Citrus Sinensis ID: 031425

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
MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
cEEEcHHHHHHHHcccccccccHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccccHHHHHHHHHccc
ccHHHHHHHHHHHHHcccccccEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccHHHHHHHHcccc
MAGVAGILFTDllrvtgirelpvwyeagavefkfaSTRTLFIVQLLLMGFAETkrymdyispgsqtkegsfFGLEAALeglepgypggpllnplglAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASvthvgpidnilehlsdpwhKTIIQTLANSGS
magvagilftdllrvtgIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNIlehlsdpwhKTIIQTLANSGS
MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAAleglepgypggpllnplglAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
***VAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTL*****
MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS**
MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS
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 ?
Query160 2.2.26 [Sep-21-2011]
P27522273 Chlorophyll a-b binding p N/A no 0.962 0.564 0.451 3e-32
Q9SQL2252 Chlorophyll a-b binding p N/A no 0.937 0.595 0.455 3e-31
P27521251 Chlorophyll a-b binding p no no 0.918 0.585 0.451 2e-30
Q32904275 Chlorophyll a-b binding p N/A no 0.825 0.48 0.453 9e-30
P10708270 Chlorophyll a-b binding p N/A no 0.956 0.566 0.445 3e-28
P13869270 Chlorophyll a-b binding p N/A no 0.956 0.566 0.420 2e-27
Q36718231 Chlorophyll a-b binding p N/A no 0.918 0.636 0.403 7e-22
P27518265 Chlorophyll a-b binding p N/A no 0.806 0.486 0.385 1e-18
P10049266 Chlorophyll a-b binding p N/A no 0.862 0.518 0.421 2e-18
P27517253 Chlorophyll a-b binding p N/A no 0.806 0.509 0.406 3e-18
>sp|P27522|CB13_SOLLC Chlorophyll a-b binding protein 8, chloroplastic OS=Solanum lycopersicum GN=CAB8 PE=3 SV=1 Back     alignment and function desciption
 Score =  137 bits (345), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 74/164 (45%), Positives = 104/164 (63%), Gaps = 10/164 (6%)

Query: 1   MAGVAGILFTDLLRVTGI---RELPVWYEAGAVEFK-----FASTRTLFIVQLLLMGFAE 52
           M G AG +  ++L   G+        W++ G +        +A   TLF++++ LMGFAE
Sbjct: 108 MLGAAGAIAPEILGKAGLIPQETALAWFQTGVIPPAGTYNYWADNYTLFVLEMALMGFAE 167

Query: 53  TKRYMDYISPGSQTKEGSFFGLEAALEGL-EPGYPGGPLLNPLGLAKDIRNAREWKLKEI 111
            +R+ D+  PGS  K+  F GLE  L G  +P YPGGPL NPLG  KD ++ +E KLKEI
Sbjct: 168 HRRFQDWAKPGSMGKQ-YFLGLEKGLGGSGDPAYPGGPLFNPLGFGKDEKSMKELKLKEI 226

Query: 112 KNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTL 155
           KNGRLAM+A+LG F+QA VT VGP  N+L+HL+DP +  ++ +L
Sbjct: 227 KNGRLAMLAILGYFIQALVTGVGPYQNLLDHLADPVNNNVLTSL 270
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|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|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|P10708|CB12_SOLLC Chlorophyll a-b binding protein 7, chloroplastic OS=Solanum lycopersicum GN=CAB7 PE=3 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|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|P27518|CB21_GOSHI Chlorophyll a-b binding protein 151, chloroplastic OS=Gossypium hirsutum GN=CAB-151 PE=2 SV=2 Back     alignment and function description
>sp|P10049|CB21_PINTH Chlorophyll a-b binding protein type I, chloroplastic OS=Pinus thunbergii PE=2 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 ?
Query160
224137478 266 light-harvesting complex I protein Lhca5 1.0 0.601 0.875 3e-78
255538312 269 chlorophyll A/B binding protein, putativ 1.0 0.594 0.856 9e-78
356519222 263 PREDICTED: chlorophyll a-b binding prote 1.0 0.608 0.831 5e-74
15220077256 photosystem I light harvesting complex p 1.0 0.625 0.838 2e-73
222423311248 AT1G45474 [Arabidopsis thaliana] 1.0 0.645 0.838 2e-73
225458605 264 PREDICTED: chlorophyll a-b binding prote 0.987 0.598 0.829 2e-73
297846882256 light-harvesting complex protein [Arabid 1.0 0.625 0.838 2e-73
4741942256 Lhca5 protein [Arabidopsis thaliana] 1.0 0.625 0.832 5e-73
388510254213 unknown [Lotus japonicus] 1.0 0.751 0.831 7e-73
21593722256 light-harvesting complex protein [Arabid 1.0 0.625 0.826 1e-72
>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 =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 140/160 (87%), Positives = 154/160 (96%)

Query: 1   MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYI 60
           MAGVAGILFTDLLRVTGIR+LPVWYEAGAV+F+FASTRTL +VQLLLMGFAETKRYMD++
Sbjct: 107 MAGVAGILFTDLLRVTGIRKLPVWYEAGAVKFEFASTRTLIVVQLLLMGFAETKRYMDFV 166

Query: 61  SPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVA 120
           SPGSQ KEGSFFGLE+ALEGLEPGYPGGPLLNPLGLA+DI NA  WKLKEIKNGRLAMVA
Sbjct: 167 SPGSQAKEGSFFGLESALEGLEPGYPGGPLLNPLGLARDIENAHVWKLKEIKNGRLAMVA 226

Query: 121 MLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS 160
           M+GIFVQA+VTH GPIDN++EHLS+PWH+TIIQTLANSGS
Sbjct: 227 MVGIFVQAAVTHAGPIDNLIEHLSNPWHRTIIQTLANSGS 266

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>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|15220077|ref|NP_175137.1| photosystem I light harvesting complex protein 5 [Arabidopsis thaliana] gi|30693978|ref|NP_849778.1| photosystem I light harvesting complex protein 5 [Arabidopsis thaliana] gi|12321000|gb|AAG50618.1|AC083835_3 light-harvesting complex protein [Arabidopsis thaliana] gi|17063199|gb|AAL32974.1| At1g45474/F2G19.4 [Arabidopsis thaliana] gi|19699116|gb|AAL90924.1| At1g45474/F2G19.4 [Arabidopsis thaliana] gi|62320735|dbj|BAD95402.1| light-harvesting complex protein [Arabidopsis thaliana] gi|332193996|gb|AEE32117.1| photosystem I light harvesting complex protein 5 [Arabidopsis thaliana] gi|332193997|gb|AEE32118.1| photosystem I light harvesting complex protein 5 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|222423311|dbj|BAH19631.1| AT1G45474 [Arabidopsis thaliana] Back     alignment and taxonomy information
>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|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
>gi|4741942|gb|AAD28768.1|AF134121_1 Lhca5 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|388510254|gb|AFK43193.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|21593722|gb|AAM65689.1| light-harvesting complex protein [Arabidopsis thaliana] 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 ?
Query160
TAIR|locus:2825741256 Lhca5 "photosystem I light har 1.0 0.625 0.720 9.6e-57
TAIR|locus:2079117251 LHCA4 "light-harvesting chloro 0.912 0.581 0.383 1.8e-23
TAIR|locus:2200868273 LHCA3 "photosystem I light har 0.956 0.560 0.369 3.4e-22
TAIR|locus:2082767257 LHCA2 "photosystem I light har 0.931 0.579 0.384 1.9e-21
TAIR|locus:2202150270 Lhca6 "photosystem I light har 0.393 0.233 0.453 9e-21
TAIR|locus:2044988265 LHCB2.2 "photosystem II light 0.312 0.188 0.58 5.5e-14
TAIR|locus:2042148265 LHCB2.1 "photosystem II light 0.312 0.188 0.58 5.5e-14
UNIPROTKB|P12331261 CAB2R "Chlorophyll a-b binding 0.312 0.191 0.58 8.9e-14
UNIPROTKB|P12330265 CAB1R "Chlorophyll a-b binding 0.312 0.188 0.58 1e-13
TAIR|locus:2019287267 CAB3 "chlorophyll A/B binding 0.312 0.187 0.58 1.1e-13
TAIR|locus:2825741 Lhca5 "photosystem I light harvesting complex gene 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 584 (210.6 bits), Expect = 9.6e-57, P = 9.6e-57
 Identities = 116/161 (72%), Positives = 128/161 (79%)

Query:     1 MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYI 60
             M GVAGILFTDLLR TGIR LPVWYEAGAV+F FAST+TL +VQ LLMGFAETKRYMD++
Sbjct:    96 MLGVAGILFTDLLRTTGIRNLPVWYEAGAVKFDFASTKTLIVVQFLLMGFAETKRYMDFV 155

Query:    61 SPGSQTKEGSFF-GLEAAXXXXXXXXXXXXXXXXXXXAKDIRNAREWKLKEIKNGRLAMV 119
             SPGSQ KEGSFF GLEAA                   AKD++NA +WKLKEIKNGRLAM+
Sbjct:   156 SPGSQAKEGSFFFGLEAALEGLEPGYPGGPLLNPLGLAKDVQNAHDWKLKEIKNGRLAMM 215

Query:   120 AMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANSGS 160
             AMLG FVQASVTH GPIDN++EHLS+PWHKTIIQTL  S S
Sbjct:   216 AMLGFFVQASVTHTGPIDNLVEHLSNPWHKTIIQTLFTSTS 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:2200868 LHCA3 "photosystem I light harvesting complex gene 3" [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:2202150 Lhca6 "photosystem I light harvesting complex gene 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2044988 LHCB2.2 "photosystem II light harvesting complex gene 2.2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2042148 LHCB2.1 "photosystem II light harvesting complex gene 2.1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P12331 CAB2R "Chlorophyll a-b binding protein 2, chloroplastic" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
UNIPROTKB|P12330 CAB1R "Chlorophyll a-b binding protein 1, chloroplastic" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2019287 CAB3 "chlorophyll A/B binding protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

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

Your Input:
Lhca5-2
light-harvesting complex I protein Lhca5 (266 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query160
PLN00147252 PLN00147, PLN00147, light-harvesting complex I chl 1e-114
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 1e-43
PLN00048262 PLN00048, PLN00048, photosystem I light harvesting 3e-43
PLN00097244 PLN00097, PLN00097, photosystem I light harvesting 9e-37
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 9e-33
PLN00098267 PLN00098, PLN00098, light-harvesting complex I chl 1e-30
PLN00171324 PLN00171, PLN00171, photosystem light-harvesting c 2e-28
PLN00025262 PLN00025, PLN00025, photosystem II light harvestin 8e-27
PLN00100246 PLN00100, PLN00100, light-harvesting complex chlor 3e-23
PLN00187286 PLN00187, PLN00187, photosystem II light-harvestin 7e-22
PLN00099243 PLN00099, PLN00099, light-harvesting complex IChlo 8e-17
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 1e-16
PLN00101 250 PLN00101, PLN00101, Photosystem I light-harvesting 1e-04
PLN00089209 PLN00089, PLN00089, fucoxanthin-chlorophyll a/c bi 9e-04
PLN00170 255 PLN00170, PLN00170, photosystem II light-harvestin 0.002
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 0.003
PLN00098 267 PLN00098, PLN00098, light-harvesting complex I chl 0.003
>gnl|CDD|215076 PLN00147, PLN00147, light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information 
 Score =  322 bits (827), Expect = e-114
 Identities = 141/158 (89%), Positives = 150/158 (94%)

Query: 1   MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYI 60
           MAGVAGILFTDLLRVTGIR LPVWYEAGAV+F+FASTRTLF+VQLLLMGFAETKRYMD++
Sbjct: 95  MAGVAGILFTDLLRVTGIRNLPVWYEAGAVKFEFASTRTLFVVQLLLMGFAETKRYMDFV 154

Query: 61  SPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVA 120
           SPGSQ KEGSFFGLEAALEGLEPGYPGGPL NPLGLAKDI NA +WKLKEIKNGRLAMVA
Sbjct: 155 SPGSQAKEGSFFGLEAALEGLEPGYPGGPLFNPLGLAKDIENAHDWKLKEIKNGRLAMVA 214

Query: 121 MLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS 158
           MLG FVQASVTH GPIDN+L HLSDPWHKTIIQTL++S
Sbjct: 215 MLGFFVQASVTHTGPIDNLLTHLSDPWHKTIIQTLSHS 252

Length = 252
>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|165670 PLN00097, PLN00097, photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; 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|215088 PLN00171, PLN00171, photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; 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|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
>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|215055 PLN00101, PLN00101, Photosystem I light-harvesting complex type 4 protein; 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|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|177716 PLN00098, PLN00098, light-harvesting complex I chlorophyll a/b-binding protein (Lhac); 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 160
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 100.0
PLN00101250 Photosystem I light-harvesting complex type 4 prot 100.0
PLN00098267 light-harvesting complex I chlorophyll a/b-binding 100.0
PLN00097244 photosystem I light harvesting complex Lhca2/4, ch 100.0
PLN00048262 photosystem I light harvesting chlorophyll a/b bin 100.0
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 100.0
PLN00099243 light-harvesting complex IChlorophyll A-B binding 100.0
PLN00187286 photosystem II light-harvesting complex II protein 100.0
PLN00171324 photosystem light-harvesting complex -chlorophyll 100.0
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 100.0
PLN00170255 photosystem II light-harvesting-Chl-binding protei 99.96
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.93
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.9
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.88
PLN00098 267 light-harvesting complex I chlorophyll a/b-binding 99.73
PLN00170 255 photosystem II light-harvesting-Chl-binding protei 99.7
PLN00101 250 Photosystem I light-harvesting complex type 4 prot 99.7
PLN00147 252 light-harvesting complex I chlorophyll-a/b binding 99.66
PLN00097 244 photosystem I light harvesting complex Lhca2/4, ch 99.64
PLN00025 262 photosystem II light harvesting chlorophyll a/b bi 99.64
PLN00171 324 photosystem light-harvesting complex -chlorophyll 99.64
PLN00187286 photosystem II light-harvesting complex II protein 99.61
PLN00100 246 light-harvesting complex chlorophyll-a/b protein o 99.61
PLN00099 243 light-harvesting complex IChlorophyll A-B binding 99.6
PLN00048 262 photosystem I light harvesting chlorophyll a/b bin 99.55
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.52
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.51
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.25
PHA0233735 putative high light inducible protein 98.01
PLN00084214 photosystem II subunit S (PsbS); Provisional 97.69
PLN00014250 light-harvesting-like protein 3; Provisional 97.43
>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.9e-43  Score=291.72  Aligned_cols=158  Identities=89%  Similarity=1.426  Sum_probs=141.5

Q ss_pred             CcccchhhhhhhhccCCCCCCchhhhcchhhhcccChhHHHHHHHHHHHHHHHHhhccccCCCCCCCCCcccchhhhccC
Q 031425            1 MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEG   80 (160)
Q Consensus         1 MLA~~G~lv~E~~~~pG~~~~~~w~~ag~~~~~~~~~~~l~~~q~l~ig~~E~~r~~~~~~pg~~~~~~~f~g~~~~~~~   80 (160)
                      |||++|+++||+++.+|+...|.|++++...+.+++.++++++|+++||++|.+|+.++.+||+...++.|.+.+....+
T Consensus        95 MlA~~G~l~~e~~~~~g~~~~p~w~~ag~~~~~~~~~~~~~~~q~~~mG~~E~~R~~~~~~pg~~~~~g~~~g~~~~~~~  174 (252)
T PLN00147         95 MAGVAGILFTDLLRVTGIRNLPVWYEAGAVKFEFASTRTLFVVQLLLMGFAETKRYMDFVSPGSQAKEGSFFGLEAALEG  174 (252)
T ss_pred             HHHHhhhhHHHHhccCCCcCCcchhhcccchhccccchHHHHHHHHHHHHHHHHhhccccCCCccccccccccccccccc
Confidence            99999999999999888776788999887665566667888999999999999999999899887777777665554455


Q ss_pred             CCCCCCCCCCCccCCCcccHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhccCCCchhhHHhhhcCccchhHhhhcccc
Q 031425           81 LEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS  158 (160)
Q Consensus        81 ~~~~~PGd~~fdplgl~~~~~~~~~~~~~ElknGRlAMla~~G~~~q~~~~g~gp~~~l~~~~~~P~~~~~~~~~~~~  158 (160)
                      .++.||||++|||+||.+|+++++++|++|||||||||+|++|+++|+++||++|++||.+|++||+++||++++.++
T Consensus       175 ~~~~yPGd~~FDPlGl~~d~~~~~~~k~kEikNGRLAMlA~~G~~~q~~vtg~Gp~~nL~~hladP~~~ni~~~~~~~  252 (252)
T PLN00147        175 LEPGYPGGPLFNPLGLAKDIENAHDWKLKEIKNGRLAMVAMLGFFVQASVTHTGPIDNLLTHLSDPWHKTIIQTLSHS  252 (252)
T ss_pred             cCCCCcccccCCccccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCCChHHHHHHHhcCcccchhhhhhcCC
Confidence            667899999999999999999999999999999999999999999999999999999999999999999999998775

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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query160
2o01_4165 The Structure Of A Plant Photosystem I Supercomplex 1e-26
2wsc_4251 Improved Model Of Plant Photosystem I Length = 251 8e-25
3lw5_4166 Improved Model Of Plant Photosystem I Length = 166 1e-23
2wsc_3276 Improved Model Of Plant Photosystem I Length = 276 8e-23
3lw5_2176 Improved Model Of Plant Photosystem I Length = 176 9e-22
2o01_2186 The Structure Of A Plant Photosystem I Supercomplex 8e-21
2o01_3165 The Structure Of A Plant Photosystem I Supercomplex 8e-20
2wsc_2269 Improved Model Of Plant Photosystem I Length = 269 1e-19
3lw5_3172 Improved Model Of Plant Photosystem I Length = 172 2e-16
1rwt_A232 Crystal Structure Of Spinach Major Light-harvesting 5e-12
1vcr_A232 An Icosahedral Assembly Of Light-Harvesting Chlorop 1e-11
2bhw_A232 Pea Light-Harvesting Complex Ii At 2.5 Angstrom Res 2e-11
2wsc_1241 Improved Model Of Plant Photosystem I Length = 241 4e-11
2o01_1187 The Structure Of A Plant Photosystem I Supercomplex 5e-11
3lw5_1170 Improved Model Of Plant Photosystem I Length = 170 2e-10
3pl9_A243 Crystal Structure Of Spinach Minor Light-Harvesting 9e-10
>pdb|2O01|4 Chain 4, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 165 Back     alignment and structure 
Iteration: 1

 Score =  115 bits (287), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 63/157 (40%), Positives = 88/157 (56%), Gaps = 12/157 (7%)
Query: 1   MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYI 60
           M GVAG+L  ++    GI  +P WY AG  E+ FAS+ TLF+++ +L  + E +R+ D  
Sbjct: 19  MLGVAGMLLPEVFTSIGIINVPKWYAAGKEEY-FASSSTLFVIEFILSHYVEIRRWQDIK 77
Query: 61  SPGSQTKEGSF--FGLEAAXXXXXXXXXXXXXXXXXXXAKDIRNAREWKLKEIKNGRLAM 118
           +PGS  ++  F  + L A                    AK+         KEI NGRLAM
Sbjct: 78  NPGSVNQDPIFKQYSLPAGEVGYPGGIFNPLNFAPTLEAKE---------KEIANGRLAM 128
Query: 119 VAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTL 155
           +A LG  +Q +VT  GP DN+L+H+SDPWH TI+QTL
Sbjct: 129 LAFLGFIIQHNVTGKGPFDNLLQHISDPWHNTIVQTL 165
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I Length = 251 Back     alignment and structure
>pdb|3LW5|4 Chain 4, Improved Model Of Plant Photosystem I Length = 166 Back     alignment and structure
>pdb|2WSC|3 Chain 3, Improved Model Of Plant Photosystem I Length = 276 Back     alignment and structure
>pdb|3LW5|2 Chain 2, Improved Model Of Plant Photosystem I Length = 176 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|2O01|3 Chain 3, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 165 Back     alignment and structure
>pdb|2WSC|2 Chain 2, Improved Model Of Plant Photosystem I Length = 269 Back     alignment and structure
>pdb|3LW5|3 Chain 3, Improved Model Of Plant Photosystem I Length = 172 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|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|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query160
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 1e-36
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 4e-34
2wsc_4 251 Chlorophyll A-B binding protein P4, chloroplastic; 2e-07
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 1e-32
2wsc_2 269 LHCA2, type II chlorophyll A/B binding protein fro 3e-04
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 2e-29
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 3e-25
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 6e-25
2wsc_1 241 AT3G54890, LHCA1; photosynthesis, electron transfe 5e-04
>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
 Score =  126 bits (317), Expect = 1e-36
 Identities = 68/164 (41%), Positives = 96/164 (58%), Gaps = 8/164 (4%)

Query: 1   MAGVAGILFTDLLRVTGIRELP---VWYEAGAVE-----FKFASTRTLFIVQLLLMGFAE 52
           M G  G +  ++L   G+        W+  G +        +A + TLF+ ++ LMGFAE
Sbjct: 111 MLGAVGAIAPEILGKAGLIPQETALPWFRTGFIPPAGTYNYWADSYTLFVFEMALMGFAE 170

Query: 53  TKRYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIK 112
            +R+ D+  PGS  K+      +      EP YPGGP  NPLG  KD ++ ++ KLKE+K
Sbjct: 171 HRRFQDWAKPGSMGKQYFLGLEKGLGGSGEPAYPGGPFFNPLGFGKDEKSLKDLKLKEVK 230

Query: 113 NGRLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLA 156
           NGRLAM+A+LG FVQA VT VGP  N+L+HL+DP H  I+ +L 
Sbjct: 231 NGRLAMLAILGYFVQALVTGVGPYQNLLDHLTDPVHNNILTSLK 274
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Length = 251 Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Length = 251 Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Length = 269 Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Length = 269 Back     alignment and structure
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Length = 232 Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Length = 243 Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Length = 241 Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Length = 241 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query160
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 100.0
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 100.0
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 100.0
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 100.0
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 100.0
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.97
2bhw_A 232 Chlorophyll A-B binding protein AB80; LHC-II, phot 99.65
2wsc_4 251 Chlorophyll A-B binding protein P4, chloroplastic; 99.59
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.58
2wsc_2 269 LHCA2, type II chlorophyll A/B binding protein fro 99.57
2wsc_1 241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.53
2wsc_3 276 LHCA3, type II chlorophyll A/B binding protein fro 99.41
>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=4.2e-39  Score=268.15  Aligned_cols=153  Identities=44%  Similarity=0.812  Sum_probs=131.3

Q ss_pred             CcccchhhhhhhhccCCCCCCchhhhcchhhhcccChhHHHHHHHHHHHHHHHHhhccccCCCCCCCCCcccchhhhccC
Q 031425            1 MAGVAGILFTDLLRVTGIRELPVWYEAGAVEFKFASTRTLFIVQLLLMGFAETKRYMDYISPGSQTKEGSFFGLEAALEG   80 (160)
Q Consensus         1 MLA~~G~lv~E~~~~pG~~~~~~w~~ag~~~~~~~~~~~l~~~q~l~ig~~E~~r~~~~~~pg~~~~~~~f~g~~~~~~~   80 (160)
                      |||++|+++||+++..|..+.|.|++++...+ +.+.++++++|+++||++|++|++++.+||+++.++.|.+.  ....
T Consensus       114 MLA~~G~l~~E~l~~~G~~~~p~w~~aG~~~~-~~~~~~l~~~qi~liG~~E~~r~~~~~~pG~~g~~p~f~~~--~~~~  190 (269)
T 2wsc_2          114 MLGAAGIFIPEFLTKLGILNTPSWYTAGEQEY-FTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTDPIFPNN--KLTG  190 (269)
T ss_dssp             TTTTHHHHHHHHHCCTTSSSCCCCCSTTSSSS-CCCTTSHHHHHTTHHHHHHHHHHTTSSCCCCCSSSCCSSSC--CSST
T ss_pred             HHHHHHhHhHHhhccCCcccCccccccchhhh-hcchHHHHHHHHHHHHHHHHHHHhccccCCccccccccccc--cccc
Confidence            99999999999998888876688999876544 55567788999999999999999998888887666555321  1123


Q ss_pred             CCCCCCCCCCCccCCCcc-cHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhccCCCchhhHH-hhhcCccchhHhhhccc
Q 031425           81 LEPGYPGGPLLNPLGLAK-DIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNIL-EHLSDPWHKTIIQTLAN  157 (160)
Q Consensus        81 ~~~~~PGd~~fdplgl~~-~~~~~~~~~~~ElknGRlAMla~~G~~~q~~~~g~gp~~~l~-~~~~~P~~~~~~~~~~~  157 (160)
                      .+..||||++|||+||.+ |+++++++|.+|||||||||+|++|+++|+.+||++|++||. +|++|| ++||++++..
T Consensus       191 ~d~~~PG~~~fDPlgl~~~~~e~~~~~~~~Ei~nGRlAMla~~g~~~~~~~tg~g~l~~l~~~HladP-~~n~~~~~~~  268 (269)
T 2wsc_2          191 TDVGYPGGLWFDPLGWGSASPQKLKELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFAAHLADP-HATIFAAFTP  268 (269)
T ss_dssp             TSCSCTTCSSCCCSSSSSSCCCSCTTSTTTTHHHHHHHHTTTSSSCHHHHHTTTCSSCCCSCCCCCCS-CCCCCSSSCC
T ss_pred             cccCCCCCcccCccccCcccHHHHHHHHHhhcccchHHHHHHHHHHHHHHhcCCChHHHHHHHHhcCc-ccchhhhccC
Confidence            456799999999999985 788899999999999999999999999999999999999999 999999 9999998764
>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
>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_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
>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_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 160
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 1e-30
d1rwta_ 218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 3e-07
>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 =  108 bits (270), Expect = 1e-30
 Identities = 59/164 (35%), Positives = 82/164 (50%), Gaps = 14/164 (8%)

Query: 1   MAGVAGILFTDLLRVTGIR-ELPVWYEAGAVEFK-----FASTRTLFIVQLLLMGFAETK 54
           M G  G +F +LL   G++    VW++AG+  F      +    +L   Q +L  +A   
Sbjct: 60  MLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQV 119

Query: 55  RYMDYISPGSQTKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNG 114
             M  +       EG         E ++P YPGG   +PLGLA D     E K+KEIKNG
Sbjct: 120 ILMGAV-------EGYRIAGGPLGEVVDPLYPGGSF-DPLGLADDPEAFAELKVKEIKNG 171

Query: 115 RLAMVAMLGIFVQASVTHVGPIDNILEHLSDPWHKTIIQTLANS 158
           RLAM +M G FVQA VT  GP++N+ +HL+DP +        N 
Sbjct: 172 RLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWNFATNF 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 ?
Query160
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 100.0
d1rwta_ 218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.7
>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=1.4e-33  Score=226.46  Aligned_cols=141  Identities=43%  Similarity=0.684  Sum_probs=108.0

Q ss_pred             CcccchhhhhhhhccCCCC-CCchhhhcchhhhc--------------ccChhHHHHHHHHHHHHHHHHhhccccCCCCC
Q 031425            1 MAGVAGILFTDLLRVTGIR-ELPVWYEAGAVEFK--------------FASTRTLFIVQLLLMGFAETKRYMDYISPGSQ   65 (160)
Q Consensus         1 MLA~~G~lv~E~~~~pG~~-~~~~w~~ag~~~~~--------------~~~~~~l~~~q~l~ig~~E~~r~~~~~~pg~~   65 (160)
                      |||++|+++||+++.++.. ..+.|+++......              ++.+...+.+++.+++.+|..|....  +.  
T Consensus        60 MLA~vG~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~--~~--  135 (218)
T d1rwta_          60 MLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGG--PL--  135 (218)
T ss_dssp             HHHHHHHHHHHHHHTTTCCCSCCSHHHHGGGGGSTTCBCGGGCTTSCCBCCHHHHHHHHHHHHHHHHHHHHHCB--TT--
T ss_pred             HhhhcceeehhhhccCCCCCCCcccccccccccCcchhhhhcCchHHHHHHHHHHHHHHHHHHhhhhhhcccCC--Cc--
Confidence            9999999999998766543 33457764432211              11223334445678999998876541  10  


Q ss_pred             CCCCcccchhhhccCCCCCCCCCCCCccCCCcccHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhccCCCchhhHHhhhcC
Q 031425           66 TKEGSFFGLEAALEGLEPGYPGGPLLNPLGLAKDIRNAREWKLKEIKNGRLAMVAMLGIFVQASVTHVGPIDNILEHLSD  145 (160)
Q Consensus        66 ~~~~~f~g~~~~~~~~~~~~PGd~~fdplgl~~~~~~~~~~~~~ElknGRlAMla~~G~~~q~~~~g~gp~~~l~~~~~~  145 (160)
                                  ....+..|||+ +|||+++.+++++++++|++|||||||||||++|+++|+++||++|++||.+|++|
T Consensus       136 ------------~~~~~~~~~~g-~fdPlg~~~~~e~~~~~k~kElkNGRLAMlAi~G~~~qe~vtG~gp~~nl~~h~~~  202 (218)
T d1rwta_         136 ------------GEVVDPLYPGG-SFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLAD  202 (218)
T ss_dssp             ------------BCCSSSSCCCG-GGCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCHHHHHHHHHHC
T ss_pred             ------------ccccCCCCCCC-CccccccCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhcCCCHHHHHHHHhcC
Confidence                        01234567777 69999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhHhhhcccc
Q 031425          146 PWHKTIIQTLANS  158 (160)
Q Consensus       146 P~~~~~~~~~~~~  158 (160)
                      |+++||++....+
T Consensus       203 P~~~n~~~~~~~~  215 (218)
T d1rwta_         203 PVNNNAWNFATNF  215 (218)
T ss_dssp             TTTSSGGGGTTSS
T ss_pred             chhhhHHHHHhcc
Confidence            9999999765543
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure