Citrus Sinensis ID: 024588

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-------230-------240-------250-------260-----
MAVAVGRGFLLQPSSSSSFICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
cHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHHccc
cHHHHHHHHHcccccccccccccccccHHcHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccHHHHHHHccccc
mavavgrgfllqpsssssficndvnkssigitsaflpaksgttRRYLATVVRAqqrptwlpgvdpppyldgtlagdfgfdplglgedpesLRWYVQAELVHARFAMAGVAGILFTDLlrvtgirelpvwyeagavefkfaSTRTLFIVQLLLMGFAETkrymdyispgsqtkegsfFGLEAALeglepgypggpllnplglAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASvthvgpidnilehlsdpwhKTIIQTLANSGS
mavavgrgfllqpsssssfICNDVNKSSIGItsaflpaksgttRRYLATVVraqqrptwlpgvDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNIlehlsdpwhKTIIQTLANSGS
MAVAVGRGFLLQPSSSSSFICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAAleglepgypggpllnplglAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
******************FICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTL*****
*************************************************************GVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS**
MAVAVGRGFLLQPSSSSSFICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
***************************************************RAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLAN***
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooo
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MAVAVGRGFLLQPSSSSSFICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
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 ?
Query265 2.2.26 [Sep-21-2011]
P10708270 Chlorophyll a-b binding p N/A no 0.815 0.8 0.504 5e-53
Q9SQL2252 Chlorophyll a-b binding p N/A no 0.856 0.900 0.461 8e-53
P13869270 Chlorophyll a-b binding p N/A no 0.883 0.866 0.449 1e-51
P27521251 Chlorophyll a-b binding p no no 0.747 0.788 0.5 1e-51
P27522273 Chlorophyll a-b binding p N/A no 0.788 0.765 0.442 6e-45
Q32904275 Chlorophyll a-b binding p N/A no 0.913 0.88 0.396 2e-44
Q36718231 Chlorophyll a-b binding p N/A no 0.811 0.930 0.448 6e-44
P27525256 Chlorophyll a-b binding p N/A no 0.750 0.777 0.38 7e-31
P27524256 Chlorophyll a-b binding p N/A no 0.796 0.824 0.389 2e-30
P27517253 Chlorophyll a-b binding p N/A no 0.652 0.683 0.416 3e-30
>sp|P10708|CB12_SOLLC Chlorophyll a-b binding protein 7, chloroplastic OS=Solanum lycopersicum GN=CAB7 PE=3 SV=1 Back     alignment and function desciption
 Score =  207 bits (528), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 112/222 (50%), Positives = 135/222 (60%), Gaps = 6/222 (2%)

Query: 43  TRRYLATVVRAQQ--RPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELV 100
           T R   TV  A    RP W PG  PPP+LDG+L GDFGFDPLGL  DPESLRW  QAELV
Sbjct: 50  TARSATTVCVAADPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLASDPESLRWNQQAELV 109

Query: 101 HARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKR 160
           H R+AM G AGI   +LL   GI   P WY AG  E+ F  T TLFIV+L+L+G+AE +R
Sbjct: 110 HCRWAMLGAAGIFIPELLTKIGILNTPSWYTAGEQEY-FTDTTTLFIVELVLIGWAEGRR 168

Query: 161 YMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAK-DIRNAREWKLKEIKNG 219
           + D I PG    +  F      L G + GYPGG   +PLG         +E + KEIKNG
Sbjct: 169 WADIIKPGCVNTDPIF--PNNKLTGTDVGYPGGLWFDPLGWGSGSPAKIKELRTKEIKNG 226

Query: 220 RLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLA 261
           RLAM+A++G + Q   T  GPIDN+  HL+DP H TI    +
Sbjct: 227 RLAMLAVMGAWFQHIYTGTGPIDNLFAHLADPGHATIFAAFS 268
The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated.
Solanum lycopersicum (taxid: 4081)
>sp|Q9SQL2|CB24_PEA Chlorophyll a-b binding protein P4, chloroplastic OS=Pisum sativum GN=lhcA-P4 PE=1 SV=1 Back     alignment and function description
>sp|P13869|CB12_PETHY Chlorophyll a-b binding protein, chloroplastic OS=Petunia hybrida PE=2 SV=1 Back     alignment and function description
>sp|P27521|CA4_ARATH Chlorophyll a-b binding protein 4, chloroplastic OS=Arabidopsis thaliana GN=LHCA4 PE=1 SV=1 Back     alignment and function description
>sp|P27522|CB13_SOLLC Chlorophyll a-b binding protein 8, chloroplastic OS=Solanum lycopersicum GN=CAB8 PE=3 SV=1 Back     alignment and function description
>sp|Q32904|CB23_PEA Chlorophyll a-b binding protein 3, chloroplastic OS=Pisum sativum GN=lhca3 PE=1 SV=1 Back     alignment and function description
>sp|Q36718|CB120_HORVU Chlorophyll a-b binding protein 1B-20, chloroplastic (Fragment) OS=Hordeum vulgare GN=LHC Ib-20 PE=1 SV=1 Back     alignment and function description
>sp|P27525|CB4B_SOLLC Chlorophyll a-b binding protein CP24 10B, chloroplastic OS=Solanum lycopersicum GN=CAP10B PE=3 SV=1 Back     alignment and function description
>sp|P27524|CB4A_SOLLC Chlorophyll a-b binding protein CP24 10A, chloroplastic OS=Solanum lycopersicum GN=CAP10A PE=3 SV=1 Back     alignment and function description
>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

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 ?
Query265
224137478266 light-harvesting complex I protein Lhca5 0.996 0.992 0.808 1e-121
225458605264 PREDICTED: chlorophyll a-b binding prote 0.992 0.996 0.771 1e-118
255538312269 chlorophyll A/B binding protein, putativ 1.0 0.985 0.776 1e-118
356519222263 PREDICTED: chlorophyll a-b binding prote 0.992 1.0 0.750 1e-111
124388816272 Lhca5 protein [Gentiana lutea] 0.932 0.908 0.767 1e-108
388518909266 unknown [Lotus japonicus] 0.992 0.988 0.742 1e-108
357465507267 Chlorophyll a-b binding protein [Medicag 0.981 0.973 0.715 1e-105
449466336259 PREDICTED: chlorophyll a-b binding prote 0.924 0.945 0.731 1e-104
388510254213 unknown [Lotus japonicus] 0.8 0.995 0.853 1e-103
297846882256 light-harvesting complex protein [Arabid 0.883 0.914 0.764 1e-103
>gi|224137478|ref|XP_002327136.1| light-harvesting complex I protein Lhca5 [Populus trichocarpa] gi|222835451|gb|EEE73886.1| light-harvesting complex I protein Lhca5 [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  439 bits (1130), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 216/267 (80%), Positives = 239/267 (89%), Gaps = 3/267 (1%)

Query: 1   MAVAVGRGFLLQPSSSSSFIC--NDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPT 58
           MAVA+GR F++QP  SSS      ++NKSS G    FLPAK  +TR     VV AQQRPT
Sbjct: 1   MAVAMGRPFVIQPCLSSSLCSLSKNINKSSFGAAETFLPAKPSSTR-CTPVVVHAQQRPT 59

Query: 59  WLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLL 118
           WLPG+DPPPYLDGTLAGDFGFDPLGLGEDP+SL+WYVQAELVHARFAMAGVAGILFTDLL
Sbjct: 60  WLPGLDPPPYLDGTLAGDFGFDPLGLGEDPQSLKWYVQAELVHARFAMAGVAGILFTDLL 119

Query: 119 RVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFG 178
           RVTGIR+LPVWYEAGAV+F+FASTRTL +VQLLLMGFAETKRYMD++SPGSQ KEGSFFG
Sbjct: 120 RVTGIRKLPVWYEAGAVKFEFASTRTLIVVQLLLMGFAETKRYMDFVSPGSQAKEGSFFG 179

Query: 179 LEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHV 238
           LE+ALEGLEPGYPGGPLLNPLGLA+DI NA  WKLKEIKNGRLAMVAM+GIFVQA+VTH 
Sbjct: 180 LESALEGLEPGYPGGPLLNPLGLARDIENAHVWKLKEIKNGRLAMVAMVGIFVQAAVTHA 239

Query: 239 GPIDNILEHLSDPWHKTIIQTLANSGS 265
           GPIDN++EHLS+PWH+TIIQTLANSGS
Sbjct: 240 GPIDNLIEHLSNPWHRTIIQTLANSGS 266

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225458605|ref|XP_002284724.1| PREDICTED: chlorophyll a-b binding protein 4, chloroplastic [Vitis vinifera] gi|302142320|emb|CBI19523.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255538312|ref|XP_002510221.1| chlorophyll A/B binding protein, putative [Ricinus communis] gi|223550922|gb|EEF52408.1| chlorophyll A/B binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356519222|ref|XP_003528272.1| PREDICTED: chlorophyll a-b binding protein 7, chloroplastic-like [Glycine max] Back     alignment and taxonomy information
>gi|124388816|gb|ABN10530.1| Lhca5 protein [Gentiana lutea] Back     alignment and taxonomy information
>gi|388518909|gb|AFK47516.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|357465507|ref|XP_003603038.1| Chlorophyll a-b binding protein [Medicago truncatula] gi|355492086|gb|AES73289.1| Chlorophyll a-b binding protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|449466336|ref|XP_004150882.1| PREDICTED: chlorophyll a-b binding protein 4, chloroplastic-like [Cucumis sativus] gi|449522610|ref|XP_004168319.1| PREDICTED: chlorophyll a-b binding protein 4, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|388510254|gb|AFK43193.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|297846882|ref|XP_002891322.1| light-harvesting complex protein [Arabidopsis lyrata subsp. lyrata] gi|297337164|gb|EFH67581.1| light-harvesting complex protein [Arabidopsis lyrata subsp. lyrata] 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 ?
Query265
TAIR|locus:2825741256 Lhca5 "photosystem I light har 0.803 0.832 0.747 7.2e-84
TAIR|locus:2079117251 LHCA4 "light-harvesting chloro 0.792 0.836 0.433 2.8e-43
TAIR|locus:2202150270 Lhca6 "photosystem I light har 0.426 0.418 0.543 3.2e-43
TAIR|locus:2082767257 LHCA2 "photosystem I light har 0.750 0.774 0.457 1.2e-42
TAIR|locus:2200868273 LHCA3 "photosystem I light har 0.826 0.802 0.383 1.2e-35
TAIR|locus:2122794280 LHCB5 "light harvesting comple 0.264 0.25 0.458 3.6e-26
TAIR|locus:2082717241 LHCA1 "photosystem I light har 0.705 0.775 0.348 1.4e-25
TAIR|locus:2036209258 LHCB6 "light harvesting comple 0.845 0.868 0.345 3.6e-25
TAIR|locus:2097608287 LHCB4.2 "light harvesting comp 0.267 0.247 0.386 2.6e-24
TAIR|locus:2011691327 AT1G76570 [Arabidopsis thalian 0.301 0.244 0.404 4.3e-23
TAIR|locus:2825741 Lhca5 "photosystem I light harvesting complex gene 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 = 160/214 (74%), Positives = 178/214 (83%)

Query:    53 AQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGI 112
             A +R TWLPG++PPPYLDG LAGD+GFDPLGLGEDPESL+WYVQAELVH+RFAM GVAGI
Sbjct:    43 AVERATWLPGLNPPPYLDGNLAGDYGFDPLGLGEDPESLKWYVQAELVHSRFAMLGVAGI 102

Query:   113 LFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTK 172
             LFTDLLR TGIR LPVWYEAGAV+F FAST+TL +VQ LLMGFAETKRYMD++SPGSQ K
Sbjct:   103 LFTDLLRTTGIRNLPVWYEAGAVKFDFASTKTLIVVQFLLMGFAETKRYMDFVSPGSQAK 162

Query:   173 EGSFF-GLEAAXXXXXXXXXXXXXXXXXXXAKDIRNAREWKLKEIKNGRLAMVAMLGIFV 231
             EGSFF GLEAA                   AKD++NA +WKLKEIKNGRLAM+AMLG FV
Sbjct:   163 EGSFFFGLEAALEGLEPGYPGGPLLNPLGLAKDVQNAHDWKLKEIKNGRLAMMAMLGFFV 222

Query:   232 QASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS 265
             QASVTH GPIDN++EHLS+PWHKTIIQTL  S S
Sbjct:   223 QASVTHTGPIDNLVEHLSNPWHKTIIQTLFTSTS 256
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0009765 "photosynthesis, light harvesting" evidence=IEA
GO:0015979 "photosynthesis" evidence=ISS
GO:0016020 "membrane" evidence=IEA;IDA
GO:0030076 "light-harvesting complex" evidence=ISS
GO:0009535 "chloroplast thylakoid membrane" evidence=IDA
GO:0009782 "photosystem I antenna complex" evidence=IDA
GO:0031409 "pigment binding" evidence=IDA
GO:0009768 "photosynthesis, light harvesting in photosystem I" evidence=IGI
GO:0006364 "rRNA processing" evidence=RCA
GO:0009657 "plastid organization" evidence=RCA
GO:0010027 "thylakoid membrane organization" evidence=RCA
GO:0010207 "photosystem II assembly" evidence=RCA
TAIR|locus:2079117 LHCA4 "light-harvesting chlorophyll-protein complex I subunit A4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2202150 Lhca6 "photosystem I light harvesting complex gene 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2082767 LHCA2 "photosystem I light harvesting complex gene 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2200868 LHCA3 "photosystem I light harvesting complex gene 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2122794 LHCB5 "light harvesting complex of photosystem II 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2082717 LHCA1 "photosystem I light harvesting complex gene 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2036209 LHCB6 "light harvesting complex photosystem II subunit 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2097608 LHCB4.2 "light harvesting complex photosystem II" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2011691 AT1G76570 [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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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 ?
Query265
PLN00147252 PLN00147, PLN00147, light-harvesting complex I chl 1e-163
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 3e-73
PLN00097244 PLN00097, PLN00097, photosystem I light harvesting 6e-67
PLN00098267 PLN00098, PLN00098, light-harvesting complex I chl 3e-62
PLN00048262 PLN00048, PLN00048, photosystem I light harvesting 1e-60
PLN00100246 PLN00100, PLN00100, light-harvesting complex chlor 2e-51
PLN00171324 PLN00171, PLN00171, photosystem light-harvesting c 6e-47
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 1e-44
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 6e-43
PLN00025262 PLN00025, PLN00025, photosystem II light harvestin 2e-42
PLN00099243 PLN00099, PLN00099, light-harvesting complex IChlo 1e-39
PLN00187286 PLN00187, PLN00187, photosystem II light-harvestin 1e-38
PLN00089209 PLN00089, PLN00089, fucoxanthin-chlorophyll a/c bi 1e-14
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 1e-08
PLN00120202 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c bi 0.001
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 0.004
>gnl|CDD|215076 PLN00147, PLN00147, light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information 
 Score =  451 bits (1162), Expect = e-163
 Identities = 202/265 (76%), Positives = 217/265 (81%), Gaps = 18/265 (6%)

Query: 1   MAVAVGRGFLLQPSSSSSFIC--NDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPT 58
           MA     GFL QP  SSS          +S G                    V AQ+RPT
Sbjct: 4   MAGGTTGGFLHQPRDSSSHCTRSISSVAASSGG----------------INPVVAQERPT 47

Query: 59  WLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLL 118
           WLPG+DPPP+LDGTLAGDFGFDPLGLGEDPESL+WYVQAELVH+RFAMAGVAGILFTDLL
Sbjct: 48  WLPGLDPPPHLDGTLAGDFGFDPLGLGEDPESLKWYVQAELVHSRFAMAGVAGILFTDLL 107

Query: 119 RVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFG 178
           RVTGIR LPVWYEAGAV+F+FASTRTLF+VQLLLMGFAETKRYMD++SPGSQ KEGSFFG
Sbjct: 108 RVTGIRNLPVWYEAGAVKFEFASTRTLFVVQLLLMGFAETKRYMDFVSPGSQAKEGSFFG 167

Query: 179 LEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHV 238
           LEAALEGLEPGYPGGPL NPLGLAKDI NA +WKLKEIKNGRLAMVAMLG FVQASVTH 
Sbjct: 168 LEAALEGLEPGYPGGPLFNPLGLAKDIENAHDWKLKEIKNGRLAMVAMLGFFVQASVTHT 227

Query: 239 GPIDNILEHLSDPWHKTIIQTLANS 263
           GPIDN+L HLSDPWHKTIIQTL++S
Sbjct: 228 GPIDNLLTHLSDPWHKTIIQTLSHS 252

Length = 252
>gnl|CDD|215055 PLN00101, PLN00101, Photosystem I light-harvesting complex type 4 protein; 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|177716 PLN00098, PLN00098, light-harvesting complex I chlorophyll a/b-binding protein (Lhac); 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|215054 PLN00100, PLN00100, light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>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|215087 PLN00170, PLN00170, photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>gnl|CDD|215033 PLN00025, PLN00025, photosystem II light harvesting chlorophyll a/b binding protein; 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|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II protein Lhcb4; 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|215956 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein 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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 265
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
PLN00187286 photosystem II light-harvesting complex II protein 100.0
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 100.0
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
PLN00170255 photosystem II light-harvesting-Chl-binding protei 100.0
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 100.0
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 100.0
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 100.0
PLN00098 267 light-harvesting complex I chlorophyll a/b-binding 99.64
PLN00101 250 Photosystem I light-harvesting complex type 4 prot 99.61
PLN00170 255 photosystem II light-harvesting-Chl-binding protei 99.6
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 99.55
PLN00171 324 photosystem light-harvesting complex -chlorophyll 99.51
PLN00097 244 photosystem I light harvesting complex Lhca2/4, ch 99.51
PLN00048262 photosystem I light harvesting chlorophyll a/b bin 99.51
PLN00025 262 photosystem II light harvesting chlorophyll a/b bi 99.49
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.49
PLN00100 246 light-harvesting complex chlorophyll-a/b protein o 99.48
PLN00099 243 light-harvesting complex IChlorophyll A-B binding 99.44
PLN00187286 photosystem II light-harvesting complex II protein 99.44
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.36
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.15
PHA0233735 putative high light inducible protein 98.01
PLN00084214 photosystem II subunit S (PsbS); Provisional 97.92
PLN00014250 light-harvesting-like protein 3; Provisional 97.46
PHA0233735 putative high light inducible protein 97.46
PLN00014250 light-harvesting-like protein 3; Provisional 95.25
PLN00084214 photosystem II subunit S (PsbS); Provisional 95.03
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1e-69  Score=492.64  Aligned_cols=249  Identities=81%  Similarity=1.309  Sum_probs=215.4

Q ss_pred             CceeccccceeccCCCCcccccccCCCcccccccCCCCCcccCccchhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCcC
Q 024588            1 MAVAVGRGFLLQPSSSSSFICNDVNKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFD   80 (265)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~r~~~lP~~~~p~~l~G~~pGd~GfD   80 (265)
                      |++.+.+++..+++.+++..+..  +++.+          ..+.|.  +..++++|++|+|+.++|+||||++|||+|||
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~----------~~~~~~--~~~~~~~R~~wlP~~~~P~~Ldg~~pGD~GFD   69 (252)
T PLN00147          4 MAGGTTGGFLHQPRDSSSHCTRS--ISSVA----------ASSGGI--NPVVAQERPTWLPGLDPPPHLDGTLAGDFGFD   69 (252)
T ss_pred             eeeccCCceeeecccccchhhhh--hhhhh----------hccccC--cccCCCCccccCCCCCCCCcCCCCCCCccCCC
Confidence            55666777777777655555443  22221          012332  22346899999999999999999999999999


Q ss_pred             CCCCCCCHHHHHHHHHHHHhhccchhhhhhhHhhhhhhhccCCCCCcchhccccccccccchhhHHHHHHHHhHhhhhhh
Q 024588           81 PLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKR  160 (265)
Q Consensus        81 Plgl~~~~~~l~~~r~aElkHGRlAMlA~~G~~~~e~~~~~G~~~~P~w~~aG~~~~~f~~~~~l~~~ql~~~G~~E~~r  160 (265)
                      |+||++|+++++|||++|||||||||||++|+++||+++..|....|.|+++|...+++.+.++++++|+++||++|..|
T Consensus        70 Plgl~~d~~~~~~~r~aElkhGR~AMlA~~G~l~~e~~~~~g~~~~p~w~~ag~~~~~~~~~~~~~~~q~~~mG~~E~~R  149 (252)
T PLN00147         70 PLGLGEDPESLKWYVQAELVHSRFAMAGVAGILFTDLLRVTGIRNLPVWYEAGAVKFEFASTRTLFVVQLLLMGFAETKR  149 (252)
T ss_pred             cccccCCHHHHHHHHHHHhhccHHHHHHHhhhhHHHHhccCCCcCCcchhhcccchhccccchHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999888877788999988766666677888899999999999999


Q ss_pred             hccccCCCCCCCCCcccchhhhhcCCCCCCCCCCCCCccCCchhHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhccCCcc
Q 024588          161 YMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGP  240 (265)
Q Consensus       161 ~~~~~~pg~~~~~~~f~G~~~~~~g~~~~yPGd~gFDPLgl~~d~e~~~~~k~kELkNGRLAMlAi~G~~~Qe~vtG~gP  240 (265)
                      |.++.+||++..++.|+|.+...++.+++||||++||||||.+|+++++++|+||||||||||+|++||++|+++||++|
T Consensus       150 ~~~~~~pg~~~~~g~~~g~~~~~~~~~~~yPGd~~FDPlGl~~d~~~~~~~k~kEikNGRLAMlA~~G~~~q~~vtg~Gp  229 (252)
T PLN00147        150 YMDFVSPGSQAKEGSFFGLEAALEGLEPGYPGGPLFNPLGLAKDIENAHDWKLKEIKNGRLAMVAMLGFFVQASVTHTGP  229 (252)
T ss_pred             hccccCCCccccccccccccccccccCCCCcccccCCccccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCCCh
Confidence            99999999988888887776666667788999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhcCccccchhhccccC
Q 024588          241 IDNILEHLSDPWHKTIIQTLANS  263 (265)
Q Consensus       241 l~nL~~hl~dP~~~ni~~~~~~~  263 (265)
                      ++||.+||+||+|+||+++++++
T Consensus       230 ~~nL~~hladP~~~ni~~~~~~~  252 (252)
T PLN00147        230 IDNLLTHLSDPWHKTIIQTLSHS  252 (252)
T ss_pred             HHHHHHHhcCcccchhhhhhcCC
Confidence            99999999999999999999875

>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
>PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional Back     alignment and domain information
>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional Back     alignment and domain information
>PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional Back     alignment and domain information
>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
>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
>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
>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
>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
>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
>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
>PLN00089 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
>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
>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
>PHA02337 putative high light inducible protein Back     alignment and domain information
>PLN00084 photosystem II subunit S (PsbS); Provisional 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 ?
Query265
2wsc_4251 Improved Model Of Plant Photosystem I Length = 251 2e-46
2wsc_2269 Improved Model Of Plant Photosystem I Length = 269 3e-46
2o01_2186 The Structure Of A Plant Photosystem I Supercomplex 6e-40
2wsc_3276 Improved Model Of Plant Photosystem I Length = 276 5e-36
2o01_4165 The Structure Of A Plant Photosystem I Supercomplex 2e-34
3lw5_4166 Improved Model Of Plant Photosystem I Length = 166 2e-33
3lw5_2176 Improved Model Of Plant Photosystem I Length = 176 2e-31
2wsc_1241 Improved Model Of Plant Photosystem I Length = 241 3e-28
2o01_1187 The Structure Of A Plant Photosystem I Supercomplex 1e-26
2o01_3165 The Structure Of A Plant Photosystem I Supercomplex 3e-23
3lw5_1170 Improved Model Of Plant Photosystem I Length = 170 4e-22
1rwt_A232 Crystal Structure Of Spinach Major Light-harvesting 4e-22
1vcr_A232 An Icosahedral Assembly Of Light-Harvesting Chlorop 6e-22
2bhw_A232 Pea Light-Harvesting Complex Ii At 2.5 Angstrom Res 1e-21
3pl9_A243 Crystal Structure Of Spinach Minor Light-Harvesting 2e-21
3lw5_3172 Improved Model Of Plant Photosystem I Length = 172 6e-21
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I Length = 251 Back     alignment and structure 
Iteration: 1

 Score =  182 bits (461), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 103/247 (41%), Positives = 140/247 (56%), Gaps = 23/247 (9%)
Query: 29  IGITSAFLPAKSGTTRRYLA----------TVVRAQQRPTWLPGVDPPPYLDGTLAGDFG 78
            G+ S FL   SG   R +A          +     ++  WLPG+  P YL G+L GD G
Sbjct: 16  CGLKSRFLGGSSGKLNRGVAFRPVGCSPSASFKVEAKKGEWLPGLASPGYLTGSLPGDNG 75
Query: 79  FDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFK 138
           FDPLGL EDPE+LRW+VQAELV+ R+AM GVAG+L  ++    GI  +P WY AG  E+ 
Sbjct: 76  FDPLGLAEDPENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIGIINVPKWYAAGKEEY- 134
Query: 139 FASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSF--FGLEAAXXXXXXXXXXXXXX 196
           FAS+ TLF+++ +L  + E +R+ D  +PGS  ++  F  + L A               
Sbjct: 135 FASSSTLFVIEFILSHYVEIRRWQDIKNPGSVNQDPIFKQYSLPAGEVGYPGGIFNPLNF 194
Query: 197 XXXXXAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTI 256
                AK+         KEI NGRL M+A LG  +Q +VT  GP DN+L+H+SDPWH TI
Sbjct: 195 APTLEAKE---------KEIANGRL-MLAFLGFIIQHNVTGKGPFDNLLQHISDPWHNTI 244
Query: 257 IQTLANS 263
           +QTL  +
Sbjct: 245 VQTLGGN 251
>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|3 Chain 3, Improved Model Of Plant Photosystem I Length = 276 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|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I Length = 166 Back     alignment and structure
>pdb|3LW5|2 Chain 2, Improved Model Of Plant Photosystem I Length = 176 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|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|1 Chain 1, Improved Model Of Plant Photosystem I Length = 170 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|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|2BHW|A Chain A, Pea Light-Harvesting Complex Ii At 2.5 Angstrom Resolution Length = 232 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|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 ?
Query265
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 3e-57
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 1e-56
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 2e-56
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 3e-52
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 3e-50
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 4e-43
>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
 Score =  182 bits (463), Expect = 3e-57
 Identities = 108/239 (45%), Positives = 147/239 (61%), Gaps = 13/239 (5%)

Query: 25  NKSSIGITSAFLPAKSGTTRRYLATVVRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGL 84
           +   +    AF P     +    A+     ++  WLPG+  P YL G+L GD GFDPLGL
Sbjct: 26  SSGKLNRGVAFRPVGCSPS----ASFKVEAKKGEWLPGLASPGYLTGSLPGDNGFDPLGL 81

Query: 85  GEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRT 144
            EDPE+LRW+VQAELV+ R+AM GVAG+L  ++    GI  +P WY AG  E+ FAS+ T
Sbjct: 82  AEDPENLRWFVQAELVNGRWAMLGVAGMLLPEVFTSIGIINVPKWYAAGKEEY-FASSST 140

Query: 145 LFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKD 204
           LF+++ +L  + E +R+ D  +PGS  ++  F   + +L   E GYPGG + NPL  A  
Sbjct: 141 LFVIEFILSHYVEIRRWQDIKNPGSVNQDPIF--KQYSLPAGEVGYPGG-IFNPLNFAPT 197

Query: 205 IRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS 263
                E K KEI NGRL M+A LG  +Q +VT  GP DN+L+H+SDPWH TI+QTL  +
Sbjct: 198 ----LEAKEKEIANGRL-MLAFLGFIIQHNVTGKGPFDNLLQHISDPWHNTIVQTLGGN 251
>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_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
>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_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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query265
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 100.0
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 100.0
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 100.0
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 100.0
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 100.0
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 100.0
2bhw_A 232 Chlorophyll A-B binding protein AB80; LHC-II, phot 99.48
2wsc_4 251 Chlorophyll A-B binding protein P4, chloroplastic; 99.44
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.43
2wsc_2 269 LHCA2, type II chlorophyll A/B binding protein fro 99.42
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 99.4
2wsc_1 241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.33
>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
Probab=100.00  E-value=5.6e-64  Score=458.04  Aligned_cols=208  Identities=51%  Similarity=0.976  Sum_probs=154.0

Q ss_pred             hccCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCHHHHHHHHHHHHhhccchhhhhhhHhhhhhhhccCCCCCcchh
Q 024588           51 VRAQQRPTWLPGVDPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIRELPVWY  130 (265)
Q Consensus        51 ~~~~~r~~~lP~~~~p~~l~G~~pGd~GfDPlgl~~~~~~l~~~r~aElkHGRlAMlA~~G~~~~e~~~~~G~~~~P~w~  130 (265)
                      +..++|++|+|+.+.|.||||++|||||||||||++|+|+++|||++|||||||||||++|++++|+++..|+.+.|.|+
T Consensus        59 ~~~~~r~~wlpg~~~P~~L~G~~pGD~GfDPlGL~~d~e~~~~~r~aElkHGR~AMLA~~G~l~~E~l~~~G~~~~p~w~  138 (269)
T 2wsc_2           59 VAEPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLGAAGIFIPEFLTKLGILNTPSWY  138 (269)
T ss_dssp             -----------------------------------CCCSCCTTTHHHHHHTHHHHTTTTHHHHHHHHHCCTTSSSCCCCC
T ss_pred             ccCCCcccccCCCCCcccccCcCCCCCCCCccccCCCHHHHHHHHHHHHhcchHHHHHHHHhHhHHhhccCCcccCcccc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999988888788999


Q ss_pred             ccccccccccchhhHHHHHHHHhHhhhhhhhccccCCCCCCCCCcccchhhhhcCCCCCCCCCCCCCccCCch-hHHHHH
Q 024588          131 EAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAK-DIRNAR  209 (265)
Q Consensus       131 ~aG~~~~~f~~~~~l~~~ql~~~G~~E~~r~~~~~~pg~~~~~~~f~G~~~~~~g~~~~yPGd~gFDPLgl~~-d~e~~~  209 (265)
                      ++|...+ |.+.++++++|+++||++|++|+.++.+||+...++.|.+  ....+.|.+||||++||||||.+ |+++++
T Consensus       139 ~aG~~~~-~~~~~~l~~~qi~liG~~E~~r~~~~~~pG~~g~~p~f~~--~~~~~~d~~~PG~~~fDPlgl~~~~~e~~~  215 (269)
T 2wsc_2          139 TAGEQEY-FTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTDPIFPN--NKLTGTDVGYPGGLWFDPLGWGSASPQKLK  215 (269)
T ss_dssp             STTSSSS-CCCTTSHHHHHTTHHHHHHHHHHTTSSCCCCCSSSCCSSS--CCSSTTSCSCTTCSSCCCSSSSSSCCCSCT
T ss_pred             ccchhhh-hcchHHHHHHHHHHHHHHHHHHHhccccCCcccccccccc--ccccccccCCCCCcccCccccCcccHHHHH
Confidence            9876554 6666788899999999999999999989998776666532  22234567899999999999986 788889


Q ss_pred             HHHHHHHhhhhHHHHHHHHHHHHhhccCCcchhhhh-hhhcCccccchhhcccc
Q 024588          210 EWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNIL-EHLSDPWHKTIIQTLAN  262 (265)
Q Consensus       210 ~~k~kELkNGRLAMlAi~G~~~Qe~vtG~gPl~nL~-~hl~dP~~~ni~~~~~~  262 (265)
                      ++|.+||||||||||||+|+++|+.+||++|++||. +||+|| |+||++++.+
T Consensus       216 ~~~~~Ei~nGRlAMla~~g~~~~~~~tg~g~l~~l~~~HladP-~~n~~~~~~~  268 (269)
T 2wsc_2          216 ELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFAAHLADP-HATIFAAFTP  268 (269)
T ss_dssp             TSTTTTHHHHHHHHTTTSSSCHHHHHTTTCSSCCCSCCCCCCS-CCCCCSSSCC
T ss_pred             HHHHhhcccchHHHHHHHHHHHHHHhcCCChHHHHHHHHhcCc-ccchhhhccC
Confidence            999999999999999999999999999999999999 999999 9999998865
>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
>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_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
>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
>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_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

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 265
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 2e-58
d1rwta_ 218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 2e-06
>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 =  183 bits (465), Expect = 2e-58
 Identities = 78/216 (36%), Positives = 110/216 (50%), Gaps = 16/216 (7%)

Query: 56  RPTWLPGV--DPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGIL 113
           R  +L     + P YL G   GD+G+D  GL  DPE+     + E++H R+AM G  G +
Sbjct: 8   RVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCV 67

Query: 114 FTDLLRVTGIR-ELPVWYEAGAVEFK-----FASTRTLFIVQLLLMGFAETKRYMDYISP 167
           F +LL   G++    VW++AG+  F      +    +L   Q +L  +A     M  +  
Sbjct: 68  FPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAV-- 125

Query: 168 GSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAML 227
                EG         E ++P YPGG   +PLGLA D     E K+KEIKNGRLAM +M 
Sbjct: 126 -----EGYRIAGGPLGEVVDPLYPGGS-FDPLGLADDPEAFAELKVKEIKNGRLAMFSMF 179

Query: 228 GIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS 263
           G FVQA VT  GP++N+ +HL+DP +        N 
Sbjct: 180 GFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNF 215
>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 ?
Query265
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 100.0
d1rwta_ 218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.55
>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=6.8e-59  Score=410.62  Aligned_cols=195  Identities=41%  Similarity=0.697  Sum_probs=156.1

Q ss_pred             ccCCCCCCCCCC--CCCCCCCCCCCCCCCcCCCCCCCCHHHHHHHHHHHHhhccchhhhhhhHhhhhhhhccCCC-CCcc
Q 024588           52 RAQQRPTWLPGV--DPPPYLDGTLAGDFGFDPLGLGEDPESLRWYVQAELVHARFAMAGVAGILFTDLLRVTGIR-ELPV  128 (265)
Q Consensus        52 ~~~~r~~~lP~~--~~p~~l~G~~pGd~GfDPlgl~~~~~~l~~~r~aElkHGRlAMlA~~G~~~~e~~~~~G~~-~~P~  128 (265)
                      ..++|++|+|..  +.|+||||++|||+|||||||++|+++++||||+|||||||||||++|++++|+++..+.. ..+.
T Consensus         4 ~~~~r~~~~~~~~~~~P~~LdGs~pGD~GFDPLgls~d~~~~~~~ReaELKHGR~AMLA~vG~~~~E~~~~~~~~~~~~~   83 (218)
T d1rwta_           4 YGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAV   83 (218)
T ss_dssp             SSTTCCCTTGGGGCSCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCSCCS
T ss_pred             CCCCCcccCCccccCCCcccCCCCCCCCCcCCcccCCCHHHHHHHHHHHHhhceehHhhhcceeehhhhccCCCCCCCcc
Confidence            457899999743  5799999999999999999999999999999999999999999999999999998865442 3344


Q ss_pred             hhcccccccc--------------ccchhhHHHHHHHHhHhhhhhhhccccCCCCCCCCCcccchhhhhcCCCCCCCCCC
Q 024588          129 WYEAGAVEFK--------------FASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGP  194 (265)
Q Consensus       129 w~~aG~~~~~--------------f~~~~~l~~~ql~~~G~~E~~r~~~~~~pg~~~~~~~f~G~~~~~~g~~~~yPGd~  194 (265)
                      |++++.....              +..+...+.+++.+++.+|..+...-  +.              ....+..|||+ 
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~--~~--------------~~~~~~~~~~g-  146 (218)
T d1rwta_          84 WFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGG--PL--------------GEVVDPLYPGG-  146 (218)
T ss_dssp             HHHHGGGGGSTTCBCGGGCTTSCCBCCHHHHHHHHHHHHHHHHHHHHHCB--TT--------------BCCSSSSCCCG-
T ss_pred             cccccccccCcchhhhhcCchHHHHHHHHHHHHHHHHHHhhhhhhcccCC--Cc--------------ccccCCCCCCC-
Confidence            6654332110              11111222334567888888765421  10              01134567777 


Q ss_pred             CCCccCCchhHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhccCCcchhhhhhhhcCccccchhhccccC
Q 024588          195 LLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS  263 (265)
Q Consensus       195 gFDPLgl~~d~e~~~~~k~kELkNGRLAMlAi~G~~~Qe~vtG~gPl~nL~~hl~dP~~~ni~~~~~~~  263 (265)
                      +|||+++.+|+++++++|+|||||||||||||+||++||++||++|++||.+|++||+|+||++.++.+
T Consensus       147 ~fdPlg~~~~~e~~~~~k~kElkNGRLAMlAi~G~~~qe~vtG~gp~~nl~~h~~~P~~~n~~~~~~~~  215 (218)
T d1rwta_         147 SFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNF  215 (218)
T ss_dssp             GGCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCHHHHHHHHHHCTTTSSGGGGTTSS
T ss_pred             CccccccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhcCCCHHHHHHHHhcCchhhhHHHHHhcc
Confidence            599999999999999999999999999999999999999999999999999999999999999887764
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure