Citrus Sinensis ID: 009540

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-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530--

MTGMAVPTIALYASPPSSVCSATHQINAHTTYDFDLNSRSSASTSSTAAAPSSQKQTIGGLSCLFSSSSEMGSYRSEELKELSSSFGYAYSPSKLCGSSSSLKRDQSPVSVFQGPVSCSGNGSYSYSRSSPPIRTAREKADVNVNFHTFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHGSQFDE

ccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccccccccHHcHHHHHHHHHHccccHHHHHHHHcccccccccccHHHHHHHHcHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHcHHEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEcccccccHHHHHHHHHHccccccccEEEEEEEEEcccccHHHHHHHcccccEEEEccccccccccccccccEEEEEEccccccccc

ccccEEHHEHHEcccccccccccccccccccccccccccccccccccccccccccccEcccHHcccccHHccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccHEEEcccccccccccccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccccccEEEcHHHHHHHHHHccccHHHHHHHHHHHcHccccccHHHHHHHHcHHHHHHHccccccccEEEccHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHEccHHHHHHHHHHHHHccccccccEEEEEEEEEEEEEcccccccc

mtgmavptialyasppssvcsathqinahttydfdlnsrssastsstaaapssqkqtigglsclfssssemgsyRSEELKELSssfgyayspsklcgsssslkrdqspvsvfqgpvscsgngsysysrssppirtarekadvnvnfhtffkgssglfNGFVRNALgscvdydsssfrvhngdavlnvgssaALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAhrgqmrasgdpylLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNmmtldalplckrQRFAKETLEIFVPLANRLGISTWKVQLENLcfkhlnpdqhtELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKyalpslpnlirESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVpvclshgsqfde

MTGMAVPTIALYASPPSSVCSATHQINAHTTYDFDLNSRSSASTSStaaapssqkqtiggLSCLFSSSSEMGSYRSEELKELSSSFGYAYSPSKLCGSSSSLKRDQSPVSVFqgpvscsgngsysysrsspPIRTAREKADVNVNFHTFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQlsklarenntasktveadrLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHGSQFDE

MTGMAVPTIALYASPPSSVCSATHQINAHTTYDFDLNsrssastsstaaapssQKQTIGGLSCLFssssemgsyrseeLKELSSSFGYAYspsklcgsssslkRDQSPVSVFQGPVscsgngsysysrssPPIRTAREKADVNVNFHTFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHGSQFDE

********IALY*******CSATHQINAHTTYD***********************************************************************************************************DVNVNFHTFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLS***************VEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLS*******

****AVP*IALYASPPSSVCSATHQINA************************************************************************************************************************************VRNALGSC*************************************VEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLAREN*****TVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHG*****

MTGMAVPTIALYASPPSSVCSATHQINAHTTYDFDLN********************IGGLSCLFSS****************SSFGYAYSPSK****************VFQGPVSCSG*************RTAREKADVNVNFHTFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHGSQFDE

**GMAVPTIALYASPPSSVCSA**********************************************************************************DQSPVSVFQGP********************************TFFKGSSGLFNGFVRNALGSCVDYDSSSFRVHN*DAVL**GSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYALPSLPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQLVPVCLSHG*****

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SSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		532	2.2.26 [Sep-21-2011]
P74007		760	Probable guanosine-3',5'-	N/A	no	0.421	0.294	0.433	5e-43
O54408		734	GTP pyrophosphokinase OS=	yes	no	0.421	0.305	0.401	5e-41
Q8CS97		729	GTP pyrophosphokinase OS=	yes	no	0.424	0.310	0.364	7e-40
Q5HNR8		729	GTP pyrophosphokinase OS=	yes	no	0.424	0.310	0.364	7e-40
P0AG26		702	Guanosine-3',5'-bis(dipho	yes	no	0.415	0.314	0.411	4e-39
P0AG24		702	Bifunctional (p)ppGpp syn	N/A	no	0.415	0.314	0.411	4e-39
P0AG25		702	Guanosine-3',5'-bis(dipho	N/A	no	0.415	0.314	0.411	4e-39
O52177		757	GTP pyrophosphokinase OS=	yes	no	0.426	0.299	0.384	5e-39
P0A0E9		736	GTP pyrophosphokinase OS=	yes	no	0.424	0.307	0.355	1e-38
P0A0F0		736	GTP pyrophosphokinase OS=	yes	no	0.424	0.307	0.355	1e-38

>sp\|P74007\|SPOT_SYNY3 Probable guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=spoT PE=3 SV=1	Back alignment and function desciption

 Score =  176 bits (446), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 101/233 (43%), Positives = 142/233 (60%), Gaps = 9/233 (3%)

Query: 232 FVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLS 291
            + +AF  A   H  Q R SG+PY+ H V  A LL  +G +  ++AAG LHD ++D  +S
Sbjct: 53  LICRAFCFAYDLHAQQRRKSGEPYIAHPVAVAGLLRDLGGDEAMIAAGFLHDVVEDTDIS 112

Query: 292 YDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLI 350
            + I   FG   A LVEGV+KLS+       N +++   +A+    MFLAMA D R +++
Sbjct: 113 IEQIEALFGEETASLVEGVTKLSKF------NFSSTTEHQAENFRRMFLAMAKDIRVIVV 166

Query: 351 KLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQH 410
           KLADRLHNM TLDAL   K++R A+ET +IF PLANRLGI  +K +LE+L FK+L PD +
Sbjct: 167 KLADRLHNMRTLDALSPEKQRRIARETKDIFAPLANRLGIWRFKWELEDLSFKYLEPDSY 226

Query: 411 TELSSKLVECFD--EAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKM 461
            ++ S +VE     E+ + +  + L   L+D+ I    L GR K LY I+ KM
Sbjct: 227 RKIQSLVVEKRGDRESRLETVKDMLRFRLRDEGIEHFELQGRPKHLYGIYYKM 279

In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes the degradation of ppGpp into GDP. It may also be capable of catalyzing the synthesis of ppGpp.
Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)
EC: 3EC: .EC: 1EC: .EC: 7EC: .EC: 2

>sp\|O54408\|RELA_BACSU GTP pyrophosphokinase OS=Bacillus subtilis (strain 168) GN=relA PE=3 SV=3	Back alignment and function description

>sp\|Q8CS97\|RELA_STAES GTP pyrophosphokinase OS=Staphylococcus epidermidis (strain ATCC 12228) GN=relA PE=3 SV=1	Back alignment and function description

>sp\|Q5HNR8\|RELA_STAEQ GTP pyrophosphokinase OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) GN=relA PE=3 SV=1	Back alignment and function description

