Citrus Sinensis ID: 027278

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-------190-------200-------210-------220-----
MASLAASSTPAASIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKKAAPPAKSKPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
ccccccccHHHHHHHHHHHHcccHHHHHHHHHcccccccccccccHHHHHcccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccEEHHcccccHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccc
cccHcccccHHHHHcHHHHHHHHHHHHHHHHHHcHHccccccccccccHccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcc
maslaasstpaasigakemlgnplnvssavrtsapgasnpstfkpvalfskkkaappakskpvavspvneelakwygpdrriflpeglldrseipeyltgevpgdygydpfglskkpddfskYQAYELIHARWAMLGaagfiipeafnkfgancgpeavwFKTGAllldgntlnyfgknipiNLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
maslaasstpaasigakemlGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKkaappakskpvavspvneelakwygpdrRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
MaslaasstpaasIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFskkkaappakskpvavspvNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGlvivfvlllinitytlltW
**********************************************************************ELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLT*
*********************************************************************************IFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
************SIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSK***************PVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
************************************************************************AKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiHHHHHHHHHHHHHHHHHHHHoo
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiHHHHHHHHHHHHHHHHoooo
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MASLAASSTPAASIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKKAAPPAKSKPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITNGLVIVFVLLLINITYTLLTW
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 ?
Query225 2.2.26 [Sep-21-2011]
Q9XF89280 Chlorophyll a-b binding p yes no 0.857 0.689 0.801 2e-72
P27517253 Chlorophyll a-b binding p N/A no 0.688 0.612 0.406 2e-26
P12330265 Chlorophyll a-b binding p no no 0.782 0.664 0.403 2e-25
P27490268 Chlorophyll a-b binding p N/A no 0.76 0.638 0.408 4e-25
P22686256 Chlorophyll a-b binding p N/A no 0.688 0.605 0.402 1e-24
P04782266 Chlorophyll a-b binding p N/A no 0.613 0.518 0.430 1e-24
P07371269 Chlorophyll a-b binding p N/A no 0.693 0.579 0.418 2e-24
P06671265 Chlorophyll a-b binding p N/A no 0.568 0.483 0.474 2e-24
P15194274 Chlorophyll a-b binding p N/A no 0.568 0.467 0.451 3e-24
P04781267 Chlorophyll a-b binding p N/A no 0.613 0.516 0.430 4e-24
>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 =  271 bits (694), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 157/196 (80%), Positives = 173/196 (88%), Gaps = 3/196 (1%)

Query: 12  ASIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKKAAPPAKSKPVAVSPVNEE 71
           AS+G  EMLG PLN  +  R+SAP AS+PSTFK VALFSKKK A    +K  AVS  ++E
Sbjct: 2   ASLGVSEMLGTPLNFRAVSRSSAPLASSPSTFKTVALFSKKKPA---PAKSKAVSETSDE 58

Query: 72  LAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHA 131
           LAKWYGPDRRIFLP+GLLDRSEIPEYL GEV GDYGYDPFGL KKP++F+KYQA+ELIHA
Sbjct: 59  LAKWYGPDRRIFLPDGLLDRSEIPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHA 118

Query: 132 RWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAE 191
           RWAMLGAAGFIIPEA NK+GANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLV AV+AE
Sbjct: 119 RWAMLGAAGFIIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVLAVVAE 178

Query: 192 IVLVGGAEYYRITNGL 207
           +VL+GGAEYYRITNGL
Sbjct: 179 VVLLGGAEYYRITNGL 194
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|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
>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|P22686|CB2_CHLMO Chlorophyll a-b binding protein of LHCII type I, chloroplastic OS=Chlamydomonas moewusii PE=2 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|P07371|CB22_PEA Chlorophyll a-b binding protein AB80, chloroplastic OS=Pisum sativum GN=AB80 PE=1 SV=1 Back     alignment and function description
>sp|P06671|CB22_MAIZE Chlorophyll a-b binding protein, chloroplastic OS=Zea mays PE=2 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|P04781|CB23_PETSP Chlorophyll a-b binding protein 22R, chloroplastic OS=Petunia sp. GN=CAB22R PE=3 SV=1 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 ?
Query225
255557841292 chlorophyll A/B binding protein, putativ 0.915 0.705 0.845 4e-89
225459918290 PREDICTED: chlorophyll a-b binding prote 0.848 0.658 0.860 5e-86
224127848290 light-harvesting complex II protein Lhcb 0.848 0.658 0.849 2e-85
118489770302 unknown [Populus trichocarpa x Populus d 0.848 0.632 0.849 2e-85
356535308287 PREDICTED: chlorophyll a-b binding prote 0.893 0.700 0.816 2e-84
255638437287 unknown [Glycine max] 0.893 0.700 0.811 7e-84
356576567288 PREDICTED: chlorophyll a-b binding prote 0.893 0.697 0.812 8e-83
261351266287 chloroplast pigment-binding protein CP26 0.875 0.686 0.808 3e-80
1644289283 chlorophyll a/b-binding protein CP26 in 0.866 0.689 0.776 1e-79
449447521288 PREDICTED: chlorophyll a-b binding prote 0.84 0.656 0.808 6e-79
>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
 Score =  333 bits (853), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 175/207 (84%), Positives = 188/207 (90%), Gaps = 1/207 (0%)

Query: 1   MASLAASSTPAASIGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKKAAPPAKS 60
           MASLAAS   A S+G  EMLGNPLN S A R++AP +S PST K VALFSKKKAAPP K+
Sbjct: 1   MASLAASRA-AGSLGVSEMLGNPLNFSGATRSAAPTSSTPSTLKTVALFSKKKAAPPPKA 59

Query: 61  KPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDF 120
           KP AVSPV++ELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKP+DF
Sbjct: 60  KPAAVSPVDDELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPEDF 119

Query: 121 SKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNI 180
           +KYQAYELIHARWAMLGAAGFI+PEAFNKFGANCGPEAVWFKTGALLLDG TLNYFG +I
Sbjct: 120 AKYQAYELIHARWAMLGAAGFIVPEAFNKFGANCGPEAVWFKTGALLLDGGTLNYFGNSI 179

Query: 181 PINLVFAVIAEIVLVGGAEYYRITNGL 207
           PINLV AVIAE+VL+GGAEYYRI NGL
Sbjct: 180 PINLVVAVIAEVVLLGGAEYYRIINGL 206

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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
>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|118489770|gb|ABK96685.1| unknown [Populus trichocarpa x Populus deltoides] Back     alignment and taxonomy information
>gi|356535308|ref|XP_003536189.1| 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|356576567|ref|XP_003556402.1| PREDICTED: chlorophyll a-b binding protein CP26, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|261351266|gb|ACX71300.1| chloroplast pigment-binding protein CP26 [Capsicum annuum] Back     alignment and taxonomy information
>gi|1644289|emb|CAA65042.1| chlorophyll a/b-binding protein CP26 in PS II [Brassica juncea] 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

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 ?
Query225
TAIR|locus:2122794280 LHCB5 "light harvesting comple 0.844 0.678 0.751 2.4e-76
UNIPROTKB|P12330265 CAB1R "Chlorophyll a-b binding 0.568 0.483 0.466 1.8e-25
UNIPROTKB|P12331261 CAB2R "Chlorophyll a-b binding 0.568 0.490 0.466 1.8e-25
TAIR|locus:2044988265 LHCB2.2 "photosystem II light 0.568 0.483 0.474 5.9e-25
TAIR|locus:2042148265 LHCB2.1 "photosystem II light 0.568 0.483 0.474 5.9e-25
TAIR|locus:2089139266 LHCB2.3 "photosystem II light 0.568 0.481 0.474 5.9e-25
TAIR|locus:2019287267 CAB3 "chlorophyll A/B binding 0.568 0.479 0.433 8.7e-24
TAIR|locus:2019372267 CAB2 "chlorophyll A/B-binding 0.568 0.479 0.433 8.7e-24
TAIR|locus:2019322267 CAB1 "chlorophyll A/B binding 0.568 0.479 0.433 8.7e-24
TAIR|locus:2040934265 LHB1B2 "photosystem II light h 0.555 0.471 0.431 2.3e-23
TAIR|locus:2122794 LHCB5 "light harvesting complex of photosystem II 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 769 (275.8 bits), Expect = 2.4e-76, P = 2.4e-76
 Identities = 145/193 (75%), Positives = 160/193 (82%)

