Citrus Sinensis ID: 023799

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------

MAQTMLLMSGVSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMFNPLSNESLTAAAASSSSKAFSTVALFKSKTKAPPKTKKPKVEDGIFGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKFVTDEDEE

cccccccccccccccccccccccHHHHccccccccccccccccccccccHHHcccccccccHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccc

cccEEEEEcccccccccccccccHHcccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccEccccccccccHcHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccccEccccccccccccccccccccHHHHccccccccccccccHcHHHHHHHHHHHHHHHHHHHHHccccHHHHHcccccccHcHHHHHHHHHHHHHHHHHHccccccEccccccc

MAQTMLLMSgvstshagnlkrdSLVTFqtqmlrpkpfshlmfnplsneSLTAAAASSSSKAFSTVALFksktkappktkkpkvedgifgtsggfgftkqneLFVGRVAMIGFAASLlgegitgkgILAQLNletgipiyeaePLLLFFILFTLLGAIgalgdrgkfvdepdeptglggavippgkglrsalglkeggpifgftksneLFVGRLAQLGIAFSLIGEIItgkgalaqlnietgipineieplvLFNVIFFFVAalnpgtgkfvtdedee

MAQTMLLMSgvstshagnlkRDSLVTFQTQMLRPKPFSHLMFNPLSNESLTAAAASSSSKAFSTVAlfksktkappktkkpkvedgifgtsggfGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTglggavippgKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGtgkfvtdedee

MAQTMLLMSGVSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMFNPLSNEsltaaaasssskafstvalFksktkappktkkpkVEDgifgtsggfgftKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPlllffilftllGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKFVTDEDEE

*************************************************************************************GIFGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVD*******LGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKF*******

***************************************************************************************FGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVD*************************KEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTG*********

MAQTMLLMSGVSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMFNPLSNES*************STVALFKS************VEDGIFGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKFVTDEDEE

**********VSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMF*******************FSTVALFKS**************DGIFGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGK********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiii

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHoooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiii

SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		277	2.2.26 [Sep-21-2011]
Q02060		274	Photosystem II 22 kDa pro	N/A	no	0.967	0.978	0.748	2e-98
Q9SMB4		274	Photosystem II 22 kDa pro	N/A	no	0.974	0.985	0.722	3e-88
Q9XF91		265	Photosystem II 22 kDa pro	yes	no	0.942	0.984	0.725	3e-87
P54773		276	Photosystem II 22 kDa pro	N/A	no	0.971	0.974	0.728	3e-83
Q9FPP4		276	Photosystem II 22 kDa pro	N/A	no	0.971	0.974	0.718	3e-82

>sp\|Q02060\|PSBS_SPIOL Photosystem II 22 kDa protein, chloroplastic OS=Spinacia oleracea GN=PSBS PE=1 SV=1	Back alignment and function desciption

 Score =  358 bits (919), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 211/282 (74%), Positives = 237/282 (84%), Gaps = 14/282 (4%)

Query: 1   MAQTMLLM-SGVSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMFNPLSNESLTAAAASSSS 59
           MAQ MLLM  GVST++  +LKR++L+  Q Q ++PK       +  SN   +   +SSSS
Sbjct: 1   MAQAMLLMMPGVSTTNTIDLKRNALLKLQIQKIKPK-------SSTSNLFFSPLPSSSSS 53

Query: 60  K--AFSTVALFKSKTKAPPKTKKPK--VEDGIFGTSGGFGFTKQNELFVGRVAMIGFAAS 115
               F T+ALFKSK KAP K +KPK  VEDG+FGTSGG GFTK+NELFVGRVAMIGFAAS
Sbjct: 54  SSTVFKTLALFKSKAKAPKKVEKPKLKVEDGLFGTSGGIGFTKENELFVGRVAMIGFAAS 113

Query: 116 LLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTG 175
           LLGEGITGKGIL+QLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRG+FVDEP   TG
Sbjct: 114 LLGEGITGKGILSQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGRFVDEPT--TG 171

Query: 176 LGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQ 235
           L  AVIPPGK +RSALGLK  GP+FGFTKSNELFVGRLAQLG AFSLIGEIITGKGALAQ
Sbjct: 172 LEKAVIPPGKDVRSALGLKTKGPLFGFTKSNELFVGRLAQLGFAFSLIGEIITGKGALAQ 231

