Citrus Sinensis ID: 022739

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-------280-------290---

MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAALGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTAENFDPTARSDDGSCQYTL

cccccEEccccccccccccccHHHHHHHHHHHHHHHHHcccEEEEcccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccEEEcccccccccccccccccccEEEEcccHHHHHHHHHHHHccccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccccEEEEEcccccccccccHHHHHHHHHHHHHHHHHcccEEEEEEEcccccccccccccEEEEccHHHHHHHHHccccccccEccccccccccccccEEEEccccHHcccHHcccccccEEEccccHHHHHEEHHHHEccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHccccccccccccccccccccccccccccccccccccccccEEEEc

mginpimmsagelesgnagepAKLIRQRYREAADIIKKGKMCCLMINDLdagagrmggttqYTVNNQMVNATLmniadnptcvqlpgmynkeenprvpiivtgndfstlyaplirdgrmekfywaptredrigvckgifrndnvadddIVKLvdtfpgqsidfFGALRARVYDDEVRKWISGVGVgsigkslvnskeaaptfeqprMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAAlgeanedaiqsgnfygkaaqqmnvpvpegctdptaenfdptarsddgscqytl

mginpimmsagelesgnagePAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISgvgvgsigkslvnskeaaptfeqpRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAALGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTaenfdptarsddgscqytl

MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWisgvgvgsigKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAALGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTAENFDPTARSDDGSCQYTL

***********************LIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISGVGVGSIGKSLV*****************KLLEYGNMIVQEQENVKRVQLADKYLSEA******************************************************

**INPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGA****************NATLMNIADNPTCVQ*******EENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISGVGVGSI***********************LLEYGNMIVQEQEN****QLA**Y**********************************************************

*GINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAALGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTAENFDPTARSDDGSCQYTL

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		293	2.2.26 [Sep-21-2011]
Q7X9A0		476	Ribulose bisphosphate car	N/A	no	1.0	0.615	0.884	1e-153
P93431		466	Ribulose bisphosphate car	yes	no	1.0	0.628	0.853	1e-151
P10896		474	Ribulose bisphosphate car	yes	no	1.0	0.618	0.846	1e-148
Q40073		464	Ribulose bisphosphate car	N/A	no	1.0	0.631	0.825	1e-148
P10871		472	Ribulose bisphosphate car	N/A	no	1.0	0.620	0.805	1e-144
Q40281		437	Ribulose bisphosphate car	N/A	no	0.873	0.585	0.902	1e-136
Q7X999		435	Ribulose bisphosphate car	N/A	no	0.866	0.583	0.893	1e-135
O98997		439	Ribulose bisphosphate car	N/A	no	0.870	0.580	0.870	1e-133
Q42450		425	Ribulose bisphosphate car	N/A	no	0.873	0.602	0.867	1e-131
Q9ZT00		433	Ribulose bisphosphate car	N/A	no	0.870	0.588	0.850	1e-130

>sp\|Q7X9A0\|RCA1_LARTR Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic OS=Larrea tridentata GN=RCA1 PE=1 SV=1	Back alignment and function desciption

 Score =  541 bits (1394), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 261/295 (88%), Positives = 274/295 (92%), Gaps = 2/295 (0%)

Query: 1   MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60
           MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCL INDLDAGAGRMGGTT
Sbjct: 182 MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLFINDLDAGAGRMGGTT 241

Query: 61  QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 120
           QYTVNNQMVNATLMNIADNPT VQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME
Sbjct: 242 QYTVNNQMVNATLMNIADNPTNVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 301

Query: 121 KFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWI 180
           KFYWAPTREDRIGVCKGIFR DNVADDDIVKLVDTFPGQSIDFFGALRARVY DEVRKW+
Sbjct: 302 KFYWAPTREDRIGVCKGIFRTDNVADDDIVKLVDTFPGQSIDFFGALRARVYHDEVRKWV 361

Query: 181 SGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAA 240
           S VGV +IGK LVNSKE  P+FEQP+MT++KLL YG M+VQEQENVKRVQLADKY+SEAA
Sbjct: 362 SEVGVDTIGKKLVNSKEGPPSFEQPKMTIDKLLGYGGMLVQEQENVKRVQLADKYMSEAA 421

Query: 241 LGEANEDAIQSGNFY-GKAAQQM-NVPVPEGCTDPTAENFDPTARSDDGSCQYTL 293
           LG+AN DAI+ G FY G+AAQQ+ NVPVPEGCTDP A N+DPTARSDDGSC Y  
Sbjct: 422 LGDANNDAIKRGTFYGGQAAQQVGNVPVPEGCTDPQATNYDPTARSDDGSCVYKF 476