Query:    14 IGAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFXXXXXXXXXXXXXXXXXXXNEELA 73
             +G  EMLG PLN  +  R+SAP AS+PSTFK VALF                   ++ELA
Sbjct:     4 LGVSEMLGTPLNFRAVSRSSAPLASSPSTFKTVALFSKKKPAPAKSKAVSET---SDELA 60

Query:    74 KWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARW 133
             KWYGPDRRIFLP+GLLDRSEIPEYL GEV GDYGYDPFGL KKP++F+KYQA+ELIHARW
Sbjct:    61 KWYGPDRRIFLPDGLLDRSEIPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHARW 120

Query:   134 AMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIV 193
             AMLGAAGFIIPEA NK+GANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLV AV+AE+V
Sbjct:   121 AMLGAAGFIIPEALNKYGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVLAVVAEVV 180

Query:   194 LVGGAEYYRITNG 206
             L+GGAEYYRITNG
Sbjct:   181 LLGGAEYYRITNG 193
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: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
TAIR|locus:2089139 LHCB2.3 "photosystem II light harvesting complex gene 2.3" [Arabidopsis thaliana (taxid:3702)] 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

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 number0.80100.85770.6892yesno

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 ?Alignment Graph ?Length ? Definition ? E-value ?
Query225
PLN00025262 PLN00025, PLN00025, photosystem II light harvestin 8e-35
PLN00171324 PLN00171, PLN00171, photosystem light-harvesting c 2e-29
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 7e-18
PLN00098267 PLN00098, PLN00098, light-harvesting complex I chl 8e-17
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 1e-15
PLN00048262 PLN00048, PLN00048, photosystem I light harvesting 8e-15
PLN00147252 PLN00147, PLN00147, light-harvesting complex I chl 3e-14
PLN00097244 PLN00097, PLN00097, photosystem I light harvesting 4e-14
PLN00187286 PLN00187, PLN00187, photosystem II light-harvestin 5e-14
PLN00099243 PLN00099, PLN00099, light-harvesting complex IChlo 3e-13
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 4e-12
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 6e-09
PLN00100246 PLN00100, PLN00100, light-harvesting complex chlor 3e-08
PLN00187286 PLN00187, PLN00187, 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 =  124 bits (312), Expect = 8e-35
 Identities = 67/161 (41%), Positives = 88/161 (54%), Gaps = 13/161 (8%)

Query: 52  KKAAPPAKSKPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPF 111
           +K      +    V+      + WYGPDR  +L  G     E P YLTGE PGDYG+D  
Sbjct: 23  RKVGNGRVTMRKTVAKAAGSGSIWYGPDRPKYL--GPFS-GETPSYLTGEFPGDYGWDTA 79

Query: 112 GLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGN 171
           GLS  P+ F++ +  E+IHARWAMLGA G + PE   K G   G EAVWFK GA +    
Sbjct: 80  GLSADPETFARNRELEVIHARWAMLGALGCVTPELLAKNGVKFG-EAVWFKAGAQIFSEG 138

Query: 172 TLNYFGKNIPINLVFA--VIA----EIVLVGGAEYYRITNG 206
            L+Y G     +LV A  ++A    ++VL+G  E YR+  G
Sbjct: 139 GLDYLGNP---SLVHAQSILAIWACQVVLMGAVEGYRVNGG 176

