi|157678732|dbj|BAF80471.1| PSI reaction center subunit II [Citrus sinensis] gi|157678950|dbj|BAF80473.1| PSI reaction center subunit II [Citrus sinensis]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 200/207 (96%), Positives = 202/207 (97%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP
Sbjct: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60

Query: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120
           TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI
Sbjct: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120

Query: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180
           MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180

Query: 181 QGVGVNYRSIGKNVSPIEHKTELKKFH 207
           QGVGVNYRSIGKNVSPIE K   K+ +
Sbjct: 181 QGVGVNYRSIGKNVSPIEVKFTGKQVY 207

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|157678962|dbj|BAF80479.1| PSI reaction center subunit II [Citrus sinensis]

 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 194/207 (93%), Positives = 197/207 (95%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQAGLFTPSI TTKTSKL LNPWKPTSSFSFTSPKPLTFSM QRTVRAA AE KTEAP
Sbjct: 1   MATQAGLFTPSITTTKTSKLPLNPWKPTSSFSFTSPKPLTFSMGQRTVRAAGAEGKTEAP 60

Query: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120
           TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI
Sbjct: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120

Query: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180
           MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180

Query: 181 QGVGVNYRSIGKNVSPIEHKTELKKFH 207
           QGVG+NYRSIGKNVSPIE K   K+ +
Sbjct: 181 QGVGLNYRSIGKNVSPIEVKFTGKQVY 207

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559414|ref|XP_002520727.1| Photosystem I reaction center subunit II, chloroplast precursor, putative [Ricinus communis] gi|223540112|gb|EEF41689.1| Photosystem I reaction center subunit II, chloroplast precursor, putative [Ricinus communis]

 Score =  333 bits (854), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 177/209 (84%), Positives = 189/209 (90%), Gaps = 4/209 (1%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSP-KPLTFSMAQRTVR-AAAAEEKTE 58
           MATQ+GLFTP+ IT     L+  PWKPTSSFSFTS  KPLTFS  QR+++ AAAAEEKTE
Sbjct: 1   MATQSGLFTPTTITAPKPNLI--PWKPTSSFSFTSTTKPLTFSTTQRSLKVAAAAEEKTE 58

Query: 59  APTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 118
            PTKEAPVGFTPP+LDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGA
Sbjct: 59  TPTKEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGA 118

Query: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178
           AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP
Sbjct: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178

Query: 179 GRQGVGVNYRSIGKNVSPIEHKTELKKFH 207
           GRQGVG N+RSIGKNVSPIE K   K+ +
Sbjct: 179 GRQGVGQNFRSIGKNVSPIEVKFTGKQVY 207

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255551453|ref|XP_002516772.1| Photosystem I reaction center subunit II, chloroplast precursor, putative [Ricinus communis] gi|223543860|gb|EEF45386.1| Photosystem I reaction center subunit II, chloroplast precursor, putative [Ricinus communis]

 Score =  328 bits (840), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 163/208 (78%), Positives = 182/208 (87%), Gaps = 5/208 (2%)

Query: 1   MATQAGLFTPSIITT-KTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEA 59
           MATQA LFTP+ ++T K+S   + PWK +S  S  + KP  +S+AQ+T++AAAAE KT  
Sbjct: 3   MATQASLFTPTTLSTPKSSNHAIVPWKQSSFLSIPTAKPRKYSIAQKTIKAAAAEGKT-- 60

Query: 60  PTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
             KEAPVGFTPP+LDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAA
Sbjct: 61  --KEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAA 118

Query: 120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
           IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG
Sbjct: 119 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 178

Query: 180 RQGVGVNYRSIGKNVSPIEHKTELKKFH 207
           R+GVG N+RSIGKNVSPIE K   K+ +
Sbjct: 179 REGVGQNFRSIGKNVSPIEVKFTGKQVY 206

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225432620|ref|XP_002281825.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 1 [Vitis vinifera] gi|359477510|ref|XP_003631987.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 2 [Vitis vinifera] gi|359477512|ref|XP_003631988.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 3 [Vitis vinifera] gi|359477514|ref|XP_003631989.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 4 [Vitis vinifera] gi|147800882|emb|CAN62373.1| hypothetical protein VITISV_036477 [Vitis vinifera]

 Score =  326 bits (836), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 164/200 (82%), Positives = 175/200 (87%), Gaps = 7/200 (3%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQA LFTP++    +   +  PWK +SS SFT+PK    S+A RT   A AEE   AP
Sbjct: 3   MATQASLFTPTL----SGDRVTVPWKSSSSLSFTTPKLPKSSVAPRTTIRAMAEE---AP 55

Query: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120
           TKEAPVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 56  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 115

Query: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180
           MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 116 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 175

Query: 181 QGVGVNYRSIGKNVSPIEHK 200
           QGVGVN+RSIGKNV+PIE K
Sbjct: 176 QGVGVNFRSIGKNVNPIEVK 195

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575833|ref|XP_003556041.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic-like [Glycine max]

 Score =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 160/200 (80%), Positives = 172/200 (86%), Gaps = 8/200 (4%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQA LFTP +   K S     PWK +S+ SF++ KPL FS   RT+RAAA ++ TEAP
Sbjct: 3   MATQASLFTPPLSGLKPSDRATAPWKQSSTLSFSTSKPLKFS---RTIRAAATDQTTEAP 59

Query: 61  TKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 120
                VGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 60  -----VGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 114

Query: 121 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 180
           MR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN GR
Sbjct: 115 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGR 174

Query: 181 QGVGVNYRSIGKNVSPIEHK 200
           QGVG N+RSIGKNVSPIE K
Sbjct: 175 QGVGQNFRSIGKNVSPIEVK 194

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|157678954|dbj|BAF80475.1| PSI reaction center subunit II [Citrus sinensis]

 Score =  316 bits (810), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 160/205 (78%), Positives = 171/205 (83%), Gaps = 6/205 (2%)

Query: 3   TQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTK 62
           TQA LF P+  +T  S     PWK +SSFS    +PL  +  +     A AE KTE PTK
Sbjct: 7   TQASLFAPANFSTTKSSA---PWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKTETPTK 60

Query: 63  EAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 122
           EAPVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR
Sbjct: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120

Query: 123 QGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQG 182
           +GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR+G
Sbjct: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180

Query: 183 VGVNYRSIGKNVSPIEHKTELKKFH 207
           VG NYRSIGKNVSPIE K   K+ +
Sbjct: 181 VGQNYRSIGKNVSPIEVKFTGKQVY 205

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|157678730|dbj|BAF80470.1| PSI reaction center subunit II [Citrus sinensis] gi|157678958|dbj|BAF80477.1| PSI reaction center subunit II [Citrus sinensis]

 Score =  316 bits (809), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 160/205 (78%), Positives = 171/205 (83%), Gaps = 6/205 (2%)

Query: 3   TQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTK 62
           TQA LF P+  +T  S     PWK +SSFS    +PL  +  +     A AE KTE PTK
Sbjct: 7   TQASLFAPANFSTTKSSA---PWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKTETPTK 60

Query: 63  EAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 122
           EAPVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR
Sbjct: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120

Query: 123 QGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQG 182
           +GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR+G
Sbjct: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180

Query: 183 VGVNYRSIGKNVSPIEHKTELKKFH 207
           VG NYRSIGKNVSPIE K   K+ +
Sbjct: 181 VGQNYRSIGKNVSPIEVKFTGKQVY 205

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727030|ref|NP_001235355.1| photosystem I subunit PsaD [Glycine max] gi|148372347|gb|ABQ63097.1| photosystem I subunit PsaD [Glycine max] gi|255627695|gb|ACU14192.1| unknown [Glycine max]

 Score =  315 bits (808), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 167/202 (82%), Positives = 175/202 (86%), Gaps = 5/202 (2%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQA L TP +   K S     PWK  SS SF+SPKPL FS   RT+RAAAA+E TEAP
Sbjct: 3   MATQASLLTPPLSGLKASDRASVPWKQNSSLSFSSPKPLKFS---RTIRAAAADETTEAP 59

Query: 61  TK--EAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 118
            K   APVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGA
Sbjct: 60  AKVEAAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGA 119

Query: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178
           AIMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN 
Sbjct: 120 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNA 179

Query: 179 GRQGVGVNYRSIGKNVSPIEHK 200
           GRQGVG N+RSIGKNVSPIE K
Sbjct: 180 GRQGVGQNFRSIGKNVSPIEVK 201

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357480841|ref|XP_003610706.1| Photosystem I reaction center subunit II [Medicago truncatula] gi|355512041|gb|AES93664.1| Photosystem I reaction center subunit II [Medicago truncatula] gi|388519753|gb|AFK47938.1| unknown [Medicago truncatula]

 Score =  314 bits (804), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 162/207 (78%), Positives = 174/207 (84%), Gaps = 16/207 (7%)

Query: 1   MATQAGLFTPSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAP 60
           MATQA LFTP + + K       PWK  S+ SF S KP+ F+   +T + +AA+EKTEA 
Sbjct: 3   MATQASLFTPPLSSPK-------PWKQPSTLSFISLKPIKFTT--KTTKISAADEKTEAA 53

Query: 61  ---TKE----APVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEM 113
              TKE    APVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEM
Sbjct: 54  SVTTKEEAPAAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEM 113

Query: 114 PTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP 173
           PTGGAAIMR+GPNLLKLARKEQCLALG RLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP
Sbjct: 114 PTGGAAIMREGPNLLKLARKEQCLALGNRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP 173

Query: 174 EKVNPGRQGVGVNYRSIGKNVSPIEHK 200
           EKVNPGRQGVG N+RSIGKNVSPIE K
Sbjct: 174 EKVNPGRQGVGQNFRSIGKNVSPIEVK 200

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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	229
TAIR|locus:2140255	208	PSAD-1 "AT4G02770" [Arabidopsi	0.864	0.951	0.691	3.5e-68
UNIPROTKB|P12353	212	psaD "Photosystem I reaction c	0.873	0.943	0.691	4.4e-68
TAIR|locus:2007519	204	PSAD-2 "AT1G03130" [Arabidopsi	0.847	0.950	0.696	5.6e-68
UNIPROTKB|Q39615	196	psaD "Photosystem I reaction c	0.580	0.678	0.751	5.1e-51
UNIPROTKB|P19569	141	psaD "Photosystem I reaction c	0.528	0.858	0.669	8.7e-40

TAIR|locus:2140255 PSAD-1 "AT4G02770" [Arabidopsis thaliana (taxid:3702)]

 Score = 692 (248.7 bits), Expect = 3.5e-68, P = 3.5e-68
 Identities = 139/201 (69%), Positives = 148/201 (73%)

Query:     1 MATQA-GLFTPSIITTKTSKLLLNPWXXXXXXXXXXXXXXXXXMAQRTVRXXXXXXXXXX 59
             MATQA G+F  +I T  TS +    +                  A++T            
Sbjct:     1 MATQAAGIFNSAITTAATSGVKKLHFFSTTHRPKSLSFTKTAIRAEKT--DSSAAAAAAP 58

Query:    60 XXXXXXVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
                   VGFTPPQLDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAA
Sbjct:    59 ATKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAA 118

Query:   120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
             IMR+GPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPG
Sbjct:   119 IMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPG 178

Query:   180 RQGVGVNYRSIGKNVSPIEHK 200
             R+GVG+N RSIGKNVSPIE K
Sbjct:   179 REGVGLNMRSIGKNVSPIEVK 199

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009522 "photosystem I" evidence=IEA

GO:0009538 "photosystem I reaction center" evidence=IEA;ISS

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

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0010287 "plastoglobule" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" 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

UNIPROTKB|P12353 psaD "Photosystem I reaction center subunit II, chloroplastic" [Spinacia oleracea (taxid:3562)]

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 139/201 (69%), Positives = 148/201 (73%)

Query:     1 MATQAGLFTPSIITT-KTSKLLLNPWXXXXXXXXXXXXXXXXXMAQRTVRXXXXXXXXXX 59
             MATQA LF+PS +++ K     L                     + R             
Sbjct:     3 MATQATLFSPSSLSSAKPIDTRLTTSFKQPSAVTFASKPASRHHSIRAAAAAEGKAAAAT 62

Query:    60 XXXXXXVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
                    GFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA
Sbjct:    63 ETKEAPKGFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 122

Query:   120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
             IMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNPG
Sbjct:   123 IMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPG 182

Query:   180 RQGVGVNYRSIGKNVSPIEHK 200
             RQGVG+N RSIGKNVSPIE K
Sbjct:   183 RQGVGLNMRSIGKNVSPIEVK 203

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2007519 PSAD-2 "AT1G03130" [Arabidopsis thaliana (taxid:3702)]

 Score = 690 (248.0 bits), Expect = 5.6e-68, P = 5.6e-68
 Identities = 140/201 (69%), Positives = 152/201 (75%)

Query:     1 MATQA-GLFTPSIITTKTSKLLLNPWXXXXXXXXXXXXXXXXXMAQRTVRXXXXXXXXXX 59
             MATQA G+F+P+I TT ++   L+ +                  A++T            
Sbjct:     1 MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIR-AEKT-----ESSSAAP 54

Query:    60 XXXXXXVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAA 119
                   VGFTPPQLDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAA
Sbjct:    55 AVKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAA 114

Query:   120 IMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPG 179
             IMR+GPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPG
Sbjct:   115 IMREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPG 174

Query:   180 RQGVGVNYRSIGKNVSPIEHK 200
             R+GVG+N RSIGKNVSPIE K
Sbjct:   175 REGVGLNMRSIGKNVSPIEVK 195

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009522 "photosystem I" evidence=IEA

GO:0009538 "photosystem I reaction center" evidence=IEA;ISS

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

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

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

GO:0030003 "cellular cation homeostasis" evidence=RCA

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

GO:0070838 "divalent metal ion transport" evidence=RCA

UNIPROTKB|Q39615 psaD "Photosystem I reaction center subunit II, chloroplastic" [Chlamydomonas reinhardtii (taxid:3055)]

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 100/133 (75%), Positives = 114/133 (85%)

Query:    68 FTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNL 127
             +T P L+P+TPSPIFGGSTGGLLRKAQ EEFYVITWE+ KEQIFEMPTGGAAIMRQGPNL
Sbjct:    53 WTVPTLNPDTPSPIFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNL 112

Query:   128 LKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNY 187
             LK  +KEQCLAL T+LR+K+K+   FYRVFP+G+VQYLHP DGVYPEKVN GR G   N 
Sbjct:   113 LKFGKKEQCLALTTQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNM 172

Query:   188 RSIGKNVSPIEHK 200
             R IG+NV+PI+ K
Sbjct:   173 RRIGQNVNPIKVK 185

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|P19569 psaD "Photosystem I reaction center subunit II" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 424 (154.3 bits), Expect = 8.7e-40, P = 8.7e-40
 Identities = 83/124 (66%), Positives = 95/124 (76%)

Query:    80 PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLAL 139
             P FGGSTGGLL KA  EE Y ITW S  EQ+FEMPTGGAAIM +G NLL LARKEQCLAL
Sbjct:     9 PKFGGSTGGLLSKANREEKYAITWTSASEQVFEMPTGGAAIMNEGENLLYLARKEQCLAL 68

Query:   140 GTRLRSKYKIK---YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSP 196
             GT+LR+K+K K   Y+ YRV+P+GEVQYLHP DGV+PEKVN GR+  G   R IG+N  P
Sbjct:    69 GTQLRTKFKPKIQDYKIYRVYPSGEVQYLHPADGVFPEKVNEGREAQGTKTRRIGQNPEP 128

Query:   197 IEHK 200
             +  K
Sbjct:   129 VTIK 132


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        0.319   0.136   0.414    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      229       196   0.00080  111 3  11 22  0.48    32
                                                     31  0.44    35


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:  5
  No. of states in DFA:  596 (63 KB)
  Total size of DFA:  172 KB (2101 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:  18.00u 0.11s 18.11t   Elapsed:  00:00:01
  Total cpu time:  18.00u 0.11s 18.11t   Elapsed:  00:00:01
  Start:  Tue May 21 03:43:37 2013   End:  Tue May 21 03:43:38 2013

