Citrus Sinensis ID: 026395

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-------24
MALIQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
ccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccHHHHHHccccHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccc
ccEEEEcccccHHHHHHHHHcccccccHcccEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEHEHcHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcc
MALIQFQAHatedwlswsccssssggcslrKILAlkpsrknlllkpksslvCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESlwygeerprwlgpipydypsyltgelpgdygfdvaglskdpmafQKYFNFEILHARWAMLGALGALVPEVLDMVGAFhlvepvwwrvgysklqgetldylgipglhlagsQGVIVIAICQALLMD
MALIQFQahatedwlswSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNeslwygeerprwlGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
MALIQFQAHATEDwlswsccssssggcslRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
***IQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQN************************NESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALL**
*ALI***AHATEDWLSWSCCSSSSGGCSL********************************VLVFSAIPF****************************************************RWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
MALIQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
*ALIQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIAN************************************LWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooo
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MALIQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD
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 ?
Query239 2.2.26 [Sep-21-2011]
P22686256 Chlorophyll a-b binding p N/A no 0.640 0.597 0.445 6e-31
P14278265 Chlorophyll a-b binding p N/A no 0.514 0.464 0.492 1e-28
P12332205 Chlorophyll a-b binding p N/A no 0.514 0.6 0.507 2e-28
P07370265 Chlorophyll a-b binding p N/A no 0.552 0.498 0.488 6e-28
P20866269 Chlorophyll a-b binding p N/A no 0.552 0.490 0.459 6e-28
P12328264 Chlorophyll a-b binding p N/A no 0.631 0.571 0.428 8e-28
P04784266 Chlorophyll a-b binding p N/A no 0.652 0.586 0.431 1e-27
P27518265 Chlorophyll a-b binding p N/A no 0.510 0.460 0.496 1e-27
P12062265 Chlorophyll a-b binding p N/A no 0.514 0.464 0.484 2e-27
P07369267 Chlorophyll a-b binding p N/A no 0.652 0.584 0.434 2e-27
>sp|P22686|CB2_CHLMO Chlorophyll a-b binding protein of LHCII type I, chloroplastic OS=Chlamydomonas moewusii PE=2 SV=1 Back     alignment and function desciption
 Score =  134 bits (337), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 70/157 (44%), Positives = 93/157 (59%), Gaps = 4/157 (2%)

Query: 84  LLQNRMLETK-KAALQDSSKFKALARQARNESL-WYGEERPRWLGPIPYDYPSYLTGELP 141
           L+ NR L  K +AA + +   +  A  A++  + WYG +R +WLGP   + P+YLTGE P
Sbjct: 5   LISNRALTVKVEAAKKAAGTKQTKAAPAKSAGIEWYGPDRAKWLGPFSTNTPAYLTGEFP 64

Query: 142 GDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRV 201
           GDYG+D AGLS DP  F+KY   E++HARWA+LGALG L PE+L         EPVW++ 
Sbjct: 65  GDYGWDTAGLSADPETFKKYRELEVIHARWALLGALGILTPELLSTYAGVKFGEPVWFKA 124

