Citrus Sinensis ID: 029740

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------19
MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL
cccEEcccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHcccccccccccccccccccHHHHHHHHHHHHHHHccccccEEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHcccccHHHHHHHHHccccccccc
ccEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHccccccccc
MVTILLVSARNQTTSASIYQAYELIHARWAMLGaagfiipeafnkfgancgpeavwFKTGAllldgntlnyfgknipiNLVFAVIAEIVLVGGAeyyritngldledklhpggpfdplglakdpdQFALLKVKEIKNGRLAMFAMLGFFLQAYvtgegpvenlakhlsdpfannLLTVISgnaeraptl
MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLltvisgnaeraptl
MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL
***********************LIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVI**********
MVTILL*SARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPT*
MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL
MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAER****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVTILLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query189 2.2.26 [Sep-21-2011]
Q9XF89280 Chlorophyll a-b binding p yes no 0.904 0.610 0.918 3e-83
P27517253 Chlorophyll a-b binding p N/A no 0.878 0.656 0.525 3e-41
P20866269 Chlorophyll a-b binding p N/A no 0.798 0.561 0.560 9e-41
P04781267 Chlorophyll a-b binding p N/A no 0.798 0.565 0.554 3e-40
P27490268 Chlorophyll a-b binding p N/A no 0.798 0.563 0.541 8e-40
P15193278 Chlorophyll a-b binding p N/A no 0.798 0.543 0.547 9e-40
P12328264 Chlorophyll a-b binding p N/A no 0.798 0.571 0.566 1e-39
P04782266 Chlorophyll a-b binding p N/A no 0.798 0.567 0.547 1e-39
P15194274 Chlorophyll a-b binding p N/A no 0.798 0.551 0.541 1e-39
P12330265 Chlorophyll a-b binding p no no 0.798 0.569 0.554 1e-39
>sp|Q9XF89|CB5_ARATH Chlorophyll a-b binding protein CP26, chloroplastic OS=Arabidopsis thaliana GN=LHCB5 PE=2 SV=1 Back     alignment and function desciption
 Score =  307 bits (786), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 157/171 (91%), Positives = 165/171 (96%)

Query: 19  YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
           YQA+ELIHARWAMLGAAGFIIPEA NK+GANCGPEAVWFKTGALLLDGNTLNYFGKNIPI
Sbjct: 110 YQAFELIHARWAMLGAAGFIIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 169

Query: 79  NLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNG 138
           NLV AV+AE+VL+GGAEYYRITNGLD EDKLHPGGPFDPLGLAKDP+Q ALLKVKEIKNG
Sbjct: 170 NLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDPLGLAKDPEQGALLKVKEIKNG 229

Query: 139 RLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL 189
           RLAMFAMLGFF+QAYVTGEGPVENLAKHLSDPF NNLLTVI+G AERAPTL
Sbjct: 230 RLAMFAMLGFFIQAYVTGEGPVENLAKHLSDPFGNNLLTVIAGTAERAPTL 280
The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated.
Arabidopsis thaliana (taxid: 3702)
>sp|P27517|CB2_DUNTE Chlorophyll a-b binding protein of LHCII type I, chloroplastic OS=Dunaliella tertiolecta PE=2 SV=1 Back     alignment and function description
>sp|P20866|CB2_PHYPA Chlorophyll a-b binding protein, chloroplastic OS=Physcomitrella patens subsp. patens PE=3 SV=1 Back     alignment and function description
>sp|P04781|CB23_PETSP Chlorophyll a-b binding protein 22R, chloroplastic OS=Petunia sp. GN=CAB22R PE=3 SV=1 Back     alignment and function description
>sp|P27490|CB28_PEA Chlorophyll a-b binding protein 8, chloroplastic OS=Pisum sativum GN=CAB8 PE=1 SV=1 Back     alignment and function description
>sp|P15193|CB2A_PINSY Chlorophyll a-b binding protein type 2 member 1A, chloroplastic OS=Pinus sylvestris PE=2 SV=1 Back     alignment and function description
>sp|P12328|CB21_LEMGI Chlorophyll a-b binding protein of LHCII type I, chloroplastic OS=Lemna gibba PE=3 SV=1 Back     alignment and function description
>sp|P04782|CB24_PETSP Chlorophyll a-b binding protein 25, chloroplastic OS=Petunia sp. GN=CAB25 PE=3 SV=1 Back     alignment and function description
>sp|P15194|CB2B_PINSY Chlorophyll a-b binding protein type 2 member 1B, chloroplastic OS=Pinus sylvestris PE=2 SV=1 Back     alignment and function description
>sp|P12330|CB21_ORYSJ Chlorophyll a-b binding protein 1, chloroplastic OS=Oryza sativa subsp. japonica GN=CAB1R PE=2 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query189
225459918 290 PREDICTED: chlorophyll a-b binding prote 0.904 0.589 0.935 3e-89
356535308287 PREDICTED: chlorophyll a-b binding prote 0.904 0.595 0.918 2e-87
339716054279 putative chlorophyll a/b binding protein 0.904 0.612 0.923 2e-87
224127848 290 light-harvesting complex II protein Lhcb 0.904 0.589 0.912 3e-87
255557841 292 chlorophyll A/B binding protein, putativ 0.904 0.585 0.906 3e-87
356576567288 PREDICTED: chlorophyll a-b binding prote 0.904 0.593 0.912 5e-87
255638437287 unknown [Glycine max] 0.904 0.595 0.912 6e-87
449447521288 PREDICTED: chlorophyll a-b binding prote 0.904 0.593 0.912 1e-86
261351266287 chloroplast pigment-binding protein CP26 0.904 0.595 0.912 2e-86
255645788289 unknown [Glycine max] 0.915 0.598 0.907 6e-86
>gi|225459918|ref|XP_002264295.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic [Vitis vinifera] gi|147770824|emb|CAN76428.1| hypothetical protein VITISV_023565 [Vitis vinifera] gi|297734735|emb|CBI16969.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  333 bits (853), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 160/171 (93%), Positives = 165/171 (96%)

