Citrus Sinensis ID: 030062

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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---
Protein Sequence
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccEEcccccEEEEEccccccccccEEEEEccccccEEEEEEEccccccccccccccEEEEEEEEcccEEEEEEccEEEEcccccEEEEEEEEcccHHHHHHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHccccccccccccccccccccccHHHccccccccccccccccccccccccccccccHHHHHHcccEEEEEccccccccccEEEEEccccccEEEEEEEcccHHHccccccccEEEEEEEccccEEEEEEEEEEEEcccccEEEEEEEEccHHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MAALRSLAlaspishcwhpqsrspslsgiVTWAvhgsaqspfngqsvhmprmrlspvtrnskvsgpitmavkptiqfiqgtdeltvpdvkltksrdgsngmaifsfsepsvfdssgeigditgfymideegtlqsvdvsakfvngrpsrieakyimrSPREWDRFMRFMERYANQnglqfvkk
Flexible Loop (DISEMBL)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKptiqfiqgtdeltvpdVKLTKSRDGSNGMAIfsfsepsvfdsSGEIGDITGFYMIDEEGTlqsvdvsakfvngrpsrieakyimrsprEWDRFMRFMERYanqnglqfvkk
Low Complexity Region (SEG)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK
Disordered region (IsUnstruct)
************ISHCW*********SGIVTWAVH*******************************ITMAVKPTIQFIQGTDELTVPDVK**********MAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYAN*********
Disordered Region (DISOPRED)
*********************************************************************AVKPTIQFIQGTDELTVPDVKLTKS**GSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF***
Disordered Region (DISEMBL)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK
Disordered Region (DISPRO)
***************************************************************SGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGL*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK
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	183	2.2.26 [Sep-21-2011]
Q0JG75	180	Photosystem II reaction c	yes	no	0.972	0.988	0.604	1e-58
Q8W0Y8	183	Photosystem II reaction c	yes	no	0.967	0.967	0.595	9e-56
Q00UI6	147	Photosystem II reaction c	yes	no	0.732	0.911	0.503	4e-35
P49508	115	Photosystem II reaction c	N/A	no	0.612	0.973	0.575	2e-34
Q1XDE0	115	Photosystem II reaction c	N/A	no	0.595	0.947	0.581	1e-33
P51347	115	Photosystem II reaction c	N/A	no	0.595	0.947	0.581	1e-33
A0T0H5	115	Photosystem II reaction c	yes	no	0.612	0.973	0.566	1e-33
O78418	116	Photosystem II reaction c	yes	no	0.606	0.956	0.591	2e-33
A0T0W9	114	Photosystem II reaction c	N/A	no	0.590	0.947	0.596	3e-33
Q6B8Z7	114	Photosystem II reaction c	N/A	no	0.606	0.973	0.591	5e-33

>sp|Q0JG75|PSB28_ORYSJ Photosystem II reaction center PSB28 protein, chloroplastic OS=Oryza sativa subsp. japonica GN=PSB28 PE=2 SV=2

 Score =  225 bits (574), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 110/182 (60%), Positives = 138/182 (75%), Gaps = 4/182 (2%)

Query: 2   AALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNS 61
           A +++LA+ASPIS    P+      SG  + ++H S    F G S+   R + + + R+ 
Sbjct: 3   AVMKALAVASPISARAQPRRCPAGSSGGPSQSLHSS----FGGVSLQCRRTKPASLHRSR 58

Query: 62  KVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDI 121
                + MA +P IQFIQGTDE T+PDV+LTKSRDG+NG+AIF+F +PSVFDSS E+GDI
Sbjct: 59  PSMQVVMMAARPAIQFIQGTDEQTIPDVRLTKSRDGTNGVAIFTFDQPSVFDSSAELGDI 118

Query: 122 TGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFV 181
           TGFYMID+EG LQSVDVSAKFVNG+P+ IEAKY+MR+PREWDRFMRFMERY+  NGLQFV
Sbjct: 119 TGFYMIDDEGVLQSVDVSAKFVNGKPALIEAKYVMRTPREWDRFMRFMERYSQANGLQFV 178

Query: 182 KK 183
           KK
Sbjct: 179 KK 180

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8W0Y8|PSB28_ARATH Photosystem II reaction center PSB28 protein, chloroplastic OS=Arabidopsis thaliana GN=PSB28 PE=1 SV=1

 Score =  216 bits (549), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 112/188 (59%), Positives = 141/188 (75%), Gaps = 11/188 (5%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIV--TWAVHGSAQSPFNGQSVHMPRMRLSPVT 58
           MA +RS+   + ++H      R+   SGIV  + +V     S F G  V +PR +  P +
Sbjct: 1   MACVRSIGSLTSVNH----SQRNVPRSGIVLSSCSVLPIKSSSFTGSPVSLPRAQ--PSS 54

Query: 59  RNS-KVSGP--ITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS 115
           R + +   P  ITM VKP +QFIQGTDE+T+PDVKLT+SRDGSNGMA+FSF +PSVFDSS
Sbjct: 55  RTALRPMKPVSITMMVKPALQFIQGTDEMTIPDVKLTRSRDGSNGMALFSFDQPSVFDSS 114

Query: 116 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQ 175
           GE+G+ITG YMIDEEG +QS DV+A+FVNG+P  I AK+IMRSP+EWDRFMRFMERY++Q
Sbjct: 115 GEVGEITGLYMIDEEGVIQSTDVNARFVNGKPEGIVAKHIMRSPKEWDRFMRFMERYSDQ 174

Query: 176 NGLQFVKK 183
           NGLQFVKK
Sbjct: 175 NGLQFVKK 182

Arabidopsis thaliana (taxid: 3702)

>sp|Q00UI6|PSB28_OSTTA Photosystem II reaction center psb28 protein, chloroplastic OS=Ostreococcus tauri GN=psb28 PE=3 SV=1

 Score =  147 bits (371), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 70/139 (50%), Positives = 97/139 (69%), Gaps = 5/139 (3%)

Query: 45  QSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIF 104
           +S +    R S   R S V   +      +IQF++G +E  VP+V+LT+S+DGSNG A F
Sbjct: 14  RSFNASTKRFSKSARRSVV---VRAGTTTSIQFVKGQNETAVPEVRLTRSKDGSNGTAFF 70

Query: 105 SFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDR 164
            FS+P VF++    GDITG ++ DEEG + +VDV+AKFVNG+P+ IEA+Y+M++  +W+R
Sbjct: 71  IFSDPDVFENGQ--GDITGMFLTDEEGEMSTVDVNAKFVNGKPTGIEARYVMKTEADWNR 128

Query: 165 FMRFMERYANQNGLQFVKK 183
           FMRFMERYA  NGL F KK
Sbjct: 129 FMRFMERYAEDNGLGFSKK 147

Ostreococcus tauri (taxid: 70448)