Query: 202 GYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLM 238
           G        LDYLG P L  A  Q ++     Q +LM
Sbjct: 125 GAQIFSEGGLDYLGSPALIHA--QNIVATLAVQVVLM 159
The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated.
Chlamydomonas moewusii (taxid: 3054)
>sp|P14278|CB24_SOLLC Chlorophyll a-b binding protein 4, chloroplastic OS=Solanum lycopersicum GN=CAB4 PE=2 SV=1 Back     alignment and function description
>sp|P12332|CB21_SILPR Chlorophyll a-b binding protein, chloroplastic (Fragment) OS=Silene pratensis PE=2 SV=2 Back     alignment and function description
>sp|P07370|CB2B_SOLLC Chlorophyll a-b binding protein 1B, chloroplastic OS=Solanum lycopersicum GN=CAB1B PE=3 SV=1 Back     alignment and function description
>sp|P20866|CB2_PHYPA Chlorophyll a-b binding protein, chloroplastic OS=Physcomitrella patens subsp. patens PE=3 SV=1 Back     alignment and function description
>sp|P12328|CB21_LEMGI Chlorophyll a-b binding protein of LHCII type I, chloroplastic OS=Lemna gibba PE=3 SV=1 Back     alignment and function description
>sp|P04784|CB21_WHEAT Chlorophyll a-b binding protein, chloroplastic OS=Triticum aestivum GN=WHAB1.6 PE=3 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|P12062|CB26_PETSP Chlorophyll a-b binding protein 37, chloroplastic OS=Petunia sp. GN=CAB37 PE=3 SV=1 Back     alignment and function description
>sp|P07369|CB2G_SOLLC Chlorophyll a-b binding protein 3C, chloroplastic OS=Solanum lycopersicum GN=CAB3C PE=3 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query239
255539358329 chlorophyll A/B binding protein, putativ 0.949 0.689 0.736 2e-89
297839529330 chlorophyll A-B binding family protein [ 0.870 0.630 0.746 2e-88
224083380338 light-harvesting complex II protein Lhcb 0.786 0.556 0.808 3e-88
449525738338 PREDICTED: chlorophyll a-b binding prote 0.853 0.603 0.740 6e-88
449455655338 PREDICTED: chlorophyll a-b binding prote 0.853 0.603 0.740 6e-88
15223108327 putative chlorophyll a/b-binding protein 0.861 0.629 0.735 1e-86
358248178331 uncharacterized protein LOC100786260 [Gl 0.811 0.586 0.773 6e-85
225457685331 PREDICTED: chlorophyll a-b binding prote 0.782 0.564 0.866 4e-84
414884910315 TPA: hypothetical protein ZEAMMB73_23528 0.857 0.650 0.668 2e-74
168049357 348 predicted protein [Physcomitrella patens 0.933 0.640 0.580 3e-74
>gi|255539358|ref|XP_002510744.1| chlorophyll A/B binding protein, putative [Ricinus communis] gi|223551445|gb|EEF52931.1| chlorophyll A/B binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  333 bits (855), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 173/235 (73%), Positives = 195/235 (82%), Gaps = 8/235 (3%)

Query: 4   IQFQAHATEDWLSWSCCSSSSGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVL 63
           +  Q H +  W+S S  S  S      K+LALKP  + +L     S  CKASWQELAGVL
Sbjct: 3   VLLQPHPSFSWISSSLFSQGS------KLLALKP--RKILFNGNPSSPCKASWQELAGVL 54

Query: 64  VFSAIPFTAVKAIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPR 123
           VFSAIPFTAVKA+ANSPLGE LQ R+ E+KK A+++SSKF+AL  +AR ESLWYGEERPR
Sbjct: 55  VFSAIPFTAVKALANSPLGESLQRRLEESKKVAVKESSKFQALTAKARKESLWYGEERPR 114

Query: 124 WLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPE 183
           WLGPIPYDYP+YLTGELPGDYGFDVAGLSKD +AFQ+YFNFEILHARWAML ALGAL PE
Sbjct: 115 WLGPIPYDYPAYLTGELPGDYGFDVAGLSKDSVAFQRYFNFEILHARWAMLAALGALAPE 174

Query: 184 VLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLM 238
           VLD+ GAFH +EPVWWRVGYSKL+G+TLDYLGIPGLH AGSQGV+VIAICQALLM
Sbjct: 175 VLDLSGAFHFIEPVWWRVGYSKLKGDTLDYLGIPGLHFAGSQGVLVIAICQALLM 229

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297839529|ref|XP_002887646.1| chlorophyll A-B binding family protein [Arabidopsis lyrata subsp. lyrata] gi|297333487|gb|EFH63905.1| chlorophyll A-B binding family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|224083380|ref|XP_002307004.1| light-harvesting complex II protein Lhcb7 [Populus trichocarpa] gi|222856453|gb|EEE94000.1| light-harvesting complex II protein Lhcb7 [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449525738|ref|XP_004169873.1| PREDICTED: chlorophyll a-b binding protein of LHCII type I, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449455655|ref|XP_004145567.1| PREDICTED: chlorophyll a-b binding protein of LHCII type I, chloroplastic-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|15223108|ref|NP_177783.1| putative chlorophyll a/b-binding protein [Arabidopsis thaliana] gi|12323973|gb|AAG51944.1|AC015450_5 putative chlorophyll A-B binding protein; 65434-67056 [Arabidopsis thaliana] gi|332197739|gb|AEE35860.1| putative chlorophyll a/b-binding protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|358248178|ref|NP_001240088.1| uncharacterized protein LOC100786260 [Glycine max] gi|255636882|gb|ACU18774.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|225457685|ref|XP_002276647.1| PREDICTED: chlorophyll a-b binding protein of LHCII type I, chloroplastic [Vitis vinifera] gi|297745621|emb|CBI40786.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|414884910|tpg|DAA60924.1| TPA: hypothetical protein ZEAMMB73_235289 [Zea mays] Back     alignment and taxonomy information
>gi|168049357|ref|XP_001777130.1| predicted protein [Physcomitrella patens subsp. patens] gi|162671573|gb|EDQ58123.1| predicted protein [Physcomitrella patens subsp. patens] 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 ?
Query239
TAIR|locus:2011691327 AT1G76570 [Arabidopsis thalian 0.861 0.629 0.735 6.4e-83
TAIR|locus:2089139266 LHCB2.3 "photosystem II light 0.514 0.462 0.492 1.2e-28
TAIR|locus:2044988265 LHCB2.2 "photosystem II light 0.514 0.464 0.484 1.3e-27
TAIR|locus:2042148265 LHCB2.1 "photosystem II light 0.514 0.464 0.484 1.3e-27
TAIR|locus:2162540265 LHCB3 "light-harvesting chloro 0.510 0.460 0.483 3.5e-27
UNIPROTKB|P12331261 CAB2R "Chlorophyll a-b binding 0.560 0.513 0.467 5.2e-26
TAIR|locus:2019287267 CAB3 "chlorophyll A/B binding 0.552 0.494 0.448 6.6e-26
TAIR|locus:2019372267 CAB2 "chlorophyll A/B-binding 0.552 0.494 0.448 6.6e-26
TAIR|locus:2019322267 CAB1 "chlorophyll A/B binding 0.552 0.494 0.448 6.6e-26
TAIR|locus:2040934265 LHB1B2 "photosystem II light h 0.552 0.498 0.448 8.4e-26
TAIR|locus:2011691 AT1G76570 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 831 (297.6 bits), Expect = 6.4e-83, P = 6.4e-83
 Identities = 153/208 (73%), Positives = 176/208 (84%)

Query:    31 KILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRML 90
             +IL  KP  +N +   KS  +C+ASWQELAGVLVFSAIPFTAVKAIANS +G  L+ R+ 
Sbjct:    23 RILVSKP--RNRIAVTKSRSICRASWQELAGVLVFSAIPFTAVKAIANSSIGVSLRRRLE 80

Query:    91 ETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAG 150
             E KK A+++SS+FK+ A++ARN+S WYG+ERPRW GPIPYDYP YLTGELPGDYGFD+AG
Sbjct:    81 EKKKEAVENSSRFKSKAQEARNDSKWYGKERPRWFGPIPYDYPPYLTGELPGDYGFDIAG 140

Query:   151 LSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGET 210
             L KD + F KYFNFEILHARWAML ALGAL+PEV D+ G FH  EPVWWRVGYSKLQGET
Sbjct:   141 LGKDRLTFDKYFNFEILHARWAMLAALGALIPEVFDLTGTFHFAEPVWWRVGYSKLQGET 200

Query:   211 LDYLGIPGLHLAGSQGVIVIAICQALLM 238
             L+YLGIPGLH+AGSQGVIVIAICQ LLM
Sbjct:   201 LEYLGIPGLHVAGSQGVIVIAICQVLLM 228
GO:0009507 "chloroplast" evidence=ISM
GO:0009765 "photosynthesis, light harvesting" evidence=IEA
GO:0015979 "photosynthesis" evidence=ISS
GO:0016020 "membrane" evidence=IEA
GO:0016168 "chlorophyll binding" evidence=ISS
GO:0030076 "light-harvesting complex" evidence=ISS
GO:0009637 "response to blue light" evidence=IEP
GO:0010218 "response to far red light" evidence=IEP
GO:0010264 "myo-inositol hexakisphosphate biosynthetic process" evidence=RCA
GO:0015996 "chlorophyll catabolic process" evidence=RCA
TAIR|locus:2089139 LHCB2.3 "photosystem II light harvesting complex gene 2.3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2044988 LHCB2.2 "photosystem II light harvesting complex gene 2.2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2042148 LHCB2.1 "photosystem II light harvesting complex gene 2.1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2162540 LHCB3 "light-harvesting chlorophyll B-binding protein 3" [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
TAIR|locus:2019287 CAB3 "chlorophyll A/B binding protein 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019372 CAB2 "chlorophyll A/B-binding protein 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019322 CAB1 "chlorophyll A/B binding protein 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2040934 LHB1B2 "photosystem II light harvesting complex gene B1B2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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 ?
Query239
PLN00171324 PLN00171, PLN00171, photosystem light-harvesting c 1e-140
PLN00025262 PLN00025, PLN00025, photosystem II light harvestin 8e-44
PLN00101250 PLN00101, PLN00101, Photosystem I light-harvesting 4e-17
PLN00147252 PLN00147, PLN00147, light-harvesting complex I chl 9e-17
PLN00097244 PLN00097, PLN00097, photosystem I light harvesting 8e-14
PLN00098267 PLN00098, PLN00098, light-harvesting complex I chl 1e-13
PLN00048262 PLN00048, PLN00048, photosystem I light harvesting 5e-13
PLN00099243 PLN00099, PLN00099, light-harvesting complex IChlo 9e-11
PLN00170255 PLN00170, PLN00170, photosystem II light-harvestin 4e-10
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 6e-10
PLN00187286 PLN00187, PLN00187, photosystem II light-harvestin 6e-08
PLN00100 246 PLN00100, PLN00100, light-harvesting complex chlor 2e-07
pfam00504135 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding 1e-06
>gnl|CDD|215088 PLN00171, PLN00171, photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information 
 Score =  396 bits (1020), Expect = e-140
 Identities = 173/224 (77%), Positives = 192/224 (85%), Gaps = 3/224 (1%)

Query: 16  SWSCCSSS-SGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVK 74
           S S  SSS SG  SL +ILA KP R+    +P SS  C+ASWQELAGVLVFSAIPFTAVK
Sbjct: 4   SVSSSSSSFSGQHSLPRILASKPRRRRATRRPASS--CRASWQELAGVLVFSAIPFTAVK 61

Query: 75  AIANSPLGELLQNRMLETKKAALQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPS 134
           AIANS LGE LQ R+ ETKKAA+++SS FKA A++ARNES WYGEERPRWLGPIPYDYP 
Sbjct: 62  AIANSSLGESLQRRLEETKKAAVEESSAFKAAAQKARNESFWYGEERPRWLGPIPYDYPD 121

Query: 135 YLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHLV 194
           +LTGELPGDYGFD+AGL KDP+AF KYFNFEILHARWAML ALG ++PEVLD+ GA H  
Sbjct: 122 HLTGELPGDYGFDIAGLGKDPVAFDKYFNFEILHARWAMLAALGVVIPEVLDLFGAVHFA 181

Query: 195 EPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLM 238
           EPVWWRVGY+KLQG+TLDYLGIPGLH+AGSQGVIVIAICQALLM
Sbjct: 182 EPVWWRVGYAKLQGDTLDYLGIPGLHIAGSQGVIVIAICQALLM 225

Length = 324
>gnl|CDD|215033 PLN00025, PLN00025, photosystem II light harvesting chlorophyll a/b binding protein; 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|215076 PLN00147, PLN00147, light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional Back     alignment and domain information
>gnl|CDD|165670 PLN00097, PLN00097, photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional Back     alignment and domain information
>gnl|CDD|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|177717 PLN00099, PLN00099, light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional Back     alignment and domain information
>gnl|CDD|215087 PLN00170, PLN00170, photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional Back     alignment and domain information
>gnl|CDD|215956 pfam00504, Chloroa_b-bind, Chlorophyll A-B binding protein Back     alignment and domain information
>gnl|CDD|177781 PLN00187, PLN00187, photosystem II light-harvesting complex II protein Lhcb4; 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|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 239
PLN00171324 photosystem light-harvesting complex -chlorophyll 100.0
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 100.0
PLN00187286 photosystem II light-harvesting complex II protein 100.0
PLN00048 262 photosystem I light harvesting chlorophyll a/b bin 99.96
PLN00098 267 light-harvesting complex I chlorophyll a/b-binding 99.96
PLN00097 244 photosystem I light harvesting complex Lhca2/4, ch 99.96
PLN00101250 Photosystem I light-harvesting complex type 4 prot 99.95
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 99.94
PLN00099243 light-harvesting complex IChlorophyll A-B binding 99.94
PLN00170 255 photosystem II light-harvesting-Chl-binding protei 99.93
PLN00100 246 light-harvesting complex chlorophyll-a/b protein o 99.92
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.82
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.7
PLN00147252 light-harvesting complex I chlorophyll-a/b binding 99.58
PLN00089209 fucoxanthin-chlorophyll a/c binding protein; Provi 99.57
PLN00048262 photosystem I light harvesting chlorophyll a/b bin 99.53
PLN00025262 photosystem II light harvesting chlorophyll a/b bi 99.48
PLN00187286 photosystem II light-harvesting complex II protein 99.47
PLN00099243 light-harvesting complex IChlorophyll A-B binding 99.44
PF00504156 Chloroa_b-bind: Chlorophyll A-B binding protein; I 99.44
PLN00098267 light-harvesting complex I chlorophyll a/b-binding 99.42
PLN00171324 photosystem light-harvesting complex -chlorophyll 99.39
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.38
PLN00097244 photosystem I light harvesting complex Lhca2/4, ch 99.32
PLN00120202 fucoxanthin-chlorophyll a-c binding protein; Provi 99.31
PLN00100246 light-harvesting complex chlorophyll-a/b protein o 99.27
PLN00101250 Photosystem I light-harvesting complex type 4 prot 99.17
PLN00170255 photosystem II light-harvesting-Chl-binding protei 99.16
PHA0233735 putative high light inducible protein 97.61
PLN00014250 light-harvesting-like protein 3; Provisional 97.46
PLN00084214 photosystem II subunit S (PsbS); Provisional 95.09
>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.3e-65  Score=472.36  Aligned_cols=220  Identities=77%  Similarity=1.275  Sum_probs=205.6

Q ss_pred             ccccCC-CCCcchhHHHhcCccccccccCCCCcchhhhhHhhhhhhheecccchhHHHHhhcCchhHHHHHhHHHhhHHh
Q 026395           18 SCCSSS-SGGCSLRKILALKPSRKNLLLKPKSSLVCKASWQELAGVLVFSAIPFTAVKAIANSPLGELLQNRMLETKKAA   96 (239)
Q Consensus        18 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sa~p~ta~~a~a~s~fg~~l~~r~~~~k~~a   96 (239)
                      ||-+|+ ++.-+++++++.++|++..  +++.+++|||||||+|||+||||+|||+++|||||+||++||+||+++|+++
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (324)
T PLN00171          6 SSSSSSFSGQHSLPRILASKPRRRRA--TRRPASSCRASWQELAGVLVFSAIPFTAVKAIANSSLGESLQRRLEETKKAA   83 (324)
T ss_pred             cccccccccccccchhhccccccccc--cCCCCccchhhHHhhhheeeeecccHHHHHHHhcCcHHHHHHHHHHHhhHHH
Confidence            343333 3445789999999999988  7778899999999999999999999999999999999999999999999999


Q ss_pred             hhhchHHHHHHHhhcccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcCccCCCCCCChHHHHHHHHHHHhhhhhHHHhh
Q 026395           97 LQDSSKFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGA  176 (239)
Q Consensus        97 ~~~a~~~~~~~~~a~~~s~wyg~~R~~wlg~~~~~~P~yL~G~~PGD~GFDPLGLs~dpe~~~r~reaELkHGRwAMLA~  176 (239)
                      +++++++++.++.+++.+.|||++|++|||++++++|+||||++||||||||+||++||+++++||++|||||||||||+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~g~~R~~wl~~~~~~~P~yLdG~lpGD~GFDPLGL~~dp~~l~~~reaELkHGR~AMLA~  163 (324)
T PLN00171         84 VEESSAFKAAAQKARNESFWYGEERPRWLGPIPYDYPDHLTGELPGDYGFDIAGLGKDPVAFDKYFNFEILHARWAMLAA  163 (324)
T ss_pred             HHhHHHHHHHHHhhcccCcccCCCCccccCCCCCCCCcccCCCCCcccCCCccccccCHHHHHHHHHHHhccchHHHHHH
Confidence            99999999999999999999999999999998889999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhhcccCcccCCCcccccccccccCCCcccccCCCcccccCcchhHHHhhhhhhccC
Q 026395          177 LGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD  239 (239)
Q Consensus       177 lG~vv~Ell~~~G~i~~~~~vWf~aGa~~~~~~~l~YlG~P~l~~ag~q~i~aI~~~qvlLMg  239 (239)
                      +|+++||++++.|++.+.+++||++|...++++.++|+++|++++++.|.+.+|.++|+++|+
T Consensus       164 ~G~lv~e~l~~~g~~~~~~p~W~~aG~~~~~g~~~~y~~~p~~~~~~~q~l~~i~~iEillm~  226 (324)
T PLN00171        164 LGVVIPEVLDLFGAVHFAEPVWWRVGYAKLQGDTLDYLGIPGLHIAGSQGVIVIAICQALLMV  226 (324)
T ss_pred             hhHHHHHHhccCCccccCccchhhcccccccccchhhccCCccccchhHHHHHHHHHHHHHhh
Confidence            999999999988887778899999999888888899999998877788999999999999985

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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query239
1rwt_A232 Crystal Structure Of Spinach Major Light-harvesting 1e-27
2bhw_A232 Pea Light-Harvesting Complex Ii At 2.5 Angstrom Res 6e-27
1vcr_A232 An Icosahedral Assembly Of Light-Harvesting Chlorop 9e-27
2wsc_2269 Improved Model Of Plant Photosystem I Length = 269 2e-12
2wsc_4251 Improved Model Of Plant Photosystem I Length = 251 3e-12
2o01_2186 The Structure Of A Plant Photosystem I Supercomplex 7e-12
2wsc_1241 Improved Model Of Plant Photosystem I Length = 241 4e-10
2o01_1187 The Structure Of A Plant Photosystem I Supercomplex 5e-10
2wsc_3276 Improved Model Of Plant Photosystem I Length = 276 6e-10
3lw5_1170 Improved Model Of Plant Photosystem I Length = 170 1e-07
3lw5_4166 Improved Model Of Plant Photosystem I Length = 166 5e-04
3lw5_2176 Improved Model Of Plant Photosystem I Length = 176 7e-04
>pdb|1RWT|A Chain A, Crystal Structure Of Spinach Major Light-harvesting Complex At 2.72 Angstrom Resolution Length = 232 Back     alignment and structure 
Iteration: 1

 Score =  119 bits (298), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 62/131 (47%), Positives = 79/131 (60%), Gaps = 3/131 (2%)
Query: 108 RQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEIL 167
           +  ++ S WYG +R ++LGP   + PSYLTGE PGDYG+D AGLS DP  F K    E++
Sbjct: 8   KTVQSSSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVI 67
Query: 168 HARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGV 227
           H RWAMLGALG + PE+L   G     E VW++ G        LDYLG P L  A  Q +
Sbjct: 68  HCRWAMLGALGCVFPELLARNGV-KFGEAVWFKAGSQIFSEGGLDYLGNPSLVHA--QSI 124
Query: 228 IVIAICQALLM 238
           + I  CQ +LM
Sbjct: 125 LAIWACQVILM 135
>pdb|2BHW|A Chain A, Pea Light-Harvesting Complex Ii At 2.5 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|2WSC|2 Chain 2, Improved Model Of Plant Photosystem I Length = 269 Back     alignment and structure
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I Length = 251 Back     alignment and structure
>pdb|2O01|2 Chain 2, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 186 Back     alignment and structure
>pdb|2WSC|1 Chain 1, Improved Model Of Plant Photosystem I Length = 241 Back     alignment and structure
>pdb|2O01|1 Chain 1, The Structure Of A Plant Photosystem I Supercomplex At 3.4 Angstrom Resolution Length = 187 Back     alignment and structure
>pdb|2WSC|3 Chain 3, Improved Model Of Plant Photosystem I Length = 276 Back     alignment and structure
>pdb|3LW5|1 Chain 1, Improved Model Of Plant Photosystem I Length = 170 Back     alignment and structure
>pdb|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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query239
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 3e-31
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 2e-04
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 2e-25
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 3e-22
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 1e-21
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 1e-06
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 1e-15
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 2e-04
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 2e-15
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 2e-04
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Length = 232 Back     alignment and structure
 Score =  113 bits (284), Expect = 3e-31
 Identities = 62/138 (44%), Positives = 81/138 (58%), Gaps = 3/138 (2%)

Query: 102 KFKALARQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKY 161
           K     + A + S WYG +R ++LGP   + PSYLTGE PGDYG+D AGLS DP  F K 
Sbjct: 2   KSATTKKVASSGSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFSKN 61

Query: 162 FNFEILHARWAMLGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHL 221
              E++H+RWAMLGALG++ PE+L   G     E VW++ G        LDYLG P   L
Sbjct: 62  RELEVIHSRWAMLGALGSVFPELLSRNGVKFG-EAVWFKAGSQIFSEGGLDYLGNPS--L 118

Query: 222 AGSQGVIVIAICQALLMD 239
             +Q ++ I   Q +LM 
Sbjct: 119 VHAQSILAIWATQVILMG 136
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Length = 232 Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Length = 269 Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Length = 251 Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Length = 276 Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Length = 276 Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Length = 243 Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Length = 243 Back     alignment and structure
>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 ?
Query239
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 100.0
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.97
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 99.95
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 99.95
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 99.95
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.92
3pl9_A243 Chlorophyll A-B binding protein; CP29, light-harve 99.45
2wsc_3276 LHCA3, type II chlorophyll A/B binding protein fro 99.44
2wsc_2269 LHCA2, type II chlorophyll A/B binding protein fro 99.42
2bhw_A232 Chlorophyll A-B binding protein AB80; LHC-II, phot 99.41
2wsc_1241 AT3G54890, LHCA1; photosynthesis, electron transfe 99.27
2wsc_4251 Chlorophyll A-B binding protein P4, chloroplastic; 99.11
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Back     alignment and structure
Probab=100.00  E-value=2.7e-40  Score=291.10  Aligned_cols=129  Identities=47%  Similarity=0.896  Sum_probs=117.4

Q ss_pred             HhhcccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCcCccCCCCCCChHHHHHHHHHHHhhhhhHHHhhhhhhhhhhhcc
Q 026395          108 RQARNESLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDM  187 (239)
Q Consensus       108 ~~a~~~s~wyg~~R~~wlg~~~~~~P~yL~G~~PGD~GFDPLGLs~dpe~~~r~reaELkHGRwAMLA~lG~vv~Ell~~  187 (239)
                      +++.+++.||+++|++|||+++.+.|+||||++||||||||+||++|+|+++|||++|||||||||||++|+++||++++
T Consensus         8 ~~~~~~~~~~~~~r~~~l~~~~~~~P~~LdG~~pGD~GFDPLGLs~d~e~~~r~ReaELkHGR~AMLA~~G~lv~E~l~~   87 (232)
T 2bhw_A            8 KVASSGSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFSKNRELEVIHSRWAMLGALGSVFPELLSR   87 (232)
T ss_dssp             --CCTTCTTSSTTCCCTTGGGCCSCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCcccCCcccCCCcccccCccccCCccccCCcCCCCCCCCCCcCCCCHHHHHHHHHHHHhccchHHHhhhhhhhHHHhcc
Confidence            34456789999999999998877899999999999999999999999999999999999999999999999999999988


Q ss_pred             cCcccCCCcccccccccccCCCcccccCCCcccccCcchhHHHhhhhhhccC
Q 026395          188 VGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD  239 (239)
Q Consensus       188 ~G~i~~~~~vWf~aGa~~~~~~~l~YlG~P~l~~ag~q~i~aI~~~qvlLMg  239 (239)
                      .|+ .+++++||++|.+.++..+++|+++|.+.+  .|.|.+|+++|+++||
T Consensus        88 ~G~-~~~~~~w~~ag~~~~~~~~~~~~~~P~~~~--~q~i~~~~~~q~~~~g  136 (232)
T 2bhw_A           88 NGV-KFGEAVWFKAGSQIFSEGGLDYLGNPSLVH--AQSILAIWATQVILMG  136 (232)
T ss_dssp             TTC-CCSCCSGGGSGGGGGSTTCEEGGGCTTSEE--ECCHHHHHHHHHHHHH
T ss_pred             CCc-CCcccccccccchhccccchhcccCcchhh--HHHHHHHHHHHHHHHH
Confidence            774 577889999999888877899999998875  7999999999999986
>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_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Back     alignment and structure
>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea} Back     alignment and structure
>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Back     alignment and structure
>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2* Back     alignment and structure
>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A* Back     alignment and structure
>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Back     alignment and structure
>2wsc_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 239
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 4e-38
d1rwta_218 f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi 4e-04
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 218 Back     information, alignment and structure

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

 Score =  130 bits (328), Expect = 4e-38
 Identities = 61/126 (48%), Positives = 76/126 (60%), Gaps = 3/126 (2%)

Query: 114 SLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAM 173
           S WYG +R ++LGP   + PSYLTGE PGDYG+D AGLS DP  F K    E++H RWAM
Sbjct: 1   SPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAM 60

Query: 174 LGALGALVPEVLDMVGAFHLVEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAIC 233
           LGALG + PE+L   G     E VW++ G        LDYLG P   L  +Q ++ I  C
Sbjct: 61  LGALGCVFPELLARNG-VKFGEAVWFKAGSQIFSEGGLDYLGNPS--LVHAQSILAIWAC 117

Query: 234 QALLMD 239
           Q +LM 
Sbjct: 118 QVILMG 123
>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 ?
Query239
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 100.0
d1rwta_218 Chlorophyll a-b binding protein {Spinach (Spinacia 99.47
>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=7.8e-37  Score=262.21  Aligned_cols=123  Identities=50%  Similarity=0.956  Sum_probs=111.2

Q ss_pred             CcccCCCCCCCCCCCCCCCCCCCCCCCCCCcCccCCCCCCChHHHHHHHHHHHhhhhhHHHhhhhhhhhhhhcccCcccC
Q 026395          114 SLWYGEERPRWLGPIPYDYPSYLTGELPGDYGFDVAGLSKDPMAFQKYFNFEILHARWAMLGALGALVPEVLDMVGAFHL  193 (239)
Q Consensus       114 s~wyg~~R~~wlg~~~~~~P~yL~G~~PGD~GFDPLGLs~dpe~~~r~reaELkHGRwAMLA~lG~vv~Ell~~~G~i~~  193 (239)
                      ++||||||++||||++.++|+||||++|||||||||||++|+++++||||+|||||||||||++|++++|++++.+. .+
T Consensus         1 ~~~~~~~r~~~~~~~~~~~P~~LdGs~pGD~GFDPLgls~d~~~~~~~ReaELKHGR~AMLA~vG~~~~E~~~~~~~-~~   79 (218)
T d1rwta_           1 SPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGV-KF   79 (218)
T ss_dssp             CTTSSTTCCCTTGGGGCSCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC-CC
T ss_pred             CCCCCCCCcccCCccccCCCcccCCCCCCCCCcCCcccCCCHHHHHHHHHHHHhhceehHhhhcceeehhhhccCCC-CC
Confidence            58999999999999988999999999999999999999999999999999999999999999999999999987654 35


Q ss_pred             CCcccccccccccCCCcccccCCCcccccCcchhHHHhhhhhhccC
Q 026395          194 VEPVWWRVGYSKLQGETLDYLGIPGLHLAGSQGVIVIAICQALLMD  239 (239)
Q Consensus       194 ~~~vWf~aGa~~~~~~~l~YlG~P~l~~ag~q~i~aI~~~qvlLMg  239 (239)
                      ..+.|++++......+.++|++.|.+..  .|.++.++++++++++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~  123 (218)
T d1rwta_          80 GEAVWFKAGSQIFSEGGLDYLGNPSLVH--AQSILAIWACQVILMG  123 (218)
T ss_dssp             SCCSHHHHGGGGGSTTCBCGGGCTTSCC--BCCHHHHHHHHHHHHH
T ss_pred             CCcccccccccccCcchhhhhcCchHHH--HHHHHHHHHHHHHHHh
Confidence            6788999988877778899999987765  7999999999887653
>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Back     information, alignment and structure