Query: 19  YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
           YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI
Sbjct: 120 YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 179

Query: 79  NLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNG 138
           NL+FAV+AE+VLVGGAEYYRI NGLDLEDKLHPGGPFDPLGLA DPDQ ALLKVKEIKNG
Sbjct: 180 NLIFAVVAEVVLVGGAEYYRIINGLDLEDKLHPGGPFDPLGLANDPDQAALLKVKEIKNG 239

Query: 139 RLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL 189
           RLAMFAMLGFF+QAYVTGEGPVENLA HLSDPF NNLLTVI+G AERAPTL
Sbjct: 240 RLAMFAMLGFFIQAYVTGEGPVENLAAHLSDPFGNNLLTVIAGTAERAPTL 290

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356535308|ref|XP_003536189.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|339716054|gb|AEJ88274.1| putative chlorophyll a/b binding protein [Wolffia australiana] Back     alignment and taxonomy information
>gi|224127848|ref|XP_002329192.1| light-harvesting complex II protein Lhcb5 [Populus trichocarpa] gi|118487642|gb|ABK95646.1| unknown [Populus trichocarpa] gi|222870973|gb|EEF08104.1| light-harvesting complex II protein Lhcb5 [Populus trichocarpa] Back     alignment and taxonomy information
>gi|255557841|ref|XP_002519950.1| chlorophyll A/B binding protein, putative [Ricinus communis] gi|223540996|gb|EEF42554.1| chlorophyll A/B binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356576567|ref|XP_003556402.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|255638437|gb|ACU19528.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|449447521|ref|XP_004141516.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic-like [Cucumis sativus] gi|449510691|ref|XP_004163735.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|261351266|gb|ACX71300.1| chloroplast pigment-binding protein CP26 [Capsicum annuum] Back     alignment and taxonomy information
>gi|255645788|gb|ACU23386.1| unknown [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query189
TAIR|locus:2122794280 LHCB5 "light harvesting comple 0.904 0.610 0.918 7.2e-84
UNIPROTKB|P12330265 CAB1R "Chlorophyll a-b binding 0.798 0.569 0.554 3.7e-39
UNIPROTKB|P12331261 CAB2R "Chlorophyll a-b binding 0.798 0.578 0.554 3.7e-39
TAIR|locus:2019287267 CAB3 "chlorophyll A/B binding 0.798 0.565 0.537 4.8e-39
TAIR|locus:2019372267 CAB2 "chlorophyll A/B-binding 0.798 0.565 0.537 4.8e-39
TAIR|locus:2019322267 CAB1 "chlorophyll A/B binding 0.798 0.565 0.537 4.8e-39
TAIR|locus:2040934265 LHB1B2 "photosystem II light h 0.798 0.569 0.531 2.6e-38
TAIR|locus:2040944266 LHB1B1 "light-harvesting chlor 0.798 0.567 0.531 2.6e-38
TAIR|locus:2044988265 LHCB2.2 "photosystem II light 0.798 0.569 0.554 1.1e-37
TAIR|locus:2042148265 LHCB2.1 "photosystem II light 0.798 0.569 0.554 1.1e-37
TAIR|locus:2122794 LHCB5 "light harvesting complex of photosystem II 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 840 (300.8 bits), Expect = 7.2e-84, P = 7.2e-84
 Identities = 157/171 (91%), Positives = 165/171 (96%)

Query:    19 YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
             YQA+ELIHARWAMLGAAGFIIPEA NK+GANCGPEAVWFKTGALLLDGNTLNYFGKNIPI
Sbjct:   110 YQAFELIHARWAMLGAAGFIIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 169

Query:    79 NLVFAVIAEIVLVGGAEYYRITNGLDLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNG 138
             NLV AV+AE+VL+GGAEYYRITNGLD EDKLHPGGPFDPLGLAKDP+Q ALLKVKEIKNG
Sbjct:   170 NLVLAVVAEVVLLGGAEYYRITNGLDFEDKLHPGGPFDPLGLAKDPEQGALLKVKEIKNG 229

Query:   139 RLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLTVISGNAERAPTL 189
             RLAMFAMLGFF+QAYVTGEGPVENLAKHLSDPF NNLLTVI+G AERAPTL
Sbjct:   230 RLAMFAMLGFFIQAYVTGEGPVENLAKHLSDPFGNNLLTVIAGTAERAPTL 280
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0009533 "chloroplast stromal thylakoid" evidence=IDA
GO:0009765 "photosynthesis, light harvesting" evidence=IEA
GO:0015979 "photosynthesis" evidence=ISS;IMP
GO:0016020 "membrane" evidence=IEA;IDA
GO:0016168 "chlorophyll binding" evidence=ISS
GO:0030076 "light-harvesting complex" evidence=ISS
GO:0009783 "photosystem II antenna complex" evidence=IMP
GO:0009535 "chloroplast thylakoid membrane" evidence=IDA
GO:0010287 "plastoglobule" evidence=IDA
GO:0010196 "nonphotochemical quenching" evidence=IMP
GO:0009579 "thylakoid" evidence=IDA
GO:0009637 "response to blue light" evidence=IEP;RCA
GO:0010114 "response to red light" evidence=IEP;RCA
GO:0010218 "response to far red light" evidence=IEP;RCA
GO:0009534 "chloroplast thylakoid" evidence=IDA
GO:0006364 "rRNA processing" evidence=RCA
GO:0009644 "response to high light intensity" evidence=RCA
GO:0009744 "response to sucrose stimulus" evidence=RCA
GO:0010155 "regulation of proton transport" evidence=RCA
GO:0019344 "cysteine biosynthetic process" evidence=RCA
GO:0009517 "PSII associated light-harvesting complex II" evidence=IDA
UNIPROTKB|P12330 CAB1R "Chlorophyll a-b binding protein 1, chloroplastic" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
UNIPROTKB|P12331 CAB2R "Chlorophyll a-b binding protein 2, chloroplastic" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2019287 CAB3 "chlorophyll A/B binding protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019372 CAB2 "chlorophyll A/B-binding protein 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019322 CAB1 "chlorophyll A/B binding protein 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2040934 LHB1B2 "photosystem II light harvesting complex gene B1B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2040944 LHB1B1 "light-harvesting chlorophyll-protein complex II subunit B1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2044988 LHCB2.2 "photosystem II light harvesting complex gene 2.2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2042148 LHCB2.1 "photosystem II light harvesting complex gene 2.1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

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) ?
Q9XF89CB5_ARATHNo assigned EC number0.91810.90470.6107yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00031964001
SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_61, whole genome shotgun sequence); (290 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query189
PLN00025262 PLN00025, PLN00025, photosystem II light harvestin 1e-62
PLN00171324 PLN00171, PLN00171, photosystem light-harvesting c 2e-50
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 1e-41
PLN00048262 PLN00048, PLN00048, photosystem I light harvesting 6e-39
PLN00187286 PLN00187, PLN00187, photosystem II light-harvestin 2e-35
PLN00147252 PLN00147, PLN00147, light-harvesting complex I chl 4e-34
PLN00099243 PLN00099, PLN00099, light-harvesting complex IChlo 4e-33
PLN00098267 PLN00098, PLN00098, light-harvesting complex I chl 6e-27
PLN00097244 PLN00097, PLN00097, photosystem I light harvesting 4e-26
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 4e-24
PLN00100246 PLN00100, PLN00100, light-harvesting complex chlor 6e-18
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 2e-08
PLN00089209 PLN00089, PLN00089, fucoxanthin-chlorophyll a/c bi 6e-07
PLN00120202 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c bi 2e-05
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 7e-04
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 0.001
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 0.002
>gnl|CDD|215033 PLN00025, PLN00025, photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information 
 Score =  194 bits (494), Expect = 1e-62
 Identities = 93/164 (56%), Positives = 111/164 (67%), Gaps = 12/164 (7%)

Query: 19  YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
            +  E+IHARWAMLGA G + PE   K G   G EAVWFK GA +     L+Y G     
Sbjct: 91  NRELEVIHARWAMLGALGCVTPELLAKNGVKFG-EAVWFKAGAQIFSEGGLDYLGNP--- 146

Query: 79  NLVFA--VIA----EIVLVGGAEYYRITNGLDLE--DKLHPGGPFDPLGLAKDPDQFALL 130
           +LV A  ++A    ++VL+G  E YR+  G   E  D L+PGG FDPLGLA DPD FA L
Sbjct: 147 SLVHAQSILAIWACQVVLMGAVEGYRVNGGPLGEGLDPLYPGGSFDPLGLADDPDTFAEL 206