>sp\|P0AG26\|SPOT_SHIFL Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase OS=Shigella flexneri GN=spoT PE=3 SV=1	Back alignment and function description

>sp\|P0AG24\|SPOT_ECOLI Bifunctional (p)ppGpp synthase/hydrolase SpoT OS=Escherichia coli (strain K12) GN=spoT PE=1 SV=1	Back alignment and function description

>sp\|P0AG25\|SPOT_ECO57 Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase OS=Escherichia coli O157:H7 GN=spoT PE=3 SV=1	Back alignment and function description

>sp\|O52177\|RELA_MYXXA GTP pyrophosphokinase OS=Myxococcus xanthus GN=relA PE=3 SV=1	Back alignment and function description

>sp\|P0A0E9\|RELA_STAAW GTP pyrophosphokinase OS=Staphylococcus aureus (strain MW2) GN=relA PE=3 SV=1	Back alignment and function description

>sp\|P0A0F0\|RELA_STAAU GTP pyrophosphokinase OS=Staphylococcus aureus GN=relA 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
Query		532
224054061		716	predicted protein [Populus trichocarpa]	0.838	0.622	0.703	1e-176
225442114		724	PREDICTED: GTP pyrophosphokinase-like [V	0.827	0.607	0.705	1e-171
33637487		718	RSH2 [Nicotiana tabacum]	0.840	0.622	0.696	1e-169
15822693		643	relA/spoT-like protein RSH2 [Nicotiana t	0.840	0.695	0.696	1e-169
15081594		721	RSH-like protein [Capsicum annuum]	0.821	0.606	0.675	1e-169
224070802		737	predicted protein [Populus trichocarpa]	0.838	0.605	0.698	1e-167
356558920		715	PREDICTED: uncharacterized protein LOC10	0.813	0.605	0.684	1e-166
356519788		714	PREDICTED: uncharacterized protein LOC10	0.812	0.605	0.686	1e-166
449461673		733	PREDICTED: GTP pyrophosphokinase-like [C	0.849	0.616	0.656	1e-162
37196706		729	RelA-SpoT like protein PsRSH1 [Pisum sat	0.819	0.598	0.655	1e-158

>gi\|224054061\|ref\|XP_002298089.1\| predicted protein [Populus trichocarpa] gi\|222845347\|gb\|EEE82894.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  624 bits (1608), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 339/482 (70%), Positives = 388/482 (80%), Gaps = 36/482 (7%)

Query: 4   MAVPTIALYASPPSSVCSATH--QINAHTTYDFDLNSRSSASTSSTAAAPSSQKQTIGGL 61
           MAVPTIALYASPPSSVCS  +  QINAH  YDF+LNSRSS++ SS+A++  SQK  +GGL
Sbjct: 1   MAVPTIALYASPPSSVCSTPYPCQINAHANYDFELNSRSSSTASSSASS--SQKPIVGGL 58

Query: 62  SCLFSSSS-----------EMGSY-RSEELKELSSSFGYAYSPSKLCGSSSSLKRDQSPV 109
           S LFSS +           E+G + R +ELKELSSSF   Y+PSK C + SS+KRDQSPV
Sbjct: 59  SRLFSSPAVKHASFSGDREELGWHDRGDELKELSSSF--CYTPSK-CLAGSSIKRDQSPV 115

Query: 110 SVFQGPVSCSGNGSYSYSRSSPPIRTAREKADVNVNFHT-----FFKGSSGLFNGFVRNA 164
           SV QG VSCS         SSPP R ARE++  +V F +     F  G++GLFNGFVRNA
Sbjct: 116 SVLQGQVSCS---------SSPPTRIARERSGCDVGFQSSIHGSFRSGANGLFNGFVRNA 166

Query: 165 LGSCVDYDSSSFRVHNGDAVLNVGSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLK 224
           LGSCVDYDS SF VHN    ++  SS+ ++DELTF+MED+ V+ N E YAKE L  AQ +
Sbjct: 167 LGSCVDYDSPSFEVHNNG--IDEDSSSVVVDELTFSMEDSCVDANYEPYAKELLFGAQSR 224

Query: 225 HKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDT 284
           H IF +DFVIKAF+EAE+AHRGQMRASGDPYL HCVETA+LLA IGANSTVVAAGLLHDT
Sbjct: 225 HTIFCDDFVIKAFHEAEKAHRGQMRASGDPYLQHCVETAVLLAIIGANSTVVAAGLLHDT 284

Query: 285 LDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMAD 344
           LDD+F+SYD+IF+TFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMAD
Sbjct: 285 LDDSFISYDHIFKTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMAD 344

Query: 345 ARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKH 404
           ARAVLIKLADRLHNMMTLDALPL K+QRFAKET EIF PLANRLGIS+WK QLENLCFKH
Sbjct: 345 ARAVLIKLADRLHNMMTLDALPLVKQQRFAKETSEIFAPLANRLGISSWKEQLENLCFKH 404

Query: 405 LNPDQHTELSSKLVECFDEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKY 464
           LNPDQH +LS++LV+ FDEAM+ SA EKLE+AL D+ IS+  L GRHKSLYS +CKMLK 
Sbjct: 405 LNPDQHKDLSARLVDSFDEAMIASAKEKLEKALTDEAISY-DLSGRHKSLYSTYCKMLKK 463

Query: 465 AL 466
            L
Sbjct: 464 KL 465

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225442114\|ref\|XP_002273796.1\| PREDICTED: GTP pyrophosphokinase-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|33637487\|gb\|AAQ23899.1\| RSH2 [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|15822693\|gb\|AAL03950.1\| relA/spoT-like protein RSH2 [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|15081594\|gb\|AAK82651.1\| RSH-like protein [Capsicum annuum]	Back alignment and taxonomy information

>gi\|224070802\|ref\|XP_002303242.1\| predicted protein [Populus trichocarpa] gi\|222840674\|gb\|EEE78221.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356558920\|ref\|XP_003547750.1\| PREDICTED: uncharacterized protein LOC100787301 [Glycine max]	Back alignment and taxonomy information

>gi\|356519788\|ref\|XP_003528551.1\| PREDICTED: uncharacterized protein LOC100789399 [Glycine max]	Back alignment and taxonomy information

>gi\|449461673\|ref\|XP_004148566.1\| PREDICTED: GTP pyrophosphokinase-like [Cucumis sativus] gi\|449528710\|ref\|XP_004171346.1\| PREDICTED: GTP pyrophosphokinase-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|37196706\|dbj\|BAC97801.1\| RelA-SpoT like protein PsRSH1 [Pisum sativum]	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		532
TAIR\|locus:2088262		709	RSH2 "RELA/SPOT homolog 2" [Ar	0.516	0.387	0.781	1.6e-130
TAIR\|locus:2014335		715	RSH3 "RELA/SPOT homolog 3" [Ar	0.800	0.595	0.592	1.5e-129
UNIPROTKB\|Q3A9Z8		716	relA "GTP pyrophosphokinase" [	0.422	0.314	0.434	2.2e-39
TIGR_CMR\|CHY_2223		716	CHY_2223 "GTP pyrophosphokinas	0.422	0.314	0.434	2.2e-39
TIGR_CMR\|DET_0005		728	DET_0005 "GTP pyrophosphokinas	0.436	0.318	0.440	4e-39
TIGR_CMR\|GSU_2236		716	GSU_2236 "GTP pyrophosphokinas	0.419	0.311	0.404	7.4e-37
UNIPROTKB\|P0AG24		702	spoT "guanosine 3'-diphosphate	0.415	0.314	0.415	1.4e-36
TIGR_CMR\|CPS_4973		703	CPS_4973 "guanosine-3,5-bis(di	0.430	0.325	0.418	2.4e-36
TIGR_CMR\|BA_4637		727	BA_4637 "GTP pyrophosphokinase	0.411	0.301	0.410	5.9e-36
TIGR_CMR\|SO_0359		701	SO_0359 "guanosine-3,5-bis(dip	0.417	0.316	0.416	1.1e-35

TAIR\|locus:2088262 RSH2 "RELA/SPOT homolog 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1077 (384.2 bits), Expect = 1.6e-130, Sum P(2) = 1.6e-130
 Identities = 218/279 (78%), Positives = 240/279 (86%)

Query:   188 GSSAALIDELTFNMEDNIVEGNLETYAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQ 247
             GS + L+DELTF ME   V+  ++ YA++ L  AQL+HKIF ++ VIKAFYEAE+AHRGQ
Sbjct:   170 GSDSVLVDELTFPME---VD-TIKPYARDLLRRAQLRHKIFNDESVIKAFYEAEKAHRGQ 225

Query:   248 MRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLV 307
             MRAS DPYL HCVETAMLLA IGANSTVV AGLLHDT+DD+F+SYDYI R FGAGVADLV
Sbjct:   226 MRASRDPYLQHCVETAMLLANIGANSTVVVAGLLHDTIDDSFMSYDYILRNFGAGVADLV 285

Query:   308 EGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMADARAVLIKLADRLHNMMTLDALPL 367
             EGVSKLSQLSKLARENNTA KTVEADRLHTMFLAMADARAVLIKLADRLHNM TL AL  
Sbjct:   286 EGVSKLSQLSKLARENNTACKTVEADRLHTMFLAMADARAVLIKLADRLHNMKTLYALSP 345

Query:   368 CKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECFDEAMVT 427
              K+QRFAKETLEIF PLANRLGISTWKVQLENLCFKHL P+QH E+S+ L + FDEAM+T
Sbjct:   346 VKQQRFAKETLEIFAPLANRLGISTWKVQLENLCFKHLYPNQHNEMSTMLEDSFDEAMIT 405

Query:   428 SAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLKYAL 466
             SAIEKLEQALK   IS+ VLCGRHKSLYSI+ KMLK  L
Sbjct:   406 SAIEKLEQALKKAGISYHVLCGRHKSLYSIYSKMLKKKL 444

GO:0003824 "catalytic activity" evidence=IEA

GO:0008081 "phosphoric diester hydrolase activity" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0015969 "guanosine tetraphosphate metabolic process" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0008728 "GTP diphosphokinase activity" evidence=IGI

GO:0009611 "response to wounding" evidence=IEP;RCA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0007165 "signal transduction" evidence=RCA

GO:0009414 "response to water deprivation" evidence=RCA

GO:0009620 "response to fungus" evidence=RCA

GO:0009695 "jasmonic acid biosynthetic process" evidence=RCA

GO:0009723 "response to ethylene stimulus" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=RCA

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

GO:0042538 "hyperosmotic salinity response" evidence=RCA

TAIR\|locus:2014335 RSH3 "RELA/SPOT homolog 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3A9Z8 relA "GTP pyrophosphokinase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|CHY_2223 CHY_2223 "GTP pyrophosphokinase" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]	Back alignment and assigned GO terms

TIGR_CMR\|DET_0005 DET_0005 "GTP pyrophosphokinase" [Dehalococcoides ethenogenes 195 (taxid:243164)]	Back alignment and assigned GO terms

TIGR_CMR\|GSU_2236 GSU_2236 "GTP pyrophosphokinase" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

UNIPROTKB\|P0AG24 spoT "guanosine 3'-diphosphate 5'-triphosphate 3'-diphosphatase [multifunctional]" [Escherichia coli K-12 (taxid:83333)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_4973 CPS_4973 "guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

TIGR_CMR\|BA_4637 BA_4637 "GTP pyrophosphokinase" [Bacillus anthracis str. Ames (taxid:198094)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_0359 SO_0359 "guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase" [Shewanella oneidensis MR-1 (taxid:211586)]	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
Query		532
COG0317		701	COG0317, SpoT, Guanosine polyphosphate pyrophospho	1e-75
TIGR00691		683	TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/Sp	5e-62
pfam13328		156	pfam13328, HD_4, HD domain	6e-52
PRK11092		702	PRK11092, PRK11092, bifunctional (p)ppGpp syntheta	6e-51
PRK10872		743	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophos	2e-26
pfam01966		111	pfam01966, HD, HD domain	2e-08
smart00471		124	smart00471, HDc, Metal dependent phosphohydrolases	4e-05
cd00077		145	cd00077, HDc, Metal dependent phosphohydrolases wi	2e-04

>gnl\|CDD\|223394 COG0317, SpoT, Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]	Back alignment and domain information

 Score =  252 bits (645), Expect = 1e-75
 Identities = 104/254 (40%), Positives = 153/254 (60%), Gaps = 10/254 (3%)

Query: 213 YAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGAN 272
             +E L +         +  + KA+Y A +AH GQ R SG+PY+ H +E A +LA +  +
Sbjct: 8   ELEELLDSLATYLPP-VDIELKKAWYYARQAHGGQTRKSGEPYISHPLEVAEILAELHMD 66

Query: 273 STVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEA 332
              +AA LLHDT++D  ++ + I   FG  VA LVEGV+KL ++ +L+     + + ++A
Sbjct: 67  METLAAALLHDTIEDTPVTEELIEEIFGKEVAKLVEGVTKLKKIGQLS-----SEEELQA 121

Query: 333 DRLHTMFLAMA-DARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGIS 391
           + L  M LAM  D R VLIKLADRLHN+ TL  L   KR+R A+ETL+I+ PLA+RLGI 
Sbjct: 122 ENLRKMLLAMVKDIRVVLIKLADRLHNLRTLKNLDEEKRRRIARETLDIYAPLAHRLGIG 181

Query: 392 TWKVQLENLCFKHLNPDQHTELSSKLVE--CFDEAMVTSAIEKLEQALKDKNISFLVLCG 449
             K +LE+L F++L+PDQ+  ++  L E     E  + + + +L + LK   I   V  G
Sbjct: 182 QIKWELEDLSFRYLHPDQYKRIAKLLDEKRLEREQYIENVVSELREELKAAGIKAEVS-G 240

Query: 450 RHKSLYSIHCKMLK 463
           R K +YSI+ KM K
Sbjct: 241 RPKHIYSIYRKMQK 254

Length = 701

>gnl\|CDD\|213552 TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/SpoT family	Back alignment and domain information

>gnl\|CDD\|222047 pfam13328, HD_4, HD domain	Back alignment and domain information

>gnl\|CDD\|236843 PRK11092, PRK11092, bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional	Back alignment and domain information

>gnl\|CDD\|182797 PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	Back alignment and domain information

>gnl\|CDD\|216815 pfam01966, HD, HD domain	Back alignment and domain information

>gnl\|CDD\|214679 smart00471, HDc, Metal dependent phosphohydrolases with conserved 'HD' motif	Back alignment and domain information

>gnl\|CDD\|238032 cd00077, HDc, Metal dependent phosphohydrolases with conserved 'HD' motif	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		532
COG0317		701	SpoT Guanosine polyphosphate pyrophosphohydrolases	100.0
PRK10872		743	relA (p)ppGpp synthetase I/GTP pyrophosphokinase;	100.0
PRK11092		702	bifunctional (p)ppGpp synthetase II/ guanosine-3',	100.0
TIGR00691		683	spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (	100.0
KOG1157		543	consensus Predicted guanosine polyphosphate pyroph	100.0
PF13328		153	HD_4: HD domain; PDB: 3NR1_B.	100.0
cd05399		129	NT_Rel-Spo_like Nucleotidyltransferase (NT) domain	99.15
PF04607		115	RelA_SpoT: Region found in RelA / SpoT proteins; I	98.72
TIGR03276		179	Phn-HD phosphonate degradation operons associated	98.27
COG2357		231	PpGpp synthetase catalytic domain [General functio	97.29
smart00471		124	HDc Metal dependent phosphohydrolases with conserv	95.5
PF01966		122	HD: HD domain; InterPro: IPR006674 This domain is	94.94
TIGR03401		228	cyanamide_fam HD domain protein, cyanamide hydrata	93.73
PRK12703		339	tRNA 2'-O-methylase; Reviewed	93.14
cd00077		145	HDc Metal dependent phosphohydrolases with conserv	93.08
TIGR00295		164	conserved hypothetical protein TIGR00295. This set	85.5
PRK10119		231	putative hydrolase; Provisional	84.79
COG1418		222	Predicted HD superfamily hydrolase [General functi	82.3

>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]	Back alignment and domain information

Probab=100.00  E-value=8.2e-87  Score=732.42  Aligned_cols=290  Identities=39%  Similarity=0.565  Sum_probs=274.1

Q ss_pred             HHHHHHHHHHhhCChhhHHHHHHHHHHHHHHhcCCccccCcchhHHHHHHHHHHHHhCCCHHHHHHHHhhcccccccCCH
Q 009540          213 YAKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSY  292 (532)
Q Consensus       213 ~~~~Ll~~~~~~~~~~d~~ll~kA~~fA~~aH~GQ~RkSGePYI~HpleVA~ILa~Lg~D~etIaAALLHDvVEDT~vTl  292 (532)
                      ...++++.+..+.+..+.. +.+|+.||.++|.+|+|++|+|||.||++||.||+++++|.++++||||||++|||++|.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~-l~kA~~~A~q~H~~q~r~SGePYi~Hpl~Va~iLael~~d~~tl~AaLLHD~vEDt~~t~   86 (701)
T COG0317           8 ELEELLDSLATYLPPVDIE-LKKAWYYARQAHGGQTRKSGEPYISHPLEVAEILAELHMDMETLAAALLHDTIEDTPVTE   86 (701)
T ss_pred             cHHHHHHHHHhcCChHHHH-HHHHHHHHHHHhHhhcCcCCCchhhCHHHHHHHHHHccCCHHHHHHHHccchHhcCCCCH
Confidence            4557788888888766666 999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcHHHHHHHHHhhcccccchHHhhccccchHHHHHHHHHHHhhcc-CchhhHhHHhhhHhhccccCCCCHHHHH
Q 009540          293 DYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLIKLADRLHNMMTLDALPLCKRQ  371 (532)
Q Consensus       293 EeIee~FG~eVA~LVegVTKls~l~~~~r~~~~~~~~~qAE~lRKMLLAma-DiRVVLIKLADRLhNMRtL~~lp~ekq~  371 (532)
                      |+|++.||++|++||+||||+.++..+..     ....|+|++|||||||+ |+||++||||||||||||+..++++||+
T Consensus        87 e~i~~~FG~eVa~LV~GvTkl~~i~~~~~-----~~~~qaen~rkmllAm~~DiRvilIKLADRLhNmrtl~~~~~ek~~  161 (701)
T COG0317          87 ELIEEIFGKEVAKLVEGVTKLKKIGQLSS-----EEELQAENLRKMLLAMVKDIRVVLIKLADRLHNLRTLKNLDEEKRR  161 (701)
T ss_pred             HHHHHHHCHHHHHHHhhHHHhhhhhccCc-----cchhHHHHHHHHHHHhccCccEEEeehhhhhhhcccCccCCHHHHH
Confidence            99999999999999999999999842211     23458999999999997 9999999999999999999998899999


Q ss_pred             HHHHHhhhHHHHHHhhhChHHHHHHHHHHHHhhcChhhHHHHHHHHHHHH--hHHhHHHHHHHHHHHHHhcCcccccccc
Q 009540          372 RFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECF--DEAMVTSAIEKLEQALKDKNISFLVLCG  449 (532)
Q Consensus       372 riA~ETl~IYAPLA~RLGI~~iK~ELEDLsFkyL~Pe~Y~~I~~~L~e~~--re~~I~~vi~~L~~~L~~~gI~~~~V~G  449 (532)
                      ++|+||++|||||||||||+++|||||||||+||+|++|+.|+++|++++  |+++|++++.+|++.|+++||+++ |+|
T Consensus       162 riakETl~IyAPLA~RLGi~~iK~ELEDlsFr~l~P~~Y~~I~~~l~e~r~~re~~i~~~~~~l~~~L~~~gi~a~-v~g  240 (701)
T COG0317         162 RIARETLDIYAPLAHRLGIGQIKWELEDLSFRYLHPDQYKRIAKLLDEKRLEREQYIENVVSELREELKAAGIKAE-VSG  240 (701)
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHhhhhhhhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeEE-EEc
Confidence            99999999999999999999999999999999999999999999999986  899999999999999999999996 999


Q ss_pred             cccchHHHHHHHHhcCCCC--ccccccceEEecCCcchhhhhhhhhhhhhhhhhhccCccccCCcceeceec
Q 009540          450 RHKSLYSIHCKMLKYALPS--LPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQL  519 (532)
Q Consensus       450 R~KhiYSIy~KM~kK~l~f--i~Dlia~Riiv~~~~~~~~CY~a~~~~tvLGiVH~lWkPI~~~~f~dyIa~  519 (532)
                      |+|||||||+||++|++.|  |+||+||||||+   ++.+||++      ||+||++|+|+ ||+||||||+
T Consensus       241 R~KhiYSIyrKM~~k~~~f~~I~Dl~avRiIv~---~~~dCY~~------LGiVH~~~kp~-PgrFKDYIA~  302 (701)
T COG0317         241 RPKHIYSIYRKMQKKKLSFDEIYDVRAVRIIVD---TIPDCYTA------LGIVHTLWKPI-PGEFDDYIAN  302 (701)
T ss_pred             CCCcccHHHHHHHHcccChhhhhhheeEEEEEC---ChHHHHHH------HHHHHhcCcCC-CCcccccccc
Confidence            9999999999999999999  999999999997   57999998      99999999999 9999999997

>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	Back alignment and domain information

>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional	Back alignment and domain information

>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family	Back alignment and domain information

>KOG1157 consensus Predicted guanosine polyphosphate pyrophosphohydrolase/synthase [Signal transduction mechanisms]	Back alignment and domain information

>PF13328 HD_4: HD domain; PDB: 3NR1_B	Back alignment and domain information

>cd05399 NT_Rel-Spo_like Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases	Back alignment and domain information

>PF04607 RelA_SpoT: Region found in RelA / SpoT proteins; InterPro: IPR007685 The functions of Escherichia coli RelA and SpoT differ somewhat	Back alignment and domain information

>TIGR03276 Phn-HD phosphonate degradation operons associated HDIG domain protein	Back alignment and domain information

>COG2357 PpGpp synthetase catalytic domain [General function prediction only]	Back alignment and domain information

>smart00471 HDc Metal dependent phosphohydrolases with conserved 'HD' motif	Back alignment and domain information

>PF01966 HD: HD domain; InterPro: IPR006674 This domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity []	Back alignment and domain information

>TIGR03401 cyanamide_fam HD domain protein, cyanamide hydratase family	Back alignment and domain information

>PRK12703 tRNA 2'-O-methylase; Reviewed	Back alignment and domain information

>cd00077 HDc Metal dependent phosphohydrolases with conserved 'HD' motif	Back alignment and domain information

>TIGR00295 conserved hypothetical protein TIGR00295	Back alignment and domain information

>PRK10119 putative hydrolase; Provisional	Back alignment and domain information

>COG1418 Predicted HD superfamily hydrolase [General function prediction only]	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		532
1vj7_A		393	Crystal Structure Of The Bifunctional Catalytic Fra		2e-37
3nr1_A		178	A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Pl		2e-09
3nqw_A		179	A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Pl		6e-08

>pdb|1VJ7|A Chain A, Crystal Structure Of The Bifunctional Catalytic Fragment Of Relseq, The RelaSPOT HOMOLOG FROM STREPTOCOCCUS EQUISIMILIS. Length = 393

Back alignment and structure

Iteration: 1

Score = 154 bits (388), Expect = 2e-37, Method: Compositional matrix adjust. Identities = 91/233 (39%), Positives = 140/233 (60%), Gaps = 10/233 (4%) Query: 232 FVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLS 291 FV KA A AH Q+R SG+PY++H ++ A +LA + ++ VA G LHD ++D ++ Sbjct: 27 FVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDIT 86 Query: 292 YDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLI 350 D I FG V D+V+GV+KL ++ + E A M +AM+ D R +L+ Sbjct: 87 LDNIEFDFGKDVRDIVDGVTKLGKVEYKSHEEQLAENH------RKMLMAMSKDIRVILV 140 Query: 351 KLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQH 410 KLADRLHNM TL L K++R ++ET+EI+ PLA+RLGIS K +LE+L F++LN + Sbjct: 141 KLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEF 200 Query: 411 TELSSKLVECF--DEAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKM 461 ++S + E EA+V + K++ ++ + F + GR K +YSI+ KM Sbjct: 201 YKISHMMNEKRREREALVDDIVTKIKSYTTEQGL-FGDVYGRPKHIYSIYRKM 252

PyMOL of 1vj7

>pdb|3NR1|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A Role In Starvation Responses Length = 178

Back alignment and structure

>pdb|3NQW|A Chain A, A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Plays A Role In Starvation Responses Length = 179

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		532
1vj7_A		393	Bifunctional RELA/SPOT; HD domain, alpha beta 2-la	3e-86
3nr1_A		178	HD domain-containing protein 3; stringent response	1e-58
3nqw_A		179	CG11900; stringent response, pyrophosphohydrolase,	3e-55
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-13
3l9d_A		255	SMU.1046C, putative GTP pyrophosphokinase; transfe	2e-07

>1vj7_A Bifunctional RELA/SPOT; HD domain, alpha beta 2-layer sandwich, helix bundle, mangan PPG2':3'P, (P)PPGPP, PPGPP; HET: GDP GPX; 2.10A {Streptococcus dysgalactiae subsp} SCOP: a.211.1.1 d.218.1.8 Length = 393	Back alignment and structure

 Score =  270 bits (694), Expect = 3e-86
 Identities = 91/237 (38%), Positives = 140/237 (59%), Gaps = 10/237 (4%)

Query: 230 EDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAF 289
             FV KA   A  AH  Q+R SG+PY++H ++ A +LA +  ++  VA G LHD ++D  
Sbjct: 25  AAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTD 84

Query: 290 LSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAV 348
           ++ D I   FG  V D+V+GV+KL ++   + E         A+    M +AM+ D R +
Sbjct: 85  ITLDNIEFDFGKDVRDIVDGVTKLGKVEYKSHE------EQLAENHRKMLMAMSKDIRVI 138

Query: 349 LIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPD 408
           L+KLADRLHNM TL  L   K++R ++ET+EI+ PLA+RLGIS  K +LE+L F++LN  
Sbjct: 139 LVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNET 198

Query: 409 QHTELSSKLVECFD--EAMVTSAIEKLEQALKDKNISFLVLCGRHKSLYSIHCKMLK 463
           +  ++S  + E     EA+V   + K++    ++ +   V  GR K +YSI+ KM  
Sbjct: 199 EFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGDVY-GRPKHIYSIYRKMRD 254

PyMOL of 1vj7

>3nr1_A HD domain-containing protein 3; stringent response, pyrophosphohydrolase, HD (histidine and acid) family, PPGPP hydrolase, hydrolase; 1.90A {Homo sapiens} Length = 178	Back alignment and structure

>3nqw_A CG11900; stringent response, pyrophosphohydrolase, HD (histidine and acid) family ,PPGPP hydrolase, hydrolase; 2.90A {Drosophila melanogaster} Length = 179	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>3l9d_A SMU.1046C, putative GTP pyrophosphokinase; transferase; 2.48A {Streptococcus mutans} Length = 255	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		532
1vj7_A		393	Bifunctional RELA/SPOT; HD domain, alpha beta 2-la	100.0
3nqw_A		179	CG11900; stringent response, pyrophosphohydrolase,	100.0
3nr1_A		178	HD domain-containing protein 3; stringent response	100.0
3l9d_A		255	SMU.1046C, putative GTP pyrophosphokinase; transfe	99.86
2be3_A		226	GTP pyrophosphokinase; structural genomics, PSI, p	99.46
2pq7_A		220	Predicted HD superfamily hydrolase; 104161995, HD	94.89
3b57_A		209	LIN1889 protein; Q92AN1, X-RAY, NESG, structural g	94.41
3dto_A		223	BH2835 protein; all alpha-helical protein, structu	94.23
2qgs_A		225	Protein Se1688; alpha-helical protein, structural	93.7
2pjq_A		231	Uncharacterized protein LP_2664; LPR71, NESG, stru	93.48
3djb_A		223	Hydrolase, HD family; all alpha-helical protein.,	93.36
2paq_A		201	5'-deoxynucleotidase YFBR; HD domain phosphoh stru	91.9

>1vj7_A Bifunctional RELA/SPOT; HD domain, alpha beta 2-layer sandwich, helix bundle, mangan PPG2':3'P, (P)PPGPP, PPGPP; HET: GDP GPX; 2.10A {Streptococcus dysgalactiae subsp} SCOP: a.211.1.1 d.218.1.8	Back alignment and structure

Probab=100.00  E-value=7.5e-83  Score=667.56  Aligned_cols=289  Identities=35%  Similarity=0.477  Sum_probs=260.7

Q ss_pred             HHHHHHHHHhhCChhhHHHHHHHHHHHHHHhcCCccccCcchhHHHHHHHHHHHHhCCCHHHHHHHHhhcccccccCCHH
Q 009540          214 AKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYD  293 (532)
Q Consensus       214 ~~~Ll~~~~~~~~~~d~~ll~kA~~fA~~aH~GQ~RkSGePYI~HpleVA~ILa~Lg~D~etIaAALLHDvVEDT~vTlE  293 (532)
                      +++|+..+..+++..|.+++.+|+.||.++|.||+|++|+|||.||++||.||+++|+|.++++||||||++|||.+|.+
T Consensus         9 ~~~l~~~~~~~~~~~~~~~l~~A~~~A~~aH~gQ~rksGePYi~Hpl~VA~iLa~l~~D~~~i~AALLHDvvEDt~~t~e   88 (393)
T 1vj7_A            9 GEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLD   88 (393)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTCBCTTSCBTTHHHHHHHHHHHHTTCCHHHHHHHHHTTHHHHSSCCHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhccCcCCCCCcHHHHHHHHHHHHHHhcCCHHHHHHHHhhhHHhcCCCCHH
Confidence            35788888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcHHHHHHHHHhhcccccchHHhhccccchHHHHHHHHHHHhhcc-CchhhHhHHhhhHhhccccCCCCHHHHHH
Q 009540          294 YIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLIKLADRLHNMMTLDALPLCKRQR  372 (532)
Q Consensus       294 eIee~FG~eVA~LVegVTKls~l~~~~r~~~~~~~~~qAE~lRKMLLAma-DiRVVLIKLADRLhNMRtL~~lp~ekq~r  372 (532)
                      +|++.||++|+.||+||||+.++++..+      ...|+|++|||||||+ |+||++|||||||||||++..+++++|++
T Consensus        89 ~I~~~FG~~Va~lV~gvTk~~~~~~~~~------~~~qae~~Rkmllam~~D~RvvlIKLADRlhNmRtl~~~~~ek~~~  162 (393)
T 1vj7_A           89 NIEFDFGKDVRDIVDGVTKLGKVEYKSH------EEQLAENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQER  162 (393)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHC--------------------CCSCTTTSCCCHHHHHHHHHHHHHHHHTCC------HHH
T ss_pred             HHHHHhCHHHHHHHHHHHhcccCCcccH------HHHHHHHHHHHHHhhcCCcceeeeeHHHHHHccCchhhCChHHHHH
Confidence            9999999999999999999998864221      3458999999999997 99999999999999999999999999999


Q ss_pred             HHHHhhhHHHHHHhhhChHHHHHHHHHHHHhhcChhhHHHHHHHHHHHH--hHHhHHHHHHHHHHHHHhcCccccccccc
Q 009540          373 FAKETLEIFVPLANRLGISTWKVQLENLCFKHLNPDQHTELSSKLVECF--DEAMVTSAIEKLEQALKDKNISFLVLCGR  450 (532)
Q Consensus       373 iA~ETl~IYAPLA~RLGI~~iK~ELEDLsFkyL~Pe~Y~~I~~~L~e~~--re~~I~~vi~~L~~~L~~~gI~~~~V~GR  450 (532)
                      +|+||++|||||||||||++||||||||||+||+|+.|+.|+++|.+.+  ++.+|+++++.|++.|++.||+++ |+||
T Consensus       163 iA~Etl~iyaPLA~rLGi~~ik~ELEdl~f~~l~p~~y~~i~~~l~~~r~~r~~~i~~i~~~l~~~L~~~gi~~~-v~~R  241 (393)
T 1vj7_A          163 ISRETMEIYAPLAHRLGISRIKWELEDLAFRYLNETEFYKISHMMNEKRREREALVDDIVTKIKSYTTEQGLFGD-VYGR  241 (393)
T ss_dssp             HHHHHHHTHHHHHHHTTCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHTTTCCCE-EEEC
T ss_pred             HHHHHHHHHHHHHhhcChhHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCceE-EEEE
Confidence            9999999999999999999999999999999999999999999999876  789999999999999999999996 9999


Q ss_pred             ccchHHHHHHHHhcCCCC--ccccccceEEecCCcchhhhhhhhhhhhhhhhhhccCccccCCcceeceec
Q 009540          451 HKSLYSIHCKMLKYALPS--LPNLIRESFVTEYSSLSHACFQKFQLLTIHGIGHILWKILCLHYLSVNIQL  519 (532)
Q Consensus       451 ~KhiYSIy~KM~kK~l~f--i~Dlia~Riiv~~~~~~~~CY~a~~~~tvLGiVH~lWkPI~~~~f~dyIa~  519 (532)
                      +||+||||+||++|+++|  |+|++++|||+.   .+.+||++      +|+||++|+|+ +++|||||++
T Consensus       242 ~K~~~Si~~Km~rk~~~~~~i~Di~giRIi~~---~~~dcy~v------l~~i~~~~~~~-~~~~kDyIa~  302 (393)
T 1vj7_A          242 PKHIYSIYRKMRDKKKRFDQIFDLIAIRCVME---TQSDVYAM------VGYIHELWRPM-PGRFKDYIAA  302 (393)
T ss_dssp             CCCHHHHHHHHHHHGGGCCTTGGGCEEEEEES---SHHHHHHH------HHHHHHHSCBC-TTCCEETTTS
T ss_pred             eCChHHHHHHHHHhCCChhhhcccceEEEEEC---CHHHHHHH------HHHHHhcCCCC-CCcccccccC
Confidence            999999999999999988  999999999997   47999998      99999999999 8999999995

PyMOL of 1vj7

>3nqw_A CG11900; stringent response, pyrophosphohydrolase, HD (histidine and acid) family ,PPGPP hydrolase, hydrolase; 2.90A {Drosophila melanogaster}	Back alignment and structure

>3nr1_A HD domain-containing protein 3; stringent response, pyrophosphohydrolase, HD (histidine and acid) family, PPGPP hydrolase, hydrolase; 1.90A {Homo sapiens}	Back alignment and structure

>3l9d_A SMU.1046C, putative GTP pyrophosphokinase; transferase; 2.48A {Streptococcus mutans}	Back alignment and structure

>2be3_A GTP pyrophosphokinase; structural genomics, PSI, protein structure initiative, midwest center structural genomics, MCSG, transferase; HET: PG4; 2.40A {Streptococcus pneumoniae} SCOP: d.218.1.8	Back alignment and structure

>2pq7_A Predicted HD superfamily hydrolase; 104161995, HD domain, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.45A {Uncultured thermotogales bacterium} SCOP: a.211.1.1	Back alignment and structure

>3b57_A LIN1889 protein; Q92AN1, X-RAY, NESG, structural genomics, PSI-2, protein structure initiative; 3.00A {Listeria innocua CLIP11262} SCOP: a.211.1.1	Back alignment and structure

>3dto_A BH2835 protein; all alpha-helical protein, structural genomics, PSI-2, protein structure initiative; 3.30A {Bacillus halodurans} SCOP: a.211.1.1	Back alignment and structure

>2qgs_A Protein Se1688; alpha-helical protein, structural genomics, PSI-2, protein S initiative, northeast structural genomics consortium; 2.00A {Staphylococcus epidermidis} SCOP: a.211.1.1	Back alignment and structure

>2pjq_A Uncharacterized protein LP_2664; LPR71, NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Lactobacillus plantarum WCFS1} SCOP: a.211.1.1	Back alignment and structure

>3djb_A Hydrolase, HD family; all alpha-helical protein., structural genomics, PSI-2, protein structure initiative; 2.90A {Bacillus thuringiensis serovarkonkukian} SCOP: a.211.1.1	Back alignment and structure

>2paq_A 5'-deoxynucleotidase YFBR; HD domain phosphoh structural genomics, PSI, protein structure initiative, MID center for structural genomics, MCSG; 2.10A {Escherichia coli} SCOP: a.211.1.1 PDB: 2par_A* 2pau_A*	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		532
d1vj7a1		192	a.211.1.1 (A:5-196) Stringent response-like protei	1e-44

>d1vj7a1 a.211.1.1 (A:5-196) Stringent response-like protein RelA N-terminal domain {Streptococcus equisimilis [TaxId: 119602]} Length = 192	Back information, alignment and structure


class: All alpha proteins
fold: HD-domain/PDEase-like
superfamily: HD-domain/PDEase-like
family: HD domain
domain: Stringent response-like protein RelA N-terminal domain
species: Streptococcus equisimilis [TaxId: 119602]

 Score =  153 bits (388), Expect = 1e-44
 Identities = 78/194 (40%), Positives = 116/194 (59%), Gaps = 7/194 (3%)

Query: 214 AKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANS 273
            +E +A A          FV KA   A  AH  Q+R SG+PY++H ++ A +LA +  ++
Sbjct: 5   GEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDA 64

Query: 274 TVVAAGLLHDTLDDAFLSYDYIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEAD 333
             VA G LHD ++D  ++ D I   FG  V D+V+GV+KL       +    + +   A+
Sbjct: 65  VTVACGFLHDVVEDTDITLDNIEFDFGKDVRDIVDGVTKL------GKVEYKSHEEQLAE 118

Query: 334 RLHTMFLAMA-DARAVLIKLADRLHNMMTLDALPLCKRQRFAKETLEIFVPLANRLGIST 392
               M +AM+ D R +L+KLADRLHNM TL  L   K++R ++ET+EI+ PLA+RLGIS 
Sbjct: 119 NHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQERISRETMEIYAPLAHRLGISR 178

Query: 393 WKVQLENLCFKHLN 406
            K +LE+L F++LN
Sbjct: 179 IKWELEDLAFRYLN 192

PyMOL of d1vj7a1

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		532
d1vj7a1		192	Stringent response-like protein RelA N-terminal do	100.0
d1vj7a2		175	Stringent response-like protein RelA domain 2 {Str	99.93
d2be3a1		203	Putative GTP pyrophosphokinase SP1097 {Streptococc	99.23
d2qgsa1		216	Uncharacterized protein SE1688 {Staphylococcus epi	93.63
d3dtoa1		212	Uncharacterized protein BH2835 {Bacillus haloduran	93.62
d3b57a1		201	Uncharacterized protein Lin1889 {Listeria innocua	92.98
d2pq7a1		217	Predicted hydrolase mes0020 {Uncultured thermotoga	91.39
d3djba1		213	Uncharacterized protein BT9727_1981 {Bacillus thur	89.19
d2pjqa1		215	Uncharacterized protein LP2664 {Lactobacillus plan	88.91

>d1vj7a1 a.211.1.1 (A:5-196) Stringent response-like protein RelA N-terminal domain {Streptococcus equisimilis [TaxId: 119602]}	Back information, alignment and structure

class: All alpha proteins
fold: HD-domain/PDEase-like
superfamily: HD-domain/PDEase-like
family: HD domain
domain: Stringent response-like protein RelA N-terminal domain
species: Streptococcus equisimilis [TaxId: 119602]

Probab=100.00  E-value=4.3e-57  Score=428.61  Aligned_cols=187  Identities=42%  Similarity=0.608  Sum_probs=163.9

Q ss_pred             HHHHHHHHHhhCChhhHHHHHHHHHHHHHHhcCCccccCcchhHHHHHHHHHHHHhCCCHHHHHHHHhhcccccccCCHH
Q 009540          214 AKEFLANAQLKHKIFREDFVIKAFYEAERAHRGQMRASGDPYLLHCVETAMLLAAIGANSTVVAAGLLHDTLDDAFLSYD  293 (532)
Q Consensus       214 ~~~Ll~~~~~~~~~~d~~ll~kA~~fA~~aH~GQ~RkSGePYI~HpleVA~ILa~Lg~D~etIaAALLHDvVEDT~vTlE  293 (532)
                      .++++..++.|.+..|.++|++|++||.++|.||+|++|+||+.||++||.+|+++++|+++++||||||++|||.+|.+
T Consensus         5 ~e~~l~~~~~yl~~~d~~~i~~A~~~A~~~H~gq~r~sG~py~~H~~~VA~iL~~~~~d~~~i~AalLhd~~edt~~t~e   84 (192)
T d1vj7a1           5 GEEVVALAAKYMNETDAAFVKKALDYATAAHFYQVRKSGEPYIVHPIQVAGILADLHLDAVTVACGFLHDVVEDTDITLD   84 (192)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTTCBCTTSCBTTHHHHHHHHHHHHTTCCHHHHHHHHHTTHHHHSSCCHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcccChHHHHHHHHHHHHHHHHhcCChHHhhhhheechhhhchhHHH
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcHHHHHHHHHhhcccccchHHhhccccchHHHHHHHHHHHhhcc-CchhhHhHHhhhHhhccccCCCCHHHHHH
Q 009540          294 YIFRTFGAGVADLVEGVSKLSQLSKLARENNTASKTVEADRLHTMFLAMA-DARAVLIKLADRLHNMMTLDALPLCKRQR  372 (532)
Q Consensus       294 eIee~FG~eVA~LVegVTKls~l~~~~r~~~~~~~~~qAE~lRKMLLAma-DiRVVLIKLADRLhNMRtL~~lp~ekq~r  372 (532)
                      +|+++||++|+++|++|||+..+....+      ...+++++|||+++|. |+||++|||||||||||++..++++++++
T Consensus        85 ~I~~~FG~~Va~lV~~ltk~~~~~~~~~------~~~~ae~~rkmlla~~~d~rvvlIKLADRLhnlrtl~~~~~~k~~~  158 (192)
T d1vj7a1          85 NIEFDFGKDVRDIVDGVTKLGKVEYKSH------EEQLAENHRKMLMAMSKDIRVILVKLADRLHNMRTLKHLRKDKQER  158 (192)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHC--------------------CCSCTTTSCCCHHHHHHHHHHHHHHHHTCC------HHH
T ss_pred             HHHHhcchhHHHHHHHHHhhcccccccc------chHHHHHHHHHHHhhccCceeehhHHHHHHhhccccccCChHHHHH
Confidence            9999999999999999999998775332      3457899999999997 99999999999999999999999999999


Q ss_pred             HHHHhhhHHHHHHhhhChHHHHHHHHHHHHhhcC
Q 009540          373 FAKETLEIFVPLANRLGISTWKVQLENLCFKHLN  406 (532)
Q Consensus       373 iA~ETl~IYAPLA~RLGI~~iK~ELEDLsFkyL~  406 (532)
                      +|+||+++|+|||||||+|++|||||||||||||
T Consensus       159 ~a~Et~~iyaplA~rLG~~~ik~eLEdl~f~~L~  192 (192)
T d1vj7a1         159 ISRETMEIYAPLAHRLGISRIKWELEDLAFRYLN  192 (192)
T ss_dssp             HHHHHHHTHHHHHHHTTCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999986

PyMOL of d1vj7a1

>d1vj7a2 d.218.1.8 (A:197-371) Stringent response-like protein RelA domain 2 {Streptococcus equisimilis [TaxId: 119602]}	Back information, alignment and structure

>d2be3a1 d.218.1.8 (A:1-203) Putative GTP pyrophosphokinase SP1097 {Streptococcus pneumoniae [TaxId: 1313]}	Back information, alignment and structure

>d2qgsa1 a.211.1.1 (A:1-216) Uncharacterized protein SE1688 {Staphylococcus epidermidis [TaxId: 1282]}	Back information, alignment and structure

>d3dtoa1 a.211.1.1 (A:2-213) Uncharacterized protein BH2835 {Bacillus halodurans [TaxId: 86665]}	Back information, alignment and structure

>d3b57a1 a.211.1.1 (A:1-201) Uncharacterized protein Lin1889 {Listeria innocua [TaxId: 1642]}	Back information, alignment and structure

>d2pq7a1 a.211.1.1 (A:1-217) Predicted hydrolase mes0020 {Uncultured thermotogales bacterium [TaxId: 221214]}	Back information, alignment and structure

>d3djba1 a.211.1.1 (A:2-214) Uncharacterized protein BT9727_1981 {Bacillus thuringiensis [TaxId: 1428]}	Back information, alignment and structure

>d2pjqa1 a.211.1.1 (A:1-215) Uncharacterized protein LP2664 {Lactobacillus plantarum [TaxId: 1590]}	Back information, alignment and structure