>sp|P49508|PSB28_ODOSI Photosystem II reaction center psb28 protein OS=Odontella sinensis GN=psb28 PE=3 SV=1

 Score =  145 bits (365), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 65/113 (57%), Positives = 86/113 (76%), Gaps = 1/113 (0%)

Query: 71  VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFD-SSGEIGDITGFYMIDE 129
           ++  IQFI+G DE  +PDV+LT+SRDGS G A F F  P++ D S+ + G+ITG Y+ID+
Sbjct: 1   MEAKIQFIKGLDEKVLPDVRLTRSRDGSTGTATFRFKNPNILDKSTAKEGEITGMYLIDQ 60

Query: 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           EGTL++ DV+A+F+NG+P  IE+ YIM+SP  WDRFMRFMERY   NGL F K
Sbjct: 61  EGTLETRDVNAQFINGKPEAIESIYIMKSPEAWDRFMRFMERYGESNGLVFTK 113

Odontella sinensis (taxid: 2839)

>sp|Q1XDE0|PSB28_PORYE Photosystem II reaction center psb28 protein OS=Porphyra yezoensis GN=psb28 PE=3 SV=1

 Score =  142 bits (358), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 84/110 (76%), Gaps = 1/110 (0%)

Query: 74  TIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGT 132
           TIQFIQG +E  VPDV+LT+SRDGS G A F F+ P + D+S  + G+ITG Y++D EG 
Sbjct: 3   TIQFIQGINEEVVPDVRLTRSRDGSTGTATFRFTNPKILDASMADKGEITGMYLMDTEGQ 62

Query: 133 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           + + DV+AKF+NG+P  IEA ++++SP +WDRFMRFMERYA  NGL F K
Sbjct: 63  IITRDVNAKFINGKPQAIEAVHVIKSPDDWDRFMRFMERYAQDNGLTFTK 112

Porphyra yezoensis (taxid: 2788)

>sp|P51347|PSB28_PORPU Photosystem II reaction center psb28 protein OS=Porphyra purpurea GN=psb28 PE=3 SV=1

 Score =  142 bits (358), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 84/110 (76%), Gaps = 1/110 (0%)

Query: 74  TIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGT 132
           TIQFIQG +E  VPDV+LT+SRDGS G A F F+ P + D+S  + G+ITG Y++D EG 
Sbjct: 3   TIQFIQGINEEVVPDVRLTRSRDGSTGTATFRFTNPKILDASMADKGEITGMYLMDTEGQ 62

Query: 133 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           + + DV+AKF+NG+P  IEA ++++SP +WDRFMRFMERYA  NGL F K
Sbjct: 63  IITRDVNAKFINGKPQAIEAVHVIKSPDDWDRFMRFMERYAQDNGLTFTK 112

Porphyra purpurea (taxid: 2787)

>sp|A0T0H5|PSB28_PHATC Photosystem II reaction center psb28 protein OS=Phaeodactylum tricornutum (strain CCAP 1055/1) GN=psb28 PE=3 SV=1

 Score =  142 bits (358), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 64/113 (56%), Positives = 85/113 (75%), Gaps = 1/113 (0%)

Query: 71  VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFD-SSGEIGDITGFYMIDE 129
           ++  IQFI+G DE  +PDV+LT+S+DGS G A F F  P++ D ++ + G+ITG Y+IDE
Sbjct: 1   MEAKIQFIKGLDEKVLPDVRLTRSKDGSTGTATFRFKNPNILDKTTAKEGEITGMYLIDE 60

Query: 130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           EG L++ DV+A+FVNG+P  IE+ YIM+SP  WDRFMRFMERY   NGL F K
Sbjct: 61  EGILETRDVNARFVNGKPEAIESIYIMKSPEAWDRFMRFMERYGETNGLVFSK 113

Phaeodactylum tricornutum (strain CCAP 1055/1) (taxid: 556484)

>sp|O78418|PSB28_GUITH Photosystem II reaction center psb28 protein OS=Guillardia theta GN=psb28 PE=3 SV=1

 Score =  142 bits (357), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 68/115 (59%), Positives = 85/115 (73%), Gaps = 4/115 (3%)

Query: 69  MAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEI-GDITGFYMI 127
           MAV   IQFIQG +E  +PDV+LT+SRDGS G A F F+ P V ++   + G+ITG Y+I
Sbjct: 1   MAV---IQFIQGVNEDVIPDVRLTRSRDGSTGTATFRFANPKVLEAQSSVKGNITGMYLI 57

Query: 128 DEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           DEEG L + DV+A+FVNG+P  IEA YIM+S  +WDRFMRFMERY+  NGL F K
Sbjct: 58  DEEGQLVTRDVNARFVNGKPQGIEAVYIMQSKEDWDRFMRFMERYSEDNGLSFTK 112

Guillardia theta (taxid: 55529)

>sp|A0T0W9|PSB28_THAPS Photosystem II reaction center psb28 protein OS=Thalassiosira pseudonana GN=psb28 PE=3 SV=1

 Score =  141 bits (355), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 65/109 (59%), Positives = 81/109 (74%), Gaps = 1/109 (0%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEI-GDITGFYMIDEEGTL 133
           IQFI+G DE  +PDV+LT+SRDGS G A F F   ++ + S  + G+ITG YMIDEEG L
Sbjct: 5   IQFIKGIDEKVLPDVRLTRSRDGSTGTATFLFKNANLINKSLALNGEITGMYMIDEEGIL 64

Query: 134 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           ++ DVSA+FVNG+P  +E+ YIM+SP  WDRFMRFMERY   NGL F K
Sbjct: 65  ETRDVSARFVNGKPQAVESIYIMKSPEAWDRFMRFMERYGESNGLAFTK 113

Thalassiosira pseudonana (taxid: 35128)

>sp|Q6B8Z7|PSB28_GRATL Photosystem II reaction center psb28 protein OS=Gracilaria tenuistipitata var. liui GN=psb28 PE=3 SV=1

 Score =  140 bits (353), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 68/115 (59%), Positives = 84/115 (73%), Gaps = 4/115 (3%)

Query: 69  MAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGE-IGDITGFYMI 127
           MAV   IQFI+G +E  V DV LT+SRDGS G A F F+ P +  S  E  GDITG Y+ 
Sbjct: 1   MAV---IQFIKGINETVVADVSLTRSRDGSKGTATFRFNNPDILKSGMEDKGDITGMYLK 57

Query: 128 DEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           D+EG L + DVSAKF+NG+P  +EA YI++SP+EWDRFMRFME+YAN+N L F K
Sbjct: 58  DDEGELMTRDVSAKFINGKPQAVEAIYIIKSPQEWDRFMRFMEKYANENKLSFTK 112

Gracilaria tenuistipitata var. liui (taxid: 285951)

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	183
225437969	179	PREDICTED: photosystem II reaction cente	0.978	1.0	0.743	2e-74
118488045	181	unknown [Populus trichocarpa]	0.989	1.0	0.704	1e-67
351725219	179	uncharacterized protein LOC100306491 [Gl	0.978	1.0	0.672	3e-67
255571176	178	Photosystem II reaction center W protein	0.967	0.994	0.708	4e-67
388491040	179	unknown [Lotus japonicus]	0.978	1.0	0.655	5e-67
356537186	179	PREDICTED: photosystem II reaction cente	0.978	1.0	0.672	6e-66
388494372	182	unknown [Medicago truncatula]	0.972	0.978	0.643	8e-62
449445636	221	PREDICTED: photosystem II reaction cente	0.972	0.805	0.627	4e-59
449487345	226	PREDICTED: photosystem II reaction cente	0.972	0.787	0.627	6e-59
357122411	179	PREDICTED: photosystem II reaction cente	0.972	0.994	0.602	1e-57

>gi|225437969|ref|XP_002271666.1| PREDICTED: photosystem II reaction center PSB28 protein, chloroplastic [Vitis vinifera] gi|297744226|emb|CBI37196.3| unnamed protein product [Vitis vinifera]

 Score =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/183 (74%), Positives = 158/183 (86%), Gaps = 4/183 (2%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MAAL+SLA  SP+SHC     +SP LSG+ +WAVH SA S FNG+S+H+PR + + + R+
Sbjct: 1   MAALQSLAFTSPLSHCC---KQSP-LSGLSSWAVHRSAHSSFNGRSLHLPRPQWAALKRS 56

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
           S  SG ITM VKPTIQFIQGTDE TVPDV+LT+SRDG+NGMAIF F +PSVFDSSGE+GD
Sbjct: 57  SSTSGLITMMVKPTIQFIQGTDEQTVPDVRLTQSRDGTNGMAIFKFEQPSVFDSSGEVGD 116

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITGFYMIDEEG LQSVDVSAKF+NG+PS IEAKY+MRSPREWDRFMRFMERY+N+NGLQF
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFINGKPSGIEAKYVMRSPREWDRFMRFMERYSNENGLQF 176

Query: 181 VKK 183
           VKK
Sbjct: 177 VKK 179

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488045|gb|ABK95843.1| unknown [Populus trichocarpa]

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 129/183 (70%), Positives = 153/183 (83%), Gaps = 2/183 (1%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MA L+SLALASP++   H Q ++ S SG  +WAV+ S+ S FNGQS+ +PR+RL  + R 
Sbjct: 1   MATLQSLALASPVAQ--HLQHQTRSFSGSGSWAVNKSSYSLFNGQSLCLPRLRLPLIRRK 58

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
            + SG +TM VKP IQF+QG DE TVPDV+LTKSRDG+NGMAIF+F +PSVFDSS E+GD
Sbjct: 59  LRTSGLVTMMVKPAIQFVQGADEQTVPDVRLTKSRDGTNGMAIFTFDQPSVFDSSAEVGD 118

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITGFYMIDEEG LQSVDV+AKFVNG+P RIEAKYIMR+PREWDRFMRFME+YAN NGLQF
Sbjct: 119 ITGFYMIDEEGILQSVDVNAKFVNGKPERIEAKYIMRTPREWDRFMRFMEKYANANGLQF 178

Query: 181 VKK 183
           VKK
Sbjct: 179 VKK 181

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725219|ref|NP_001235805.1| uncharacterized protein LOC100306491 [Glycine max] gi|255628701|gb|ACU14695.1| unknown [Glycine max]

 Score =  259 bits (662), Expect = 3e-67,   Method: Compositional matrix adjust.
 Identities = 123/183 (67%), Positives = 148/183 (80%), Gaps = 4/183 (2%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MA L SLAL+SP+S+      + P    + +  VH S  S FNGQ++H+P +RL  + +N
Sbjct: 1   MATLHSLALSSPLSNSL----QKPRSCAVPSSIVHQSTNSSFNGQTLHLPCLRLPVLRQN 56

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
           + +  P+ M VKP IQFIQGTDE T+PDV+LTKSRDG+NGMAIF+F +PSVFDSSGEIGD
Sbjct: 57  TPMHMPVIMMVKPKIQFIQGTDEQTIPDVRLTKSRDGTNGMAIFTFDQPSVFDSSGEIGD 116

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITGFYMIDEEG LQSVDVSAKFVNG+PS IEAKY+MRSPR+WDRFMRFMERY+N NGLQF
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFVNGKPSIIEAKYVMRSPRDWDRFMRFMERYSNANGLQF 176

Query: 181 VKK 183
           +KK
Sbjct: 177 IKK 179

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255571176|ref|XP_002526538.1| Photosystem II reaction center W protein, putative [Ricinus communis] gi|223534099|gb|EEF35816.1| Photosystem II reaction center W protein, putative [Ricinus communis]

 Score =  259 bits (661), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 129/182 (70%), Positives = 149/182 (81%), Gaps = 5/182 (2%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MA L+SLA ASP+SH  H Q+RS    G   WAVH  A+SPF+G+S+ +   +L+   + 
Sbjct: 1   MATLQSLAFASPVSHYSH-QTRS--FPGSFCWAVHRIARSPFSGKSLRLSHPQLTSTRQK 57

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
           S  S  ITM  KP+IQFIQGTDE T+PDV+LTKSRDG+NGMAIF+F EPSVFDSS E+GD
Sbjct: 58  S--SRFITMMAKPSIQFIQGTDEQTIPDVRLTKSRDGTNGMAIFTFDEPSVFDSSAELGD 115

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITGFYMIDEEG LQSVDVSAKFVNG+P+RIEAKY+MRSPREWDRFMRFMERYAN NGLQF
Sbjct: 116 ITGFYMIDEEGVLQSVDVSAKFVNGKPARIEAKYVMRSPREWDRFMRFMERYANANGLQF 175

Query: 181 VK 182
           VK
Sbjct: 176 VK 177

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491040|gb|AFK33586.1| unknown [Lotus japonicus]

 Score =  258 bits (660), Expect = 5e-67,   Method: Compositional matrix adjust.
 Identities = 120/183 (65%), Positives = 146/183 (79%), Gaps = 4/183 (2%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MA L SLAL+SP+S+      + P L  + +  V  S+ S FNGQ +H+P +RL  +T+N
Sbjct: 1   MATLHSLALSSPLSNSI----QKPRLYSVPSSIVQRSSNSSFNGQHLHLPHLRLPKLTQN 56

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
           + +  P+ M VKP IQFIQG DELT+PDV+LTKSRDG+NGMAIF F +PSVFD+SGE+GD
Sbjct: 57  TAMHTPVIMMVKPAIQFIQGNDELTIPDVRLTKSRDGTNGMAIFKFEQPSVFDASGEVGD 116

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITG YMIDEEG LQS DVSAKF+NG+PS IEAKYIMR+PREWDRFMRFMERY+N NGLQF
Sbjct: 117 ITGLYMIDEEGVLQSTDVSAKFINGKPSIIEAKYIMRTPREWDRFMRFMERYSNANGLQF 176

Query: 181 VKK 183
           +KK
Sbjct: 177 IKK 179

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537186|ref|XP_003537110.1| PREDICTED: photosystem II reaction center PSB28 protein, chloroplastic-like [Glycine max]

 Score =  255 bits (651), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 123/183 (67%), Positives = 146/183 (79%), Gaps = 4/183 (2%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRN 60
           MA L SLAL+SP+S+      + P    + +  VH S  S FNGQ++ MP +RL  + ++
Sbjct: 1   MATLHSLALSSPLSNSL----QKPHSYAVPSSIVHQSTNSSFNGQTLRMPCLRLPVLRQS 56

Query: 61  SKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGD 120
           + +  P+ M  KP IQFIQGTDE T+PDV+LTKSRDG+NGMAIF+F +PSVFDSSGEIGD
Sbjct: 57  TPMHMPVIMMAKPKIQFIQGTDEQTIPDVRLTKSRDGTNGMAIFTFDQPSVFDSSGEIGD 116

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
           ITGFYMIDEEG LQSVDVSAKFVNG+PS IEAKY+MRSPREWDRFMRFMERY+N NGLQF
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFVNGKPSIIEAKYVMRSPREWDRFMRFMERYSNANGLQF 176

Query: 181 VKK 183
           VKK
Sbjct: 177 VKK 179

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494372|gb|AFK35252.1| unknown [Medicago truncatula]

 Score =  241 bits (615), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 119/185 (64%), Positives = 148/185 (80%), Gaps = 7/185 (3%)

Query: 1   MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQ--SPFNGQSVHMPRMRLSPVT 58
           MA + SLA +SP+ +    + RS S + ++   +HGS    S FNGQ +H+P +RL  +T
Sbjct: 1   MATMHSLAFSSPLYNSIQ-KPRSYSATSLI---IHGSLNLNSSFNGQHLHVPSLRLPMIT 56

Query: 59  RNSKVSGP-ITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGE 117
           + + +  P I MA KP IQFIQG+DELT+PDVKLTKS+DG+NGMAIF F +PSVFDSSGE
Sbjct: 57  QKTPMHMPVIMMAGKPKIQFIQGSDELTIPDVKLTKSKDGTNGMAIFRFDQPSVFDSSGE 116

Query: 118 IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNG 177
           +GDITGFYMIDEEG LQSVDV+AKFVNG+PS IEAKYIMR+PR+WDRFMRFMERY++ NG
Sbjct: 117 VGDITGFYMIDEEGVLQSVDVNAKFVNGKPSGIEAKYIMRTPRDWDRFMRFMERYSDANG 176

Query: 178 LQFVK 182
           LQF+K
Sbjct: 177 LQFIK 181

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445636|ref|XP_004140578.1| PREDICTED: photosystem II reaction center PSB28 protein, chloroplastic-like [Cucumis sativus]

 Score =  232 bits (592), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 118/188 (62%), Positives = 145/188 (77%), Gaps = 10/188 (5%)

Query: 1   MAALRSLA-LASPIS-HCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVT 58
           MA+L+SLA   SP S H  HP S  P LS    +++H SA S F+G+S+ +   +   +T
Sbjct: 39  MASLQSLASTTSPSSPHLLHPSSTKPKLS----YSLHSSAFSSFHGRSLSLSTTKCHTLT 94

Query: 59  RNS---KVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS 115
           R +   +   PI M V P IQFIQGTDE T+PDV+LTKSRDG+NGMAIF F +PSVFDSS
Sbjct: 95  RRTYRQRSWNPILM-VLPKIQFIQGTDEQTIPDVRLTKSRDGTNGMAIFRFEQPSVFDSS 153

Query: 116 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQ 175
            E+GDITGFYMIDEEG +QSVDV+AKF+NG+P+ IEAKY+MR+PREWDRFMRFMERY+N 
Sbjct: 154 AEVGDITGFYMIDEEGMIQSVDVNAKFINGKPAGIEAKYVMRTPREWDRFMRFMERYSNA 213

Query: 176 NGLQFVKK 183
           NG+QFVKK
Sbjct: 214 NGMQFVKK 221

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487345|ref|XP_004157580.1| PREDICTED: photosystem II reaction center PSB28 protein, chloroplastic-like [Cucumis sativus]

 Score =  232 bits (591), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 118/188 (62%), Positives = 145/188 (77%), Gaps = 10/188 (5%)

Query: 1   MAALRSLA-LASPIS-HCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVT 58
           MA+L+SLA   SP S H  HP S  P LS    +++H SA S F+G+S+ +   +   +T
Sbjct: 44  MASLQSLASTTSPSSPHLLHPSSTKPKLS----YSLHSSAFSSFHGRSLSLSTTKCHTLT 99

Query: 59  RNS---KVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS 115
           R +   +   PI M V P IQFIQGTDE T+PDV+LTKSRDG+NGMAIF F +PSVFDSS
Sbjct: 100 RRTYRQRSWNPILM-VLPKIQFIQGTDEQTIPDVRLTKSRDGTNGMAIFRFEQPSVFDSS 158

Query: 116 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQ 175
            E+GDITGFYMIDEEG +QSVDV+AKF+NG+P+ IEAKY+MR+PREWDRFMRFMERY+N 
Sbjct: 159 AEVGDITGFYMIDEEGMIQSVDVNAKFINGKPAGIEAKYVMRTPREWDRFMRFMERYSNA 218

Query: 176 NGLQFVKK 183
           NG+QFVKK
Sbjct: 219 NGMQFVKK 226

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357122411|ref|XP_003562909.1| PREDICTED: photosystem II reaction center PSB28 protein, chloroplastic-like [Brachypodium distachyon]

 Score =  228 bits (580), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 109/181 (60%), Positives = 142/181 (78%), Gaps = 3/181 (1%)

Query: 4   LRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSA-QSPFNGQSVHMPRMRLSPVTRNSK 62
           +++LA+ASP++    P+ R  +++G+    +     Q+ F G S+H  R +  P TR S 
Sbjct: 1   MKALAVASPVAAA-QPRRRCLAVAGVPCHRIMSQQLQTSFTGVSLHR-RQQHKPSTRPSS 58

Query: 63  VSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDIT 122
               + MA +P+IQFIQGTDE TVPDV+LTKSRDGSNG+A+F+F +PSVFDSS E+GDIT
Sbjct: 59  SVVAMAMASRPSIQFIQGTDEQTVPDVRLTKSRDGSNGVAVFTFDQPSVFDSSAELGDIT 118

Query: 123 GFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           GFYMIDEEGTLQ+VDVSAKFVNG+P+ +EAKY+MR+PR+WDRFMRFMERY+  NGLQF+K
Sbjct: 119 GFYMIDEEGTLQTVDVSAKFVNGKPAAVEAKYVMRTPRDWDRFMRFMERYSQANGLQFLK 178

Query: 183 K 183
           K
Sbjct: 179 K 179

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	183
UNIPROTKB|Q55356	112	psb28 "Photosystem II reaction	0.584	0.955	0.527	5.2e-26

UNIPROTKB|Q55356 psb28 "Photosystem II reaction center Psb28 protein" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 57/108 (52%), Positives = 76/108 (70%)

Query:    75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQ 134
             IQF +G  E  VP+V+L+KS++G +GMA F F EP++  +     DITG Y+ID+EG + 
Sbjct:     4 IQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTIL-AKESTDDITGMYLIDDEGEII 62

Query:   135 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
             + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMERY  +NGL F K
Sbjct:    63 TREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMERYGAENGLGFSK 110


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.131   0.390    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      183       183   0.00076  110 3  11 22  0.43    32
                                                     31  0.40    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:  1
  No. of states in DFA:  601 (64 KB)
  Total size of DFA:  154 KB (2092 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:  17.54u 0.12s 17.66t   Elapsed:  00:00:01
  Total cpu time:  17.54u 0.12s 17.66t   Elapsed:  00:00:01
  Start:  Fri May 10 06:40:42 2013   End:  Fri May 10 06:40:43 2013

GO:0030096 "plasma membrane-derived thylakoid photosystem II" 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)
Q8DLJ8	PSB28_THEEB	No assigned EC number	0.5438	0.6120	0.9655	yes	no
Q0JG75	PSB28_ORYSJ	No assigned EC number	0.6043	0.9726	0.9888	yes	no
Q8W0Y8	PSB28_ARATH	No assigned EC number	0.5957	0.9672	0.9672	yes	no
O78418	PSB28_GUITH	No assigned EC number	0.5913	0.6065	0.9568	yes	no
Q00UI6	PSB28_OSTTA	No assigned EC number	0.5035	0.7322	0.9115	yes	no
A0T0H5	PSB28_PHATC	No assigned EC number	0.5663	0.6120	0.9739	yes	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	183
PLN00039	111	PLN00039, PLN00039, photosystem II reaction center	1e-78
CHL00128	113	CHL00128, psbW, photosystem II protein W; Reviewed	3e-59
pfam03912	108	pfam03912, Psb28, Psb28 protein	2e-57
TIGR03047	109	TIGR03047, PS_II_psb28, photosystem II reaction ce	6e-57
PRK13612	113	PRK13612, PRK13612, photosystem II reaction center	4e-55
PRK13611	104	PRK13611, PRK13611, photosystem II reaction center	6e-20
PRK13610	113	PRK13610, PRK13610, photosystem II reaction center	1e-13

>gnl|CDD|177673 PLN00039, PLN00039, photosystem II reaction center Psb28 protein; Provisional

 Score =  229 bits (585), Expect = 1e-78
 Identities = 90/111 (81%), Positives = 102/111 (91%)

Query: 73  PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGT 132
           P+IQFI+GTDE TVPDV+LT+SRDG+NG AIF F +PSVFDSSGE+GDITG YMIDEEG 
Sbjct: 1   PSIQFIKGTDETTVPDVRLTRSRDGTNGTAIFVFDQPSVFDSSGELGDITGLYMIDEEGV 60

Query: 133 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183
           LQ+VDVSAKFVNG+P+ IEAKY+MRSPREWDRFMRFMERYA +NGL FVKK
Sbjct: 61  LQTVDVSAKFVNGKPAGIEAKYVMRSPREWDRFMRFMERYAEENGLGFVKK 111

Length = 111

>gnl|CDD|177050 CHL00128, psbW, photosystem II protein W; Reviewed

 Score =  179 bits (457), Expect = 3e-59
 Identities = 67/113 (59%), Positives = 81/113 (71%), Gaps = 1/113 (0%)

Query: 72  KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEI-GDITGFYMIDEE 130
              IQFI+G DE  +PDV+LT+SRDGS G A F F  P++ D S    G+ITG Y+IDEE
Sbjct: 1   MAKIQFIKGIDEEVIPDVRLTRSRDGSTGTATFRFKNPNILDKSTAKQGEITGMYLIDEE 60

Query: 131 GTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183
           G L + DV+AKF+NG+P  IEA YIM++P  WDRFMRFMERYA  NGL F K 
Sbjct: 61  GELSTRDVNAKFINGKPQAIEAIYIMKNPEAWDRFMRFMERYAEDNGLTFTKA 113

Length = 113

>gnl|CDD|190791 pfam03912, Psb28, Psb28 protein

 Score =  175 bits (446), Expect = 2e-57
 Identities = 62/107 (57%), Positives = 75/107 (70%), Gaps = 1/107 (0%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDS-SGEIGDITGFYMIDEEGTL 133
           IQFI+G DE  VPDV+LT+SRDG  G A+F F  P   D  +   G+ITG Y+IDEEG +
Sbjct: 1   IQFIKGIDEEVVPDVRLTRSRDGGTGTAVFRFENPKALDKFTSGSGEITGMYLIDEEGEI 60

Query: 134 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQF 180
            +  VSAKFVNG P  +EA Y M+S  EW+RFMRFMERYA  NGL +
Sbjct: 61  STRPVSAKFVNGEPKAVEATYEMKSEEEWERFMRFMERYAEANGLGY 107

Psb28 is a 13 kDa soluble protein that is directly assembled in dimeric PSII supercomplexes. The negatively charged N-terminal region is essential for this process. This protein was formerly known as PsbW, but PsbW is now reserved for pfam07123. Length = 108

>gnl|CDD|213763 TIGR03047, PS_II_psb28, photosystem II reaction center protein Psb28

 Score =  174 bits (443), Expect = 6e-57
 Identities = 62/109 (56%), Positives = 76/109 (69%), Gaps = 1/109 (0%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGE-IGDITGFYMIDEEGTL 133
           IQF +G DE  +PDV+LT+SRDG  G A+F F  P   D      G+ITG Y+IDEEG +
Sbjct: 1   IQFFRGIDEEVIPDVRLTRSRDGGTGTALFRFENPKALDKFNSDTGEITGMYLIDEEGEI 60

Query: 134 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
            + +V AKFVNG+P  +EA YIM+S  EWDRFMRFMERYA  NGL + K
Sbjct: 61  STREVKAKFVNGKPKALEAVYIMKSEDEWDRFMRFMERYAEANGLGYSK 109

Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW [Energy metabolism, Photosynthesis]. Length = 109

>gnl|CDD|237446 PRK13612, PRK13612, photosystem II reaction center protein Psb28; Provisional

 Score =  169 bits (431), Expect = 4e-55
 Identities = 63/112 (56%), Positives = 78/112 (69%), Gaps = 1/112 (0%)

Query: 72  KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEG 131
              IQF +G DE  VPD++LT+SRDG  G A F F +P    +    G+ITG YMIDEEG
Sbjct: 3   MAAIQFSRGVDEPVVPDIRLTRSRDGRTGQATFYFEQPQAL-APETTGEITGMYMIDEEG 61

Query: 132 TLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183
            + + +V AKFVNG+PS +EA YI +S +EWDRFMRFMERYA +NGL F K 
Sbjct: 62  EIVTREVKAKFVNGKPSALEATYIWKSEQEWDRFMRFMERYAKENGLGFSKS 113

Length = 113

>gnl|CDD|106556 PRK13611, PRK13611, photosystem II reaction center protein Psb28; Provisional

 Score = 79.8 bits (196), Expect = 6e-20
 Identities = 46/107 (42%), Positives = 62/107 (57%), Gaps = 8/107 (7%)

Query: 74  TIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTL 133
           +I+F  G  E+    V+L KS+ G  G AIF F      D   +  +I G  MIDEEG L
Sbjct: 3   SIEFSPGIPEVPT-QVRLLKSKTGKRGSAIFRFE-----DLKSDTQNILGMRMIDEEGEL 56

Query: 134 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERY--ANQNGL 178
            + ++ AKF+NG    +E  Y M +  EWDRF+RFMER+  ANQ G+
Sbjct: 57  TTRNIKAKFLNGEFKALEVIYDMETEAEWDRFLRFMERFSAANQMGM 103

Length = 104

>gnl|CDD|139699 PRK13610, PRK13610, photosystem II reaction center protein Psb28; Provisional

 Score = 63.6 bits (154), Expect = 1e-13
 Identities = 29/100 (29%), Positives = 51/100 (51%), Gaps = 1/100 (1%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQ 134
           IQF++G +E   P+++L ++ DG  G A++ F +P     +     +   ++ID EG L 
Sbjct: 10  IQFVKGENEKDQPEIRLFRNLDGKKGKAVYKFYKPKTITLT-NYKSVQRMFLIDSEGVLS 68

Query: 135 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYAN 174
           +  +           +++ Y   S   ++RFMRF  RYAN
Sbjct: 69  TKKIDLSISEDHVKEVKSTYNWNSEEAFERFMRFASRYAN 108

Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
PLN00039	111	photosystem II reaction center Psb28 protein; Prov	100.0
CHL00128	113	psbW photosystem II protein W; Reviewed	100.0
PRK13612	113	photosystem II reaction center protein Psb28; Prov	100.0
TIGR03047	109	PS_II_psb28 photosystem II reaction center protein	100.0
PF03912	108	Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic	100.0
PRK13611	104	photosystem II reaction center protein Psb28; Prov	100.0
PRK13610	113	photosystem II reaction center protein Psb28; Prov	100.0
PF08722	88	Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; Inte	80.5

>PLN00039 photosystem II reaction center Psb28 protein; Provisional

Probab=100.00  E-value=3.1e-67  Score=407.49  Aligned_cols=111  Identities=81%  Similarity=1.333  Sum_probs=108.5

Q ss_pred             ceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeEE
Q 030062           73 PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEA  152 (183)
Q Consensus        73 asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa  152 (183)
                      |+||||+||||++||||||||||||++|+|+|+|++|++|++++.+++|||||||||||||+|+|||+|||||||++|||
T Consensus         1 a~IQF~~Gi~E~~vp~VrLtRsrdg~~g~a~f~F~~p~~l~~~~~~~~itgm~liDeEGei~tr~v~~KFvnGkp~~iEa   80 (111)
T PLN00039          1 PSIQFIKGTDETTVPDVRLTRSRDGTNGTAIFVFDQPSVFDSSGELGDITGLYMIDEEGVLQTVDVSAKFVNGKPAGIEA   80 (111)
T ss_pred             CcEEEecCCCCCcCCceEEEEccCCCccEEEEEECCchhhccccccCceeeEEEEccCccEEEEecceEEECCCccEEEE
Confidence            68999999999999999999999999999999999999999875689999999999999999999999999999999999


Q ss_pred             EEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062          153 KYIMRSPREWDRFMRFMERYANQNGLQFVKK  183 (183)
Q Consensus       153 ~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~  183 (183)
                      +|+|+|++|||||||||||||++|||+|+|+
T Consensus        81 ~y~m~s~~~WdRFMRFMeRYA~~ngl~f~k~  111 (111)
T PLN00039         81 KYVMRSPREWDRFMRFMERYAEENGLGFVKK  111 (111)
T ss_pred             EEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            9999999999999999999999999999986

>CHL00128 psbW photosystem II protein W; Reviewed

Probab=100.00  E-value=5.2e-67  Score=407.23  Aligned_cols=112  Identities=60%  Similarity=1.073  Sum_probs=108.9

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccC-CcccceeeEEEEecCceEEeEeceeEEEcCCccee
Q 030062           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI  150 (183)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~-~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~i  150 (183)
                      +|+||||+||||++||||||||||||++|+|+|+|++|++|+++ +.+++|||||||||||||+|+|||+|||||||++|
T Consensus         1 ~a~IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itgm~LiDeEGei~tr~v~~KFvnGkp~~i   80 (113)
T CHL00128          1 MAKIQFIKGIDEEVIPDVRLTRSRDGSTGTATFRFKNPNILDKSTAKQGEITGMYLIDEEGELSTRDVNAKFINGKPQAI   80 (113)
T ss_pred             CCeEEEecCCCCCcCCceEEEEccCCCceEEEEEECCchhhhhccccccceeeEEEEccCccEEEEecceEEECCCccEE
Confidence            48999999999999999999999999999999999999999986 46899999999999999999999999999999999


Q ss_pred             EEEEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062          151 EAKYIMRSPREWDRFMRFMERYANQNGLQFVKK  183 (183)
Q Consensus       151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~  183 (183)
                      ||+|+|+|++|||||||||||||++|||+|+|+
T Consensus        81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~  113 (113)
T CHL00128         81 EAIYIMKNPEAWDRFMRFMERYAEDNGLTFTKA  113 (113)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            999999999999999999999999999999986

>PRK13612 photosystem II reaction center protein Psb28; Provisional

Probab=100.00  E-value=7.5e-67  Score=406.32  Aligned_cols=112  Identities=56%  Similarity=0.986  Sum_probs=108.8

Q ss_pred             eeceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCccee
Q 030062           71 VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI  150 (183)
Q Consensus        71 ~~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~i  150 (183)
                      ++|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++|
T Consensus         2 ~~a~IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~-~~~~itgm~LiDeEGei~tr~v~~KFvnGkp~~i   80 (113)
T PRK13612          2 KMAAIQFSRGVDEPVVPDIRLTRSRDGRTGQATFYFEQPQALAPE-TTGEITGMYMIDEEGEIVTREVKAKFVNGKPSAL   80 (113)
T ss_pred             CcceEEEecCCCCCcCCceEEEEccCCCeeEEEEEECCccccCcc-ccCceeeEEEEccCccEEEEecceEEECCCccEE
Confidence            459999999999999999999999999999999999999999984 5899999999999999999999999999999999


Q ss_pred             EEEEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062          151 EAKYIMRSPREWDRFMRFMERYANQNGLQFVKK  183 (183)
Q Consensus       151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~  183 (183)
                      ||+|+|+|++|||||||||||||++|||+|+|+
T Consensus        81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~  113 (113)
T PRK13612         81 EATYIWKSEQEWDRFMRFMERYAKENGLGFSKS  113 (113)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            999999999999999999999999999999986

>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28

Probab=100.00  E-value=2.3e-65  Score=395.95  Aligned_cols=108  Identities=57%  Similarity=1.048  Sum_probs=105.5

Q ss_pred             eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-cccceeeEEEEecCceEEeEeceeEEEcCCcceeEEE
Q 030062           75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK  153 (183)
Q Consensus        75 IQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~-~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~  153 (183)
                      ||||+||||++||||||||||||++|+|+|+|++|++|++++ .+++|||||||||||||+|+|||+|||||||++|||+
T Consensus         1 IQF~~Gi~E~~ip~VrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itGm~LiDeEGei~tr~v~~KFvnGkp~~iEa~   80 (109)
T TIGR03047         1 IQFFRGIDEEVIPDVRLTRSRDGGTGTALFRFENPKALDKFNSDTGEITGMYLIDEEGEIVTREVKAKFVNGKPKALEAV   80 (109)
T ss_pred             CccccCCCCCcCCceEEEEccCCCceEEEEEECCchhhhhccccccceeeEEEEccCccEEEEecceEEECCCccEEEEE
Confidence            899999999999999999999999999999999999999874 5789999999999999999999999999999999999


Q ss_pred             EEecCchhHHHHHHHHHhhhhhcCcceec
Q 030062          154 YIMRSPREWDRFMRFMERYANQNGLQFVK  182 (183)
Q Consensus       154 y~m~s~~eWdRFMRFMeRYAe~NGL~f~k  182 (183)
                      |+|+|++|||||||||||||++|||+|+|
T Consensus        81 y~m~s~~~WdRFMRFmeRYA~~ngl~f~~  109 (109)
T TIGR03047        81 YIMKSEDEWDRFMRFMERYAEANGLGYSK  109 (109)
T ss_pred             EEECCHHHHHHHHHHHHHHHHhcCCcccC
Confidence            99999999999999999999999999986

Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.

>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae

Probab=100.00  E-value=1.2e-64  Score=391.33  Aligned_cols=107  Identities=61%  Similarity=1.063  Sum_probs=82.0

Q ss_pred             eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-cccceeeEEEEecCceEEeEeceeEEEcCCcceeEEE
Q 030062           75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK  153 (183)
Q Consensus        75 IQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~-~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iEa~  153 (183)
                      ||||+||||+++|||||||||||++|+|+|+|++|++|++++ ++++|||||||||||||+|+||++|||||||++|||+
T Consensus         1 IQF~~Gi~E~~~pdVrLtRsrdg~~g~a~f~F~~p~al~~~~~~~~~itgm~liDeEGei~t~~v~~kFvnG~p~~iEa~   80 (108)
T PF03912_consen    1 IQFIKGIDEEVVPDVRLTRSRDGGTGTATFYFENPKALEKFSSDKGEITGMYLIDEEGEISTRDVNAKFVNGKPQAIEAT   80 (108)
T ss_dssp             EESSSS-------EEEEEE-TTS-SEEEEEEEES-GGGTSS-GG--G---EEEE-SS-EEEE--EEEEEETTEEEEEEEE
T ss_pred             CccccCCCCccCCCeEEEEccCCCceEEEEEECCCcccccccccccccceEEEEccCccEEEEecceEEECCceEEEEEE
Confidence            899999999999999999999999999999999999999986 4689999999999999999999999999999999999


Q ss_pred             EEecCchhHHHHHHHHHhhhhhcCccee
Q 030062          154 YIMRSPREWDRFMRFMERYANQNGLQFV  181 (183)
Q Consensus       154 y~m~s~~eWdRFMRFMeRYAe~NGL~f~  181 (183)
                      |+|+|++|||||||||||||++|||+|+
T Consensus        81 y~m~s~~~WdRFMRFMeRYA~~Ngl~f~  108 (108)
T PF03912_consen   81 YIMKSEEEWDRFMRFMERYAEANGLGFS  108 (108)
T ss_dssp             EEE-SSHHHHHHHHHHHHHHHH--SSS-
T ss_pred             EEECCHHHHHHHHHHHHHHHHhcCCccC
Confidence            9999999999999999999999999996

Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.

>PRK13611 photosystem II reaction center protein Psb28; Provisional

Probab=100.00  E-value=9.9e-63  Score=378.84  Aligned_cols=104  Identities=40%  Similarity=0.723  Sum_probs=100.7

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeE
Q 030062           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (183)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iE  151 (183)
                      +|+||||+||||+ +|||||||||||++|+|+|+|++|++     .+++|||||||||||||+|+||++|||||||++||
T Consensus         1 ma~IQF~~Gi~E~-~p~VrLtRsrdg~~g~a~f~F~~~~~-----~~~~itgm~liDeEGei~tr~v~~KFvnGkp~~iE   74 (104)
T PRK13611          1 MASIEFSPGIPEV-PTQVRLLKSKTGKRGSAIFRFEDLKS-----DTQNILGMRMIDEEGELTTRNIKAKFLNGEFKALE   74 (104)
T ss_pred             CCeEEEecCCCCC-CCceEEEEccCCCccEEEEEEcCCcc-----cccceeeEEEEccCCcEEEEecceEEECCCccEEE
Confidence            3899999999999 99999999999999999999999998     35899999999999999999999999999999999


Q ss_pred             EEEEecCchhHHHHHHHHHhhhhhcCccee
Q 030062          152 AKYIMRSPREWDRFMRFMERYANQNGLQFV  181 (183)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~NGL~f~  181 (183)
                      |+|+|+|++|||||||||||||++|||+|.
T Consensus        75 a~y~m~s~~~wdRFMRFmeRYA~~Ngl~f~  104 (104)
T PRK13611         75 VIYDMETEAEWDRFLRFMERFSAANQMGMA  104 (104)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHhcCCccC
Confidence            999999999999999999999999999983

>PRK13610 photosystem II reaction center protein Psb28; Provisional

Probab=100.00  E-value=2.3e-61  Score=375.64  Aligned_cols=104  Identities=28%  Similarity=0.601  Sum_probs=101.1

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeE
Q 030062           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (183)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iE  151 (183)
                      .|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++||
T Consensus         7 ~a~IQF~~Gi~E~~vp~VrLtRsrdG~tG~A~f~F~~p~~l~~~-~~~~ItGM~LiDeEGei~tr~v~aKFvnGkp~~iE   85 (113)
T PRK13610          7 NVAIQFVKGENEKDQPEIRLFRNLDGKKGKAVYKFYKPKTITLT-NYKSVQRMFLIDSEGVLSTKKIDLSISEDHVKEVK   85 (113)
T ss_pred             CcEEEEecCCCCCcCCceEEEEccCCCccEEEEEECCchhcccc-cccceeeeEEEccCceEEEEeeeEEEEcCCccEEE
Confidence            58999999999999999999999999999999999999999984 58999999999999999999999999999999999


Q ss_pred             EEEEecCchhHHHHHHHHHhhhhhc
Q 030062          152 AKYIMRSPREWDRFMRFMERYANQN  176 (183)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~N  176 (183)
                      |+|+|+|++|||||||||||||++.
T Consensus        86 a~y~m~s~~~WdRFMRFMeRYA~~~  110 (113)
T PRK13610         86 STYNWNSEEAFERFMRFASRYANSL  110 (113)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999974

>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB

Probab=80.50  E-value=2.6  Score=30.03  Aligned_cols=54  Identities=17%  Similarity=0.265  Sum_probs=33.2

Q ss_pred             ecCceEEeEeceeEEEcC---CcceeEEEEEecCch-hHHHHHHHHHhhhhhcCccee
Q 030062          128 DEEGTLQSVDVSAKFVNG---RPSRIEAKYIMRSPR-EWDRFMRFMERYANQNGLQFV  181 (183)
Q Consensus       128 DEEGeI~Tr~V~aKFvnG---kp~~iEa~y~m~s~~-eWdRFMRFMeRYAe~NGL~f~  181 (183)
                      +.....-|.|.=+.+-+|   ++..+|+++.-+-.. .+..=.....+|++++|..|.
T Consensus        27 ~~~~~~yTpDFlv~~~~g~~~~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f~   84 (88)
T PF08722_consen   27 TGVPIVYTPDFLVTYRDGNGKKPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPFR   84 (88)
T ss_dssp             TTEE---EEEEEEEESSS--SSEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--EE
T ss_pred             CCCccEEeccEEEEEccCCcceEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeEE
Confidence            445566788888888898   888899888654444 333334556789999999884

DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
2kvo_A	120	Solution Nmr Structure Of Photosystem Ii Reaction C		4e-28

>pdb|2KVO|A Chain A, Solution Nmr Structure Of Photosystem Ii Reaction Center Psb28 Protein From Synechocystis Sp.(Strain Pcc 6803), Northeast Structural Genomics Consortium Target Sgr171 Length = 120

Iteration: 1
 Score =  120 bits (301), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 57/108 (52%), Positives = 76/108 (70%), Gaps = 1/108 (0%)
Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQ 134
           IQF +G  E  VP+V+L+KS++G +GMA F F EP++  +     DITG Y+ID+EG + 
Sbjct: 4   IQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTIL-AKESTDDITGMYLIDDEGEII 62
Query: 135 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVK 182
           + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMERY  +NGL F K
Sbjct: 63  TREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMERYGAENGLGFSK 110

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
2kvo_A	120	Photosystem II reaction center PSB28 protein; memb	1e-55

>2kvo_A Photosystem II reaction center PSB28 protein; membrane, photosynthesis, thylakoid, structural genom 2, protein structure initiative; NMR {Synechocystis SP} Length = 120

 Score =  170 bits (432), Expect = 1e-55
 Identities = 57/111 (51%), Positives = 75/111 (67%), Gaps = 1/111 (0%)

Query: 73  PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGT 132
             IQF +G  E  VP+V+L+KS++G +GMA F F EP++        DITG Y+ID+EG 
Sbjct: 2   AEIQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTILAKEST-DDITGMYLIDDEGE 60

Query: 133 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERYANQNGLQFVKK 183
           + + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMERY  +NGL F K 
Sbjct: 61  IITREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMERYGAENGLGFSKS 111

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
2kvo_A	120	Photosystem II reaction center PSB28 protein; memb	100.0

>2kvo_A Photosystem II reaction center PSB28 protein; membrane, photosynthesis, thylakoid, structural genom 2, protein structure initiative; NMR {Synechocystis SP}

Probab=100.00  E-value=5.2e-67  Score=409.54  Aligned_cols=111  Identities=51%  Similarity=0.932  Sum_probs=108.6

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCcccceeeEEEEecCceEEeEeceeEEEcCCcceeE
Q 030062           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (183)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLtRSrdG~~GtA~F~Fe~p~a~~~~~~~~~ItGMyLiDEEGeI~Tr~V~aKFvnGkp~~iE  151 (183)
                      +|+||||+||||++||||||||||||++|+|+|+|++|++|+++ ++++|||||||||||||+|+||++|||||||++||
T Consensus         1 ~a~IQF~~Gi~E~~vpdVrLtRsrdg~~g~A~f~F~~p~al~~~-~~~~itgm~LiDeEGei~t~~v~aKFvnGkp~~iE   79 (120)
T 2kvo_A            1 MAEIQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTILAKE-STDDITGMYLIDDEGEIITREVKGKFINGRPTAIE   79 (120)
T ss_dssp             CCEEESSSSCCCCCCCEEEEEECTTSCSEEEEEEEESCGGGTSS-CGGGCCCEEEECSSCEEEECCEEEEEETTEEEEEE
T ss_pred             CCcEEEecCCCCCcCCceEEEEcccCCccEEEEEECCchhcccc-ccCcceeEEEEccCccEEEEecceEEECCceeEEE
Confidence            48999999999999999999999999999999999999999997 58999999999999999999999999999999999


Q ss_pred             EEEEecCchhHHHHHHHHHhhhhhcCcceecC
Q 030062          152 AKYIMRSPREWDRFMRFMERYANQNGLQFVKK  183 (183)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~NGL~f~k~  183 (183)
                      |+|+|+|+++||||||||||||++|||+|+|+
T Consensus        80 a~y~m~s~~~WdRFMRFMeRYA~~Ngl~f~k~  111 (120)
T 2kvo_A           80 ATVILNSQPEWDRFMRFMERYGAENGLGFSKS  111 (120)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHHHCCSSSCST
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            99999999999999999999999999999985

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00