Query: 131 KVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANN 174
           KVKEIKNGRLAMF+M GFF+QA VTG+GP+ENLA HL+DP ANN
Sbjct: 207 KVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVANN 250

Length = 262
>gnl|CDD|215088 PLN00171, PLN00171, photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information
>gnl|CDD|215956 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein Back     alignment and domain information
>gnl|CDD|177680 PLN00048, PLN00048, photosystem I light harvesting chlorophyll a/b binding protein 3; Provisional Back     alignment and domain information
>gnl|CDD|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information
>gnl|CDD|215076 PLN00147, PLN00147, light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>gnl|CDD|177717 PLN00099, PLN00099, light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>gnl|CDD|177716 PLN00098, PLN00098, light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional Back     alignment and domain information
>gnl|CDD|165670 PLN00097, PLN00097, photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional Back     alignment and domain information
>gnl|CDD|215055 PLN00101, PLN00101, Photosystem I light-harvesting complex type 4 protein; Provisional Back     alignment and domain information
>gnl|CDD|215054 PLN00100, PLN00100, light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>gnl|CDD|215087 PLN00170, PLN00170, photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>gnl|CDD|177710 PLN00089, PLN00089, fucoxanthin-chlorophyll a/c binding protein; Provisional Back     alignment and domain information
>gnl|CDD|215063 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c binding protein; Provisional Back     alignment and domain information
>gnl|CDD|215956 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein Back     alignment and domain information
>gnl|CDD|215055 PLN00101, PLN00101, Photosystem I light-harvesting complex type 4 protein; Provisional Back     alignment and domain information
>gnl|CDD|215087 PLN00170, PLN00170, photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 189
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 100.0
PLN00099243 light-harvesting complex IChlorophyll A-B binding 100.0
PLN00171324 photosystem light-harvesting complex -chlorophyll 100.0
PLN00187286 photosystem II light-harvesting complex II protein 100.0
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 100.0
PLN00098267 light-harvesting complex I chlorophyll a/b-binding 100.0
PLN00101250 Photosystem I light-harvesting complex type 4 prot 100.0
PLN00097244 photosystem I light harvesting complex Lhca2/4, ch 100.0
PLN00048262 photosystem I light harvesting chlorophyll a/b bin 100.0
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 100.0
PLN00170255 photosystem II light-harvesting-Chl-binding protei 100.0
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 100.0
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 100.0
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 100.0
PLN00098 267 light-harvesting complex I chlorophyll a/b-binding 99.62
PLN00101250 Photosystem I light-harvesting complex type 4 prot 99.6
PLN00147 252 light-harvesting complex I chlorophyll-a/b binding 99.56
PLN00097 244 photosystem I light harvesting complex Lhca2/4, ch 99.53
PLN00171 324 photosystem light-harvesting complex -chlorophyll 99.53
PLN00025 262 photosystem II light harvesting chlorophyll a/b bi 99.52
PLN00170 255 photosystem II light-harvesting-Chl-binding protei 99.52
PLN00100 246 light-harvesting complex chlorophyll-a/b protein o 99.49
PLN00099 243 light-harvesting complex IChlorophyll A-B binding 99.47
PLN00187286 photosystem II light-harvesting complex II protein 99.46
PLN00048 262 photosystem I light harvesting chlorophyll a/b bin 99.42
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.4
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.39
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.17
PLN00084214 photosystem II subunit S (PsbS); Provisional 98.16
PHA0233735 putative high light inducible protein 98.12
PLN00014250 light-harvesting-like protein 3; Provisional 97.51
PHA0233735 putative high light inducible protein 97.16
PLN00014250 light-harvesting-like protein 3; Provisional 94.88
PLN00084214 photosystem II subunit S (PsbS); Provisional 91.95
>PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.8e-47  Score=327.02  Aligned_cols=172  Identities=52%  Similarity=0.847  Sum_probs=145.1

Q ss_pred             EeeccCCChhhHHHHHHHHhhhhhhHHhhhhhhhhhhccccCCCCCCCcchhhhccccccCCcccccccccchH--HH-H
Q 029740            5 LLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI--NL-V   81 (189)
Q Consensus         5 ~~~~~~~~~~~l~~~REaELkHGRvAMLA~vG~lv~e~~~~~g~~~~p~~~w~~ag~~~~~~~~~~~~~~~~p~--~~-~   81 (189)
                      |.++  .|+++++||||+|||||||||||++|+++||+++..|..+. +..|+++|...++.+.++|++++..+  +. .
T Consensus        79 lGls--~dp~~~~~~re~El~hGR~AMLa~~G~i~~e~l~~~g~~~~-~~~W~~ag~~~~~~gg~~y~~~p~~~~~~~~~  155 (262)
T PLN00025         79 AGLS--ADPETFARNRELEVIHARWAMLGALGCVTPELLAKNGVKFG-EAVWFKAGAQIFSEGGLDYLGNPSLVHAQSIL  155 (262)
T ss_pred             cccc--cCHHHHHHHHHHHHhccHHHHHHHhhhhhHHHhhcCCcCcC-cccccccccccccccccccccCcccchhhhHH
Confidence            3454  48999999999999999999999999999999876554332 45799999877777778898876432  22 2


Q ss_pred             HHHHHHHHHHhhhhhhhcccCc--CCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhchhhHHHHHHHHHHHhhhcCCcc
Q 029740           82 FAVIAEIVLVGGAEYYRITNGL--DLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGP  159 (189)
Q Consensus        82 ~a~~~qv~~~g~~E~~~~~~g~--~~~~~~~PG~~fDPlgl~~d~~~~~~~~~~ElkNGRLAMla~~G~i~q~~v~g~gp  159 (189)
                      ..+++|++++|++|.+|..++.  ...+..||||.||||||.+|+++++++|++|||||||||+|++||++|+.+||++|
T Consensus       156 a~~~~qv~lmg~~E~~r~~~~~~~~~~d~~yPG~~FDPlGl~~d~~~~~~~k~kEikNGRLAMlA~~G~~~q~~vTG~GP  235 (262)
T PLN00025        156 AIWACQVVLMGAVEGYRVNGGPLGEGLDPLYPGGSFDPLGLADDPDTFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGP  235 (262)
T ss_pred             HHHHHHHHHHHHHHHhcccCCcccccccCcCCcccCCccccCCCHHHHHHHHHHHHhhhhHHHHHHHHHhhhhhhcCCCh
Confidence            3347788899999999876532  11256899999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhCCcccchhhhhh
Q 029740          160 VENLAKHLSDPFANNLLTVI  179 (189)
Q Consensus       160 l~~l~~~~~~P~~~~~~~~~  179 (189)
                      ++||.+|++||+++|++++.
T Consensus       236 lenL~~hladP~~~n~~~~~  255 (262)
T PLN00025        236 LENLADHLADPVANNAWAYA  255 (262)
T ss_pred             HHHHHHHhcCccccchhhhh
Confidence            99999999999999998875

>PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information
>PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional Back     alignment and domain information
>PLN00101 Photosystem I light-harvesting complex type 4 protein; Provisional Back     alignment and domain information
>PLN00097 photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional Back     alignment and domain information
>PLN00048 photosystem I light harvesting chlorophyll a/b binding protein 3; Provisional Back     alignment and domain information
>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional Back     alignment and domain information
>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional Back     alignment and domain information
>PF00504 Chloroa_b-bind: Chlorophyll A-B binding protein; InterPro: IPR022796 The light-harvesting complex (LHC) consists of chlorophylls A and B and the chlorophyll A-B binding protein Back     alignment and domain information
>PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional Back     alignment and domain information
>PLN00101 Photosystem I light-harvesting complex type 4 protein; Provisional Back     alignment and domain information
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>PLN00097 photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional Back     alignment and domain information
>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information
>PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information
>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information
>PLN00048 photosystem I light harvesting chlorophyll a/b binding protein 3; Provisional Back     alignment and domain information
>PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional Back     alignment and domain information
>PF00504 Chloroa_b-bind: Chlorophyll A-B binding protein; InterPro: IPR022796 The light-harvesting complex (LHC) consists of chlorophylls A and B and the chlorophyll A-B binding protein Back     alignment and domain information
>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional Back     alignment and domain information
>PLN00084 photosystem II subunit S (PsbS); Provisional Back     alignment and domain information
>PHA02337 putative high light inducible protein Back     alignment and domain information
>PLN00014 light-harvesting-like protein 3; Provisional Back     alignment and domain information
>PHA02337 putative high light inducible protein Back     alignment and domain information
>PLN00014 light-harvesting-like protein 3; Provisional Back     alignment and domain information
>PLN00084 photosystem II subunit S (PsbS); Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query189
2bhw_A232 Pea Light-Harvesting Complex Ii At 2.5 Angstrom Res 4e-40
1vcr_A232 An Icosahedral Assembly Of Light-Harvesting Chlorop 4e-40
1rwt_A232 Crystal Structure Of Spinach Major Light-harvesting 1e-39
2wsc_1241 Improved Model Of Plant Photosystem I Length = 241 4e-27
3pl9_A243 Crystal Structure Of Spinach Minor Light-Harvesting 6e-27
2o01_1187 The Structure Of A Plant Photosystem I Supercomplex 8e-27
2wsc_3276 Improved Model Of Plant Photosystem I Length = 276 9e-26
3lw5_1170 Improved Model Of Plant Photosystem I Length = 170 1e-25
2o01_3165 The Structure Of A Plant Photosystem I Supercomplex 7e-22
3lw5_2176 Improved Model Of Plant Photosystem I Length = 176 9e-21
2wsc_2269 Improved Model Of Plant Photosystem I Length = 269 1e-20
2o01_2186 The Structure Of A Plant Photosystem I Supercomplex 2e-20
3lw5_3172 Improved Model Of Plant Photosystem I Length = 172 2e-19
2o01_4165 The Structure Of A Plant Photosystem I Supercomplex 7e-18
2wsc_4251 Improved Model Of Plant Photosystem I Length = 251 5e-17
3lw5_4166 Improved Model Of Plant Photosystem I Length = 166 8e-16
>pdb|2BHW|A Chain A, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution Length = 232 Back     alignment and structure 
Iteration: 1

 Score =  160 bits (405), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 88/176 (50%), Positives = 118/176 (67%), Gaps = 8/176 (4%)
Query: 7   VSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDG 66
           +SA  +T S +  +  E+IH+RWAMLGA G + PE  ++ G   G EAVWFK G+ +   
Sbjct: 51  LSADPETFSKN--RELEVIHSRWAMLGALGSVFPELLSRNGVKFG-EAVWFKAGSQIFSE 107
Query: 67  NTLNYFGKN--IPINLVFAVIA-EIVLVGGAEYYRITNGL--DLEDKLHPGGPFDPLGLA 121
             L+Y G    +    + A+ A +++L+G  E YRI  G   ++ D L+PGG FDPLGLA
Sbjct: 108 GGLDYLGNPSLVHAQSILAIWATQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLA 167
Query: 122 KDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLT 177
            DP+ FA LKVKE+KNGRLAMF+M GFF+QA VTG+GP+ENLA HL+DP  NN  +
Sbjct: 168 DDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWS 223
>pdb|1VCR|A Chain A, An Icosahedral Assembly Of Light-Harvesting Chlorophyll AB Protein Complex From Pea Thylakoid Membranes Length = 232 Back     alignment and structure
>pdb|1RWT|A Chain A, Crystal Structure Of Spinach Major Light-harvesting Complex At 2.72 Angstrom Resolution Length = 232 Back     alignment and structure
>pdb|2WSC|1 Chain 1, Improved Model Of Plant Photosystem I Length = 241 Back     alignment and structure
>pdb|3PL9|A Chain A, Crystal Structure Of Spinach Minor Light-Harvesting Complex Cp29 At 2.80 Angstrom Resolution Length = 243 Back     alignment and structure
>pdb|2O01|1 Chain 1, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 187 Back     alignment and structure
>pdb|2WSC|3 Chain 3, Improved Model Of Plant Photosystem I Length = 276 Back     alignment and structure
>pdb|3LW5|1 Chain 1, Improved Model Of Plant Photosystem I Length = 170 Back     alignment and structure
>pdb|2O01|3 Chain 3, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 165 Back     alignment and structure
>pdb|3LW5|2 Chain 2, Improved Model Of Plant Photosystem I Length = 176 Back     alignment and structure
>pdb|2WSC|2 Chain 2, Improved Model Of Plant Photosystem I Length = 269 Back     alignment and structure
>pdb|2O01|2 Chain 2, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 186 Back     alignment and structure
>pdb|3LW5|3 Chain 3, Improved Model Of Plant Photosystem I Length = 172 Back     alignment and structure
>pdb|2O01|4 Chain 4, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 165 Back     alignment and structure
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I Length = 251 Back     alignment and structure
>pdb|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I Length = 166 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query189
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 9e-44
2bhw_A 232 Chlorophyll A-B binding protein AB80; LHC-II, phot 2e-06
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 1e-39
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 2e-37
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 1e-04
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 2e-37
2wsc_3 276 LHCA3, type II chlorophyll A/B binding protein fro 3e-04
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 2e-36
2wsc_4 251 Chlorophyll A-B binding protein P4, chloroplastic; 8e-08
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 5e-36
2wsc_2 269 LHCA2, type II chlorophyll A/B binding protein fro 9e-06
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Length = 232 Back     alignment and structure
 Score =  144 bits (364), Expect = 9e-44
 Identities = 80/164 (48%), Positives = 108/164 (65%), Gaps = 6/164 (3%)

Query: 19  YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
            +  E+IH+RWAMLGA G + PE  ++ G     EAVWFK G+ +     L+Y G    +
Sbjct: 61  NRELEVIHSRWAMLGALGSVFPELLSRNGVKF-GEAVWFKAGSQIFSEGGLDYLGNPSLV 119

Query: 79  N---LVFAVIAEIVLVGGAEYYRITN--GLDLEDKLHPGGPFDPLGLAKDPDQFALLKVK 133
           +   ++     +++L+G  E YRI      ++ D L+PGG FDPLGLA DP+ FA LKVK
Sbjct: 120 HAQSILAIWATQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVK 179

Query: 134 EIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLT 177
           E+KNGRLAMF+M GFF+QA VTG+GP+ENLA HL+DP  NN  +
Sbjct: 180 ELKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWS 223
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Length = 232 Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Length = 243 Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Length = 241 Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Length = 241 Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Length = 276 Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Length = 276 Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Length = 251 Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Length = 251 Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Length = 269 Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Length = 269 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query189
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 100.0
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 100.0
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 100.0
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 100.0
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 100.0
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 100.0
2bhw_A 232 Chlorophyll A-B binding protein AB80; LHC-II, phot 99.54
2wsc_4 251 Chlorophyll A-B binding protein P4, chloroplastic; 99.46
2wsc_2 269 LHCA2, type II chlorophyll A/B binding protein fro 99.46
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.42
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.37
2wsc_3 276 LHCA3, type II chlorophyll A/B binding protein fro 99.24
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Back     alignment and structure
Probab=100.00  E-value=7.1e-48  Score=324.59  Aligned_cols=173  Identities=48%  Similarity=0.835  Sum_probs=144.2

Q ss_pred             EeeccCCChhhHHHHHHHHhhhhhhHHhhhhhhhhhhccccCCCCCCCcchhhhccccccCCcccccccccch--HH-HH
Q 029740            5 LLVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIP--IN-LV   81 (189)
Q Consensus         5 ~~~~~~~~~~~l~~~REaELkHGRvAMLA~vG~lv~e~~~~~g~~~~p~~~w~~ag~~~~~~~~~~~~~~~~p--~~-~~   81 (189)
                      |.|+  +|+++++||||||||||||||||++||++||+++++|..+ ++..|+++|...+++..++|++.+..  .+ +.
T Consensus        49 LGLs--~d~e~~~r~ReaELkHGR~AMLA~~G~lv~E~l~~~G~~~-~~~~w~~ag~~~~~~~~~~~~~~P~~~~~q~i~  125 (232)
T 2bhw_A           49 AGLS--ADPETFSKNRELEVIHSRWAMLGALGSVFPELLSRNGVKF-GEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSIL  125 (232)
T ss_dssp             TCTT--CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCC-SCCSGGGSGGGGGSTTCEEGGGCTTSEEECCHH
T ss_pred             CcCC--CCHHHHHHHHHHHHhccchHHHhhhhhhhHHHhccCCcCC-cccccccccchhccccchhcccCcchhhHHHHH
Confidence            3455  4899999999999999999999999999999998776543 24579998876676656677765431  12 22


Q ss_pred             HHHHHHHHHHhhhhhhhcccCc--CCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhchhhHHHHHHHHHHHhhhcCCcc
Q 029740           82 FAVIAEIVLVGGAEYYRITNGL--DLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGP  159 (189)
Q Consensus        82 ~a~~~qv~~~g~~E~~~~~~g~--~~~~~~~PG~~fDPlgl~~d~~~~~~~~~~ElkNGRLAMla~~G~i~q~~v~g~gp  159 (189)
                      ..+++|++++|++|.+|..++.  ...+..+|||.|||||+.+|+++++++|.+|||||||||+|++|+++|+.+||++|
T Consensus       126 ~~~~~q~~~~g~~E~~r~~~g~~g~~~d~~~Pg~~fdPlgl~~~~~~~~~~~~~E~~nGRlAM~~~~g~~~~~~~tg~g~  205 (232)
T 2bhw_A          126 AIWATQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKELKNGRLAMFSMFGFFVQAIVTGKGP  205 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHEETTEECSSSSCCCTTSCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCS
T ss_pred             HHHHHHHHHHHHHHHHhhccCcccccccccCCCcccccchhccchHHHHHHHHhhhhccchHHHHHHHHHHHHHhcCCCh
Confidence            3347888899999999876532  12356799999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhCCcccchhhhhhc
Q 029740          160 VENLAKHLSDPFANNLLTVIS  180 (189)
Q Consensus       160 l~~l~~~~~~P~~~~~~~~~~  180 (189)
                      ++||.+|+++|+++|+++++.
T Consensus       206 ~~~l~~~~adP~~~n~~~~~~  226 (232)
T 2bhw_A          206 LENLADHLADPVNNNAWSYAT  226 (232)
T ss_dssp             HHHHHHHHHCTTTSSGGGGTT
T ss_pred             HHHHHHHhcChHHhHHHHHHH
Confidence            999999999999999999854
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Back     alignment and structure
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 189
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 1e-47
d1rwta_ 218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 1e-09
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 218 Back     information, alignment and structure

class: Membrane and cell surface proteins and peptides
fold: Chlorophyll a-b binding protein
superfamily: Chlorophyll a-b binding protein
family: Chlorophyll a-b binding protein
domain: Chlorophyll a-b binding protein
species: Spinach (Spinacia oleracea) [TaxId: 3562]

 Score =  152 bits (386), Expect = 1e-47
 Identities = 83/164 (50%), Positives = 107/164 (65%), Gaps = 6/164 (3%)

Query: 19  YQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPI 78
            +  E+IH RWAMLGA G + PE   + G   G EAVWFK G+ +     L+Y G    +
Sbjct: 48  NRELEVIHCRWAMLGALGCVFPELLARNGVKFG-EAVWFKAGSQIFSEGGLDYLGNPSLV 106

Query: 79  N---LVFAVIAEIVLVGGAEYYRITNG--LDLEDKLHPGGPFDPLGLAKDPDQFALLKVK 133
           +   ++     +++L+G  E YRI  G   ++ D L+PGG FDPLGLA DP+ FA LKVK
Sbjct: 107 HAQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVK 166

Query: 134 EIKNGRLAMFAMLGFFLQAYVTGEGPVENLAKHLSDPFANNLLT 177
           EIKNGRLAMF+M GFF+QA VTG+GP+ENLA HL+DP  NN   
Sbjct: 167 EIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWN 210
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 218 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query189
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 100.0
d1rwta_ 218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.59
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure
class: Membrane and cell surface proteins and peptides
fold: Chlorophyll a-b binding protein
superfamily: Chlorophyll a-b binding protein
family: Chlorophyll a-b binding protein
domain: Chlorophyll a-b binding protein
species: Spinach (Spinacia oleracea) [TaxId: 3562]

Probab=100.00  E-value=4.3e-48  Score=320.95  Aligned_cols=173  Identities=49%  Similarity=0.873  Sum_probs=135.0

Q ss_pred             eeccCCChhhHHHHHHHHhhhhhhHHhhhhhhhhhhccccCCCCCCCcchhhhccccccCCcccccccccch--HHHHHH
Q 029740            6 LVSARNQTTSASIYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIP--INLVFA   83 (189)
Q Consensus         6 ~~~~~~~~~~l~~~REaELkHGRvAMLA~vG~lv~e~~~~~g~~~~p~~~w~~ag~~~~~~~~~~~~~~~~p--~~~~~a   83 (189)
                      .|+  +|+++++||||||||||||||||++||+++|++++++.... ...|+.++........+.++..+..  .+.+..
T Consensus        37 gls--~d~~~~~~~ReaELKHGR~AMLA~vG~~~~E~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (218)
T d1rwta_          37 GLS--ADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFG-EAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILA  113 (218)
T ss_dssp             CTT--CSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCS-CCSHHHHGGGGGSTTCBCGGGCTTSCCBCCHHH
T ss_pred             ccC--CCHHHHHHHHHHHHhhceehHhhhcceeehhhhccCCCCCC-CcccccccccccCcchhhhhcCchHHHHHHHHH
Confidence            455  37899999999999999999999999999999987755432 3467776655454444444433221  112222


Q ss_pred             H-HHHHHHHhhhhhhhcccCc--CCCCCCCCCCCCCCCCCCCChHHHHHHHHHHHhchhhHHHHHHHHHHHhhhcCCcch
Q 029740           84 V-IAEIVLVGGAEYYRITNGL--DLEDKLHPGGPFDPLGLAKDPDQFALLKVKEIKNGRLAMFAMLGFFLQAYVTGEGPV  160 (189)
Q Consensus        84 ~-~~qv~~~g~~E~~~~~~g~--~~~~~~~PG~~fDPlgl~~d~~~~~~~~~~ElkNGRLAMla~~G~i~q~~v~g~gpl  160 (189)
                      + +.++..++.+|.++..++.  ...+..+||++|||+++.+++++++++|++||||||||||||+||++|+.+||++|+
T Consensus       114 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~g~fdPlg~~~~~e~~~~~k~kElkNGRLAMlAi~G~~~qe~vtG~gp~  193 (218)
T d1rwta_         114 IWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPL  193 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHCBTTBCCSSSSCCCGGGCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCHH
T ss_pred             HHHHHHHHHhhhhhhcccCCCcccccCCCCCCCCccccccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhcCCCHH
Confidence            3 4455568888888765432  233566788899999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhCCcccchhhhhhcc
Q 029740          161 ENLAKHLSDPFANNLLTVISG  181 (189)
Q Consensus       161 ~~l~~~~~~P~~~~~~~~~~~  181 (189)
                      +||++|+++|+++|+++.+.+
T Consensus       194 ~nl~~h~~~P~~~n~~~~~~~  214 (218)
T d1rwta_         194 ENLADHLADPVNNNAWNFATN  214 (218)
T ss_dssp             HHHHHHHHCTTTSSGGGGTTS
T ss_pred             HHHHHHhcCchhhhHHHHHhc
Confidence            999999999999999977654
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure