Citrus Sinensis ID: 028581

---

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
MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL
Secondary Structure (PSIPRED)
ccHHHcHHHcccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccEEEEcccccHHHHccccccccccHHHHHHHHHHHHHHccccccEEEEEcccccEEEEccccccccccccccccccccccccccccccccEEEEcccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccEcccEcccEccHHHHccEEEEEEEEcccEEEEcccccEEEEccEEEEEEEccHHHHHHHHHHHcHHHccccEEEEEcccccEEEEEccccccccccccccccccEEcccHHHcccHHHHcccccccccc
Coil and Loop (DISEMBL)
mamaattqaslfapanfsttkssapwkqsssfsvrplkhnaprtnTIKAMaegktetptkeapvgftppeldpntpspifggstggllrkAQVEEFYVITwespkeqifemptggaaimregpNLLKLARKEQCLALGTRLRSKYKIKYQFYRvfpngevqylhpkdgvypekvnpgregvgqnyrsigknvspievkftgkqvydl
Flexible Loop (DISEMBL)
mamaattqaslfapanfsttkssapwkqsssfsvrplkhnaprtntikamaegktetptkeaPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVnpgregvgqnyrsigknvspievkftgkqvydl
Low Complexity Region (SEG)
MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL
Disordered region (IsUnstruct)
*********************************************************************************GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP************************************
Disordered Region (DISOPRED)
********ASLFAPA******************************************************ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPE**********Q*YRSIGKNVSPIEVKFTGK*VYD*
Disordered Region (DISEMBL)
********ASLFAPANF***************SVRPLKHNAPRTNTIKAMAE*********APVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL
Disordered Region (DISPRO)
****************************************************************GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQ****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	207	2.2.26 [Sep-21-2011]
P32869	207	Photosystem I reaction ce	N/A	no	0.971	0.971	0.796	5e-90
P29302	204	Photosystem I reaction ce	N/A	no	0.980	0.995	0.820	2e-86
P12372	208	Photosystem I reaction ce	N/A	no	0.990	0.985	0.793	4e-85
Q9SA56	204	Photosystem I reaction ce	yes	no	0.975	0.990	0.764	1e-82
P12353	212	Photosystem I reaction ce	N/A	no	0.990	0.966	0.75	9e-82
Q9S7H1	208	Photosystem I reaction ce	no	no	0.719	0.716	0.946	1e-80
P36213	205	Photosystem I reaction ce	N/A	no	0.690	0.697	0.902	1e-74
Q39615	196	Photosystem I reaction ce	N/A	no	0.671	0.709	0.741	6e-58
Q9T4W8	220	Photosystem I reaction ce	N/A	no	0.700	0.659	0.650	3e-53
O78502	141	Photosystem I reaction ce	yes	no	0.657	0.964	0.678	1e-49

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

 Score =  330 bits (846), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 168/211 (79%), Positives = 178/211 (84%), Gaps = 10/211 (4%)

Query: 3   MAATTQASLFAPANFSTTKS---SAPWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKTE 56
           MA  TQA+LF P+  ST KS   S PWKQSS+ S    +P    A  + + K  AE +T 
Sbjct: 1   MAMATQATLFTPS-LSTPKSTGISIPWKQSSTLSFLTSKPHLKAASSSRSFKVSAEAETS 59

Query: 57  TPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 116
               EAP GF+PPELDP+TPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA
Sbjct: 60  V---EAPAGFSPPELDPSTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 116

Query: 117 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 176
           AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP
Sbjct: 117 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 176

Query: 177 GREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           GREGVGQN+RSIGKNVSPIEVKFTGKQVYDL
Sbjct: 177 GREGVGQNFRSIGKNVSPIEVKFTGKQVYDL 207

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

 Score =  318 bits (815), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 169/206 (82%), Positives = 176/206 (85%), Gaps = 3/206 (1%)

Query: 3   MAATTQASLFAPANFSTTKSSAPWKQS-SSFSVRPLKHNAPRTNTIKAMAEGKTETPTKE 61
           MA  TQASLF PA  S  KSSAPWKQS +SFS + LK        I+AMAE        E
Sbjct: 1   MAMATQASLFTPA-LSAPKSSAPWKQSLASFSPKQLKSTVSAPRPIRAMAEEAATK-EAE 58

Query: 62  APVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRE 121
           APVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRE
Sbjct: 59  APVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRE 118

Query: 122 GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGV 181
           G NLLKLARKEQCLALGTRLRSKYKI Y+FYRVFPNGEVQYLHPKDGVYPEKVN GR+GV
Sbjct: 119 GANLLKLARKEQCLALGTRLRSKYKINYRFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGV 178

Query: 182 GQNYRSIGKNVSPIEVKFTGKQVYDL 207
           GQN+RSIGKN SPIEVKFTGKQVYDL
Sbjct: 179 GQNFRSIGKNKSPIEVKFTGKQVYDL 204

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

 Score =  313 bits (803), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 165/208 (79%), Positives = 173/208 (83%), Gaps = 3/208 (1%)

Query: 3   MAATTQASLFAPANFSTTKSSAPWKQS-SSFSV-RPLKHNAPRTNTIKAMAEGKTETPT- 59
           MA  TQASLF P       ++APWKQS  SFS  + LK     T  I+AMAE        
Sbjct: 1   MAMATQASLFTPPLSVPKSTTAPWKQSLVSFSTPKQLKSTVSVTRPIRAMAEEAPAATEE 60

Query: 60  KEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM 119
           K AP GFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM
Sbjct: 61  KPAPAGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM 120

Query: 120 REGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRE 179
           R+GPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRE
Sbjct: 121 RQGPNLLKLARKEQCLALGTRLRSKYKINYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRE 180

Query: 180 GVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           GVGQN+RSIGKN S IEVKFTGKQVYD+
Sbjct: 181 GVGQNFRSIGKNKSAIEVKFTGKQVYDI 208

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

 Score =  305 bits (782), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 156/204 (76%), Positives = 164/204 (80%), Gaps = 2/204 (0%)

Query: 5   ATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETP-TKEAP 63
           AT  A +F+PA  +TT S+       S S RP   +  +T       E  +  P  KEAP
Sbjct: 2   ATQAAGIFSPA-ITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP 60

Query: 64  VGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGP 123
           VGFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAAIMREGP
Sbjct: 61  VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP 120

Query: 124 NLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQ 183
           NLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPGREGVG 
Sbjct: 121 NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL 180

Query: 184 NYRSIGKNVSPIEVKFTGKQVYDL 207
           N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 181 NMRSIGKNVSPIEVKFTGKQSYDL 204

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

 Score =  302 bits (774), Expect = 9e-82,   Method: Compositional matrix adjust.
 Identities = 159/212 (75%), Positives = 174/212 (82%), Gaps = 7/212 (3%)

Query: 3   MAATTQASLFAPANFST-----TKSSAPWKQSS--SFSVRPLKHNAPRTNTIKAMAEGKT 55
           MA  TQA+LF+P++ S+     T+ +  +KQ S  +F+ +P   +        A  +   
Sbjct: 1   MAMATQATLFSPSSLSSAKPIDTRLTTSFKQPSAVTFASKPASRHHSIRAAAAAEGKAAA 60

Query: 56  ETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG 115
            T TKEAP GFTPPELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG
Sbjct: 61  ATETKEAPKGFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG 120

Query: 116 AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN 175
           AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVN
Sbjct: 121 AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVN 180

Query: 176 PGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           PGR+GVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 181 PGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL 212

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

 Score =  298 bits (764), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 141/149 (94%), Positives = 142/149 (95%)

Query: 59  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
           TKEAPVGFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAAI
Sbjct: 60  TKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAI 119

Query: 119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
           MREGPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPGR
Sbjct: 120 MREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGR 179

Query: 179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           EGVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 180 EGVGLNMRSIGKNVSPIEVKFTGKQSYDL 208

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

 Score =  279 bits (713), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 129/143 (90%), Positives = 136/143 (95%)

Query: 65  GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN 124
           GF PP+LDP+TPSPIFGGSTGGLLRKAQVEEFYVITW SPKEQ+FEMPTGGAAIMREGPN
Sbjct: 63  GFVPPQLDPSTPSPIFGGSTGGLLRKAQVEEFYVITWTSPKEQVFEMPTGGAAIMREGPN 122

Query: 125 LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQN 184
           LLKLARKEQCLALG RLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEKVN GR+GVGQN
Sbjct: 123 LLKLARKEQCLALGNRLRSKYKIAYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQN 182

Query: 185 YRSIGKNVSPIEVKFTGKQVYDL 207
           +RSIGKNVSPIEVKFTGK  +D+
Sbjct: 183 FRSIGKNVSPIEVKFTGKNSFDI 205

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 =  223 bits (568), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 103/139 (74%), Positives = 121/139 (87%)

Query: 66  FTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNL 125
           +T P L+P+TPSPIFGGSTGGLLRKAQ EEFYVITWE+ KEQIFEMPTGGAAIMR+GPNL
Sbjct: 53  WTVPTLNPDTPSPIFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNL 112

Query: 126 LKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNY 185
           LK  +KEQCLAL T+LR+K+K+   FYRVFP+G+VQYLHP DGVYPEKVN GR G  QN 
Sbjct: 113 LKFGKKEQCLALTTQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNM 172

Query: 186 RSIGKNVSPIEVKFTGKQV 204
           R IG+NV+PI+VKF+G+ +
Sbjct: 173 RRIGQNVNPIKVKFSGRMM 191

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 =  207 bits (528), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 95/146 (65%), Positives = 117/146 (80%), Gaps = 1/146 (0%)

Query: 62  APVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRE 121
           AP  F+ P L+ N P+PIFGGSTGGLLRKA+VEEFY ITW    E +FE+PTGGAAIMR 
Sbjct: 70  APKPFSVPTLNLNAPTPIFGGSTGGLLRKAEVEEFYSITWTGKSETVFELPTGGAAIMRA 129

Query: 122 GPNLLKLARKEQCLALGTRLRSKYKI-KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180
           G NLL+LARKEQC+ALG +L+ K+KI  Y+ YRV+P+GEVQ+LHPKDGV+PEKVNPGR  
Sbjct: 130 GENLLRLARKEQCIALGAQLKDKFKITDYKIYRVYPSGEVQFLHPKDGVFPEKVNPGRVA 189

Query: 181 VGQNYRSIGKNVSPIEVKFTGKQVYD 206
           VG N R IG+N  P ++KF G++ +D
Sbjct: 190 VGSNKRRIGQNPDPAKLKFKGQETFD 215

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 =  196 bits (497), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 93/137 (67%), Positives = 110/137 (80%), Gaps = 1/137 (0%)

Query: 71  LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLAR 130
           L+   PSP F GSTGG LR A+ EE Y ITW SPKEQ+FEMPTGGAAIMR+G NLL LAR
Sbjct: 5   LNLQIPSPTFEGSTGGWLRAAETEEKYAITWTSPKEQVFEMPTGGAAIMRKGENLLYLAR 64

Query: 131 KEQCLALGTRLRSKYKI-KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           KEQCLALGT++++ +KI  Y+ YR+FP+GEVQYLHPKDGV+PEKVNPGR GVG    SIG
Sbjct: 65  KEQCLALGTQVKTSFKITDYKIYRIFPSGEVQYLHPKDGVFPEKVNPGRIGVGNVSHSIG 124

Query: 190 KNVSPIEVKFTGKQVYD 206
           KN++P ++KFT K   D
Sbjct: 125 KNLNPAQIKFTNKSFCD 141

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	207
157678730	207	PSI reaction center subunit II [Citrus s	1.0	1.0	1.0	1e-117
157678954	207	PSI reaction center subunit II [Citrus s	1.0	1.0	0.995	1e-117
255551453	208	Photosystem I reaction center subunit II	0.971	0.966	0.816	5e-92
157678962	209	PSI reaction center subunit II [Citrus s	0.966	0.956	0.826	4e-91
225432620	204	PREDICTED: photosystem I reaction center	0.966	0.980	0.822	7e-91
224099787	204	hypothetical protein POPTRDRAFT_564827 [	0.966	0.980	0.808	8e-90
118489639	201	unknown [Populus trichocarpa x Populus d	0.951	0.980	0.822	3e-89
449432708	207	PREDICTED: photosystem I reaction center	0.971	0.971	0.796	2e-88
407769	214	PSI-D1 precursor [Nicotiana sylvestris]	0.985	0.953	0.781	6e-88
224111204	201	hypothetical protein POPTRDRAFT_566261 [	0.951	0.980	0.808	7e-88

>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 =  426 bits (1096), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 207/207 (100%), Positives = 207/207 (100%)

Query: 1   MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK 60
           MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK
Sbjct: 1   MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK 60

Query: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120
           EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR
Sbjct: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120

Query: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180
           EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG
Sbjct: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180

Query: 181 VGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           VGQNYRSIGKNVSPIEVKFTGKQVYDL
Sbjct: 181 VGQNYRSIGKNVSPIEVKFTGKQVYDL 207