GO:0005515 "protein binding" evidence=IPI

GO:0030094 "plasma membrane-derived photosystem I" 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)
P84563	PSAD_POPEU	No assigned EC number	0.9310	0.1266	1.0	N/A	no
P12372	PSAD_SOLLC	No assigned EC number	0.7451	0.8864	0.9759	N/A	no
P12353	PSAD_SPIOL	No assigned EC number	0.7475	0.8689	0.9386	N/A	no
Q9S7H1	PSAD1_ARATH	No assigned EC number	0.7320	0.8296	0.9134	no	no
P36213	PSAD_HORVU	No assigned EC number	0.6826	0.8122	0.9073	N/A	no
Q9SA56	PSAD2_ARATH	No assigned EC number	0.7425	0.8427	0.9460	yes	no
P32869	PSAD_CUCSA	No assigned EC number	0.7355	0.8820	0.9758	N/A	no
P29302	PSAD_NICSY	No assigned EC number	0.75	0.8689	0.9754	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

Fail to connect to STRING server

---

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	229
PLN00041	196	PLN00041, PLN00041, photosystem I reaction center	1e-112
pfam02531	139	pfam02531, PsaD, PsaD	2e-87
CHL00145	139	CHL00145, psaD, photosystem I subunit II; Validate	3e-74

>gnl|CDD|215039 PLN00041, PLN00041, photosystem I reaction center subunit II; Provisional

 Score =  318 bits (817), Expect = e-112
 Identities = 154/191 (80%), Positives = 159/191 (83%), Gaps = 4/191 (2%)

Query: 10  PSIITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTKEAPVGFT 69
            +I T  +S   L PW    S S TS  P + S A R VRAAAA E  EA  KEAPVGFT
Sbjct: 1   TTITTPASSGRKLVPWASFLSKS-TSKAPASLS-ATRAVRAAAAAE--EAAAKEAPVGFT 56

Query: 70  PPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLK 129
           PP L+PNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLK
Sbjct: 57  PPTLNPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLK 116

Query: 130 LARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRS 189
           LARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEKVNPGR GVG N RS
Sbjct: 117 LARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRVGVGQNMRS 176

Query: 190 IGKNVSPIEHK 200
           IGKNV+PIE K
Sbjct: 177 IGKNVNPIEVK 187

Length = 196

>gnl|CDD|145591 pfam02531, PsaD, PsaD

 Score =  254 bits (651), Expect = 2e-87
 Identities = 97/131 (74%), Positives = 110/131 (83%), Gaps = 1/131 (0%)

Query: 71  PQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKL 130
           P L+ NTPSPIFGGSTGGLLRKA+ EE Y ITW S KEQ+FEMPTGGAAIMR+G NLL L
Sbjct: 1   PTLNGNTPSPIFGGSTGGLLRKAETEEKYAITWTSKKEQVFEMPTGGAAIMREGENLLYL 60

Query: 131 ARKEQCLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRS 189
           ARKEQCLALGT+LR+K+KI+ Y+ YR+FP GEVQYLHPKDGV+PEKVN GR+GVG   R 
Sbjct: 61  ARKEQCLALGTQLRTKFKIEDYKIYRIFPGGEVQYLHPKDGVFPEKVNEGREGVGSVPRR 120

Query: 190 IGKNVSPIEHK 200
           IGKN +P   K
Sbjct: 121 IGKNPNPANVK 131

This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the electrostatic binding of ferredoxin within the reaction centre. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment. Length = 139

>gnl|CDD|177067 CHL00145, psaD, photosystem I subunit II; Validated

 Score =  220 bits (563), Expect = 3e-74
 Identities = 95/129 (73%), Positives = 104/129 (80%), Gaps = 1/129 (0%)

Query: 73  LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLAR 132
           L+   PSP FGGSTGG LR A+VEE Y ITW SPKEQIFEMPTGGAAIMR G NLL LAR
Sbjct: 3   LNLQMPSPTFGGSTGGWLRAAEVEEKYAITWTSPKEQIFEMPTGGAAIMRNGENLLYLAR 62

Query: 133 KEQCLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIG 191
           KEQCLALGT+LR+K+KI  Y+ YR+FPNGEVQYLHPKDGV+PEKVNPGR  VG    SIG
Sbjct: 63  KEQCLALGTQLRTKFKINDYKIYRIFPNGEVQYLHPKDGVFPEKVNPGRVAVGSRDFSIG 122

Query: 192 KNVSPIEHK 200
           KN +P   K
Sbjct: 123 KNPNPASVK 131

Length = 139

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	229
PLN00041	196	photosystem I reaction center subunit II; Provisio	100.0
CHL00145	139	psaD photosystem I subunit II; Validated	100.0
PF02531	139	PsaD: PsaD; InterPro: IPR003685 PsaD is a small, e	100.0

>PLN00041 photosystem I reaction center subunit II; Provisional

Probab=100.00  E-value=6.5e-101  Score=650.50  Aligned_cols=192  Identities=78%  Similarity=1.166  Sum_probs=168.0

Q ss_pred             ccccCCccccccCCCCCcceecCCCCccccchhhHHHHHhhhccCCCCCCCCCCCCCCCcCCCCCCCcccccCccccccc
Q 047658           13 ITTKTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRK   92 (229)
Q Consensus        13 ~t~~~~~~~~~p~k~~s~~s~~s~~~~~~~~~~~~~~a~~~~~~a~~~~~~ap~~f~pp~l~~~tp~P~FgGSTGGlLr~   92 (229)
                      .+.+++.+...+|+++  ++++..+.....+..+..+++++++.  ++++++|++|+||++|+++|+|+||||||||||+
T Consensus         4 ~~~as~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~t~~~~~l~~~~P~FgGSTGGlL~~   79 (196)
T PLN00041          4 TTPASSGRKLVPWASF--LSKSTSKAPASLSATRAVRAAAAAEE--AAAKEAPVGFTPPTLNPNTPSPIFGGSTGGLLRK   79 (196)
T ss_pred             cccccccceeeeeccc--cccccccccccccchhHHHHHhhhcc--cccccCCCCcCCcccCCCCCCCcccccchhhhhh
Confidence            3345666777899776  44444322223333333333333322  3677899999999999999999999999999999


Q ss_pred             cccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhccccceeeeeeeeeecCCCceEeeccCCCCC
Q 047658           93 AQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVY  172 (229)
Q Consensus        93 A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI~ykiYRifP~Gevq~LHPkDGVf  172 (229)
                      ||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+|||+||||||||||||||||+||||||||||
T Consensus        80 Ae~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLlylARKEQCLALgtQLrtkfKIdykiYRifP~Ge~q~LHPkDGVf  159 (196)
T PLN00041         80 AQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVY  159 (196)
T ss_pred             hhhhhheEEEecCChhheeecCCchhhhhhcCchHHHHHHHHHHHHHHHHHhhhcccceeEEEEcCCCceEEecCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccCCCccccCcccccCCCCCCCceeeeccchhhh
Q 047658          173 PEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHK  208 (229)
Q Consensus       173 PEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d  208 (229)
                      |||||+||++||+|+|+||+|+||++||||||++||
T Consensus       160 PEKvN~GR~~vg~~~r~IG~N~nP~~vKFsgk~~yd  195 (196)
T PLN00041        160 PEKVNPGRVGVGQNMRSIGKNVNPIEVKFTGKQAYD  195 (196)
T ss_pred             ccccCCcccccCCCCccccCCCCcceEEecCCccCC
Confidence            999999999999999999999999999999999998

>CHL00145 psaD photosystem I subunit II; Validated

Probab=100.00  E-value=1.1e-94  Score=588.92  Aligned_cols=138  Identities=70%  Similarity=1.086  Sum_probs=136.2

Q ss_pred             CcCCCCCCCcccccCccccccccccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhccccceee-
Q 047658           71 PQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKI-  149 (229)
Q Consensus        71 p~l~~~tp~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-  149 (229)
                      +++++++++|+||||||||||+||+||||||||+|++||||||||||||+||+|+|||||||||||||||+|||+|||| 
T Consensus         1 m~~~l~~~~P~fgGSTGGlL~~Ae~EEkYaITWtS~keqvFEmPTGGAA~M~~G~NLlylARKEQclALgtQLrtkfKI~   80 (139)
T CHL00145          1 MTLNLQMPSPTFGGSTGGWLRAAEVEEKYAITWTSPKEQIFEMPTGGAAIMRNGENLLYLARKEQCLALGTQLRTKFKIN   80 (139)
T ss_pred             CccccCCCCccccccchhhhhcccceeeEEEEecCCccceeecCCchhhhhhcCchhhhhhHHHHHHHHHHHHhhccccc
Confidence            4689999999999999999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             eeeeeeecCCCceEeeccCCCCCCcccCCCccccCcccccCCCCCCCceeeeccchhhh
Q 047658          150 KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHK  208 (229)
Q Consensus       150 ~ykiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d  208 (229)
                      ||||||||||||+|||||||||||||||+||+.||+++|+||+||||++||||||++||
T Consensus        81 dyKIYRifP~Ge~~~LhPkDGVfpEKvN~GR~~vg~~~r~IG~NpnP~~~KFsgk~tyd  139 (139)
T CHL00145         81 DYKIYRIFPNGEVQYLHPKDGVFPEKVNPGRVAVGSRDFSIGKNPNPASVKFTGKATYD  139 (139)
T ss_pred             ccEEEEECCCCceEEecCCCCCCcccccCcccccCCCcccccCCCCcceEEecCccCCC
Confidence            89999999999999999999999999999999999999999999999999999999997

>PF02531 PsaD: PsaD; InterPro: IPR003685 PsaD is a small, extrinsic polypeptide located on the stromal side (cytoplasmic side in cyanobacteria) of the photosystem I reaction centre complex

Probab=100.00  E-value=4.1e-94  Score=585.54  Aligned_cols=137  Identities=72%  Similarity=1.140  Sum_probs=116.8

Q ss_pred             cCCCCCCCcccccCccccccccccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhccccceee-e
Q 047658           72 QLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKI-K  150 (229)
Q Consensus        72 ~l~~~tp~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-~  150 (229)
                      +||+++|+|+||||||||||+||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+|||+|||| |
T Consensus         2 tL~~~~p~P~FgGSTGGlL~~Ae~EEkYaITWts~keqvFEmPTGGAA~M~~G~NLlylARKEQclALgtQLrtkfKI~d   81 (139)
T PF02531_consen    2 TLNGKTPSPIFGGSTGGLLRSAETEEKYAITWTSPKEQVFEMPTGGAAIMREGENLLYLARKEQCLALGTQLRTKFKIED   81 (139)
T ss_dssp             --SSB--SSB---BTTSC-TCCCCT-EEEEEEEESSSEEEETTTTCEEEE-SCCEEEEESSCCCCCCCCCCTCCSCTS--
T ss_pred             ccCCCCCCCcccccchhhhhccccceeEEEEecCCcceeEeccCchhHhhhcCchhhhhHHHHHHHHHHHHHhhheeecc
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999999 8


Q ss_pred             eeeeeecCCCceEeeccCCCCCCcccCCCccccCcccccCCCCCCCceeeeccchhhh
Q 047658          151 YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHK  208 (229)
Q Consensus       151 ykiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d  208 (229)
                      |||||||||||+|||||||||||||||+||+.||+++|+||+||||++||||||++||
T Consensus        82 ykIYRifp~Ge~~~lHPkDGVfpEKvN~GR~~vg~~~r~IG~NpnP~~~KFsgk~t~d  139 (139)
T PF02531_consen   82 YKIYRIFPNGEVQYLHPKDGVFPEKVNEGREGVGKVDRSIGKNPNPATVKFSGKATYD  139 (139)
T ss_dssp             EEEEEE-TT--CEECCTTTSSSSSS-STT-S--SECSS-CCCTTSHHHCTTSTTSTT-
T ss_pred             ceEEEEcCCCceEEeccCCCCCccccCCchhhcCCCCccccCCCCccccccCCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999998

It is required for native assembly of PSI reaction clusters and is implicated in the electrostatic binding of ferredoxin within the reaction centre []. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment [].; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 2WSF_D 2O01_D 2WSC_D 2WSE_D 1JB0_D 3PCQ_D.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	229
2wsc_D	212	Improved Model Of Plant Photosystem I Length = 212		3e-72
3lw5_D	138	Improved Model Of Plant Photosystem I Length = 138		2e-68
2o01_D	138	The Structure Of A Plant Photosystem I Supercomplex		2e-68
1jb0_D	138	Crystal Structure Of Photosystem I: A Photosyntheti		9e-38

>pdb|2WSC|D Chain D, Improved Model Of Plant Photosystem I Length = 212

Iteration: 1
 Score =  267 bits (683), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 126/133 (94%), Positives = 130/133 (97%)
Query: 68  FTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNL 127
           FTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR+GPNL
Sbjct: 71  FTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNL 130
Query: 128 LKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNY 187
           LKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNPGRQGVG+N 
Sbjct: 131 LKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGLNM 190
Query: 188 RSIGKNVSPIEHK 200
           RSIGKNVSPIE K
Sbjct: 191 RSIGKNVSPIEVK 203

>pdb|3LW5|D Chain D, Improved Model Of Plant Photosystem I Length = 138

Iteration: 1
 Score =  254 bits (650), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 122/129 (94%), Positives = 126/129 (97%)
Query: 72  QLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLA 131
           +LDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAIMR+GPNLLKLA
Sbjct: 1   ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLA 60
Query: 132 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIG 191
           RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN GRQGVG N+RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIG 120
Query: 192 KNVSPIEHK 200
           KNVSPIE K
Sbjct: 121 KNVSPIEVK 129

>pdb|2O01|D Chain D, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 138

Iteration: 1
 Score =  254 bits (650), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 122/129 (94%), Positives = 126/129 (97%)
Query: 72  QLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLA 131
           +LDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR+GPNLLKLA
Sbjct: 1   ELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 60
Query: 132 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIG 191
           RKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNPGRQGVG+N RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGLNMRSIG 120
Query: 192 KNVSPIEHK 200
           KNVSPIE K
Sbjct: 121 KNVSPIEVK 129

>pdb|1JB0|D Chain D, Crystal Structure Of Photosystem I: A Photosynthetic Reaction Center And Core Antenna System From Cyanobacteria Length = 138

Iteration: 1
 Score =  153 bits (386), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 75/127 (59%), Positives = 92/127 (72%), Gaps = 1/127 (0%)
Query: 80  PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLAL 139
           P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MR+G NL+  ARKEQCLAL
Sbjct: 8   PLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLAL 67
Query: 140 GT-RLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIE 198
              +LR +    Y+ YR+FP+GE   +HPKDGV+PEKVN GR+ V    RSIG+N +P +
Sbjct: 68  AAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQ 127
Query: 199 HKTELKK 205
            K   KK
Sbjct: 128 LKFTGKK 134

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
2wsc_D	212	Photosystem I reaction center subunit II, chloropl	4e-88
1jb0_D	138	Photosystem 1 reaction centre subunit II; membrane	4e-69
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>2wsc_D Photosystem I reaction center subunit II, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Spinacia oleracea} PDB: 2wse_D* 2wsf_D* 2o01_D* 3lw5_D* Length = 212

 Score =  258 bits (659), Expect = 4e-88
 Identities = 145/202 (71%), Positives = 158/202 (78%), Gaps = 3/202 (1%)

Query: 1   MATQAGLFTPSIITT--KTSKLLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKTE 58
           M T A LF+ S +++       L   +K  S+ +F S  P +     R   AA  +    
Sbjct: 3   MGTPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFASK-PASRLHTIRAAAAAEGKAAAA 61

Query: 59  APTKEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 118
             TKEA   FTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA
Sbjct: 62  TETKEATKAFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 121

Query: 119 AIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 178
           AIMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNP
Sbjct: 122 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNP 181

Query: 179 GRQGVGVNYRSIGKNVSPIEHK 200
           GRQGVG+N RSIGKNVSPIE K
Sbjct: 182 GRQGVGLNMRSIGKNVSPIEVK 203

>1jb0_D Photosystem 1 reaction centre subunit II; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.187.1.1 PDB: 3pcq_D* Length = 138

 Score =  207 bits (528), Expect = 4e-69
 Identities = 73/126 (57%), Positives = 89/126 (70%), Gaps = 1/126 (0%)

Query: 76  NTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQ 135
               P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MR+G NL+  ARKEQ
Sbjct: 4   TGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQ 63

Query: 136 CLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNV 194
           CLAL  +     KI  Y+ YR+FP+GE   +HPKDGV+PEKVN GR+ V    RSIG+N 
Sbjct: 64  CLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNP 123

Query: 195 SPIEHK 200
           +P + K
Sbjct: 124 NPSQLK 129

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.0 bits (95), Expect = 2e-04
 Identities = 35/223 (15%), Positives = 65/223 (29%), Gaps = 53/223 (23%)

Query: 16  KTSKLLL-NPWKPT--SSFSFTSPKPLTFSMAQRTVRAAAAEEKTEAPTKEAPVGFTPPQ 72
           +   L+L N       ++F+ +  K L  +  ++     +A   T        +  TP +
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSC-KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE 302

Query: 73  LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMP---TGGAAIMRQGPNLLK 129
                           LL K           + P+E +   P   +  A  +R G     
Sbjct: 303 -------------VKSLLLKY----LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 130 LARKEQCLALGTRLRSKYKI-----KYQFYR---VFPNGEVQYLHPKDGVY-PEKVNPGR 180
             +   C  L T + S   +       + +    VFP             + P  +    
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP----------PSAHIPTIL---- 391

Query: 181 QGVGVNYRSIGKNVSPIEHKTELKKFHKRWLHMEHLIKSLCSV 223
                    I  +V   +    + K HK  L  +   +S  S+
Sbjct: 392 ------LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
2wsc_D	212	Photosystem I reaction center subunit II, chloropl	100.0
1jb0_D	138	Photosystem 1 reaction centre subunit II; membrane	100.0

>2wsc_D Photosystem I reaction center subunit II, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Spinacia oleracea} PDB: 2wse_D* 2wsf_D* 2o01_D* 3lw5_D*

Probab=100.00  E-value=1.4e-107  Score=696.61  Aligned_cols=205  Identities=74%  Similarity=1.105  Sum_probs=136.8

Q ss_pred             CccccccCCCccccc-cCCc-cccccCCCCCcceecCCCCccccchhhHHHHHhhhccC-CCC-CCCCCCCCCCCcCCCC
Q 047658            1 MATQAGLFTPSIITT-KTSK-LLLNPWKPTSSFSFTSPKPLTFSMAQRTVRAAAAEEKT-EAP-TKEAPVGFTPPQLDPN   76 (229)
Q Consensus         1 MAtQas~~tp~~~t~-~~~~-~~~~p~k~~s~~s~~s~~~~~~~~~~~~~~a~~~~~~a-~~~-~~~ap~~f~pp~l~~~   76 (229)
                      |||||++|+|+++++ +++. .+..|||++++++|+ +++  ..++.+.++++++|+++ +++ ++++|++|+||+||++
T Consensus         3 matqa~~~~~~~~s~~~~~~~~~~~~w~~s~~~~~~-~k~--~~~~~~~~~a~~ae~~~a~~~~~~~ap~~f~p~~~~l~   79 (212)
T 2wsc_D            3 MGTPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFA-SKP--ASRLHTIRAAAAAEGKAAAATETKEATKAFTPPELDPN   79 (212)
T ss_dssp             ---------------------------------------------------------------------------CCSSC
T ss_pred             cccccccccccccccccccccccccccccccccccc-ccc--cccccchhhhhhcccccccccccccCCCccCCccccCC
Confidence            789999999998776 3333 236799999999997 444  33333444443555433 333 3689999999999999


Q ss_pred             CCCcccccCccccccccccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhccccceeeeeeeeee
Q 047658           77 TPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRV  156 (229)
Q Consensus        77 tp~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI~ykiYRi  156 (229)
                      +|+|+||||||||||+||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+|||+|||||||||||
T Consensus        80 ~~~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKIdykiYRi  159 (212)
T 2wsc_D           80 TPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRV  159 (212)
T ss_dssp             CCCSCCCCCSSSCCSTTTSSCCCEEECCCSSCCCCCTTTTCCCCCCCSSCEEECSSTTTTSHHHHTTTSSCCSCCEEECC
T ss_pred             CCCcccccccccccccccceeeEEEEecCChhheeecCCCcchhhccCcchheehhHHHHHHHHHhhhhccccccceEee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCceEeeccCCCCCCcccCCCccccCcccccCCCCCCCceeeeccchhhh
Q 047658          157 FPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHK  208 (229)
Q Consensus       157 fP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d  208 (229)
                      |||||+|||||||||||||||+||++||+|+|+||+|+||++|||+||++||
T Consensus       160 fP~Ge~q~LhPkDGVfPEKVN~GR~~vg~~~r~IG~N~nP~~~KFsgk~~yd  211 (212)
T 2wsc_D          160 FPSGEVQYLHPKDGVYPEKVNPGRQGVGLNMRSIGKNVSPIEVKFTGKQPYD  211 (212)
T ss_dssp             CSSCCSCCTTTSSSCSSSCCSCCCSCCCCSSSCSTTTTSCCCSCCCTTSSCC
T ss_pred             cCCCceEEecCcCCCCccccCCcccccCcCcccccCCCCcceEEecCccccc
Confidence            9999999999999999999999999999999999999999999999999998

>1jb0_D Photosystem 1 reaction centre subunit II; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.187.1.1 PDB: 3pcq_D*

Probab=100.00  E-value=1.9e-92  Score=574.18  Aligned_cols=135  Identities=57%  Similarity=0.934  Sum_probs=133.2

Q ss_pred             CCCCCCcccccCccccccccccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhc-cccceee-ee
Q 047658           74 DPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTR-LRSKYKI-KY  151 (229)
Q Consensus        74 ~~~tp~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtq-LrtkfKI-~y  151 (229)
                      ++++++|+||||||||||+||+||||||||+|++||||||||||||+||+|+|||||||||||||||+| ||+ ||| ||
T Consensus         2 ~l~~~~P~fgGSTGGlL~~A~~EEkYaITWtS~keQvFEmPTGGAA~M~~G~NLlylARKEQclALgtQqLrt-fKI~dy   80 (138)
T 1jb0_D            2 TLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLALAAQQLRP-RKINDY   80 (138)
T ss_dssp             CCCCBCCBCCCBTTSBCTHHHHTCEEEEEEEESSCEEEECTTSSEEEECSEEEEEEESSHHHHHHHHHHHTGG-GTCCCC
T ss_pred             CcCCCCCccccccccccccccceeeEEEEecCChhhheecCCCchhhhccCcceeEeecHHHHHHhhhcceee-eecccc
Confidence            588999999999999999999999999999999999999999999999999999999999999999999 999 999 89


Q ss_pred             eeeeecCCCceEeeccCCCCCCcccCCCccccCcccccCCCCCCCceeeeccchhhhh
Q 047658          152 QFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHKR  209 (229)
Q Consensus       152 kiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d~  209 (229)
                      ||||||||||+|||||||||||||||+||.+||+++|+||+||||++||||||++||+
T Consensus        81 kiYRifP~Ge~~~LhPkDGVfpEKvN~GR~~vg~~~r~IG~NpnP~~~KFsgk~t~d~  138 (138)
T 1jb0_D           81 KIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQLKFTGKKPYDP  138 (138)
T ss_dssp             EEEEECTTCCEEEEETTTSSCSSSCCTTCCCCSEESSCGGGCCCHHHHTTSCCCTTCC
T ss_pred             eEEEEcCCCceEEecCCCCCCcccccCcccccCcCcccccCCCCcceEEecCcccCCC
Confidence            9999999999999999999999999999999999999999999999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	229
d1jb0d_	138	d.187.1.1 (D:) Photosystem I subunit PsaD {Synecho	2e-74

>d1jb0d_ d.187.1.1 (D:) Photosystem I subunit PsaD {Synechococcus elongatus [TaxId: 32046]} Length = 138

class: Alpha and beta proteins (a+b)
fold: Photosystem I subunit PsaD
superfamily: Photosystem I subunit PsaD
family: Photosystem I subunit PsaD
domain: Photosystem I subunit PsaD
species: Synechococcus elongatus [TaxId: 32046]

 Score =  219 bits (560), Expect = 2e-74
 Identities = 73/126 (57%), Positives = 89/126 (70%), Gaps = 1/126 (0%)

Query: 76  NTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQ 135
               P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MR+G NL+  ARKEQ
Sbjct: 4   TGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQ 63

Query: 136 CLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNV 194
           CLAL  +     KI  Y+ YR+FP+GE   +HPKDGV+PEKVN GR+ V    RSIG+N 
Sbjct: 64  CLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNP 123

Query: 195 SPIEHK 200
           +P + K
Sbjct: 124 NPSQLK 129

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	229
d1jb0d_	138	Photosystem I subunit PsaD {Synechococcus elongatu	100.0

>d1jb0d_ d.187.1.1 (D:) Photosystem I subunit PsaD {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a+b)
fold: Photosystem I subunit PsaD
superfamily: Photosystem I subunit PsaD
family: Photosystem I subunit PsaD
domain: Photosystem I subunit PsaD
species: Synechococcus elongatus [TaxId: 32046]

Probab=100.00  E-value=7.2e-91  Score=562.75  Aligned_cols=134  Identities=56%  Similarity=0.909  Sum_probs=132.0

Q ss_pred             CCCCCcccccCccccccccccceeEEEEecCCcceeeeccCCcchhcccCcchhhhhhhhhHHHhhhccccceee-eeee
Q 047658           75 PNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKI-KYQF  153 (229)
Q Consensus        75 ~~tp~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-~yki  153 (229)
                      ++..+|+||||||||||+||+||||||||+|+|||||||||||||+|++|+|||||||||||||||+|++++||| ||||
T Consensus         3 l~g~~P~f~GSTGGlL~~Ae~EEkYaITWts~keqvFEmPTGGAA~M~~G~Nlly~ARKEQclALgtQ~~~~~KI~dyKi   82 (138)
T d1jb0d_           3 LTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLALAAQQLRPRKINDYKI   82 (138)
T ss_dssp             CCCBCCBCCCBTTSBCTHHHHTCEEEEEEEESSCEEEECTTSSEEEECSEEEEEEESSHHHHHHHHHHHTGGGTCCCCEE
T ss_pred             ccCCCccccccccchhhhhhhheeEEEEecCCccceeeccCchhhhhccCcchhhhhHHHHHHHhhhhhcccccccccEE
Confidence            567899999999999999999999999999999999999999999999999999999999999999999999999 8999


Q ss_pred             eeecCCCceEeeccCCCCCCcccCCCccccCcccccCCCCCCCceeeeccchhhh
Q 047658          154 YRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGVNYRSIGKNVSPIEHKTELKKFHK  208 (229)
Q Consensus       154 YRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFsgk~t~d  208 (229)
                      ||||||||+|||||||||||||||+||++||+|+|+||+||||++||||||+|||
T Consensus        83 YRifp~Ge~~~lhPkDGVfpEKVN~GR~~vg~~~r~IG~NpnP~~~KFsgk~tyd  137 (138)
T d1jb0d_          83 YRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQLKFTGKKPYD  137 (138)
T ss_dssp             EEECTTCCEEEEETTTSSCSSSCCTTCCCCSEESSCGGGCCCHHHHTTSCCCTTC
T ss_pred             EEEcCCCceEEeccCCCCCccccCCcccccCCCcccccCCCCcceEEecCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999998