Query: 236 LNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKFVTDEDEE 277
           LNIETG+PINEIEPLVL NV+FFF+AA+NPGTGKF+TD++EE
Sbjct: 232 LNIETGVPINEIEPLVLLNVVFFFIAAINPGTGKFITDDEEE 273

Seems to be involved in non-photochemical quenching, a process maintains the balance between dissipation and utilization of light energy to minimize generation of oxidizing molecules, thereby protecting the plant against photo-oxidative damage.
Spinacia oleracea (taxid: 3562)

>sp\|Q9SMB4\|PSBS_TOBAC Photosystem II 22 kDa protein, chloroplastic OS=Nicotiana tabacum GN=PSBS PE=2 SV=1	Back alignment and function description

>sp\|Q9XF91\|PSBS_ARATH Photosystem II 22 kDa protein, chloroplastic OS=Arabidopsis thaliana GN=PSBS PE=1 SV=1	Back alignment and function description

>sp\|P54773\|PSBS_SOLLC Photosystem II 22 kDa protein, chloroplastic OS=Solanum lycopersicum GN=PSBS PE=3 SV=1	Back alignment and function description

>sp\|Q9FPP4\|PSBS_SOLSG Photosystem II 22 kDa protein, chloroplastic OS=Solanum sogarandinum GN=PSBS 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
Query		277
255545402		275	Photosystem II 22 kDa protein, chloropla	0.967	0.974	0.792	1e-106
224063082		272	hypothetical protein POPTRDRAFT_816277 [	0.967	0.985	0.793	1e-105
357463499		270	Photosystem II 22 kDa protein [Medicago	0.963	0.988	0.764	1e-105
388510160		273	unknown [Lotus japonicus]	0.971	0.985	0.800	1e-104
188509922		277	putative photosystem II protein [Gossypi	0.974	0.974	0.820	1e-103
133902325		278	putative photosystem II protein [Gossypi	0.974	0.971	0.816	1e-100
217072844		262	unknown [Medicago truncatula]	0.924	0.977	0.765	1e-100
449465453		272	PREDICTED: photosystem II 22 kDa protein	0.956	0.974	0.757	2e-99
225459564		270	PREDICTED: photosystem II 22 kDa protein	0.960	0.985	0.761	5e-99
400890		274	RecName: Full=Photosystem II 22 kDa prot	0.967	0.978	0.748	1e-96

>gi\|255545402\|ref\|XP_002513761.1\| Photosystem II 22 kDa protein, chloroplast precursor, putative [Ricinus communis] gi\|223546847\|gb\|EEF48344.1\| Photosystem II 22 kDa protein, chloroplast precursor, putative [Ricinus communis]	Back alignment and taxonomy information

 Score =  389 bits (999), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 225/284 (79%), Positives = 244/284 (85%), Gaps = 16/284 (5%)

Query: 1   MAQTMLLMSGVSTSHAGNLKRDSLVTFQTQMLRPKPFSHLMFNPLSNESLTAAAASSSSK 60
           MAQTML MSGVST H  +LKRD L+ FQ   LRPKPFS L+F+PL     T +++ + SK
Sbjct: 1   MAQTMLFMSGVSTRHVVDLKRDPLLQFQVDRLRPKPFSSLLFSPLP----TNSSSFAPSK 56

Query: 61  AFSTVALFKSK-------TKAPPKTKKPKVEDGIFGTSGGFGFTKQNELFVGRVAMIGFA 113
            F+T ALFKSK       T   PK K   VEDG+FGTSGG GFTKQNELFVGRVAM+GFA
Sbjct: 57  TFTTFALFKSKAKAAPKKTVVKPKQK---VEDGVFGTSGGIGFTKQNELFVGRVAMLGFA 113

Query: 114 ASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEP 173
           ASLLGEG+TGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVD+P  P
Sbjct: 114 ASLLGEGLTGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDDP--P 171

Query: 174 TGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGAL 233
           TG+ GAVIPPGKG R+ALGLKEGGP+FGFTKSNELFVGRLAQLGIAFSLIGEIITGKGAL
Sbjct: 172 TGIEGAVIPPGKGFRAALGLKEGGPLFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGAL 231

Query: 234 AQLNIETGIPINEIEPLVLFNVIFFFVAALNPGTGKFVTDEDEE 277
           AQLNIETGIP+NEIEPLVLFNVIFFF AALNPGTGKFVTDE++E
Sbjct: 232 AQLNIETGIPVNEIEPLVLFNVIFFFFAALNPGTGKFVTDEEDE 275

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224063082\|ref\|XP_002300987.1\| hypothetical protein POPTRDRAFT_816277 [Populus trichocarpa] gi\|118488707\|gb\|ABK96164.1\| unknown [Populus trichocarpa] gi\|222842713\|gb\|EEE80260.1\| hypothetical protein POPTRDRAFT_816277 [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|357463499\|ref\|XP_003602031.1\| Photosystem II 22 kDa protein [Medicago truncatula] gi\|355491079\|gb\|AES72282.1\| Photosystem II 22 kDa protein [Medicago truncatula] gi\|388508062\|gb\|AFK42097.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|388510160\|gb\|AFK43146.1\| unknown [Lotus japonicus]	Back alignment and taxonomy information

>gi\|188509922\|gb\|ACD56611.1\| putative photosystem II protein [Gossypioides kirkii]	Back alignment and taxonomy information

>gi\|133902325\|gb\|ABO41853.1\| putative photosystem II protein [Gossypium hirsutum]	Back alignment and taxonomy information

>gi\|217072844\|gb\|ACJ84782.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449465453\|ref\|XP_004150442.1\| PREDICTED: photosystem II 22 kDa protein, chloroplastic-like [Cucumis sativus] gi\|449529497\|ref\|XP_004171736.1\| PREDICTED: photosystem II 22 kDa protein, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|225459564\|ref\|XP_002285857.1\| PREDICTED: photosystem II 22 kDa protein, chloroplastic [Vitis vinifera] gi\|302141814\|emb\|CBI19017.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|400890\|sp\|Q02060.1\|PSBS_SPIOL RecName: Full=Photosystem II 22 kDa protein, chloroplastic; AltName: Full=CP22; Flags: Precursor gi\|21307\|emb\|CAA48557.1\| 22kD-protein of PSII [Spinacia oleracea] gi\|260917\|gb\|AAB24338.1\| photosystem II 22 kda polypeptide [Spinacia oleracea]	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
Query		277
TAIR\|locus:2823639		265	NPQ4 "NONPHOTOCHEMICAL QUENCHI	0.696	0.728	0.764	5.9e-76

TAIR\|locus:2823639 NPQ4 "NONPHOTOCHEMICAL QUENCHING 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 730 (262.0 bits), Expect = 5.9e-76, Sum P(2) = 5.9e-76
 Identities = 149/195 (76%), Positives = 158/195 (81%)

Query:    83 VEDXXXXXXXXXXXXKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAE 142
             VED            K NELFVGRVAMIGFAASLLGE +TGKGILAQLNLETGIPIYEAE
Sbjct:    72 VEDGIFGTSGGIGFTKANELFVGRVAMIGFAASLLGEALTGKGILAQLNLETGIPIYEAE 131

Query:   143 PXXXXXXXXXXXGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGF 202
             P           GAIGALGDRGKFVD+P  PTGL  AVIPPGK +RSALGLKE GP+FGF
Sbjct:   132 PLLLFFILFTLLGAIGALGDRGKFVDDP--PTGLEKAVIPPGKNVRSALGLKEQGPLFGF 189

Query:   203 TKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAA 262
             TK+NELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPI +IEPLVL NV FFF AA
Sbjct:   190 TKANELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPIQDIEPLVLLNVAFFFFAA 249

Query:   263 LNPGTGKFVTDEDEE 277
             +NPG GKF+TD+ EE
Sbjct:   250 INPGNGKFITDDGEE 264

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009517 "PSII associated light-harvesting complex II" evidence=TAS

GO:0010196 "nonphotochemical quenching" evidence=IMP

GO:0016168 "chlorophyll binding" evidence=TAS

GO:0051738 "xanthophyll binding" evidence=TAS

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0080167 "response to karrikin" evidence=IEP

GO:0010027 "thylakoid membrane organization" evidence=IMP

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0043085 "positive regulation of catalytic activity" evidence=RCA

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9XF91	PSBS_ARATH	No assigned EC number	0.725	0.9422	0.9849	yes	no
Q02060	PSBS_SPIOL	No assigned EC number	0.7482	0.9675	0.9781	N/A	no
P54773	PSBS_SOLLC	No assigned EC number	0.7288	0.9711	0.9746	N/A	no
Q9FPP4	PSBS_SOLSG	No assigned EC number	0.7183	0.9711	0.9746	N/A	no
Q9SMB4	PSBS_TOBAC	No assigned EC number	0.7224	0.9747	0.9854	N/A	no

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
Query		277
PLN00084		214	PLN00084, PLN00084, photosystem II subunit S (PsbS	3e-09
PLN00084		214	PLN00084, PLN00084, photosystem II subunit S (PsbS	1e-08
pfam00504		135	pfam00504, Chloroa_b-bind, Chlorophyll A-B binding	9e-06

>gnl\|CDD\|177707 PLN00084, PLN00084, photosystem II subunit S (PsbS); Provisional	Back alignment and domain information

 Score = 55.5 bits (133), Expect = 3e-09
 Identities = 30/62 (48%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 204 KSNELFVGRLAQLGIAFSLIGEIITGK-GALAQLNIETGIPINEIE---PLVLFNVIFFF 259
           K  ELF GRLA LG AF++ G+ +TG  G L Q N ETG+P+ + E      LF V F  
Sbjct: 136 KPYELFNGRLAMLGFAFAIAGDAVTGGMGPLEQFNGETGVPVIDEELFAAFFLFGVFFNV 195

Query: 260 VA 261
           VA
Sbjct: 196 VA 197

Length = 214

>gnl\|CDD\|177707 PLN00084, PLN00084, photosystem II subunit S (PsbS); 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		277
PLN00099		243	light-harvesting complex IChlorophyll A-B binding	100.0
PLN00101		250	Photosystem I light-harvesting complex type 4 prot	100.0
PLN00147		252	light-harvesting complex I chlorophyll-a/b binding	100.0
PLN00098		267	light-harvesting complex I chlorophyll a/b-binding	99.98
PLN00100		246	light-harvesting complex chlorophyll-a/b protein o	99.98
PLN00097		244	photosystem I light harvesting complex Lhca2/4, ch	99.97
PLN00048		262	photosystem I light harvesting chlorophyll a/b bin	99.97
PLN00025		262	photosystem II light harvesting chlorophyll a/b bi	99.97
PLN00187		286	photosystem II light-harvesting complex II protein	99.97
PLN00171		324	photosystem light-harvesting complex -chlorophyll	99.96
PLN00089		209	fucoxanthin-chlorophyll a/c binding protein; Provi	99.96
PF00504		156	Chloroa_b-bind: Chlorophyll A-B binding protein; I	99.95
PLN00170		255	photosystem II light-harvesting-Chl-binding protei	99.94
PLN00120		202	fucoxanthin-chlorophyll a-c binding protein; Provi	99.89
PLN00084		214	photosystem II subunit S (PsbS); Provisional	99.51
PLN00098		267	light-harvesting complex I chlorophyll a/b-binding	99.39
PLN00101		250	Photosystem I light-harvesting complex type 4 prot	99.36
PLN00097		244	photosystem I light harvesting complex Lhca2/4, ch	99.26
PLN00147		252	light-harvesting complex I chlorophyll-a/b binding	99.26
PLN00170		255	photosystem II light-harvesting-Chl-binding protei	99.24
PLN00187		286	photosystem II light-harvesting complex II protein	99.17
PLN00048		262	photosystem I light harvesting chlorophyll a/b bin	99.16
PLN00025		262	photosystem II light harvesting chlorophyll a/b bi	99.15
PLN00100		246	light-harvesting complex chlorophyll-a/b protein o	99.15
PLN00171		324	photosystem light-harvesting complex -chlorophyll	99.14
PLN00099		243	light-harvesting complex IChlorophyll A-B binding	99.13
PF00504		156	Chloroa_b-bind: Chlorophyll A-B binding protein; I	99.12
PLN00089		209	fucoxanthin-chlorophyll a/c binding protein; Provi	99.02
PHA02337		35	putative high light inducible protein	98.95
PHA02337		35	putative high light inducible protein	98.88
PLN00084		214	photosystem II subunit S (PsbS); Provisional	98.86
PLN00120		202	fucoxanthin-chlorophyll a-c binding protein; Provi	98.67
PLN00014		250	light-harvesting-like protein 3; Provisional	98.28
PLN00014		250	light-harvesting-like protein 3; Provisional	98.24
PLN02449		485	ferrochelatase	82.51

>PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional	Back alignment and domain information

Probab=100.00  E-value=1.5e-33  Score=256.84  Aligned_cols=165  Identities=22%  Similarity=0.251  Sum_probs=117.9

Q ss_pred             ccCCCCCCCCCCCCCCCcCCCCCCC------------CccchhhhhhhHHHHHHHHHHHHhhhhhccchhhhh---cccc
Q 023799           70 SKTKAPPKTKKPKVEDGIFGTSGGF------------GFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQL---NLET  134 (277)
Q Consensus        70 ~ks~a~p~~~~p~~~dg~~~~~~~f------------Gf~r~aEl~nGR~AMLG~~g~lv~E~~tg~g~~~q~---~~~~  134 (277)
                      .+....|+.+.|+++||.+.+|.+|            .|+|++|||||||||||++|++++|.++...+.+..   ....
T Consensus        43 ~~~~w~P~~~~P~~Ldg~~pgd~GfDPlgls~~~~~~~~~r~~ELkHGR~AMLAv~G~i~~E~l~~~~w~~a~~~~~~~~  122 (243)
T PLN00099         43 MSADWMPGQPRPPYLDGSAPGDFGFDPLRLGEVPENLERYKESELIHCRWAMLAVPGILVPEALGLGNWVKAQEWAAIPG  122 (243)
T ss_pred             ccccccCCCCCCccCCCCCCcccCCCccccccCHHHHHHHHHHhccCCcHHHHHHhhHHHHHHhccCCcccccchhccCc
Confidence            3456789999999999999887554            355899999999999999999999987642211100   0011


Q ss_pred             Ccccccc-----hhH-HHHHHHHHHHHHHhhhccCCCccCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccchhhh
Q 023799          135 GIPIYEA-----EPL-LLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNEL  208 (277)
Q Consensus       135 G~p~~~~-----~pl-~l~~i~~~llgai~~~~~~~~~~~~~~~p~g~~~~~~~PGd~~~dPlGL~~~~~~~~~~k~kEL  208 (277)
                      |...+..     ..+ .++++.+.+++++|....    ....  +    ....|||| .|||+|+++++++++.+|.|||
T Consensus       123 g~~~~~g~~~~~~~l~~~~~iqvl~ig~~E~~r~----~~~~--~----~~~~yPGd-~FDPlGl~kd~~~~~~~k~kEL  191 (243)
T PLN00099        123 GQATYLGNPVPWGTLPTILAIEFLAIAFVEHQRS----MEKD--P----EKKKYPGG-AFDPLGYSKDPKKFEEYKVKEI  191 (243)
T ss_pred             chhhhccCccchhhHHHHHHHHHHHHHHHHHHhh----ccCC--C----CCCcCCCC-cCCcccccCCHHHHHHHHHHHH
Confidence            1111100     011 122344556777764311    1100  1    11248999 6899999888778889999999


Q ss_pred             hhhhhHHHHHHHHHHHH-HhcCcChHHHhHHhhCCCcc
Q 023799          209 FVGRLAQLGIAFSLIGE-IITGKGALAQLNIETGIPIN  245 (277)
Q Consensus       209 kNGRLAMlg~~G~ivqE-~vTGkg~l~~l~~~~g~p~~  245 (277)
                      |||||||+|++|+++|+ ++||++|+++|..|++||++
T Consensus       192 kNGRLAMiA~lGf~vQ~~~~~G~gPl~nL~~hladp~~  229 (243)
T PLN00099        192 KNGRLALLAFVGFCVQQSAYPGTGPLENLATHLADPWH  229 (243)
T ss_pred             HhhHHHHHHHHHHHHhhhhcCCCChHHHHHHHhcCCcc
Confidence            99999999999999999 57999999999999999985

>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

>PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional	Back alignment and domain information

>PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); 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

>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

>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

>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional	Back alignment and domain information

>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional	Back alignment and domain information

>PLN00084 photosystem II subunit S (PsbS); Provisional	Back alignment and domain information

>PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional	Back alignment and domain information

>PLN00101 Photosystem I light-harvesting complex type 4 protein; Provisional	Back alignment and domain information

>PLN00097 photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional	Back alignment and domain information

>PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional	Back alignment and domain information

>PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); 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

>PLN00025 photosystem II light harvesting chlorophyll a/b 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

>PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; 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

>PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional	Back alignment and domain information

>PHA02337 putative high light inducible protein	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

>PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional	Back alignment and domain information

>PLN00014 light-harvesting-like protein 3; Provisional	Back alignment and domain information

>PLN00014 light-harvesting-like protein 3; Provisional	Back alignment and domain information

>PLN02449 ferrochelatase	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		277
2bhw_A		232	Chlorophyll A-B binding protein AB80; LHC-II, phot	6e-11
2wsc_2		269	LHCA2, type II chlorophyll A/B binding protein fro	1e-10
3pl9_A		243	Chlorophyll A-B binding protein; CP29, light-harve	6e-10
2wsc_4		251	Chlorophyll A-B binding protein P4, chloroplastic;	4e-09
2wsc_1		241	AT3G54890, LHCA1; photosynthesis, electron transfe	3e-08
2wsc_3		276	LHCA3, type II chlorophyll A/B binding protein fro	3e-08

>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 = 60.0 bits (144), Expect = 6e-11
 Identities = 43/242 (17%), Positives = 70/242 (28%), Gaps = 39/242 (16%)

Query: 51  TAAAASSSSKAFSTVALFKSKTKAPPKTKKPKVEDGIFGTSGGF---GFTK--------- 98
           +A     +S         + K   P   + P    G F    G+   G +          
Sbjct: 3   SATTKKVASSGSPWYGPDRVKYLGPFSGESPSYLTGEFPGDYGWDTAGLSADPETFSKNR 62

Query: 99  QNELFVGRVAMIGFAASLLGEGITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIG 158
           + E+   R AM+G   S+  E ++  G+            ++A   +        LG   
Sbjct: 63  ELEVIHSRWAMLGALGSVFPELLSRNGVK-----FGEAVWFKAGSQIFSEGGLDYLGNPS 117

Query: 159 ALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFT--------------K 204
            +  +        +   +G        G      +    P   F               K
Sbjct: 118 LVHAQSILAIWATQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELK 177

Query: 205 SNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPINEIEPLVLFNVIFFFVAALN 264
             EL  GRLA   +    +  I+TGKG L  L      P+N        N  + +     
Sbjct: 178 VKELKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVN--------NNAWSYATNFV 229

Query: 265 PG 266
           PG
Sbjct: 230 PG 231

PyMOL of 2bhw

>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

>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_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_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1* Length = 241	Back alignment and structure

>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3* Length = 276	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		277
3pl9_A		243	Chlorophyll A-B binding protein; CP29, light-harve	99.97
2bhw_A		232	Chlorophyll A-B binding protein AB80; LHC-II, phot	99.97
2wsc_1		241	AT3G54890, LHCA1; photosynthesis, electron transfe	99.96
2wsc_3		276	LHCA3, type II chlorophyll A/B binding protein fro	99.96
2wsc_2		269	LHCA2, type II chlorophyll A/B binding protein fro	99.96
2wsc_4		251	Chlorophyll A-B binding protein P4, chloroplastic;	99.96
2wsc_4		251	Chlorophyll A-B binding protein P4, chloroplastic;	99.2
2wsc_2		269	LHCA2, type II chlorophyll A/B binding protein fro	99.2
2bhw_A		232	Chlorophyll A-B binding protein AB80; LHC-II, phot	99.14
3pl9_A		243	Chlorophyll A-B binding protein; CP29, light-harve	99.07
2wsc_1		241	AT3G54890, LHCA1; photosynthesis, electron transfe	98.94
2wsc_3		276	LHCA3, type II chlorophyll A/B binding protein fro	98.94

>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

Probab=99.97  E-value=2.7e-31  Score=240.50  Aligned_cols=139  Identities=24%  Similarity=0.266  Sum_probs=101.8

Q ss_pred             CCccchhhhhhhHHHHHHHHHHHHhhhhhccchhhhhcc--------ccCcccccchhHHHHHHHHHHHHHHhhhccCCC
Q 023799           94 FGFTKQNELFVGRVAMIGFAASLLGEGITGKGILAQLNL--------ETGIPIYEAEPLLLFFILFTLLGAIGALGDRGK  165 (277)
Q Consensus        94 fGf~r~aEl~nGR~AMLG~~g~lv~E~~tg~g~~~q~~~--------~~G~p~~~~~pl~l~~i~~~llgai~~~~~~~~  165 (277)
                      +.|+|++|++||||||||++|++++|+++|..+.. .+.        ..+.+..... ..++++++.+++++|.+...+ 
T Consensus        89 l~r~ReaELkHGRwAMLAvlG~lvpE~l~g~~W~~-aG~~~~~~g~~y~g~p~~~~i-~~l~~~qv~lmG~~E~~R~~~-  165 (243)
T 3pl9_A           89 LQRFRECELIHGRWAMLATLGALTVEGLTGITWQD-AGKVELIEGSSYLGQPLPFSM-TTLIWIEVLVIGYIEFQRNAE-  165 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCCTTT-HHHHHHHSCEEETTEEECCCH-HHHHHHHHHHHHHHHHHHHSC-
T ss_pred             hHHHHHhhhhcchhHHHHHHHHHhHHhhcCccccc-ccccccccccccccCccchhh-HHHHHHHHHHHHHHHHHhhcc-
Confidence            44678999999999999999999999987642211 010        0111111011 123344567788887542211 


Q ss_pred             ccCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccchhhhhhhhhHHHHHHHHHHHHHhcCcChHHHhHHhhCCCcc
Q 023799          166 FVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPIN  245 (277)
Q Consensus       166 ~~~~~~~p~g~~~~~~~PGd~~~dPlGL~~~~~~~~~~k~kELkNGRLAMlg~~G~ivqE~vTGkg~l~~l~~~~g~p~~  245 (277)
                       .+    +    ....+|||. |||+|+.+++++++++|.+|||||||||+|++|+++||++||+|+++||..|+.+|++
T Consensus       166 -~~----~----~~~~~PG~~-FDPLGl~~d~e~~~~~r~~ElknGRlAMla~~g~~~q~~vtG~Gpl~~l~~HladP~~  235 (243)
T 3pl9_A          166 -LD----T----EKRLYPGGT-FDPLGLASDPEKKPILQLAEIKHARLAMVGFLGFAVQAAVTGKGPLNNWVTHLSDPLH  235 (243)
T ss_dssp             -CC----T----TTTTCCCGG-GCTTCTTCSTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHCSGG
T ss_pred             -cC----C----ccccCCCcc-hhhccccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHhcCCChHHHHHHHhcCcch
Confidence             11    1    112489995 8999999888888899999999999999999999999999999999999999999985

PyMOL of 3pl9

>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_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

>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_4 Chlorophyll A-B binding protein P4, chloroplastic; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_4* 2wsf_4* 3lw5_4* 2o01_4*	Back alignment and structure

>2wsc_2 LHCA2, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Pisum sativum} PDB: 2wse_2* 2wsf_2* 2o01_2* 3lw5_2*	Back alignment and structure

>2bhw_A Chlorophyll A-B binding protein AB80; LHC-II, photosynthesis, light-harvesting, membrane protein, chloroplast, chromophore, membrane; HET: LUX NEX XAT CLA CHL LHG DGD; 2.50A {Pisum sativum} PDB: 1vcr_A* 1rwt_A*	Back alignment and structure

>3pl9_A Chlorophyll A-B binding protein; CP29, light-harvesting COMP membrane protein, plant, photosynthesis, chloroplast, thyla photosystem II; HET: CLA CHL LUT XAT NEX G3P HTG; 2.80A {Spinacia oleracea}	Back alignment and structure

>2wsc_1 AT3G54890, LHCA1; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB: 2wse_1* 2wsf_1* 2o01_1* 3lw5_1*	Back alignment and structure

>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I; photosynthesis, electron transfer, membrane proteins, large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A {Glycine max} PDB: 2wse_3* 2wsf_3* 3lw5_3* 2o01_3*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		277
d1rwta_		218	f.43.1.1 (A:) Chlorophyll a-b binding protein {Spi	3e-05

>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 = 42.0 bits (98), Expect = 3e-05
 Identities = 35/161 (21%), Positives = 55/161 (34%), Gaps = 11/161 (6%)

Query: 86  GIFGTSGGFGFTKQNELFVGRVAMIGFAASLLGEGITGKGILA----------QLNLETG 135
           G+      F   ++ E+   R AM+G    +  E +   G+            Q+  E G
Sbjct: 37  GLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGG 96

Query: 136 IPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKE 195
           +       L+    +  +      L    +       P G     + PG      LGL +
Sbjct: 97  LDYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGGPLGEVVDPLYPGGSFDP-LGLAD 155

Query: 196 GGPIFGFTKSNELFVGRLAQLGIAFSLIGEIITGKGALAQL 236
               F   K  E+  GRLA   +    +  I+TGKG L  L
Sbjct: 156 DPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENL 196

PyMOL of d1rwta_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		277
d1rwta_		218	Chlorophyll a-b binding protein {Spinach (Spinacia	100.0
d1rwta_		218	Chlorophyll a-b binding protein {Spinach (Spinacia	99.23

>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=1.6e-33  Score=249.38  Aligned_cols=159  Identities=25%  Similarity=0.338  Sum_probs=108.4

Q ss_pred             CCCCCCCCcCCCCCCC------------CccchhhhhhhHHHHHHHHHHHHhhhhhccchh------hhhcc---c-cCc
Q 023799           79 KKPKVEDGIFGTSGGF------------GFTKQNELFVGRVAMIGFAASLLGEGITGKGIL------AQLNL---E-TGI  136 (277)
Q Consensus        79 ~~p~~~dg~~~~~~~f------------Gf~r~aEl~nGR~AMLG~~g~lv~E~~tg~g~~------~q~~~---~-~G~  136 (277)
                      ..|+++||++.+|.+|            .|+||+|||||||||||++|++++|+++..+..      .....   . .+.
T Consensus        18 ~~P~~LdGs~pGD~GFDPLgls~d~~~~~~~ReaELKHGR~AMLA~vG~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (218)
T d1rwta_          18 ESPSYLTGEFPGDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGL   97 (218)
T ss_dssp             SCCTTCCSCSTTCCSCCTTCTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCSCCSHHHHGGGGGSTTCB
T ss_pred             CCCcccCCCCCCCCCcCCcccCCCHHHHHHHHHHHHhhceehHhhhcceeehhhhccCCCCCCCcccccccccccCcchh
Confidence            5699999999888875            256999999999999999999999987643221      00000   0 000


Q ss_pred             c------cccchh-HHHHHHHHHHHHHHhhhccCCCccCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCccccchhhhh
Q 023799          137 P------IYEAEP-LLLFFILFTLLGAIGALGDRGKFVDEPDEPTGLGGAVIPPGKGLRSALGLKEGGPIFGFTKSNELF  209 (277)
Q Consensus       137 p------~~~~~p-l~l~~i~~~llgai~~~~~~~~~~~~~~~p~g~~~~~~~PGd~~~dPlGL~~~~~~~~~~k~kELk  209 (277)
                      .      ...... +..+.+.+.+++.++.+.......       +......+|++ .|||+++++++++++++|++||+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~-------~~~~~~~~~~g-~fdPlg~~~~~e~~~~~k~kElk  169 (218)
T d1rwta_          98 DYLGNPSLVHAQSILAIWACQVILMGAVEGYRIAGGPL-------GEVVDPLYPGG-SFDPLGLADDPEAFAELKVKEIK  169 (218)
T ss_dssp             CGGGCTTSCCBCCHHHHHHHHHHHHHHHHHHHHHCBTT-------BCCSSSSCCCG-GGCTTCTTCSHHHHHHHHHHHHH
T ss_pred             hhhcCchHHHHHHHHHHHHHHHHHHhhhhhhcccCCCc-------ccccCCCCCCC-CccccccCCCHHHHHHHHHHHHH
Confidence            0      001111 111223333444444321111111       11112235665 57999998887777889999999


Q ss_pred             hhhhHHHHHHHHHHHHHhcCcChHHHhHHhhCCCcc
Q 023799          210 VGRLAQLGIAFSLIGEIITGKGALAQLNIETGIPIN  245 (277)
Q Consensus       210 NGRLAMlg~~G~ivqE~vTGkg~l~~l~~~~g~p~~  245 (277)
                      ||||||||++|+++||.+||++|++||.+|+.+|++
T Consensus       170 NGRLAMlAi~G~~~qe~vtG~gp~~nl~~h~~~P~~  205 (218)
T d1rwta_         170 NGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVN  205 (218)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSCHHHHHHHHHHCTTT
T ss_pred             HhHHHHHHHHHHHHhhhhcCCCHHHHHHHHhcCchh
Confidence            999999999999999999999999999999999985

PyMOL of d1rwta_

>d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]}	Back information, alignment and structure