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  425 bits (1093), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 206/207 (99%), Positives = 207/207 (100%)

Query: 1   MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK 60
           MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK
Sbjct: 1   MAMAATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTK 60

Query: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120
           EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR
Sbjct: 61  EAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR 120

Query: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180
           EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG
Sbjct: 121 EGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREG 180

Query: 181 VGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           VGQNYRSIGKNVSPIEVKFTGKQVYD+
Sbjct: 181 VGQNYRSIGKNVSPIEVKFTGKQVYDV 207

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

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 =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 173/212 (81%), Positives = 182/212 (85%), Gaps = 11/212 (5%)

Query: 3   MAATTQASLFAPANFSTTKSS----APWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKT 55
           MA  TQASLF P   ST KSS     PWKQSS  S+   +P K++  +     A AEGKT
Sbjct: 1   MAMATQASLFTPTTLSTPKSSNHAIVPWKQSSFLSIPTAKPRKYSIAQKTIKAAAAEGKT 60

Query: 56  ETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG 115
               KEAPVGFTPPELDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGG
Sbjct: 61  ----KEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGG 116

Query: 116 AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN 175
           AAIMR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN
Sbjct: 117 AAIMRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN 176

Query: 176 PGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           PGREGVGQN+RSIGKNVSPIEVKFTGKQVYDL
Sbjct: 177 PGREGVGQNFRSIGKNVSPIEVKFTGKQVYDL 208

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  339 bits (869), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 172/208 (82%), Positives = 182/208 (87%), Gaps = 8/208 (3%)

Query: 7   TQASLFAPANFSTTKSSA----PWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKTETPT 59
           TQA LF P+  +TTK+S     PWK +SSFS    +PL  +  +     A AEGKTE PT
Sbjct: 3   TQAGLFTPS-ITTTKTSKLPLNPWKPTSSFSFTSPKPLTFSMGQRTVRAAGAEGKTEAPT 61

Query: 60  KEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM 119
           KEAPVGFTPP+LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM
Sbjct: 62  KEAPVGFTPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIM 121

Query: 120 REGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRE 179
           R+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR+
Sbjct: 122 RQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQ 181

Query: 180 GVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           GVG NYRSIGKNVSPIEVKFTGKQVYDL
Sbjct: 182 GVGLNYRSIGKNVSPIEVKFTGKQVYDL 209

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

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 =  338 bits (868), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 172/209 (82%), Positives = 180/209 (86%), Gaps = 9/209 (4%)

Query: 3   MAATTQASLFAPANFSTTKSSAPWKQSSSFSVR----PLKHNAPRTNTIKAMAEGKTETP 58
           MA  TQASLF P   S  + + PWK SSS S      P    APRT TI+AMAE   E P
Sbjct: 1   MAMATQASLFTP-TLSGDRVTVPWKSSSSLSFTTPKLPKSSVAPRT-TIRAMAE---EAP 55

Query: 59  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
           TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 56  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 115

Query: 119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
           MR+GPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 116 MRQGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 175

Query: 179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           +GVG N+RSIGKNV+PIEVKFTGKQ YDL
Sbjct: 176 QGVGVNFRSIGKNVNPIEVKFTGKQAYDL 204

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224099787|ref|XP_002311618.1| hypothetical protein POPTRDRAFT_564827 [Populus trichocarpa] gi|222851438|gb|EEE88985.1| hypothetical protein POPTRDRAFT_564827 [Populus trichocarpa]

 Score =  335 bits (858), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 169/209 (80%), Positives = 179/209 (85%), Gaps = 9/209 (4%)

Query: 3   MAATTQASLFAPANFSTTKSS----APWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETP 58
           MA  TQASLF P   ST KSS      WKQSS   +  +K  A R+  + A+ E   +T 
Sbjct: 1   MAMATQASLFTPTTLSTLKSSNQTIVQWKQSSFLPISNVK--AQRSFKVAAVEE---KTA 55

Query: 59  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
           TKEAPVGFTPPELDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 56  TKEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 115

Query: 119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
           MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 116 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 175

Query: 179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           +GVGQN+RSIGKN SPIEVKFTGKQVYDL
Sbjct: 176 QGVGQNFRSIGKNASPIEVKFTGKQVYDL 204

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118489639|gb|ABK96621.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  333 bits (854), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 172/209 (82%), Positives = 179/209 (85%), Gaps = 12/209 (5%)

Query: 3   MAATTQASLFAPANFSTTKSS----APWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETP 58
           MAA  QASLF P   ST KSS    APWKQSS     P+ +  P+     A AE   ET 
Sbjct: 1   MAA--QASLFTPPTLSTLKSSNQAIAPWKQSSFL---PISNVKPQRTMKVAAAE---ETA 52

Query: 59  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
            KEAPVGFTPPELDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 53  VKEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 112

Query: 119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
           MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 113 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 172

Query: 179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           +GVGQN+RSIGKNVSPIEVKFTGKQVYDL
Sbjct: 173 QGVGQNFRSIGKNVSPIEVKFTGKQVYDL 201

Source: Populus trichocarpa x Populus deltoides

Species: Populus trichocarpa x Populus deltoides

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432708|ref|XP_004134141.1| PREDICTED: photosystem I reaction center subunit II, chloroplastic-like [Cucumis sativus] gi|417544|sp|P32869.1|PSAD_CUCSA RecName: Full=Photosystem I reaction center subunit II, chloroplastic; AltName: Full=PS I subunit 5; AltName: Full=Photosystem I 20 kDa subunit; Short=PSI-D; Flags: Precursor gi|227772|prf||1710320A photosystem I 20kD protein

 Score =  330 bits (846), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 168/211 (79%), Positives = 178/211 (84%), Gaps = 10/211 (4%)

Query: 3   MAATTQASLFAPANFSTTKS---SAPWKQSSSFSV---RPLKHNAPRTNTIKAMAEGKTE 56
           MA  TQA+LF P+  ST KS   S PWKQSS+ S    +P    A  + + K  AE +T 
Sbjct: 1   MAMATQATLFTPS-LSTPKSTGISIPWKQSSTLSFLTSKPHLKAASSSRSFKVSAEAETS 59

Query: 57  TPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 116
               EAP GF+PPELDP+TPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA
Sbjct: 60  V---EAPAGFSPPELDPSTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGA 116

Query: 117 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 176
           AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP
Sbjct: 117 AIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNP 176

Query: 177 GREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           GREGVGQN+RSIGKNVSPIEVKFTGKQVYDL
Sbjct: 177 GREGVGQNFRSIGKNVSPIEVKFTGKQVYDL 207

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|407769|dbj|BAA02871.1| PSI-D1 precursor [Nicotiana sylvestris]

 Score =  328 bits (842), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 168/215 (78%), Positives = 183/215 (85%), Gaps = 11/215 (5%)

Query: 3   MAATTQASLFAPANFSTTKSS-----APWKQS-SSFSVRPLKHNAPRTNTIKAMAEGKTE 56
           MA  +QASLF P + ST+K++     APWKQS SSFS   L  +      IKAMA  K +
Sbjct: 1   MAMASQASLFTP-SISTSKTADPRVVAPWKQSASSFSAPKLSKSVVAYRPIKAMAVEKAQ 59

Query: 57  TPTKE----APVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMP 112
           + TKE    APVGFTPP+LDP+TPSPIFGGSTGGLLRKAQV+EFYVITWESPKEQIFEMP
Sbjct: 60  SATKEAEPAAPVGFTPPQLDPSTPSPIFGGSTGGLLRKAQVDEFYVITWESPKEQIFEMP 119

Query: 113 TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPE 172
           TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKI Y+FYRVFPNGEVQYLHPKDGVYPE
Sbjct: 120 TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKINYRFYRVFPNGEVQYLHPKDGVYPE 179

Query: 173 KVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           KVNPGR+GVGQN+RSIGKN SPIEVKFTGKQVYD+
Sbjct: 180 KVNPGRQGVGQNFRSIGKNKSPIEVKFTGKQVYDI 214

Source: Nicotiana sylvestris

Species: Nicotiana sylvestris

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111204|ref|XP_002315779.1| hypothetical protein POPTRDRAFT_566261 [Populus trichocarpa] gi|118487204|gb|ABK95430.1| unknown [Populus trichocarpa] gi|118487687|gb|ABK95668.1| unknown [Populus trichocarpa] gi|222864819|gb|EEF01950.1| hypothetical protein POPTRDRAFT_566261 [Populus trichocarpa]

 Score =  328 bits (841), Expect = 7e-88,   Method: Compositional matrix adjust.
 Identities = 169/209 (80%), Positives = 177/209 (84%), Gaps = 12/209 (5%)

Query: 3   MAATTQASLFAPANFSTTKSS----APWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETP 58
           MAA  QASLF P   ST KSS     PWKQ+S     P+ +  P+     A AE   ET 
Sbjct: 1   MAA--QASLFTPPTLSTLKSSNQAFVPWKQASFL---PISNVKPQRTMKVAAAE---ETA 52

Query: 59  TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
            KEAPVGFTPPELDP+TPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAI
Sbjct: 53  VKEAPVGFTPPELDPSTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAI 112

Query: 119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
           MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR
Sbjct: 113 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 172

Query: 179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           +GVGQN+RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 173 QGVGQNFRSIGKNVSPIEVKFTGKQAYDL 201

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	207
UNIPROTKB|P12353	212	psaD "Photosystem I reaction c	0.975	0.952	0.767	8.5e-81
TAIR|locus:2007519	204	PSAD-2 "AT1G03130" [Arabidopsi	0.975	0.990	0.764	2.1e-77
TAIR|locus:2140255	208	PSAD-1 "AT4G02770" [Arabidopsi	0.971	0.966	0.746	2.7e-75
UNIPROTKB|Q39615	196	psaD "Photosystem I reaction c	0.888	0.938	0.618	1.1e-55
UNIPROTKB|P19569	141	psaD "Photosystem I reaction c	0.628	0.921	0.669	1.3e-43

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

 Score = 811 (290.5 bits), Expect = 8.5e-81, P = 8.5e-81
 Identities = 165/215 (76%), Positives = 181/215 (84%)

Query:     3 MAATTQASLFAPANFST-----TKSSAPWKQSSS--FSVRPL-KHNAPRTNTIKAMAEGK 54
             MA  TQA+LF+P++ S+     T+ +  +KQ S+  F+ +P  +H++ R     A AEGK
Sbjct:     1 MAMATQATLFSPSSLSSAKPIDTRLTTSFKQPSAVTFASKPASRHHSIRA---AAAAEGK 57

Query:    55 TE--TPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMP 112
                 T TKEAP GFTPPELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMP
Sbjct:    58 AAAATETKEAPKGFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMP 117

Query:   113 TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPE 172
             TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPE
Sbjct:   118 TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPE 177

Query:   173 KVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
             KVNPGR+GVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct:   178 KVNPGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL 212

GO:0005515 "protein binding" evidence=IPI

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

 Score = 779 (279.3 bits), Expect = 2.1e-77, P = 2.1e-77
 Identities = 156/204 (76%), Positives = 164/204 (80%)

Query:     5 ATTQASLFAPANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPT-KEAP 63
             AT  A +F+PA  +TT S+       S S RP   +  +T       E  +  P  KEAP
Sbjct:     2 ATQAAGIFSPA-ITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP 60

Query:    64 VGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGP 123
             VGFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAAIMREGP
Sbjct:    61 VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP 120

Query:   124 NLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQ 183
             NLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPGREGVG 
Sbjct:   121 NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL 180

Query:   184 NYRSIGKNVSPIEVKFTGKQVYDL 207
             N RSIGKNVSPIEVKFTGKQ YDL
Sbjct:   181 NMRSIGKNVSPIEVKFTGKQSYDL 204

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

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

 Score = 759 (272.2 bits), Expect = 2.7e-75, P = 2.7e-75
 Identities = 156/209 (74%), Positives = 163/209 (77%)

Query:     5 ATTQASLFAPANFSTTKSSAPWKQSSSFSV--RP----LKHNAPRTNTIKAMAEGKTETP 58
             AT  A +F  A   TT +++  K+   FS   RP        A R     + A       
Sbjct:     2 ATQAAGIFNSA--ITTAATSGVKKLHFFSTTHRPKSLSFTKTAIRAEKTDSSAAAAAAPA 59

Query:    59 TKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAI 118
             TKEAPVGFTPP+LDPNTPSPIF GSTGGLLRKAQVEEFYVITW SPKEQIFEMPTGGAAI
Sbjct:    60 TKEAPVGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAI 119

Query:   119 MREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGR 178
             MREGPNLLKLARKEQCLALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEK NPGR
Sbjct:   120 MREGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGR 179

Query:   179 EGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
             EGVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct:   180 EGVGLNMRSIGKNVSPIEVKFTGKQSYDL 208

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

 Score = 574 (207.1 bits), Expect = 1.1e-55, P = 1.1e-55
 Identities = 115/186 (61%), Positives = 140/186 (75%)

Query:    20 TKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPV-GFTPPELDPNTPSP 78
             T++ A  + SS  +V   +  A R   ++A AE       K A    +T P L+P+TPSP
Sbjct:     7 TQAPAATRASSRVAVAA-RPAARRAVVVRAEAEAAPAAAKKAAEKPAWTVPTLNPDTPSP 65

Query:    79 IFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALG 138
             IFGGSTGGLLRKAQ EEFYVITWE+ KEQIFEMPTGGAAIMR+GPNLLK  +KEQCLAL 
Sbjct:    66 IFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNLLKFGKKEQCLALT 125

Query:   139 TRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVK 198
             T+LR+K+K+   FYRVFP+G+VQYLHP DGVYPEKVN GR G  QN R IG+NV+PI+VK
Sbjct:   126 TQLRNKFKLTPCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNMRRIGQNVNPIKVK 185

Query:   199 FTGKQV 204
             F+G+ +
Sbjct:   186 FSGRMM 191

GO:0005515 "protein binding" evidence=IPI

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

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 89/133 (66%), Positives = 103/133 (77%)

Query:    78 PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLAL 137
             P FGGSTGGLL KA  EE Y ITW S  EQ+FEMPTGGAAIM EG NLL LARKEQCLAL
Sbjct:     9 PKFGGSTGGLLSKANREEKYAITWTSASEQVFEMPTGGAAIMNEGENLLYLARKEQCLAL 68

Query:   138 GTRLRSKYKIK---YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSP 194
             GT+LR+K+K K   Y+ YRV+P+GEVQYLHP DGV+PEKVN GRE  G   R IG+N  P
Sbjct:    69 GTQLRTKFKPKIQDYKIYRVYPSGEVQYLHPADGVFPEKVNEGREAQGTKTRRIGQNPEP 128

Query:   195 IEVKFTGKQVYDL 207
             + +KF+GK  Y++
Sbjct:   129 VTIKFSGKAPYEV 141


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        0.314   0.131   0.388    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      207       207   0.00099  111 3  11 23  0.42    33
                                                     31  0.47    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:  587 (62 KB)
  Total size of DFA:  164 KB (2097 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:  20.53u 0.10s 20.63t   Elapsed:  00:00:01
  Total cpu time:  20.53u 0.10s 20.63t   Elapsed:  00:00:01
  Start:  Sat May 11 02:32:21 2013   End:  Sat May 11 02:32:22 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)
Q39615	PSAD_CHLRE	No assigned EC number	0.7410	0.6714	0.7091	N/A	no
P84563	PSAD_POPEU	No assigned EC number	0.9655	0.1400	1.0	N/A	no
P58573	PSAD_NOSS1	No assigned EC number	0.6183	0.6231	0.9280	yes	no
Q7NF26	PSAD_GLOVI	No assigned EC number	0.6060	0.6328	0.9097	yes	no
P12372	PSAD_SOLLC	No assigned EC number	0.7932	0.9903	0.9855	N/A	no
O78502	PSAD_GUITH	No assigned EC number	0.6788	0.6570	0.9645	yes	no
P0A420	PSAD_THEEB	No assigned EC number	0.6230	0.6231	0.9280	yes	no
P12353	PSAD_SPIOL	No assigned EC number	0.75	0.9903	0.9669	N/A	no
P23076	PSAD_SYNP6	No assigned EC number	0.6363	0.6231	0.9084	yes	no
Q9S7H1	PSAD1_ARATH	No assigned EC number	0.9463	0.7198	0.7163	no	no
P36213	PSAD_HORVU	No assigned EC number	0.9020	0.6908	0.6975	N/A	no
Q9SA56	PSAD2_ARATH	No assigned EC number	0.7647	0.9758	0.9901	yes	no
P31089	PSAD_ANAVT	No assigned EC number	0.6259	0.6231	0.9280	yes	no
P32869	PSAD_CUCSA	No assigned EC number	0.7962	0.9710	0.9710	N/A	no
P29302	PSAD_NICSY	No assigned EC number	0.8203	0.9806	0.9950	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:
	GSVIVG00019961001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_2, whole genome shotgun sequence); (204 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00035532001	SubName- Full=Chromosome undetermined scaffold_79, whole genome shotgun sequence; (221 aa)			•	•	•		•		0.879
	GSVIVG00025097001	SubName- Full=Putative uncharacterized protein (Chromosome chr4 scaffold_32, whole genome shotg [...] (221 aa)			•	•	•		•		0.865
	psaA	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence;; PsaA and psaB bind P7 [...] (307 aa)			•		•		•		0.771
	psaC	RecName- Full=Photosystem I iron-sulfur center; AltName- Full=Photosystem I subunit VII; AltNam [...] (81 aa)					•		•		0.756
	psaB	RecName- Full=Photosystem I P700 chlorophyll A apoprotein;; PsaA and psaB bind P700, the primar [...] (347 aa)			•		•		•		0.713
	GSVIVG00013467001	SubName- Full=Chromosome undetermined scaffold_484, whole genome shotgun sequence; (332 aa)			•	•			•		0.667
	GSVIVG00012660001	SubName- Full=Chromosome undetermined scaffold_3171, whole genome shotgun sequence; (161 aa)			•			•	•		0.665
	GSVIVG00014701001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (331 aa)			•	•			•		0.660
	GSVIVG00038544001	SubName- Full=Chromosome chr3 scaffold_95, whole genome shotgun sequence; (84 aa)			•				•		0.658
	GSVIVG00028499001	RecName- Full=Photosystem II reaction center psb28 protein; (179 aa)			•	•			•		0.641

---

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	207
PLN00041	196	PLN00041, PLN00041, photosystem I reaction center	1e-113
pfam02531	139	pfam02531, PsaD, PsaD	1e-94
CHL00145	139	CHL00145, psaD, photosystem I subunit II; Validate	7e-80

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

 Score =  321 bits (823), Expect = e-113
 Identities = 147/193 (76%), Positives = 153/193 (79%), Gaps = 1/193 (0%)

Query: 15  ANFSTTKSSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPVGFTPPELDPN 74
              S+ +   PW    S S       +         A    E   KEAPVGFTPP L+PN
Sbjct: 5   TPASSGRKLVPWASFLSKSTSKAP-ASLSATRAVRAAAAAEEAAAKEAPVGFTPPTLNPN 63

Query: 75  TPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQC 134
           TPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMR+GPNLLKLARKEQC
Sbjct: 64  TPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQC 123

Query: 135 LALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSP 194
           LALGTRLRSKYKI YQFYRVFPNGEVQYLHPKDGVYPEKVNPGR GVGQN RSIGKNV+P
Sbjct: 124 LALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRVGVGQNMRSIGKNVNP 183

Query: 195 IEVKFTGKQVYDL 207
           IEVKFTGKQ YDL
Sbjct: 184 IEVKFTGKQAYDL 196

Length = 196

>gnl|CDD|145591 pfam02531, PsaD, PsaD

 Score =  271 bits (695), Expect = 1e-94
 Identities = 106/139 (76%), Positives = 117/139 (84%), Gaps = 1/139 (0%)

Query: 69  PELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKL 128
           P L+ NTPSPIFGGSTGGLLRKA+ EE Y ITW S KEQ+FEMPTGGAAIMREG NLL L
Sbjct: 1   PTLNGNTPSPIFGGSTGGLLRKAETEEKYAITWTSKKEQVFEMPTGGAAIMREGENLLYL 60

Query: 129 ARKEQCLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRS 187
           ARKEQCLALGT+LR+K+KI+ Y+ YR+FP GEVQYLHPKDGV+PEKVN GREGVG   R 
Sbjct: 61  ARKEQCLALGTQLRTKFKIEDYKIYRIFPGGEVQYLHPKDGVFPEKVNEGREGVGSVPRR 120

Query: 188 IGKNVSPIEVKFTGKQVYD 206
           IGKN +P  VKFTGK  YD
Sbjct: 121 IGKNPNPANVKFTGKATYD 139

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 =  234 bits (598), Expect = 7e-80
 Identities = 102/137 (74%), Positives = 111/137 (81%), Gaps = 1/137 (0%)

Query: 71  LDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLAR 130
           L+   PSP FGGSTGG LR A+VEE Y ITW SPKEQIFEMPTGGAAIMR G NLL LAR
Sbjct: 3   LNLQMPSPTFGGSTGGWLRAAEVEEKYAITWTSPKEQIFEMPTGGAAIMRNGENLLYLAR 62

Query: 131 KEQCLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           KEQCLALGT+LR+K+KI  Y+ YR+FPNGEVQYLHPKDGV+PEKVNPGR  VG    SIG
Sbjct: 63  KEQCLALGTQLRTKFKINDYKIYRIFPNGEVQYLHPKDGVFPEKVNPGRVAVGSRDFSIG 122

Query: 190 KNVSPIEVKFTGKQVYD 206
           KN +P  VKFTGK  YD
Sbjct: 123 KNPNPASVKFTGKATYD 139

Length = 139

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	207
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=5e-101  Score=644.47  Aligned_cols=185  Identities=80%  Similarity=1.261  Sum_probs=162.3

Q ss_pred             cccccccCccccccCCCCCCCccchhhhhhcCCCCCCCccCCCcCCCCCCCCCCCCCccccCccccccccccceeEEEEe
Q 028581           22 SSAPWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITW  101 (207)
Q Consensus        22 ~~~~w~~ss~~s~~~~~~~~~~~~~~~a~~~~~~~~~~~~ap~~f~p~~l~~~~p~P~FgGSTGGlLr~A~~EEkYaITW  101 (207)
                      ...+|++++..+...........+..++.++ +++++++++|++|+||+||+++|+|+||||||||||+||+||||+|||
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~t~~~~~l~~~~P~FgGSTGGlL~~Ae~EEkYaITW   90 (196)
T PLN00041         12 KLVPWASFLSKSTSKAPASLSATRAVRAAAA-AEEAAAKEAPVGFTPPTLNPNTPSPIFGGSTGGLLRKAQVEEFYVITW   90 (196)
T ss_pred             eeeeeccccccccccccccccchhHHHHHhh-hcccccccCCCCcCCcccCCCCCCCcccccchhhhhhhhhhhheEEEe
Confidence            4578987633333222222222233333322 223467889999999999999999999999999999999999999999


Q ss_pred             cCCcceeeeccCCceeecccCccceeehhhhhHHHHhhccccceeeeeEeeeecCCCceEeeccCCCCCCcccCCCcccc
Q 028581          102 ESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGV  181 (207)
Q Consensus       102 tS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI~ykiYRifP~Gevq~LHPkDGVfPEKVN~GR~~v  181 (207)
                      +|+|||||||||||||+||+|+|||||||||||||||+|||+||||||||||||||||+|||||||||||||||+||++|
T Consensus        91 tS~keQvFEmPTGGAAiM~~G~NLlylARKEQCLALgtQLrtkfKIdykiYRifP~Ge~q~LHPkDGVfPEKvN~GR~~v  170 (196)
T PLN00041         91 ESPKEQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKVNPGRVGV  170 (196)
T ss_pred             cCChhheeecCCchhhhhhcCchHHHHHHHHHHHHHHHHHhhhcccceeEEEEcCCCceEEecCCCCCCccccCCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccccCCCCCCcceEEecccccccC
Q 028581          182 GQNYRSIGKNVSPIEVKFTGKQVYDL  207 (207)
Q Consensus       182 g~~~r~IGkN~nP~~vKFtgk~tyd~  207 (207)
                      |+|+|+||+|+||++||||||++||+
T Consensus       171 g~~~r~IG~N~nP~~vKFsgk~~yd~  196 (196)
T PLN00041        171 GQNMRSIGKNVNPIEVKFTGKQAYDL  196 (196)
T ss_pred             CCCCccccCCCCcceEEecCCccCCC
Confidence            99999999999999999999999995

>CHL00145 psaD photosystem I subunit II; Validated

Probab=100.00  E-value=9.5e-96  Score=588.90  Aligned_cols=138  Identities=74%  Similarity=1.196  Sum_probs=136.3

Q ss_pred             CCCCCCCCCCccccCccccccccccceeEEEEecCCcceeeeccCCceeecccCccceeehhhhhHHHHhhccccceee-
Q 028581           69 PELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKI-  147 (207)
Q Consensus        69 ~~l~~~~p~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-  147 (207)
                      +++++++++|+||||||||||+||+||||||||+|++||||||||||||+||+|+|||||||||||||||+|||+|||| 
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             eeEeeeecCCCceEeeccCCCCCCcccCCCccccCCccccCCCCCCcceEEeccccccc
Q 028581          148 KYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYD  206 (207)
Q Consensus       148 ~ykiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFtgk~tyd  206 (207)
                      ||||||||||||+|||||||||||||||+||+.||+++|+||+||||++||||||++||
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            89999999999999999999999999999999999999999999999999999999998

>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=3.4e-95  Score=585.68  Aligned_cols=137  Identities=77%  Similarity=1.262  Sum_probs=116.8

Q ss_pred             CCCCCCCCCccccCccccccccccceeEEEEecCCcceeeeccCCceeecccCccceeehhhhhHHHHhhccccceee-e
Q 028581           70 ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKI-K  148 (207)
Q Consensus        70 ~l~~~~p~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-~  148 (207)
                      +||+++|+|+||||||||||+||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+|||+|||| |
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             eEeeeecCCCceEeeccCCCCCCcccCCCccccCCccccCCCCCCcceEEeccccccc
Q 028581          149 YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYD  206 (207)
Q Consensus       149 ykiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFtgk~tyd  206 (207)
                      |||||||||||+|||||||||||||||+||+.||+++|+||+|+||++||||||++||
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	207
2wsc_D	212	Improved Model Of Plant Photosystem I Length = 212		3e-79
3lw5_D	138	Improved Model Of Plant Photosystem I Length = 138		1e-75
2o01_D	138	The Structure Of A Plant Photosystem I Supercomplex		3e-74
1jb0_D	138	Crystal Structure Of Photosystem I: A Photosyntheti		1e-42

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

Iteration: 1
 Score =  290 bits (743), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 155/216 (71%), Positives = 172/216 (79%), Gaps = 15/216 (6%)
Query: 3   MAATTQASLFAPANFST-----TKSSAPWKQSS--SFSVRPLKHNAPRTNTIKAMAEGKT 55
           MA  T A+LF+ ++ S+     T+ +  +KQ S  +F+ +P    A R +TI+A A  + 
Sbjct: 1   MAMGTPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFASKP----ASRLHTIRAAAAAEG 56
Query: 56  ETPTKEAPVG----FTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEM 111
           +             FTPPELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEM
Sbjct: 57  KAAAATETKEATKAFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEM 116
Query: 112 PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYP 171
           PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYP
Sbjct: 117 PTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYP 176
Query: 172 EKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           EKVNPGR+GVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 177 EKVNPGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL 212

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

Iteration: 1
 Score =  278 bits (711), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 133/138 (96%), Positives = 136/138 (98%)
Query: 70  ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 129
           ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITW+SPKEQIFEMPTGGAAIMREGPNLLKLA
Sbjct: 1   ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLA 60
Query: 130 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN GR+GVGQN+RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIG 120
Query: 190 KNVSPIEVKFTGKQVYDL 207
           KNVSPIEVKFTGKQ YDL
Sbjct: 121 KNVSPIEVKFTGKQPYDL 138

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

Iteration: 1
 Score =  274 bits (700), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 132/138 (95%), Positives = 134/138 (97%)
Query: 70  ELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 129
           ELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA
Sbjct: 1   ELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLA 60
Query: 130 RKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIG 189
           RKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVNPGR+GVG N RSIG
Sbjct: 61  RKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGLNMRSIG 120
Query: 190 KNVSPIEVKFTGKQVYDL 207
           KNVSPIEVKFTGKQ YDL
Sbjct: 121 KNVSPIEVKFTGKQPYDL 138

>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 =  169 bits (427), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 81/130 (62%), Positives = 98/130 (75%), Gaps = 1/130 (0%)
Query: 78  PIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLAL 137
           P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MREG NL+  ARKEQCLAL
Sbjct: 8   PLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQCLAL 67
Query: 138 GT-RLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIE 196
              +LR +    Y+ YR+FP+GE   +HPKDGV+PEKVN GRE V    RSIG+N +P +
Sbjct: 68  AAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQ 127
Query: 197 VKFTGKQVYD 206
           +KFTGK+ YD
Sbjct: 128 LKFTGKKPYD 137

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	207
2wsc_D	212	Photosystem I reaction center subunit II, chloropl	1e-88
1jb0_D	138	Photosystem 1 reaction centre subunit II; membrane	6e-74
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-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 =  259 bits (661), Expect = 1e-88
 Identities = 158/212 (74%), Positives = 169/212 (79%), Gaps = 7/212 (3%)

Query: 3   MAATTQASLFAPANFSTTKSS-----APWKQSSSFSVRPLKHNAPRTNTIKAMAEGKTE- 56
           MA  T A+LF+ ++ S+ K         +KQ S+ +      +   T    A AEGK   
Sbjct: 1   MAMGTPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFASKPASRLHTIRAAAAAEGKAAA 60

Query: 57  -TPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG 115
            T TKEA   FTPPELDPNTPSPIF GSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG
Sbjct: 61  ATETKEATKAFTPPELDPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGG 120

Query: 116 AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVN 175
           AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFP+GEVQYLHPKDGVYPEKVN
Sbjct: 121 AAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVN 180

Query: 176 PGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL 207
           PGR+GVG N RSIGKNVSPIEVKFTGKQ YDL
Sbjct: 181 PGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL 212

>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 =  219 bits (558), Expect = 6e-74
 Identities = 81/134 (60%), Positives = 97/134 (72%), Gaps = 1/134 (0%)

Query: 74  NTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQ 133
               P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MREG NL+  ARKEQ
Sbjct: 4   TGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQ 63

Query: 134 CLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNV 192
           CLAL  +     KI  Y+ YR+FP+GE   +HPKDGV+PEKVN GRE V    RSIG+N 
Sbjct: 64  CLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNP 123

Query: 193 SPIEVKFTGKQVYD 206
           +P ++KFTGK+ YD
Sbjct: 124 NPSQLKFTGKKPYD 137

>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 = 38.7 bits (89), Expect = 8e-04
 Identities = 23/144 (15%), Positives = 38/144 (26%), Gaps = 39/144 (27%)

Query: 43  RTNTIKAMAEGKTETPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWE 102
           +  T    A   T        +  TP E                LL K           +
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDE-------------VKSLLLKY----LDCRPQD 317

Query: 103 SPKEQIFEMP---TGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKI-----KYQFYR- 153
            P+E +   P   +  A  +R+G       +   C  L T + S   +       + +  
Sbjct: 318 LPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377

Query: 154 --VFPNGEVQYLHPKDGVY-PEKV 174
             VFP             + P  +
Sbjct: 378 LSVFP----------PSAHIPTIL 391

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	207
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=9.4e-109  Score=696.55  Aligned_cols=203  Identities=79%  Similarity=1.207  Sum_probs=137.5

Q ss_pred             CcchhchhcccccccccCCCC-----cccccccCccccccCCCCCCCccchhhhh-hcC-CCC--CCCccCCCcCCCCCC
Q 028581            1 MAMAATTQASLFAPANFSTTK-----SSAPWKQSSSFSVRPLKHNAPRTNTIKAM-AEG-KTE--TPTKEAPVGFTPPEL   71 (207)
Q Consensus         1 mamA~~tqas~~tp~~~~~~~-----~~~~w~~ss~~s~~~~~~~~~~~~~~~a~-~~~-~~~--~~~~~ap~~f~p~~l   71 (207)
                      ||||  |||++|+++++++..     +..||++|++++|. .+. +...++++++ +++ +++  ++++++|++|+||+|
T Consensus         1 mama--tqa~~~~~~~~s~~~~~~~~~~~~w~~s~~~~~~-~k~-~~~~~~~~~a~~ae~~~a~~~~~~~ap~~f~p~~~   76 (212)
T 2wsc_D            1 MAMG--TPATLFSRSSLSSAKPIETRLTTSFKQPSAVTFA-SKP-ASRLHTIRAAAAAEGKAAAATETKEATKAFTPPEL   76 (212)
T ss_dssp             ------------------------------------------------------------------------------CC
T ss_pred             Cccc--cccccccccccccccccccccccccccccccccc-ccc-cccccchhhhhhcccccccccccccCCCccCCccc
Confidence            8999  999999999887533     24599999999996 222 2333444444 332 222  234689999999999


Q ss_pred             CCCCCCCccccCccccccccccceeEEEEecCCcceeeeccCCceeecccCccceeehhhhhHHHHhhccccceeeeeEe
Q 028581           72 DPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQF  151 (207)
Q Consensus        72 ~~~~p~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI~yki  151 (207)
                      |+++|+|+||||||||||+||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+|||+||||||||
T Consensus        77 ~l~~~~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKIdyki  156 (212)
T 2wsc_D           77 DPNTPSPIFAGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIKYQF  156 (212)
T ss_dssp             SSCCCCSCCCCCSSSCCSTTTSSCCCEEECCCSSCCCCCTTTTCCCCCCCSSCEEECSSTTTTSHHHHTTTSSCCSCCEE
T ss_pred             cCCCCCcccccccccccccccceeeEEEEecCChhheeecCCCcchhhccCcchheehhHHHHHHHHHhhhhccccccce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCceEeeccCCCCCCcccCCCccccCCccccCCCCCCcceEEecccccccC
Q 028581          152 YRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL  207 (207)
Q Consensus       152 YRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFtgk~tyd~  207 (207)
                      ||||||||+|||||||||||||||+||++||+|+|+||+|+||++||||||++||+
T Consensus       157 YRifP~Ge~q~LhPkDGVfPEKVN~GR~~vg~~~r~IG~N~nP~~~KFsgk~~yd~  212 (212)
T 2wsc_D          157 YRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGLNMRSIGKNVSPIEVKFTGKQPYDL  212 (212)
T ss_dssp             ECCCSSCCSCCTTTSSSCSSSCCSCCCSCCCCSSSCSTTTTSCCCSCCCTTSSCCC
T ss_pred             EeecCCCceEEecCcCCCCccccCCcccccCcCcccccCCCCcceEEecCcccccC
Confidence            99999999999999999999999999999999999999999999999999999995

>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=1.4e-93  Score=574.61  Aligned_cols=135  Identities=61%  Similarity=1.044  Sum_probs=133.4

Q ss_pred             CCCCCCCccccCccccccccccceeEEEEecCCcceeeeccCCceeecccCccceeehhhhhHHHHhhc-cccceee-ee
Q 028581           72 DPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTR-LRSKYKI-KY  149 (207)
Q Consensus        72 ~~~~p~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtq-LrtkfKI-~y  149 (207)
                      ++++++|+||||||||||+||+||||||||+|+|||||||||||||+||+|+|||||||||||||||+| ||+ ||| ||
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             EeeeecCCCceEeeccCCCCCCcccCCCccccCCccccCCCCCCcceEEecccccccC
Q 028581          150 QFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL  207 (207)
Q Consensus       150 kiYRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFtgk~tyd~  207 (207)
                      ||||||||||+|||||||||||||||+||++||+++|+||+||||++||||||++||+
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            9999999999999999999999999999999999999999999999999999999996

---

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	207
d1jb0d_	138	d.187.1.1 (D:) Photosystem I subunit PsaD {Synecho	1e-80

>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 =  234 bits (599), Expect = 1e-80
 Identities = 81/134 (60%), Positives = 97/134 (72%), Gaps = 1/134 (0%)

Query: 74  NTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQ 133
               P++GGSTGGLL  A  EE Y ITW SPKEQ+FEMPT GAA+MREG NL+  ARKEQ
Sbjct: 4   TGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFARKEQ 63

Query: 134 CLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNV 192
           CLAL  +     KI  Y+ YR+FP+GE   +HPKDGV+PEKVN GRE V    RSIG+N 
Sbjct: 64  CLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNP 123

Query: 193 SPIEVKFTGKQVYD 206
           +P ++KFTGK+ YD
Sbjct: 124 NPSQLKFTGKKPYD 137

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	207
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=6e-92  Score=563.12  Aligned_cols=135  Identities=60%  Similarity=1.010  Sum_probs=132.6

Q ss_pred             CCCCCCccccCccccccccccceeEEEEecCCcceeeeccCCceeecccCccceeehhhhhHHHHhhccccceee-eeEe
Q 028581           73 PNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKI-KYQF  151 (207)
Q Consensus        73 ~~~p~P~FgGSTGGlLr~A~~EEkYaITWtS~keQvFEmPTGGAAiM~~G~NLLylARKEQClALgtqLrtkfKI-~yki  151 (207)
                      ++..+|+||||||||||+||+||||||||+|+|||||||||||||+|++|+|||||||||||||||+|++++||| ||||
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             eeecCCCceEeeccCCCCCCcccCCCccccCCccccCCCCCCcceEEecccccccC
Q 028581          152 YRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNYRSIGKNVSPIEVKFTGKQVYDL  207 (207)
Q Consensus       152 YRifP~Gevq~LHPkDGVfPEKVN~GR~~vg~~~r~IGkN~nP~~vKFtgk~tyd~  207 (207)
                      |||||+||+|||||||||||||||+||++||+|+|+||+|+||++||||||++||.
T Consensus        83 YRifp~Ge~~~lhPkDGVfpEKVN~GR~~vg~~~r~IG~NpnP~~~KFsgk~tyd~  138 (138)
T d1jb0d_          83 YRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIGQNPNPSQLKFTGKKPYDP  138 (138)
T ss_dssp             EEECTTCCEEEEETTTSSCSSSCCTTCCCCSEESSCGGGCCCHHHHTTSCCCTTCC
T ss_pred             EEEcCCCceEEeccCCCCCccccCCcccccCCCcccccCCCCcceEEecCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999994