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|177716 PLN00098, PLN00098, light-harvesting complex I chlorophyll a/b-binding protein (Lhac); 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|177680 PLN00048, PLN00048, photosystem I light harvesting chlorophyll a/b binding protein 3; 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|165670 PLN00097, PLN00097, photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; 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|177717 PLN00099, PLN00099, light-harvesting complex IChlorophyll A-B binding protein Lhca1; 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|215956 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein 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|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II protein Lhcb4; 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 225
PLN00187286 photosystem II light-harvesting complex II protein 100.0
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 100.0
PLN00171324 photosystem light-harvesting complex -chlorophyll 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 99.97
PLN00170255 photosystem II light-harvesting-Chl-binding protei 99.97
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 99.96
PLN00099243 light-harvesting complex IChlorophyll A-B binding 99.95
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 99.95
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.82
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.68
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 99.61
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.58
PLN00048262 photosystem I light harvesting chlorophyll a/b bin 99.55
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 99.51
PLN00187286 photosystem II light-harvesting complex II protein 99.48
PLN00099243 light-harvesting complex IChlorophyll A-B binding 99.46
PLN00098267 light-harvesting complex I chlorophyll a/b-binding 99.45
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.41
PLN00171324 photosystem light-harvesting complex -chlorophyll 99.39
PLN00097244 photosystem I light harvesting complex Lhca2/4, ch 99.38
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.37
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 99.3
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.3
PLN00101250 Photosystem I light-harvesting complex type 4 prot 99.23
PLN00170255 photosystem II light-harvesting-Chl-binding protei 99.22
PHA0233735 putative high light inducible protein 97.96
PLN00014250 light-harvesting-like protein 3; Provisional 97.27
PLN00084214 photosystem II subunit S (PsbS); Provisional 96.26
>PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information 
Probab=100.00  E-value=3.4e-39  Score=291.63  Aligned_cols=158  Identities=30%  Similarity=0.595  Sum_probs=126.8

Q ss_pred             cchhhcCCccccccccccCCCCCCCCCCCceeEeeccCCCCCCCCCCCCcCCCchhhhhhhhcCCCcCccCcCccCCCCC
Q 027278           15 GAKEMLGNPLNVSSAVRTSAPGASNPSTFKPVALFSKKKAAPPAKSKPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEI   94 (225)
Q Consensus        15 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~a~f~~~k~~~~~~~k~~a~~~~~~~~~~wyg~~R~~~lp~G~~~~~~~   94 (225)
                      ..|.|+|.++..           +.++..+++++|+.++...++ ++++       +...+|+++|++|||+     .++
T Consensus         6 ~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~-~~~~-------~~~~~~~~~r~~w~p~-----~~~   61 (286)
T PLN00187          6 AASSFMGTRVPD-----------VASNSGRIVARFGFGKKKKAA-KKAK-------KKSSKVGADRPLWFPG-----AKA   61 (286)
T ss_pred             cchhhhhhhhcc-----------cccCccchhhhhccCcccccC-Cccc-------cCccCCCCCccccCCC-----CCC
Confidence            347788888742           344678888988743221111 1111       1246789999999996     899


Q ss_pred             CCCCCCCCCCCCccCCCCCCCChhh-------------------------------------------HHHHHHHHhhhh
Q 027278           95 PEYLTGEVPGDYGYDPFGLSKKPDD-------------------------------------------FSKYQAYELIHA  131 (225)
Q Consensus        95 P~yL~G~~PGD~GfDPlGL~~dpe~-------------------------------------------~~~~r~~EL~hG  131 (225)
                      |+||||++||||||||+||+++||.                                           ++|||++||+||
T Consensus        62 P~~LdGslpGD~GfDplgL~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~f~l~r~REaELiHG  141 (286)
T PLN00187         62 PEWLDGSLVGDYGFDPFGLGKPAEYLQFDLDSLDQNLAKNLAGDVIGTRTEASEIKSTPFQPYSEVFGLQRFRECELIHG  141 (286)
T ss_pred             cccccCCCCCcCCCCcccccCChHhhhhcccchhhhhhhcccccccccccccccccccccCcchhhhHHHHHHHHHhhhh
Confidence            9999999999999999999999986                                           599999999999


