Citrus Sinensis ID: 028962

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-
Protein Sequence
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccEEcccccEEEEEccccccccccEEEEEccccccEEEEEEEccccccccccccccEEEEEEEEcccEEEEEEccEEEEcccccEEEEEEEEcccHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHccccccccccccccccccccccHHHccccccccccccccccccccccccccccccHHHHHEEccEEEEEccccccccccEEEEEcccccccEEEEEEcccHHHccccccccEEEEEEEccccEEEEEEEEEEEEcccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEccEEEEEcc
Coil and Loop (DISEMBL)
MAALRSLAlaspishcwhpqsrspslsgiVTWAvhgsaqspfngqsvhmprmrlspvtrnskvsgpitmavkptiqfiqgtdeltvpdvkltksrdgsngmaifsfsepsvfdssgeigditgfymideegtlqsvdvsakfvngrpsrieakyimrSPREWDRFMRFMERQMVKALLDSHLslmqkpyalfsstyfcccy
Flexible Loop (DISEMBL)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKptiqfiqgtdeltvpdVKLTKSRDGSNGMAIfsfsepsvfdsSGEIGDITGFYMIDEEGTlqsvdvsakfvngrpsrieakyimrsprEWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Low Complexity Region (SEG)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Disordered region (IsUnstruct)
************ISHCW*********SGIVTWAVH*******************************ITMAVKPTIQFIQGTDELTVPDVK**********MAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCC*
Disordered Region (DISOPRED)
********************************************************************MAVKPTIQFIQGTDELTVPDVKLTKS*DGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Disordered Region (DISEMBL)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Disordered Region (DISPRO)
**************************************************************VSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAALRSLALASPISHCWHPQSRSPSLSGIVTWAVHGSAQSPFNGQSVHMPRMRLSPVTRNSKVSGPITMAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVKALLDSHLSLMQKPYALFSSTYFCCCY
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	201	2.2.26 [Sep-21-2011]
Q0JG75	180	Photosystem II reaction c	yes	no	0.825	0.922	0.594	1e-52
Q8W0Y8	183	Photosystem II reaction c	yes	no	0.820	0.901	0.579	9e-49
P49508	115	Photosystem II reaction c	N/A	no	0.502	0.878	0.578	8e-31
Q00UI6	147	Photosystem II reaction c	yes	no	0.606	0.829	0.488	8e-31
A0T0H5	115	Photosystem II reaction c	yes	no	0.502	0.878	0.568	4e-30
O78418	116	Photosystem II reaction c	yes	no	0.497	0.862	0.596	1e-29
A0T0W9	114	Photosystem II reaction c	N/A	no	0.482	0.850	0.602	2e-29
P51347	115	Photosystem II reaction c	N/A	no	0.487	0.852	0.575	3e-29
Q1XDE0	115	Photosystem II reaction c	N/A	no	0.487	0.852	0.575	3e-29
P48264	112	Photosystem II reaction c	N/A	no	0.472	0.848	0.597	6e-29

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

 Score =  206 bits (523), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 101/170 (59%), Positives = 128/170 (75%), Gaps = 4/170 (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 TGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           TGFYMID+EG LQSVDVSAKFVNG+P+ IEAKY+MR+PREWDRFMRFMER
Sbjct: 119 TGFYMIDDEGVLQSVDVSAKFVNGKPALIEAKYVMRTPREWDRFMRFMER 168

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 =  192 bits (489), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 102/176 (57%), Positives = 129/176 (73%), Gaps = 11/176 (6%)

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

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

Query: 116 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           GE+G+ITG YMIDEEG +QS DV+A+FVNG+P  I AK+IMRSP+EWDRFMRFMER
Sbjct: 115 GEVGEITGLYMIDEEGVIQSTDVNARFVNGKPEGIVAKHIMRSPKEWDRFMRFMER 170

Arabidopsis thaliana (taxid: 3702)

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

 Score =  133 bits (335), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 59/102 (57%), Positives = 80/102 (78%), Gaps = 1/102 (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 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           EGTL++ DV+A+F+NG+P  IE+ YIM+SP  WDRFMRFMER
Sbjct: 61  EGTLETRDVNAQFINGKPEAIESIYIMKSPEAWDRFMRFMER 102

Odontella sinensis (taxid: 2839)

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

 Score =  133 bits (334), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 62/127 (48%), Positives = 89/127 (70%), Gaps = 5/127 (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 FMRFMER 171
           FMRFMER
Sbjct: 129 FMRFMER 135

Ostreococcus tauri (taxid: 70448)

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

 Score =  131 bits (329), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 58/102 (56%), Positives = 79/102 (77%), Gaps = 1/102 (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 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           EG L++ DV+A+FVNG+P  IE+ YIM+SP  WDRFMRFMER
Sbjct: 61  EGILETRDVNARFVNGKPEAIESIYIMKSPEAWDRFMRFMER 102

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 =  129 bits (325), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 62/104 (59%), Positives = 78/104 (75%), Gaps = 4/104 (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 DEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           DEEG L + DV+A+FVNG+P  IEA YIM+S  +WDRFMRFMER
Sbjct: 58  DEEGQLVTRDVNARFVNGKPQGIEAVYIMQSKEDWDRFMRFMER 101

Guillardia theta (taxid: 55529)

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

 Score =  128 bits (322), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 59/98 (60%), Positives = 75/98 (76%), Gaps = 1/98 (1%)

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 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ++ DVSA+FVNG+P  +E+ YIM+SP  WDRFMRFMER
Sbjct: 65  ETRDVSARFVNGKPQAVESIYIMKSPEAWDRFMRFMER 102

Thalassiosira pseudonana (taxid: 35128)

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

 Score =  128 bits (321), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 57/99 (57%), Positives = 77/99 (77%), Gaps = 1/99 (1%)

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 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           + + DV+AKF+NG+P  IEA ++++SP +WDRFMRFMER
Sbjct: 63  IITRDVNAKFINGKPQAIEAVHVIKSPDDWDRFMRFMER 101

Porphyra purpurea (taxid: 2787)

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

 Score =  128 bits (321), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 57/99 (57%), Positives = 77/99 (77%), Gaps = 1/99 (1%)

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 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           + + DV+AKF+NG+P  IEA ++++SP +WDRFMRFMER
Sbjct: 63  IITRDVNAKFINGKPQAIEAVHVIKSPDDWDRFMRFMER 101

Porphyra yezoensis (taxid: 2788)

>sp|P48264|PSB28_CYAPA Photosystem II reaction center psb28 protein OS=Cyanophora paradoxa GN=psb28 PE=3 SV=1

 Score =  127 bits (319), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 58/97 (59%), Positives = 74/97 (76%), Gaps = 2/97 (2%)

Query: 75  IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQ 134
           IQFIQG DE  +PDVKL++S+DG+NG+A F F +P+VFD     G+ITG Y+IDEEG L 
Sbjct: 4   IQFIQGVDEEAIPDVKLSRSQDGANGIAKFYFDKPTVFDVYQ--GEITGLYLIDEEGELS 61

Query: 135 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           +  V AKF+NG+P  IEA YIM +  EW+RF+RFMER
Sbjct: 62  TRTVYAKFINGKPQSIEASYIMNNREEWERFIRFMER 98

Cyanophora paradoxa (taxid: 2762)

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	201
225437969	179	PREDICTED: photosystem II reaction cente	0.830	0.932	0.736	2e-67
118488045	181	unknown [Populus trichocarpa]	0.840	0.933	0.690	5e-61
388491040	179	unknown [Lotus japonicus]	0.830	0.932	0.649	1e-60
351725219	179	uncharacterized protein LOC100306491 [Gl	0.830	0.932	0.666	2e-60
255571176	178	Photosystem II reaction center W protein	0.825	0.932	0.695	2e-60
356537186	179	PREDICTED: photosystem II reaction cente	0.830	0.932	0.660	4e-59
388494372	182	unknown [Medicago truncatula]	0.830	0.917	0.643	1e-56
449445636	221	PREDICTED: photosystem II reaction cente	0.825	0.751	0.619	1e-52
449487345	226	PREDICTED: photosystem II reaction cente	0.825	0.734	0.619	2e-52
357122411	179	PREDICTED: photosystem II reaction cente	0.825	0.927	0.597	6e-52

>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 =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 126/171 (73%), Positives = 146/171 (85%), Gaps = 4/171 (2%)

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

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

Query: 121 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITGFYMIDEEG LQSVDVSAKF+NG+PS IEAKY+MRSPREWDRFMRFMER
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFINGKPSGIEAKYVMRSPREWDRFMRFMER 167

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 =  239 bits (609), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 118/171 (69%), Positives = 142/171 (83%), Gaps = 2/171 (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 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITGFYMIDEEG LQSVDV+AKFVNG+P RIEAKYIMR+PREWDRFMRFME+
Sbjct: 119 ITGFYMIDEEGILQSVDVNAKFVNGKPERIEAKYIMRTPREWDRFMRFMEK 169

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  238 bits (607), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 111/171 (64%), Positives = 135/171 (78%), Gaps = 4/171 (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 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITG YMIDEEG LQS DVSAKF+NG+PS IEAKYIMR+PREWDRFMRFMER
Sbjct: 117 ITGLYMIDEEGVLQSTDVSAKFINGKPSIIEAKYIMRTPREWDRFMRFMER 167

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 114/171 (66%), Positives = 137/171 (80%), Gaps = 4/171 (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 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITGFYMIDEEG LQSVDVSAKFVNG+PS IEAKY+MRSPR+WDRFMRFMER
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFVNGKPSIIEAKYVMRSPRDWDRFMRFMER 167

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 =  237 bits (605), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 119/171 (69%), Positives = 139/171 (81%), Gaps = 5/171 (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 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITGFYMIDEEG LQSVDVSAKFVNG+P+RIEAKY+MRSPREWDRFMRFMER
Sbjct: 116 ITGFYMIDEEGVLQSVDVSAKFVNGKPARIEAKYVMRSPREWDRFMRFMER 166

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 113/171 (66%), Positives = 135/171 (78%), Gaps = 4/171 (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 ITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           ITGFYMIDEEG LQSVDVSAKFVNG+PS IEAKY+MRSPREWDRFMRFMER
Sbjct: 117 ITGFYMIDEEGVLQSVDVSAKFVNGKPSIIEAKYVMRSPREWDRFMRFMER 167

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 =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 112/174 (64%), Positives = 138/174 (79%), Gaps = 7/174 (4%)

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 IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           +GDITGFYMIDEEG LQSVDV+AKFVNG+PS IEAKYIMR+PR+WDRFMRFMER
Sbjct: 117 VGDITGFYMIDEEGVLQSVDVNAKFVNGKPSGIEAKYIMRTPRDWDRFMRFMER 170

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 =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 109/176 (61%), Positives = 134/176 (76%), Gaps = 10/176 (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 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            E+GDITGFYMIDEEG +QSVDV+AKF+NG+P+ IEAKY+MR+PREWDRFMRFMER
Sbjct: 154 AEVGDITGFYMIDEEGMIQSVDVNAKFINGKPAGIEAKYVMRTPREWDRFMRFMER 209

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 =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 109/176 (61%), Positives = 134/176 (76%), Gaps = 10/176 (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 GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            E+GDITGFYMIDEEG +QSVDV+AKF+NG+P+ IEAKY+MR+PREWDRFMRFMER
Sbjct: 159 AEVGDITGFYMIDEEGMIQSVDVNAKFINGKPAGIEAKYVMRTPREWDRFMRFMER 214

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 =  209 bits (532), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 101/169 (59%), Positives = 132/169 (78%), Gaps = 3/169 (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 GFYMIDEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           GFYMIDEEGTLQ+VDVSAKFVNG+P+ +EAKY+MR+PR+WDRFMRFMER
Sbjct: 119 GFYMIDEEGTLQTVDVSAKFVNGKPAAVEAKYVMRTPRDWDRFMRFMER 167

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	201
UNIPROTKB|Q55356	112	psb28 "Photosystem II reaction	0.477	0.857	0.525	7.8e-23

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

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 51/97 (52%), Positives = 69/97 (71%)

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 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
             + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMER
Sbjct:    63 TREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMER 99


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.132   0.401    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      201       201   0.00089  111 3  11 22  0.44    32
                                                     31  0.45    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:  604 (64 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:  18.87u 0.12s 18.99t   Elapsed:  00:00:01
  Total cpu time:  18.87u 0.12s 18.99t   Elapsed:  00:00:01
  Start:  Fri May 10 00:21:43 2013   End:  Fri May 10 00:21:44 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)
Q0JG75	PSB28_ORYSJ	No assigned EC number	0.5941	0.8258	0.9222	yes	no
Q8W0Y8	PSB28_ARATH	No assigned EC number	0.5795	0.8208	0.9016	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	201
PLN00039	111	PLN00039, PLN00039, photosystem II reaction center	4e-71
CHL00128	113	CHL00128, psbW, photosystem II protein W; Reviewed	2e-53
pfam03912	108	pfam03912, Psb28, Psb28 protein	1e-52
TIGR03047	109	TIGR03047, PS_II_psb28, photosystem II reaction ce	5e-52
PRK13612	113	PRK13612, PRK13612, photosystem II reaction center	3e-50
PRK13611	104	PRK13611, PRK13611, photosystem II reaction center	9e-19
PRK13610	113	PRK13610, PRK13610, photosystem II reaction center	2e-11

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

 Score =  211 bits (538), Expect = 4e-71
 Identities = 81/99 (81%), Positives = 92/99 (92%)

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

Query: 133 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           LQ+VDVSAKFVNG+P+ IEAKY+MRSPREWDRFMRFMER
Sbjct: 61  LQTVDVSAKFVNGKPAGIEAKYVMRSPREWDRFMRFMER 99

Length = 111

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

 Score =  166 bits (422), Expect = 2e-53
 Identities = 62/104 (59%), Positives = 76/104 (73%), Gaps = 4/104 (3%)

Query: 69  MAVKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEI-GDITGFYMI 127
           MA    IQFI+G DE  +PDV+LT+SRDGS G A F F  P++ D S    G+ITG Y+I
Sbjct: 1   MAK---IQFIKGIDEEVIPDVRLTRSRDGSTGTATFRFKNPNILDKSTAKQGEITGMYLI 57

Query: 128 DEEGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           DEEG L + DV+AKF+NG+P  IEA YIM++P  WDRFMRFMER
Sbjct: 58  DEEGELSTRDVNAKFINGKPQAIEAIYIMKNPEAWDRFMRFMER 101

Length = 113

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

 Score =  163 bits (416), Expect = 1e-52
 Identities = 57/98 (58%), Positives = 69/98 (70%), Gaps = 1/98 (1%)

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 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            +  VSAKFVNG P  +EA Y M+S  EW+RFMRFMER
Sbjct: 61  STRPVSAKFVNGEPKAVEATYEMKSEEEWERFMRFMER 98

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 =  162 bits (412), Expect = 5e-52
 Identities = 56/98 (57%), Positives = 69/98 (70%), Gaps = 1/98 (1%)

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 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            + +V AKFVNG+P  +EA YIM+S  EWDRFMRFMER
Sbjct: 61  STREVKAKFVNGKPKALEAVYIMKSEDEWDRFMRFMER 98

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 =  157 bits (400), Expect = 3e-50
 Identities = 56/100 (56%), Positives = 70/100 (70%), Gaps = 1/100 (1%)

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 TLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            + + +V AKFVNG+PS +EA YI +S +EWDRFMRFMER
Sbjct: 62  EIVTREVKAKFVNGKPSALEATYIWKSEQEWDRFMRFMER 101

Length = 113

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

 Score = 77.4 bits (190), Expect = 9e-19
 Identities = 42/98 (42%), Positives = 56/98 (57%), Gaps = 6/98 (6%)

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 QSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
            + ++ AKF+NG    +E  Y M +  EWDRF+RFMER
Sbjct: 57  TTRNIKAKFLNGEFKALEVIYDMETEAEWDRFLRFMER 94

Length = 104

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

 Score = 58.6 bits (141), Expect = 2e-11
 Identities = 26/97 (26%), Positives = 48/97 (49%), Gaps = 1/97 (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 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           +  +           +++ Y   S   ++RFMRF  R
Sbjct: 69  TKKIDLSISEDHVKEVKSTYNWNSEEAFERFMRFASR 105

Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	201
PLN00039	111	photosystem II reaction center Psb28 protein; Prov	100.0
PRK13612	113	photosystem II reaction center protein Psb28; Prov	100.0
CHL00128	113	psbW photosystem II protein W; Reviewed	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
PF11497	127	NADH_Oxid_Nqo15: NADH-quinone oxidoreductase chain	83.24
TIGR02447	138	yiiD_Cterm thioesterase domain, putative. This fam	80.49

>PLN00039 photosystem II reaction center Psb28 protein; Provisional

Probab=100.00  E-value=1.6e-65  Score=402.38  Aligned_cols=111  Identities=74%  Similarity=1.172  Sum_probs=107.2

Q ss_pred             ceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEEE
Q 028962           73 PTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEA  152 (201)
Q Consensus        73 asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa  152 (201)
                      |+||||+||||++||||||||||||++|+|+|+|++|++|+++..+++|||||||||||||+|+|||+|||||||++|||
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            68999999999999999999999999999999999999998864479999999999999999999999999999999999


Q ss_pred             EEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962          153 KYIMRSPREWDRFMRFMERQMVKALLDSHLS  183 (201)
Q Consensus       153 ~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~  183 (201)
                      +|+|+|++|||||||||||||++|||+|..+
T Consensus        81 ~y~m~s~~~WdRFMRFMeRYA~~ngl~f~k~  111 (111)
T PLN00039         81 KYVMRSPREWDRFMRFMERYAEENGLGFVKK  111 (111)
T ss_pred             EEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            9999999999999999999999999999863

>PRK13612 photosystem II reaction center protein Psb28; Provisional

Probab=100.00  E-value=2.7e-65  Score=402.06  Aligned_cols=112  Identities=52%  Similarity=0.859  Sum_probs=107.9

Q ss_pred             eeceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceE
Q 028962           71 VKPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI  150 (201)
Q Consensus        71 ~~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~I  150 (201)
                      ++|+||||+||||++||||||||||||++|+|+|+|++|++|++.. +++|||||||||||||+|+||++|||||||++|
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 KMAAIQFSRGVDEPVVPDIRLTRSRDGRTGQATFYFEQPQALAPET-TGEITGMYMIDEEGEIVTREVKAKFVNGKPSAL   80 (113)
T ss_pred             CcceEEEecCCCCCcCCceEEEEccCCCeeEEEEEECCccccCccc-cCceeeEEEEccCccEEEEecceEEECCCccEE
Confidence            4599999999999999999999999999999999999999998854 699999999999999999999999999999999


Q ss_pred             EEEEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962          151 EAKYIMRSPREWDRFMRFMERQMVKALLDSHLS  183 (201)
Q Consensus       151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~  183 (201)
                      ||+|+|+|++|||||||||||||++|||+|+.+
T Consensus        81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~  113 (113)
T PRK13612         81 EATYIWKSEQEWDRFMRFMERYAKENGLGFSKS  113 (113)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            999999999999999999999999999999864

>CHL00128 psbW photosystem II protein W; Reviewed

Probab=100.00  E-value=2.4e-65  Score=402.37  Aligned_cols=112  Identities=54%  Similarity=0.940  Sum_probs=107.5

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccC-CccCceeeEEEEecCceEEeEeceeeEEcCccceE
Q 028962           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSS-GEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRI  150 (201)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~-t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~I  150 (201)
                      +|+||||+||||++||||||||||||++|+|+|+|++|++|+++ ...++|||||||||||||+|+|||+|||||||++|
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            48999999999999999999999999999999999999999875 34699999999999999999999999999999999


Q ss_pred             EEEEEeCCchhhHHHHHHHHhhhHhcCCchhhh
Q 028962          151 EAKYIMRSPREWDRFMRFMERQMVKALLDSHLS  183 (201)
Q Consensus       151 Ea~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~  183 (201)
                      ||+|+|+|++|||||||||||||++|||+|..+
T Consensus        81 Ea~y~m~s~~~WdRFMRFMeRYA~~ngl~f~~~  113 (113)
T CHL00128         81 EAIYIMKNPEAWDRFMRFMERYAEDNGLTFTKA  113 (113)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHhcCCccccC
Confidence            999999999999999999999999999999863

>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28

Probab=100.00  E-value=7.7e-64  Score=391.81  Aligned_cols=108  Identities=53%  Similarity=0.921  Sum_probs=104.1

Q ss_pred             eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCC-ccCceeeEEEEecCceEEeEeceeeEEcCccceEEEE
Q 028962           75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSG-EIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK  153 (201)
Q Consensus        75 IQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t-~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~  153 (201)
                      ||||+||||++||||||||||||++|+|+|+|++|++|++++ .+++|||||||||||||+|+|||+|||||||++|||+
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            899999999999999999999999999999999999998753 3589999999999999999999999999999999999


Q ss_pred             EEeCCchhhHHHHHHHHhhhHhcCCchhh
Q 028962          154 YIMRSPREWDRFMRFMERQMVKALLDSHL  182 (201)
Q Consensus       154 y~m~s~~eWdRFMRFMeRYAe~NGLg~~~  182 (201)
                      |+|+|++|||||||||||||++|||+|++
T Consensus        81 y~m~s~~~WdRFMRFmeRYA~~ngl~f~~  109 (109)
T TIGR03047        81 YIMKSEDEWDRFMRFMERYAEANGLGYSK  109 (109)
T ss_pred             EEECCHHHHHHHHHHHHHHHHhcCCcccC
Confidence            99999999999999999999999999973

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=1.9e-63  Score=389.03  Aligned_cols=107  Identities=56%  Similarity=0.935  Sum_probs=81.5

Q ss_pred             eEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCc-cCceeeEEEEecCceEEeEeceeeEEcCccceEEEE
Q 028962           75 IQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGE-IGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIEAK  153 (201)
Q Consensus        75 IQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~-~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IEa~  153 (201)
                      ||||+||||+++|||||||||||++|+|+|+|++|++|++++. .|+|||||||||||||+|+||++|||||||++|||+
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            8999999999999999999999999999999999999987753 579999999999999999999999999999999999


Q ss_pred             EEeCCchhhHHHHHHHHhhhHhcCCchh
Q 028962          154 YIMRSPREWDRFMRFMERQMVKALLDSH  181 (201)
Q Consensus       154 y~m~s~~eWdRFMRFMeRYAe~NGLg~~  181 (201)
                      |+|+|++|||||||||||||++|||+|+
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            9999999999999999999999999995

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=6.7e-62  Score=378.42  Aligned_cols=104  Identities=39%  Similarity=0.668  Sum_probs=100.5

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEE
Q 028962           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (201)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IE  151 (201)
                      +|+||||+||||+ +|||||||||||++|+|+|+|++|++     .+++|||||||||||||+|+||++|||||||++||
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            4899999999999 99999999999999999999999998     24899999999999999999999999999999999


Q ss_pred             EEEEeCCchhhHHHHHHHHhhhHhcCCchh
Q 028962          152 AKYIMRSPREWDRFMRFMERQMVKALLDSH  181 (201)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~NGLg~~  181 (201)
                      |+|+|+|++|||||||||||||++|||+|.
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=2.1e-60  Score=374.44  Aligned_cols=104  Identities=25%  Similarity=0.547  Sum_probs=100.6

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEE
Q 028962           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (201)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IE  151 (201)
                      .|+||||+||||++||||||||||||++|+|+|+|++|++|++. .+++|||||||||||||+|+||++|||||||++||
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            58999999999999999999999999999999999999999885 36999999999999999999999999999999999


Q ss_pred             EEEEeCCchhhHHHHHHHHhhhHhc
Q 028962          152 AKYIMRSPREWDRFMRFMERQMVKA  176 (201)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~N  176 (201)
                      |+|+|+|++|||||||||||||++.
T Consensus        86 a~y~m~s~~~WdRFMRFMeRYA~~~  110 (113)
T PRK13610         86 STYNWNSEEAFERFMRFASRYANSL  110 (113)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999974

>PF11497 NADH_Oxid_Nqo15: NADH-quinone oxidoreductase chain 15; InterPro: IPR021093 NADH:ubiquinone oxidoreductase (complex I) (1

Probab=83.24  E-value=0.79  Score=37.80  Aligned_cols=33  Identities=21%  Similarity=0.440  Sum_probs=23.4

Q ss_pred             hhhHHHHHHHHhhhHhcCCchhhhh--------cccceecc
Q 028962          160 REWDRFMRFMERQMVKALLDSHLSL--------MQKPYALF  192 (201)
Q Consensus       160 ~eWdRFMRFMeRYAe~NGLg~~~~~--------~~~~~~~~  192 (201)
                      +.|-..+-+|+-||+++|+.|..-+        |.+||-|=
T Consensus        11 ~aWvell~Wl~eyA~~~g~~fekeaDFPDyIYRMeRPydLP   51 (127)
T PF11497_consen   11 RAWVELLGWLREYAAERGLRFEKEADFPDYIYRMERPYDLP   51 (127)
T ss_dssp             HHHHHHHHHHHHHHHHTT-EEEEEEE-HHHHT--SS----S
T ss_pred             HHHHHHHHHHHHHHHHcCCceeecccccHHHHhccCcccCC
Confidence            5799999999999999999997654        88898763

6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex [].; PDB: 3M9S_7 3I9V_7 3IAM_H 2FUG_H 3IAS_7 2YBB_7.

>TIGR02447 yiiD_Cterm thioesterase domain, putative

Probab=80.49  E-value=4.7  Score=31.58  Aligned_cols=46  Identities=13%  Similarity=0.263  Sum_probs=38.4

Q ss_pred             CceEEeEeceeeEEcCccceEEEEEEeCCchhhHHHHHHHHhhhHh
Q 028962          130 EGTLQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMERQMVK  175 (201)
Q Consensus       130 EGeI~Tr~V~aKFvNGkP~~IEa~y~m~s~~eWdRFMRFMeRYAe~  175 (201)
                      ++.++|.+.+.+|+.---.++.|..+...+++||+|.+=++|-...
T Consensus        67 ~~~~vt~~~~i~yl~P~~~~~~a~~~~~~~~~~~~~~~~l~~~gr~  112 (138)
T TIGR02447        67 DGDIVIADSHIRYLAPVTGDPVANCEAPDLESWEAFLATLQRGGKA  112 (138)
T ss_pred             CCcEEEEEeeeEEcCCcCCCeEEEEEcCCHHHHHHHHHHHHhCCce
Confidence            3589999999999964445699999999999999999988885544

This family consists of a broadly distributed uncharacterized domain found often as a standalone protein. The member from Shewanella oneidensis, PDB|1T82_A (Forouhar, et al., unpublished) is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an Acetyltransf_1 domain (PFAM model pfam00583). The function of this protein is unknown.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	201
2kvo_A	120	Solution Nmr Structure Of Photosystem Ii Reaction C		2e-24

>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 =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 51/97 (52%), Positives = 69/97 (71%), Gaps = 1/97 (1%)
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 SVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMER
Sbjct: 63  TREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMER 99

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	201
2kvo_A	120	Photosystem II reaction center PSB28 protein; memb	1e-49

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

 Score =  156 bits (395), Expect = 1e-49
 Identities = 51/99 (51%), Positives = 68/99 (68%), Gaps = 1/99 (1%)

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 LQSVDVSAKFVNGRPSRIEAKYIMRSPREWDRFMRFMER 171
           + + +V  KF+NGRP+ IEA  I+ S  EWDRFMRFMER
Sbjct: 61  IITREVKGKFINGRPTAIEATVILNSQPEWDRFMRFMER 99

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	201
2kvo_A	120	Photosystem II reaction center PSB28 protein; memb	100.0
3i9v_7	129	NADH-quinone oxidoreductase subunit 15; electron t	81.92

>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=1.8e-65  Score=405.29  Aligned_cols=113  Identities=47%  Similarity=0.800  Sum_probs=109.5

Q ss_pred             eceeEeecCCCCCCCCCeeEEeccCCCcceEEEEEcCCcccccCCccCceeeEEEEecCceEEeEeceeeEEcCccceEE
Q 028962           72 KPTIQFIQGTDELTVPDVKLTKSRDGSNGMAIFSFSEPSVFDSSGEIGDITGFYMIDEEGTLQSVDVSAKFVNGRPSRIE  151 (201)
Q Consensus        72 ~asIQFi~GidEe~iPdVrLTRSrdG~~GtA~F~Fe~Pkal~s~t~~g~ITGMyLIDEEGeI~Tr~V~aKFvNGkP~~IE  151 (201)
                      +|+||||+||||++||||||||||||++|+|+|+|++|++|++++ .++|||||||||||||+|+||++|||||||++||
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 MAEIQFSKGVAETVVPEVRLSKSKNGQSGMAKFYFLEPTILAKES-TDDITGMYLIDDEGEIITREVKGKFINGRPTAIE   79 (120)
T ss_dssp             CCEEESSSSCCCCCCCEEEEEECTTSCSEEEEEEEESCGGGTSSC-GGGCCCEEEECSSCEEEECCEEEEEETTEEEEEE
T ss_pred             CCcEEEecCCCCCcCCceEEEEcccCCccEEEEEECCchhccccc-cCcceeEEEEccCccEEEEecceEEECCceeEEE
Confidence            489999999999999999999999999999999999999999884 6999999999999999999999999999999999


Q ss_pred             EEEEeCCchhhHHHHHHHHhhhHhcCCchhhhhc
Q 028962          152 AKYIMRSPREWDRFMRFMERQMVKALLDSHLSLM  185 (201)
Q Consensus       152 a~y~m~s~~eWdRFMRFMeRYAe~NGLg~~~~~~  185 (201)
                      |+|+|+|+++||||||||||||++|||+|+++..
T Consensus        80 a~y~m~s~~~WdRFMRFMeRYA~~Ngl~f~k~~~  113 (120)
T 2kvo_A           80 ATVILNSQPEWDRFMRFMERYGAENGLGFSKSEL  113 (120)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHHHCCSSSCSTTT
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHhcCCccccCch
Confidence            9999999999999999999999999999998754

>3i9v_7 NADH-quinone oxidoreductase subunit 15; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_7* 2fug_7* 3iam_7* 3ias_7* 3m9s_7*

Probab=81.92  E-value=0.68  Score=37.09  Aligned_cols=33  Identities=18%  Similarity=0.368  Sum_probs=28.5

Q ss_pred             hhhHHHHHHHHhhhHhcCCchhhhh--------cccceecc
Q 028962          160 REWDRFMRFMERQMVKALLDSHLSL--------MQKPYALF  192 (201)
Q Consensus       160 ~eWdRFMRFMeRYAe~NGLg~~~~~--------~~~~~~~~  192 (201)
                      +.|--.|-+|+-||.++|+.|..-+        |.+||-|=
T Consensus        11 ~aWvell~Wl~eyA~~~g~~FekeaDFPDyIYRMeRPydLP   51 (129)
T 3i9v_7           11 EAWVELLSWMREYAQAKGVRFEKEADFPDFIYRMERPYDLP   51 (129)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEEECHHHHSCCSSCCCCS
T ss_pred             HHHHHHHHHHHHHHHhcCCceeecccccHHHHhhcCcccCC
Confidence            5799999999999999999997654        88898774

---

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