Activation of RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) involves the ATP-dependent carboxylation of the epsilon-amino group of lysine leading to a carbamate structure.
Larrea tridentata (taxid: 66636)

>sp\|P93431\|RCA_ORYSJ Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Oryza sativa subsp. japonica GN=RCA PE=1 SV=2	Back alignment and function description

>sp\|P10896\|RCA_ARATH Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Arabidopsis thaliana GN=RCA PE=1 SV=2	Back alignment and function description

>sp\|Q40073\|RCAA_HORVU Ribulose bisphosphate carboxylase/oxygenase activase A, chloroplastic OS=Hordeum vulgare GN=RCAA PE=2 SV=1	Back alignment and function description

>sp\|P10871\|RCA_SPIOL Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Spinacia oleracea PE=1 SV=2	Back alignment and function description

>sp\|Q40281\|RCA_MALDO Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Malus domestica GN=RCA PE=2 SV=1	Back alignment and function description

>sp\|Q7X999\|RCA2_LARTR Ribulose bisphosphate carboxylase/oxygenase activase 2, chloroplastic OS=Larrea tridentata GN=RCA2 PE=2 SV=1	Back alignment and function description

>sp\|O98997\|RCA_VIGRR Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Vigna radiata var. radiata GN=RCA PE=2 SV=2	Back alignment and function description

>sp\|Q42450\|RCAB_HORVU Ribulose bisphosphate carboxylase/oxygenase activase B, chloroplastic OS=Hordeum vulgare GN=RCAB PE=2 SV=1	Back alignment and function description

>sp\|Q9ZT00\|RCA_MAIZE Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Zea mays GN=RCA1 PE=2 SV=3	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		293
115334981		474	chloroplast ribulose-1,5-bisphosphate ca	1.0	0.618	0.904	1e-158
115334977		474	chloroplast ribulose-1,5-bisphosphate ca	1.0	0.618	0.904	1e-157
255566442		473	Ribulose bisphosphate carboxylase/oxygen	1.0	0.619	0.897	1e-157
225434859		472	PREDICTED: ribulose bisphosphate carboxy	0.993	0.616	0.903	1e-156
147856329		472	hypothetical protein VITISV_039112 [Viti	0.993	0.616	0.903	1e-156
357492323		476	Ribulose-1 5-bisphosphate carboxylase/ox	1.0	0.615	0.873	1e-155
359481752		474	PREDICTED: ribulose bisphosphate carboxy	1.0	0.618	0.883	1e-155
12620883		435	ribulose-1,5-bisphosphate carboxylase/ox	1.0	0.673	0.894	1e-154
449441384		474	PREDICTED: ribulose bisphosphate carboxy	1.0	0.618	0.883	1e-154
255584538		474	Ribulose bisphosphate carboxylase/oxygen	1.0	0.618	0.880	1e-153

>gi\|115334981\|gb\|ABI94078.1\| chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase activase large protein isoform [Acer rubrum]	Back alignment and taxonomy information

 Score =  562 bits (1449), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 265/293 (90%), Positives = 282/293 (96%)

Query: 1   MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60
           MGI PIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCL INDLDAGAGRMGGTT
Sbjct: 182 MGITPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLFINDLDAGAGRMGGTT 241

Query: 61  QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 120
           QYTVNNQMVNATLMNIADNPT VQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME
Sbjct: 242 QYTVNNQMVNATLMNIADNPTSVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 301

Query: 121 KFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWI 180
           KFYWAPTREDRIGVCKGIFR+DNVAD++++KLVDTFPGQSIDFFGALRARVYDDEVRKWI
Sbjct: 302 KFYWAPTREDRIGVCKGIFRSDNVADNELIKLVDTFPGQSIDFFGALRARVYDDEVRKWI 361

Query: 181 SGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAA 240
           SG+GV SIGK+LVNSK   PTFEQP+MT++KLLEYGNM+VQEQENVKRVQLADKYLSEAA
Sbjct: 362 SGIGVDSIGKNLVNSKNGPPTFEQPKMTIDKLLEYGNMLVQEQENVKRVQLADKYLSEAA 421

Query: 241 LGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTAENFDPTARSDDGSCQYTL 293
           LG+AN+DAI+ G+FYGKAAQQ+NVPVPEGCTD  A N+DPTARSDDGSCQYTL
Sbjct: 422 LGDANDDAIKRGSFYGKAAQQVNVPVPEGCTDRNAANYDPTARSDDGSCQYTL 474

Source: Acer rubrum

Species: Acer rubrum

Genus: Acer

Family: Aceraceae

Order: Sapindales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|115334977\|gb\|ABI94076.1\| chloroplast ribulose-1,5-bisphosphate carboxylase/oxygenase activase large protein isoform [Acer rubrum]	Back alignment and taxonomy information

>gi\|255566442\|ref\|XP_002524206.1\| Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor, putative [Ricinus communis] gi\|223536483\|gb\|EEF38130.1\| Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225434859\|ref\|XP_002282236.1\| PREDICTED: ribulose bisphosphate carboxylase/oxygenase activase 2, chloroplastic isoform 1 [Vitis vinifera] gi\|297746032\|emb\|CBI16088.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147856329\|emb\|CAN83893.1\| hypothetical protein VITISV_039112 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|357492323\|ref\|XP_003616450.1\| Ribulose-1 5-bisphosphate carboxylase/oxygenase activase [Medicago truncatula] gi\|355517785\|gb\|AES99408.1\| Ribulose-1 5-bisphosphate carboxylase/oxygenase activase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|359481752\|ref\|XP_002270571.2\| PREDICTED: ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic-like [Vitis vinifera] gi\|297740331\|emb\|CBI30513.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|12620883\|gb\|AAG61121.1\|AF329935_1 ribulose-1,5-bisphosphate carboxylase/oxygenase activase 2 [Gossypium hirsutum]	Back alignment and taxonomy information

>gi\|449441384\|ref\|XP_004138462.1\| PREDICTED: ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255584538\|ref\|XP_002532996.1\| Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor, putative [Ricinus communis] gi\|223527225\|gb\|EEF29388.1\| Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplast precursor, putative [Ricinus communis]	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		293
TAIR\|locus:2063922		474	RCA "rubisco activase" [Arabid	0.993	0.613	0.838	3.9e-131
TAIR\|locus:2032687		432	AT1G73110 [Arabidopsis thalian	0.802	0.543	0.502	8.1e-60

TAIR\|locus:2063922 RCA "rubisco activase" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1286 (457.8 bits), Expect = 3.9e-131, P = 3.9e-131
 Identities = 244/291 (83%), Positives = 257/291 (88%)

Query:     1 MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60
             MGINPIMMSAGELESGNAGEPAKLIRQRYREAAD+IKKGKMCCL INDLDAGAGRMGGTT
Sbjct:   182 MGINPIMMSAGELESGNAGEPAKLIRQRYREAADLIKKGKMCCLFINDLDAGAGRMGGTT 241

Query:    61 QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 120
             QYTVNNQMVNATLMNIADNPT VQLPGMYNKEEN RVPII TGNDFSTLYAPLIRDGRME
Sbjct:   242 QYTVNNQMVNATLMNIADNPTNVQLPGMYNKEENARVPIICTGNDFSTLYAPLIRDGRME 301

Query:   121 KFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWX 180
             KFYWAPTREDRIGVCKGIFR D + D+DIV LVD FPGQSIDFFGALRARVYDDEVRK+ 
Sbjct:   302 KFYWAPTREDRIGVCKGIFRTDKIKDEDIVTLVDQFPGQSIDFFGALRARVYDDEVRKFV 361

Query:   181 XXXXXXXXXKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSEAA 240
                      K LVNS+E  P FEQP MT EKL+EYGNM+V EQENVKRVQLA+ YLS+AA
Sbjct:   362 ESLGVEKIGKRLVNSREGPPVFEQPEMTYEKLMEYGNMLVMEQENVKRVQLAETYLSQAA 421

Query:   241 LGEANEDAIQSGNFYGKAAQQMNVPVPEGCTDPTAENFDPTARSDDGSCQY 291
             LG+AN DAI  G FYGK AQQ+N+PVPEGCTDP AENFDPTARSDDG+C Y
Sbjct:   422 LGDANADAIGRGTFYGKGAQQVNLPVPEGCTDPVAENFDPTARSDDGTCVY 472

GO:0005524 "ATP binding" evidence=IEA;IDA

GO:0009507 "chloroplast" evidence=ISM;IDA;NAS

GO:0030234 "enzyme regulator activity" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0010287 "plastoglobule" evidence=IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0043531 "ADP binding" evidence=IDA

GO:0046863 "ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity" evidence=IDA

GO:0009409 "response to cold" evidence=IEP;RCA

GO:0010319 "stromule" evidence=IDA

GO:0042742 "defense response to bacterium" evidence=IEP;RCA

GO:0016020 "membrane" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0009753 "response to jasmonic acid stimulus" evidence=IEP

GO:0010150 "leaf senescence" evidence=IMP

GO:0000165 "MAPK cascade" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009595 "detection of biotic stimulus" evidence=RCA

GO:0009637 "response to blue light" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0043900 "regulation of multi-organism process" evidence=RCA

GO:0050832 "defense response to fungus" evidence=RCA

GO:0009416 "response to light stimulus" evidence=IEP

TAIR\|locus:2032687 AT1G73110 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q40073	RCAA_HORVU	No assigned EC number	0.8259	1.0	0.6314	N/A	no
Q40281	RCA_MALDO	No assigned EC number	0.9023	0.8737	0.5858	N/A	no
P10896	RCA_ARATH	No assigned EC number	0.8464	1.0	0.6181	yes	no
P10871	RCA_SPIOL	No assigned EC number	0.8054	1.0	0.6207	N/A	no
Q7X9A0	RCA1_LARTR	No assigned EC number	0.8847	1.0	0.6155	N/A	no
P93431	RCA_ORYSJ	No assigned EC number	0.8537	1.0	0.6287	yes	no
Q42450	RCAB_HORVU	No assigned EC number	0.8677	0.8737	0.6023	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		293
PLN00020		413	PLN00020, PLN00020, ribulose bisphosphate carboxyl	1e-178
pfam00004		131	pfam00004, AAA, ATPase family associated with vari	6e-13
TIGR01243		733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	7e-04

>gnl\|CDD\|215031 PLN00020, PLN00020, ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional	Back alignment and domain information

 Score =  498 bits (1283), Expect = e-178
 Identities = 197/243 (81%), Positives = 214/243 (88%), Gaps = 3/243 (1%)

Query: 1   MGINPIMMSAGELESGNAGEPAKLIRQRYREAADII-KKGKMCCLMINDLDAGAGRMGGT 59
           MGI PI+MSAGELES NAGEP KLIRQRYREAADII KKGKM CL INDLDAGAGR G T
Sbjct: 172 MGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFG-T 230

Query: 60  TQYTVNNQMVNATLMNIADNPTCVQLPGMY-NKEENPRVPIIVTGNDFSTLYAPLIRDGR 118
           TQYTVNNQMVN TLMNIADNPT V L G +  KEE PRVPIIVTGNDFSTLYAPLIRDGR
Sbjct: 231 TQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGR 290

Query: 119 MEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRK 178
           MEKFYWAPTREDRIGV  GIFR+D V+ +D+VKLVDTFPGQ +DFFGALRARVYDDEVRK
Sbjct: 291 MEKFYWAPTREDRIGVVHGIFRDDGVSREDVVKLVDTFPGQPLDFFGALRARVYDDEVRK 350

Query: 179 WISGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSE 238
           WI+ VGV ++GK LVNSK+  PTFE P+MT+EKLLEYGNM+V+EQENVKRVQL+D+YL  
Sbjct: 351 WIAEVGVENLGKKLVNSKKGPPTFEPPKMTLEKLLEYGNMLVREQENVKRVQLSDEYLKN 410

Query: 239 AAL 241
           AAL
Sbjct: 411 AAL 413

Length = 413

>gnl\|CDD\|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)	Back alignment and domain information

>gnl\|CDD\|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		293
PLN00020		413	ribulose bisphosphate carboxylase/oxygenase activa	100.0
KOG0651		388	consensus 26S proteasome regulatory complex, ATPas	100.0
PF00004		132	AAA: ATPase family associated with various cellula	98.84
PRK03992		389	proteasome-activating nucleotidase; Provisional	98.1
TIGR01242		364	26Sp45 26S proteasome subunit P45 family. Many pro	97.76
CHL00195		489	ycf46 Ycf46; Provisional	97.73
TIGR03689		512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.26
PTZ00454		398	26S protease regulatory subunit 6B-like protein; P	97.07
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.83
PRK10733		644	hflB ATP-dependent metalloprotease; Reviewed	96.23
COG0464		494	SpoVK ATPases of the AAA+ class [Posttranslational	96.19
TIGR01241		495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.16
KOG0733		802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.01
CHL00176		638	ftsH cell division protein; Validated	94.67
PTZ00361		438	26 proteosome regulatory subunit 4-like protein; P	94.32
COG1222		406	RPT1 ATP-dependent 26S proteasome regulatory subun	93.86
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	90.34
KOG0652		424	consensus 26S proteasome regulatory complex, ATPas	89.96
KOG0726		440	consensus 26S proteasome regulatory complex, ATPas	88.48
PRK04195		482	replication factor C large subunit; Provisional	87.58
KOG0743		457	consensus AAA+-type ATPase [Posttranslational modi	86.25
TIGR00763		775	lon ATP-dependent protease La. This protein is ind	85.25
PHA02544		316	44 clamp loader, small subunit; Provisional	85.1
PRK12402		337	replication factor C small subunit 2; Reviewed	83.58

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional	Back alignment and domain information

Probab=100.00  E-value=2.8e-92  Score=673.87  Aligned_cols=240  Identities=82%  Similarity=1.274  Sum_probs=235.5

Q ss_pred             CCCcceeecccccCCCCCCCchHHHHHHHHHHHHHHh-cccceEEEeecccccCCcCCCCcceeecchhhhhhhhhhccC
Q 022739            1 MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIK-KGKMCCLMINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADN   79 (293)
Q Consensus         1 MGi~pI~mSAGELEs~~AGeParLIR~RYReAae~ik-~GkM~~L~INDLDAG~Grf~~~TQ~TVNnQ~V~aTLMNiaDn   79 (293)
                      ||+++|+||+|||+|+|+|||+|+||++|++|++++| +|+||||||||||||+|+++ +||+|||+|+|++|||||+||
T Consensus       172 lg~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~-~~~~tv~~qiV~~tLLnl~D~  250 (413)
T PLN00020        172 MGIEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFG-TTQYTVNNQMVNGTLMNIADN  250 (413)
T ss_pred             cCCCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCC-CCCcchHHHHHHHHHHHHhcC
Confidence            7999999999999999999999999999999999996 99999999999999999998 799999999999999999999


Q ss_pred             CCccCCCCcCC-CCCCCCCCEEEecCCccccccccccCCCccccccCcCCccchhhhhcccccCCCChHHHHHHhhhCCC
Q 022739           80 PTCVQLPGMYN-KEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPG  158 (293)
Q Consensus        80 Pt~Vqlpg~y~-~~~~~RVPIIVTGNDfStLYAPLiRDGRMeKFYW~Ptred~i~iv~~if~~Dg~~~~dv~~LVd~Fp~  158 (293)
                      ||+||+||.|+ .+.++|||||+||||+++||+||+|+||||||||.|++++|++|++.+|++|+++.+||++||++||+
T Consensus       251 p~~v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i~lPd~e~R~eIL~~~~r~~~l~~~dv~~Lv~~f~g  330 (413)
T PLN00020        251 PTNVSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVVHGIFRDDGVSREDVVKLVDTFPG  330 (413)
T ss_pred             CccccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCceeCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHcCCC
Confidence            99999999994 56789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchhHhhhhhhhhhHHHHHHHhhhcccccccccccCCCCCCcccCCcCCHHHHHHHHHHHHHHHHHHhhhhhHHHHhcc
Q 022739          159 QSIDFFGALRARVYDDEVRKWISGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADKYLSE  238 (293)
Q Consensus       159 Q~iDFFGALRaR~YDd~Vr~wi~~vG~e~ig~~lvns~~~~p~f~~p~~tl~~Lle~G~~lv~EQe~V~~~~Ls~eYl~~  238 (293)
                      |+||||||||||+|||+||+||+++|+|+||++|||+++++|+|++|+|||++|||+|++|++|||||+++|||+|||++
T Consensus       331 q~~Df~GAlrar~yd~~v~~~i~~~g~~~~~~~l~~~~~~~p~f~~~~~t~~~l~~~g~~l~~eq~~v~~~~l~~~y~~~  410 (413)
T PLN00020        331 QPLDFFGALRARVYDDEVRKWIAEVGVENLGKKLVNSKKGPPTFEPPKMTLEKLLEYGNMLVREQENVKRVQLSDEYLKN  410 (413)
T ss_pred             CCchhhhHHHHHHHHHHHHHHHHHhhHHHHHHHHhcCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 022739          239 AAL  241 (293)
Q Consensus       239 a~l  241 (293)
                      ++|
T Consensus       411 ~~~  413 (413)
T PLN00020        411 AAL  413 (413)
T ss_pred             ccC
Confidence            875

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport	Back alignment and domain information

>PRK03992 proteasome-activating nucleotidase; Provisional	Back alignment and domain information

>TIGR01242 26Sp45 26S proteasome subunit P45 family	Back alignment and domain information

>CHL00195 ycf46 Ycf46; Provisional	Back alignment and domain information

>TIGR03689 pup_AAA proteasome ATPase	Back alignment and domain information

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	Back alignment and domain information

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed	Back alignment and domain information

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH	Back alignment and domain information

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>CHL00176 ftsH cell division protein; Validated	Back alignment and domain information

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional	Back alignment and domain information

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	Back alignment and domain information

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK04195 replication factor C large subunit; Provisional	Back alignment and domain information

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR00763 lon ATP-dependent protease La	Back alignment and domain information

>PHA02544 44 clamp loader, small subunit; Provisional	Back alignment and domain information

>PRK12402 replication factor C small subunit 2; Reviewed	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
Query		293
3t15_A		293	Structure Of Green-Type Rubisco Activase From Tobac		1e-116
3thg_A		107	Crystal Structure Of The Creosote Rubisco Activase		2e-42

>pdb|3T15|A Chain A, Structure Of Green-Type Rubisco Activase From Tobacco Length = 293

Back alignment and structure

Iteration: 1

Score = 414 bits (1065), Expect = e-116, Method: Compositional matrix adjust. Identities = 199/234 (85%), Positives = 210/234 (89%) Query: 1 MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60 MGINPIMMSAGELESGNAGEPAKLIRQRYREAA+II+KG MCCL INDLDAGAGRMGGTT Sbjct: 60 MGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTT 119 Query: 61 QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 120 QYTVNNQMVNATLMNIADNPT VQLPGMYNK+EN RVPIIVTGNDFSTLYAPLIRDGRME Sbjct: 120 QYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRME 179 Query: 121 KFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWX 180 KFYWAPTREDRIGVC GIFR DNV +D+VK+VD FPGQSIDFFGALRARVYDDEVRKW Sbjct: 180 KFYWAPTREDRIGVCTGIFRTDNVPAEDVVKIVDNFPGQSIDFFGALRARVYDDEVRKWV 239 Query: 181 XXXXXXXXXKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADK 234 L+NS + PTFEQP+MT+EKLLEYGNM+VQEQENVKRVQLADK Sbjct: 240 SGTGIEKIGDKLLNSFDGPPTFEQPKMTIEKLLEYGNMLVQEQENVKRVQLADK 293

PyMOL of 3t15

>pdb|3THG|A Chain A, Crystal Structure Of The Creosote Rubisco Activase C-Domain Length = 107

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
Query		293
3t15_A		293	Ribulose bisphosphate carboxylase/oxygenase activ	1e-121
3thg_A		107	Ribulose bisphosphate carboxylase/oxygenase activ	8e-56

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293	Back alignment and structure

 Score =  348 bits (895), Expect = e-121
 Identities = 204/234 (87%), Positives = 217/234 (92%)

Query: 1   MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60
           MGINPIMMSAGELESGNAGEPAKLIRQRYREAA+II+KG MCCL INDLDAGAGRMGGTT
Sbjct: 60  MGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTT 119

Query: 61  QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRME 120
           QYTVNNQMVNATLMNIADNPT VQLPGMYNK+EN RVPIIVTGNDFSTLYAPLIRDGRME
Sbjct: 120 QYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRME 179

Query: 121 KFYWAPTREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWI 180
           KFYWAPTREDRIGVC GIFR DNV  +D+VK+VD FPGQSIDFFGALRARVYDDEVRKW+
Sbjct: 180 KFYWAPTREDRIGVCTGIFRTDNVPAEDVVKIVDNFPGQSIDFFGALRARVYDDEVRKWV 239

Query: 181 SGVGVGSIGKSLVNSKEAAPTFEQPRMTMEKLLEYGNMIVQEQENVKRVQLADK 234
           SG G+  IG  L+NS +  PTFEQP+MT+EKLLEYGNM+VQEQENVKRVQLADK
Sbjct: 240 SGTGIEKIGDKLLNSFDGPPTFEQPKMTIEKLLEYGNMLVQEQENVKRVQLADK 293

PyMOL of 3t15

>3thg_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; four-helix bundle, rubisco reactivation, chloroplast stroma, ATPase; 1.88A {Larrea tridentata} Length = 107	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		293
3thg_A		107	Ribulose bisphosphate carboxylase/oxygenase activ	100.0
3t15_A		293	Ribulose bisphosphate carboxylase/oxygenase activ	100.0
4b4t_L		437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.86
4b4t_J		405	26S protease regulatory subunit 8 homolog; hydrola	97.8
4b4t_H		467	26S protease regulatory subunit 7 homolog; hydrola	97.79
4b4t_K		428	26S protease regulatory subunit 6B homolog; hydrol	97.79
4b4t_M		434	26S protease regulatory subunit 6A; hydrolase, AAA	97.67
4b4t_I		437	26S protease regulatory subunit 4 homolog; hydrola	97.66
3cf2_A		806	TER ATPase, transitional endoplasmic reticulum ATP	97.51
1xwi_A		322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.36
3eie_A		322	Vacuolar protein sorting-associated protein 4; AAA	97.25
2qz4_A		262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.21
3h4m_A		285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.02
2zan_A		444	Vacuolar protein sorting-associating protein 4B; S	96.84
3vfd_A		389	Spastin; ATPase, microtubule severing, hydrolase;	96.78
2qp9_X		355	Vacuolar protein sorting-associated protein 4; ATP	96.75
3cf2_A		806	TER ATPase, transitional endoplasmic reticulum ATP	96.72
1ypw_A		806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.64
3d8b_A		357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	96.46
1lv7_A		257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.33
3cf0_A		301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.26
2r62_A		268	Cell division protease FTSH homolog; ATPase domain	96.19
3b9p_A		297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.13
3hu3_A		489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.63
2ce7_A		476	Cell division protein FTSH; metalloprotease; HET:	95.08
2x8a_A		274	Nuclear valosin-containing protein-like; nuclear p	94.83
1ypw_A		806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.62
1um8_A		376	ATP-dependent CLP protease ATP-binding subunit CL;	93.57
1d2n_A		272	N-ethylmaleimide-sensitive fusion protein; hexamer	92.98
3syl_A		309	Protein CBBX; photosynthesis, rubisco activase, AA	91.75
1sxj_A		516	Activator 1 95 kDa subunit; clamp loader, processi	82.98
2chg_A		226	Replication factor C small subunit; DNA-binding pr	81.38

>3thg_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; four-helix bundle, rubisco reactivation, chloroplast stroma, ATPase; 1.88A {Larrea tridentata}	Back alignment and structure

Probab=100.00  E-value=9.2e-53  Score=342.22  Aligned_cols=102  Identities=85%  Similarity=1.341  Sum_probs=96.6

Q ss_pred             CCccchhhhhcccccCCCChHHHHHHhhhCCCCcchhHhhhhhhhhhHHHHHHHhhhcccccccccccCCCCCCcccCCc
Q 022739          127 TREDRIGVCKGIFRNDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWISGVGVGSIGKSLVNSKEAAPTFEQPR  206 (293)
Q Consensus       127 tred~i~iv~~if~~Dg~~~~dv~~LVd~Fp~Q~iDFFGALRaR~YDd~Vr~wi~~vG~e~ig~~lvns~~~~p~f~~p~  206 (293)
                      |||||++||+|||++||+|++||++|||+||+||||||||||||+||++||+||+++|+|+||++||||+++||+|++|+
T Consensus         6 treDrigiv~gif~~Dgls~~dv~~LVd~Fp~QsiDFFGALRsR~YDd~Vr~wI~~vG~e~ig~~Lvns~e~~P~F~~P~   85 (107)
T 3thg_A            6 TREDRIGVCKGIFRTDNVADDDIVKLVDTFPGQSIDFFGALRARVYDDEVRKWVSEVGVDTIGKKLVNSKEGPPSFEQPK   85 (107)
T ss_dssp             CHHHHHHHHHHHTTTTTCCHHHHHHHHHHSTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCCCCC
T ss_pred             cHHHHHHHHHHHhccCCCCHHHHHHHHHcCCCCCchHHHHHHHHHhHHHHHHHHHHhCHHHHhHHHHcCCCCCCCCCCCc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhh
Q 022739          207 MTMEKLLEYGNMIVQEQENVKR  228 (293)
Q Consensus       207 ~tl~~Lle~G~~lv~EQe~V~~  228 (293)
                      |||++|||+|++|++||||||+
T Consensus        86 ~tl~~Lle~G~~Lv~EQ~~V~~  107 (107)
T 3thg_A           86 MTIDKLLGYGGMLVQEQENVKR  107 (107)
T ss_dssp             CCHHHHHHHHHHHHTTC-----
T ss_pred             CCHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999999986

PyMOL of 3thg

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A	Back alignment and structure

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*	Back alignment and structure

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}	Back alignment and structure

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C	Back alignment and structure

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}	Back alignment and structure

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}	Back alignment and structure

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A	Back alignment and structure

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}	Back alignment and structure

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*	Back alignment and structure

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*	Back alignment and structure

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}	Back alignment and structure

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20	Back alignment and structure

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}	Back alignment and structure

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*	Back alignment and structure

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}	Back alignment and structure

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*	Back alignment and structure

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*	Back alignment and structure

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}	Back alignment and structure

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20	Back alignment and structure

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*	Back alignment and structure

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*	Back alignment and structure

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20	Back alignment and structure

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}	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		293
d1ixza_		247	c.37.1.20 (A:) AAA domain of cell division protein	4e-09
d1lv7a_		256	c.37.1.20 (A:) AAA domain of cell division protein	5e-09
d1r7ra3		265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	8e-05
d1svma_		362	c.37.1.20 (A:) Papillomavirus large T antigen heli	5e-04
d1w44a_		321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	0.001

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score = 53.7 bits (129), Expect = 4e-09
 Identities = 34/165 (20%), Positives = 61/165 (36%), Gaps = 21/165 (12%)

Query: 1   MGINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAGRMGGTT 60
             +  I  S  +      G  A  +R  +  A    K+   C + I+++DA   + G   
Sbjct: 66  ARVPFITASGSDFVEMFVGVGAARVRDLFETA----KRHAPCIVFIDEIDAVGRKRGSGV 121

Query: 61  --QYTVNNQMVNATLMNIADNPTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGR 118
                   Q +N  L         V++ G    E++  + ++   N    L   L+R GR
Sbjct: 122 GGGNDEREQTLNQLL---------VEMDGF---EKDTAIVVMAATNRPDILDPALLRPGR 169

Query: 119 MEKFYW--APTREDRIGVCKGIFRNDNVADD-DIVKLVDTFPGQS 160
            ++     AP  + R  + +   R   +A+D D+  L    PG  
Sbjct: 170 FDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFV 214

PyMOL of d1ixza_

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256	Back information, alignment and structure

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265	Back information, alignment and structure

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362	Back information, alignment and structure

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321	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
Query		293
d1lv7a_		256	AAA domain of cell division protein FtsH {Escheric	97.95
d1e32a2		258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.64
d1ixza_		247	AAA domain of cell division protein FtsH {Thermus	97.63
d1r7ra3		265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.11
d1d2na_		246	Hexamerization domain of N-ethylmalemide-sensitive	93.21
d1ofha_		309	HslU {Haemophilus influenzae [TaxId: 727]}	91.24
d1svma_		362	Papillomavirus large T antigen helicase domain {Si	88.29
d1w44a_		321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	80.26

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=97.95  E-value=1.6e-05  Score=67.78  Aligned_cols=141  Identities=23%  Similarity=0.282  Sum_probs=101.3

Q ss_pred             CCcceeecccccCCCCCCCchHHHHHHHHHHHHHHhcccceEEEeecccccCC-cCCC-CcceeecchhhhhhhhhhccC
Q 022739            2 GINPIMMSAGELESGNAGEPAKLIRQRYREAADIIKKGKMCCLMINDLDAGAG-RMGG-TTQYTVNNQMVNATLMNIADN   79 (293)
Q Consensus         2 Gi~pI~mSAGELEs~~AGeParLIR~RYReAae~ik~GkM~~L~INDLDAG~G-rf~~-~TQ~TVNnQ~V~aTLMNiaDn   79 (293)
                      |+..+.++.++|.+.+.|+-.+.||+=+..|    ++...|+|||.|+|+-.+ |-.+ ......-.+ +.++|++.-|+
T Consensus        70 ~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A----~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~-~~~~ll~~~d~  144 (256)
T d1lv7a_          70 KVPFFTISGSDFVEMFVGVGASRVRDMFEQA----KKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQ-TLNQMLVEMDG  144 (256)
T ss_dssp             TCCEEEECSCSSTTSCCCCCHHHHHHHHHHH----HTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHH-HHHHHHHHHHT
T ss_pred             CCCEEEEEhHHhhhcchhHHHHHHHHHHHHH----HHcCCEEEEEEChhhhCccCCCCCCCCcHHHHH-HHHHHHHHhhC
Confidence            6677899999999999999998888777666    567889999999998432 2211 112222223 34667666554


Q ss_pred             CCccCCCCcCCCCCCCCCCEEEecCCccccccccccCCCcccccc--CcCCccchhhhhcccccCCCC-hHHHHHHhhhC
Q 022739           80 PTCVQLPGMYNKEENPRVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGVCKGIFRNDNVA-DDDIVKLVDTF  156 (293)
Q Consensus        80 Pt~Vqlpg~y~~~~~~RVPIIVTGNDfStLYAPLiRDGRMeKFYW--~Ptred~i~iv~~if~~Dg~~-~~dv~~LVd~F  156 (293)
                      ..           ...+|=||.|-|+...|=..|+|-||.|+...  -|+.++|..|+....+.=.++ ..++..|+..-
T Consensus       145 ~~-----------~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t  213 (256)
T d1lv7a_         145 FE-----------GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGT  213 (256)
T ss_dssp             CC-----------SSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTC
T ss_pred             CC-----------CCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhC
Confidence            31           22457788899999999889999999986443  389999999998887665554 45677777655


Q ss_pred             CC
Q 022739          157 PG  158 (293)
Q Consensus       157 p~  158 (293)
                      +|
T Consensus       214 ~G  215 (256)
T d1lv7a_         214 PG  215 (256)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

PyMOL of d1lv7a_

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}	Back information, alignment and structure

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}	Back information, alignment and structure

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	Back information, alignment and structure