Q ss_pred             hhhHhhhhhhhhhhhhccCCCCCCCCcccccccccccCCCccccCCCCchhhHHHHHHHHHHHHHhhhhhhccC
Q 027278          132 RWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPINLVFAVIAEIVLVGGAEYYRITN  205 (225)
Q Consensus       132 R~AMLg~~G~lv~e~l~~~G~~~~p~~~Wf~AG~~~~~g~~l~Ylg~p~p~~~~~li~~evvLmG~~E~~R~~g  205 (225)
                      ||||||++||+++|+++        +..||++|.+.+..+ .+|++++.++.+..++++|+++||++|.+|+.+
T Consensus       142 RwAMLAvaG~lvpEll~--------G~~W~~aG~~~~~~g-~~y~g~~~p~~~~~l~~iqvllmG~~E~~R~~~  206 (286)
T PLN00187        142 RWAMLATLGALSVEALT--------GVTWQDAGKVELVDG-SSYLGQPLPFSITTLIWIEVLVIGYIEFQRNAE  206 (286)
T ss_pred             HHHHHHhhchhhHHhcc--------CCccccccccccccc-ccccccccchhHHHHHHHHHHHHHHHHhhhccC
Confidence            99999999999999985        236999998765433 469999888877888899999999999999875

>PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information
>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; 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
>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); 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
>PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional Back     alignment and domain information
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional Back     alignment and domain information
>PLN00048 photosystem I light harvesting chlorophyll a/b binding protein 3; Provisional Back     alignment and domain information
>PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information
>PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information
>PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); 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
>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information
>PLN00097 photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional Back     alignment and domain information
>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional Back     alignment and domain information
>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional Back     alignment and domain information
>PLN00101 Photosystem I light-harvesting complex type 4 protein; Provisional Back     alignment and domain information
>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); 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 ?
Query225
1vcr_A232 An Icosahedral Assembly Of Light-Harvesting Chlorop 2e-24
2bhw_A232 Pea Light-Harvesting Complex Ii At 2.5 Angstrom Res 2e-24
1rwt_A232 Crystal Structure Of Spinach Major Light-harvesting 1e-23
2wsc_2269 Improved Model Of Plant Photosystem I Length = 269 3e-14
2o01_2186 The Structure Of A Plant Photosystem I Supercomplex 3e-14
2wsc_1241 Improved Model Of Plant Photosystem I Length = 241 2e-12
2o01_1187 The Structure Of A Plant Photosystem I Supercomplex 2e-12
2wsc_4251 Improved Model Of Plant Photosystem I Length = 251 3e-12
2wsc_3276 Improved Model Of Plant Photosystem I Length = 276 4e-10
3lw5_1170 Improved Model Of Plant Photosystem I Length = 170 4e-10
3pl9_A243 Crystal Structure Of Spinach Minor Light-Harvesting 6e-07
3lw5_2176 Improved Model Of Plant Photosystem I Length = 176 4e-05
3lw5_4166 Improved Model Of Plant Photosystem I Length = 166 2e-04
2o01_3165 The Structure Of A Plant Photosystem I Supercomplex 2e-04
3lw5_3172 Improved Model Of Plant Photosystem I Length = 172 3e-04
>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 
Iteration: 1

 Score =  108 bits (271), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 61/135 (45%), Positives = 80/135 (59%), Gaps = 7/135 (5%)
Query: 75  WYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWA 134
           WYGPDR  +L        E P YLTGE PGDYG+D  GLS  P+ FSK +  E+IH+RWA
Sbjct: 16  WYGPDRVKYLGP---FSGESPSYLTGEFPGDYGWDTAGLSADPETFSKNRELEVIHSRWA 72
Query: 135 MLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKN--IPINLVFAVIA-E 191
           MLGA G + PE  ++ G   G EAVWFK G+ +     L+Y G    +    + A+ A +
Sbjct: 73  MLGALGCVFPELLSRNGVKFG-EAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWATQ 131
Query: 192 IVLVGGAEYYRITNG 206
           ++L+G  E YRI  G
Sbjct: 132 VILMGAVEGYRIAGG 146
>pdb|2BHW|A Chain A, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution 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|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|2WSC|1 Chain 1, Improved Model Of Plant Photosystem I Length = 241 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|4 Chain 4, Improved Model Of Plant Photosystem I Length = 251 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|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|3LW5|2 Chain 2, Improved Model Of Plant Photosystem I Length = 176 Back     alignment and structure
>pdb|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I Length = 166 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|3 Chain 3, Improved Model Of Plant Photosystem I Length = 172 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 ?
Query225
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 2e-29
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 8e-04
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 2e-26
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 1e-04
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 1e-23
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 2e-21
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 8e-05
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 3e-19
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 2e-16
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 8e-04
>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 =  108 bits (271), Expect = 2e-29
 Identities = 59/148 (39%), Positives = 80/148 (54%), Gaps = 7/148 (4%)

Query: 61  KPVAVSPVNEELAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDF 120
           K      V    + WYGPDR  +L        E P YLTGE PGDYG+D  GLS  P+ F
Sbjct: 2   KSATTKKVASSGSPWYGPDRVKYLGPF---SGESPSYLTGEFPGDYGWDTAGLSADPETF 58

Query: 121 SKYQAYELIHARWAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNI 180
           SK +  E+IH+RWAMLGA G + PE  ++ G     EAVWFK G+ +     L+Y G   
Sbjct: 59  SKNRELEVIHSRWAMLGALGSVFPELLSRNGVKF-GEAVWFKAGSQIFSEGGLDYLGNPS 117

Query: 181 PIN---LVFAVIAEIVLVGGAEYYRITN 205
            ++   ++     +++L+G  E YRI  
Sbjct: 118 LVHAQSILAIWATQVILMGAVEGYRIAG 145
>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
>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
>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_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_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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query225
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_2269 LHCA2, type II chlorophyll A/B binding protein fro 99.97
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 99.96
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 99.96
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.94
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.46
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 99.45
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 99.44
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 99.41
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.3
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 99.13
>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=2.3e-36  Score=264.97  Aligned_cols=130  Identities=44%  Similarity=0.866  Sum_probs=112.1

Q ss_pred             hhhhhcCCCcCccCcCccCCCCCCCCCCCCCCCCCccCCCCCCCChhhHHHHHHHHhhhhhhhHhhhhhhhhhhhhccCC
Q 027278           72 LAKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFG  151 (225)
Q Consensus        72 ~~~wyg~~R~~~lp~G~~~~~~~P~yL~G~~PGD~GfDPlGL~~dpe~~~~~r~~EL~hGR~AMLg~~G~lv~e~l~~~G  151 (225)
                      .++|||+||++|||  +++ .++|+||||++||||||||+||++|+|+++|||++||+||||||||++|++++|+++..|
T Consensus        13 ~~~~~~~~r~~~l~--~~~-~~~P~~LdG~~pGD~GFDPLGLs~d~e~~~r~ReaELkHGR~AMLA~~G~lv~E~l~~~G   89 (232)
T 2bhw_A           13 GSPWYGPDRVKYLG--PFS-GESPSYLTGEFPGDYGWDTAGLSADPETFSKNRELEVIHSRWAMLGALGSVFPELLSRNG   89 (232)
T ss_dssp             TCTTSSTTCCCTTG--GGC-CSCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCcccCCCcccccC--ccc-cCCccccCCcCCCCCCCCCCcCCCCHHHHHHHHHHHHhccchHHHhhhhhhhHHHhccCC
Confidence            35899999999994  444 589999999999999999999999999999999999999999999999999999998877


Q ss_pred             CCCCCCcccccccccccCCCccccCCCCchh---hHHHHHHHHHHHHHhhhhhhccC
Q 027278          152 ANCGPEAVWFKTGALLLDGNTLNYFGKNIPI---NLVFAVIAEIVLVGGAEYYRITN  205 (225)
Q Consensus       152 ~~~~p~~~Wf~AG~~~~~g~~l~Ylg~p~p~---~~~~li~~evvLmG~~E~~R~~g  205 (225)
                      +.. +++.||++|...+.+..++|+++|...   .+..++++|+++||++|.+|+.+
T Consensus        90 ~~~-~~~~w~~ag~~~~~~~~~~~~~~P~~~~~q~i~~~~~~q~~~~g~~E~~r~~~  145 (232)
T 2bhw_A           90 VKF-GEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWATQVILMGAVEGYRIAG  145 (232)
T ss_dssp             CCC-SCCSGGGSGGGGGSTTCEEGGGCTTSEEECCHHHHHHHHHHHHHHHHHHHHHE
T ss_pred             cCC-cccccccccchhccccchhcccCcchhhHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            643 367899999877776678899877532   23455678999999999999876
>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_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
>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_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_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
>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_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
>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_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
>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_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

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 225
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 2e-35
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 2e-04
>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 =  122 bits (308), Expect = 2e-35
 Identities = 58/137 (42%), Positives = 78/137 (56%), Gaps = 7/137 (5%)

Query: 73  AKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHAR 132
           + WYGPDR  +L        E P YLTGE PGDYG+D  GLS  P+ F+K +  E+IH R
Sbjct: 1   SPWYGPDRVKYLGP---FSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCR 57

Query: 133 WAMLGAAGFIIPEAFNKFGANCGPEAVWFKTGALLLDGNTLNYFGKNIPIN---LVFAVI 189
           WAMLGA G + PE   + G   G EAVWFK G+ +     L+Y G    ++   ++    
Sbjct: 58  WAMLGALGCVFPELLARNGVKFG-EAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWA 116

Query: 190 AEIVLVGGAEYYRITNG 206
            +++L+G  E YRI  G
Sbjct: 117 CQVILMGAVEGYRIAGG 133
>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 ?
Query225
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.98
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.48
>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=99.98  E-value=2.2e-33  Score=240.23  Aligned_cols=129  Identities=43%  Similarity=0.882  Sum_probs=107.8

Q ss_pred             hhhhcCCCcCccCcCccCCCCCCCCCCCCCCCCCccCCCCCCCChhhHHHHHHHHhhhhhhhHhhhhhhhhhhhhccCCC
Q 027278           73 AKWYGPDRRIFLPEGLLDRSEIPEYLTGEVPGDYGYDPFGLSKKPDDFSKYQAYELIHARWAMLGAAGFIIPEAFNKFGA  152 (225)
Q Consensus        73 ~~wyg~~R~~~lp~G~~~~~~~P~yL~G~~PGD~GfDPlGL~~dpe~~~~~r~~EL~hGR~AMLg~~G~lv~e~l~~~G~  152 (225)
                      ++|||+||++|||  ++. ++.|+||||++||||||||+||++|+++++|+|++||+||||||||++|++++|++++.+.
T Consensus         1 ~~~~~~~r~~~~~--~~~-~~~P~~LdGs~pGD~GFDPLgls~d~~~~~~~ReaELKHGR~AMLA~vG~~~~E~~~~~~~   77 (218)
T d1rwta_           1 SPWYGPDRVKYLG--PFS-GESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGV   77 (218)
T ss_dssp             CTTSSTTCCCTTG--GGG-CSCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCcccCC--ccc-cCCCcccCCCCCCCCCcCCcccCCCHHHHHHHHHHHHhhceehHhhhcceeehhhhccCCC
Confidence            3799999999996  233 6789999999999999999999999999999999999999999999999999999988776


Q ss_pred             CCCCCcccccccccccCCCccccCCCCchh---hHHHHHHHHHHHHHhhhhhhccC
Q 027278          153 NCGPEAVWFKTGALLLDGNTLNYFGKNIPI---NLVFAVIAEIVLVGGAEYYRITN  205 (225)
Q Consensus       153 ~~~p~~~Wf~AG~~~~~g~~l~Ylg~p~p~---~~~~li~~evvLmG~~E~~R~~g  205 (225)
                      .. .+..|++++......+.+++++.+...   .+..++++++++++.+|.+|..+
T Consensus        78 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~  132 (218)
T d1rwta_          78 KF-GEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAG  132 (218)
T ss_dssp             CC-SCCSHHHHGGGGGSTTCBCGGGCTTSCCBCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CC-CCcccccccccccCcchhhhhcCchHHHHHHHHHHHHHHHHHHhhhhhhcccC
Confidence            53 356899988877766667777655322   23344567889999999998775
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure