Citrus Sinensis ID: 003851

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-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-

MAHVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKVISPREKFPWQEEEEEEEEVQNEPETDVESRVRSEPFSSALPNRFVSAPWIHGTDSKEIKFDSPQTKITTKKEDIGDDGLLGSFEKTVVHSAVKEKTVIELDKEGDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLTGEN

cccEEEEEEccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccHHHHHHcccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccEEEccccccHHHHHHHHHHHHHcccEEEEEEEcccHHHHHHHHHHHHHHHccEEEEEEccEEEEEEcccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccEEcccccHHHHHHHHHHHHHHHccEEEEEEcccccccHHHHHHHHHHHccccEEEEEcccEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHHccEEEEEEEcccccEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccc

ccEEEEEEEEccccccccEEEccccccccccccEEEEEEEcccccccHHHHHHHHHHcccccccHHHHHHHcccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccHHccccccHHccccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccEEEEEEcccccHcHHHHHHHHHHHcccEEEEEcccEEEEEEcccccccccccccccccccccccccHHHHccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccEEccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccEEEEccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEEEEcccccEEEEEEcccccccccccccccHcHHHHHHHHHHHHHHHHHHHccccccc

MAHVVVLQakyspltqpavhylplkpqsqcsnsfrsirigicFSHLTIQAQLgttrtkrkvkpSFFEQIRhkwshkvisprekfpwqeeeeeeeevqnepetdvesrvrsepfssalpnrfvsapwihgtdskeikfdspqtkittkkedigddgllgsFEKTVVHSAVKEKTVIELdkegdynkelktdevkidanpielskdrhrevgslnqkqikgyhevddpsvlpwkrntdrrRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKlkfeephslqmKRTHEILERRTGGLVIWRSGSSVVLFRgmayklpcvqsftkhnhtqqtQDVTNEVMRnvgehpprsamesyvpdsannlenlsKEELMDLCELNYLLDelgprfkdwpgreplpvdadllppvvpdykpplrllpygikpglrdcetTEFRRLarktpphfalgRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKltggtllcrnkdyivfyrgndflppvvTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAAtsrwgrqpsyedvEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVQEsldpaelpsdletITNEERFLLRKMglsmkpylllgrrgiydgtienmHLHWKYRELVKIIVKGKSFAQVKQIAISLEaesggvlvsldktpkgIAIIVYRgknyvrplklrpqNLLTRRQALARSVELQRRTKtshlgltgen

MAHVVVLQakyspltqpaVHYLPLKPQSQCSNSFRSIRIGICFSHLTIqaqlgttrtkrkVKPSffeqirhkwshkvisprekfpwqeeeeeeeevqnepetdvesrvrsepfssalpnrfvsapwihgtdskeikfdspqtkittkkedigddgllGSFEktvvhsavkektvieldkegdynkelktdevkidanpielskdrhrevgslnqkqikgyhevddpsvlpwkrntdrrrrsntelaekmipehelqrLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLkfeephslqmkrtheilerrtgglviWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPdykpplrllpygikpglrDCETTEFRRLarktpphfalgrnrELQGLAKAMVKLWEKSaiakiaikrdvmntRNERMAEelkkltggtllcrNKDYIVFYRGNDFLPPVVTDAVKErskltdirqdeeERARHVASALIELKAKGFVGSLVAGTLAEtlaatsrwgrqpsyedVEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVqesldpaelpsdletitNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISleaesggvlvsldktpkGIAIIvyrgknyvrplklrpqnlLTRRQALarsvelqrrtktshlgltgen

MAHVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKVISPREKFPWQeeeeeeeeVQNEPETDVESRVRSEPFSSALPNRFVSAPWIHGTDSKEIKFDSPQTKITTKKEDIGDDGLLGSFEKTVVHSAVKEKTVIELDKEGDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGREplpvdadllppvvpdYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYleqklalakrklkmadkalakVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLTGEN

***VVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKV*******************************************FVSAPWIH**************************GLLGSFEKTVVHSAVKEKTVIEL********************************************************************************LRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTK*********************************************LMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAV******************HVASALIELKAKGFVGSLVAGTLAETLAATSRWG*********************SLLRYLEQKLALAK****************************ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLT**************************

**HVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRI******************************************************************************************************************************************************************************************************************IPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAY**************************************************************NYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDE****************************************************************YLEQKLALAKRKLKMADKALAKV****************TNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQAL***************G*****

MAHVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKVISPREK******************************SSALPNRFVSAPWIHGTDSKEIKFDSPQTKITTKKEDIGDDGLLGSFEKTVVHSAVKEKTVIELDKEGDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLTGEN

*AHVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKVISPREKFPWQEEE******************************************************************************VKEKTVIELDKEGDYNKELKTDEVKIDANPI*********************************************LAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPC*************************************************EELMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIEL*********VAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTS*L******

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ooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MAHVVVLQAKYSPLTQPAVHYLPLKPQSQCSNSFRSIRIGICFSHLTIQAQLGTTRTKRKVKPSFFEQIRHKWSHKVISPREKFPWQEEEEEEEEVQNEPETDVESRVRSEPFSSALPNRFVSAPWIHGTDSKEIKFDSPQTKITTKKEDIGDDGLLGSFEKTVVHSAVKEKTVIELDKEGDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLxxxxxxxxxxxxxxxxxxxxxxxxxxxxLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLTGEN

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		791	2.2.26 [Sep-21-2011]
Q6YYA3		725	Chloroplastic group IIA i	no	no	0.699	0.762	0.390	1e-102
Q9FYT6		715	Chloroplastic group IIA i	N/A	no	0.619	0.685	0.417	7e-99
Q9LF10		720	Chloroplastic group IIA i	no	no	0.634	0.697	0.393	6e-96
Q67XL4		444	Uncharacterized CRM domai	no	no	0.184	0.328	0.396	6e-22
Q9SL79		701	CRS2-associated factor 1,	no	no	0.174	0.196	0.286	3e-07
Q84N49		674	CRS2-associated factor 1,	N/A	no	0.113	0.133	0.351	4e-07
Q6Z4U2		428	CRS2-associated factor 1,	no	no	0.085	0.158	0.351	6e-07
Q5VMQ5		701	CRS2-associated factor 1,	no	no	0.118	0.134	0.336	7e-07
Q0J7J7		366	CRS2-associated factor 2,	no	no	0.077	0.166	0.373	8e-06
Q657G7		607	CRS2-associated factor 2,	no	no	0.113	0.148	0.308	9e-06

>sp\|Q6YYA3\|CRS1_ORYSJ Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os08g0360100 PE=2 SV=1	Back alignment and function desciption

 Score =  372 bits (955), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 224/574 (39%), Positives = 334/574 (58%), Gaps = 21/574 (3%)

Query: 228 VLPWKRNTDR------RRRSNTEL---AEKMIPEHELQRLRNISLRMLERTKVGSAGITQ 278
            +PW    D       RR   T +   AE  +   EL+RLR  +       +   AGIT 
Sbjct: 124 AVPWAAARDEETKVVLRREKKTRVPTRAETELEAGELERLRRAARGKERWARAKKAGITD 183

Query: 279 ALVDSIHEKW-KLDEVVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAY 337
            +V+ +  +W K  E+  ++  EP    M R  EILE +TGGLV+W  G    ++RG +Y
Sbjct: 184 EVVEEVRGQWAKGQELAGVRIVEPLRRCMDRAREILEIKTGGLVVWTRGGIHFVYRGSSY 243

Query: 338 KLPCVQSFTKH----NHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEEL 393
               +++  +H    N+ ++   VT+    + G++  +    +   D A++ ++   +  
Sbjct: 244 ----LENAKRHRDFVNYNEELSPVTSNNPTSQGKYWSKDETLTNDNDEADDKDDKPIKGT 299

Query: 394 MDLCELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCET 453
           +   E+N LLD LGPRF DW    PLPVDADLLP VVPD+K P R  P G++P L D E 
Sbjct: 300 LYEREVNRLLDSLGPRFIDWWWNTPLPVDADLLPEVVPDFKTPFRQCPPGVRPALADEEL 359

Query: 454 TEFRRLARKTPPHFALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELK 513
           T  R+ AR  P HF LGRN +LQGLA A++KLWEKS IAK+A+K  + NT +E+MA  LK
Sbjct: 360 TYLRKHARPLPTHFVLGRNTKLQGLAAAILKLWEKSLIAKVAVKVGIQNTNHEQMARNLK 419

Query: 514 KLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERAR-HVASALIEL 572
           +LTGGT++ RNKDYI+ YRG DFLP  V ++V ER      +Q +EE AR  +A +L  +
Sbjct: 420 RLTGGTVILRNKDYIIIYRGKDFLPGGVAESVIERESQVHDQQAKEEEARLKMADSLQMI 479

Query: 573 KAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYLEQKLALAK 632
                  S V GT  E         R+ + E+  ++  ++   R    L+  E +L++  
Sbjct: 480 VGLSSERSYV-GTFREYQDFHDSHARR-TTENNFRIQLEAKKHRLEKELKDQEWRLSMLT 537

Query: 633 RKLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTI 692
           +K++ +++ LAK+  S  P++   D E +T EER + RK+GL M  ++LLGRRG+++G I
Sbjct: 538 KKIERSNQVLAKLHSSWSPSKKDGDRELLTEEERRIFRKIGLKMDEHVLLGRRGVFEGVI 597

Query: 693 ENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNY 752
           E +H HWK++E+VK+I K    +Q+   ++ LE E+GG L+++++     AII+YRGKNY
Sbjct: 598 EEIHQHWKHKEVVKVITKQNQASQITYTSMMLEVETGGTLIAIERFTTSHAIILYRGKNY 657

Query: 753 VRPLKLRPQNLLTRRQALARSVELQRRTKTSHLG 786
            RP K  P NLLT+R+AL RS+E+QRR    +  
Sbjct: 658 RRPTKSAPSNLLTKREALQRSIEVQRRGSMKYFA 691

Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.
Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q9FYT6\|CRS1_MAIZE Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Zea mays GN=CRS1 PE=1 SV=1	Back alignment and function description

>sp\|Q9LF10\|CRS1_ARATH Chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic OS=Arabidopsis thaliana GN=At5g16180 PE=2 SV=2	Back alignment and function description

>sp\|Q67XL4\|Y3544_ARATH Uncharacterized CRM domain-containing protein At3g25440, chloroplastic OS=Arabidopsis thaliana GN=At3g25440 PE=2 SV=1	Back alignment and function description

>sp\|Q9SL79\|CAF1P_ARATH CRS2-associated factor 1, chloroplastic OS=Arabidopsis thaliana GN=At2g20020 PE=1 SV=2	Back alignment and function description

>sp\|Q84N49\|CAF1P_MAIZE CRS2-associated factor 1, chloroplastic OS=Zea mays GN=CAF1 PE=1 SV=1	Back alignment and function description

>sp\|Q6Z4U2\|CAF1M_ORYSJ CRS2-associated factor 1, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0174900 PE=2 SV=1	Back alignment and function description

>sp\|Q5VMQ5\|CAF1P_ORYSJ CRS2-associated factor 1, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0495900 PE=2 SV=1	Back alignment and function description

>sp\|Q0J7J7\|CAF2M_ORYSJ CRS2-associated factor 2, mitochondrial OS=Oryza sativa subsp. japonica GN=Os08g0188000 PE=2 SV=2	Back alignment and function description

>sp\|Q657G7\|CAF2P_ORYSJ CRS2-associated factor 2, chloroplastic OS=Oryza sativa subsp. japonica GN=Os01g0323300 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		791
359484307		884	PREDICTED: chloroplastic group IIA intro	0.951	0.851	0.599	0.0
297738658		881	unnamed protein product [Vitis vinifera]	0.941	0.845	0.599	0.0
255546121		930	conserved hypothetical protein [Ricinus	0.962	0.818	0.554	0.0
224091282		977	predicted protein [Populus trichocarpa]	0.811	0.657	0.612	0.0
449452735		846	PREDICTED: chloroplastic group IIA intro	0.934	0.873	0.542	0.0
449529423		789	PREDICTED: chloroplastic group IIA intro	0.898	0.901	0.564	0.0
356564786		794	PREDICTED: chloroplastic group IIA intro	0.685	0.682	0.65	0.0
334187011		841	CRS1 / YhbY (CRM) domain-containing prot	0.831	0.782	0.528	0.0
242044486		962	hypothetical protein SORBIDRAFT_02g02294	0.834	0.686	0.527	0.0
115478793		947	Os09g0363100 [Oryza sativa Japonica Grou	0.841	0.703	0.514	0.0

>gi\|359484307\|ref\|XP_002279505.2\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  902 bits (2330), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 478/797 (59%), Positives = 579/797 (72%), Gaps = 44/797 (5%)

Query: 25  KPQSQCSNSFRSIRIGICFSHLTIQAQ-------LGTTRTKRKVKPSFFEQIRHKWSHKV 77
           +PQ+  SN+FR+++     S+ +IQ         L TT+ KRK +PSFFEQIR KWS K+
Sbjct: 17  QPQAHYSNTFRTLKFNCSCSYHSIQVDTQQVKVPLKTTKAKRKPRPSFFEQIRDKWSLKI 76

Query: 78  ISPREKFPWQEEEEEEEEVQNE--PETDVESRVRSEPFSSALPNRFVSAPWIHGTDSKEI 135
            SPREKFPWQE+ EE +       P+++V       P SSA  +RFVS P IH +  +  
Sbjct: 77  NSPREKFPWQEQAEETQNSSGVVVPDSEVIDSSVGSPVSSASESRFVSVPCIHESKPRNP 136

Query: 136 KFDS-PQTKITTKKEDIGDDGLLGSFEKTVVHSAVKEKTVIELDKEGDYNKELKTDEVKI 194
           +  S P+    + ++ +   G  GS      H A  ++      KE D + + + + V++
Sbjct: 137 RLVSEPEISQNSCEQGVNVVGF-GS------HRASVDEWSKSFQKEVDSDGKFEGEGVEV 189

Query: 195 DANPIELSKDRHREVG------SLNQK---------QIKGYHEVDDPSVLPWKRNT---- 235
           D  PI +      E+       SLN+K           +G+        LPWKR      
Sbjct: 190 DEIPIGVLGTEKTEIEMGDANVSLNEKPPGGDEDFGNFEGFSGNSSLIELPWKRREGLQP 249

Query: 236 ---DRRRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDE 292
              D   R NT +AE+M+PEHEL+RL+NI+LRMLER KVG+AG+TQ+LVD+IHEKW+ DE
Sbjct: 250 VERDGWGRRNTRMAERMVPEHELRRLKNIALRMLERIKVGAAGVTQSLVDAIHEKWRKDE 309

Query: 293 VVKLKFEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKH---- 348
           VVKLKFE P S  MKRTHEILE RTGGLVIWR+GSSVVL+RGMAYKL CVQS+ K     
Sbjct: 310 VVKLKFEGPSSCNMKRTHEILETRTGGLVIWRTGSSVVLYRGMAYKLHCVQSYIKQERDN 369

Query: 349 -NHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDLCELNYLLDELG 407
            N ++ +QD  N +++++G        ES + DSA  L++LS+EELMDL ELN+LLDELG
Sbjct: 370 VNISEYSQDAANVIIQDIGVKDIVKTTESVISDSARYLKDLSEEELMDLSELNHLLDELG 429

Query: 408 PRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHF 467
           PRFKDW GREPLPVDADLLP VV +YKPP RLLPYG++  LR+ E T  RRLAR  PPHF
Sbjct: 430 PRFKDWSGREPLPVDADLLPSVVHEYKPPFRLLPYGMRHCLRNREMTFIRRLARTMPPHF 489

Query: 468 ALGRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDY 527
           ALGR+RELQGLA AMVKLWE+SAIAKIAIKR V NT N+RMAEELK LTGGTL+ RNKDY
Sbjct: 490 ALGRSRELQGLAMAMVKLWERSAIAKIAIKRGVQNTCNDRMAEELKNLTGGTLVSRNKDY 549

Query: 528 IVFYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLVAGTLA 587
           IVFYRGNDFLPP V +A+KER KL D++QDEEE+ARH ASALI+ KA+   G LVAGTLA
Sbjct: 550 IVFYRGNDFLPPHVMEALKERRKLRDLQQDEEEQARHRASALIDSKARSAKGPLVAGTLA 609

Query: 588 ETLAATSRWGRQPSYEDVEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADKALAKVQE 647
           ETLAATSRWG +PS EDV KM+RDS L+RHASL+RY+ +KLA AK KLK  +KAL KVQE
Sbjct: 610 ETLAATSRWGSEPSEEDVGKMIRDSALARHASLVRYVGKKLAHAKAKLKKTEKALRKVQE 669

Query: 648 SLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKI 707
            L+PAELP DLET+++EERFL RK+GLSMKP+LLLG RGI+DGT+ENMHLHWKYRELVKI
Sbjct: 670 DLEPAELPMDLETLSDEERFLFRKIGLSMKPFLLLGTRGIFDGTVENMHLHWKYRELVKI 729

Query: 708 IVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRR 767
           IVKGK+FAQVK IAISLEAESGGVLVS+D+TPKG AIIVYRGKNY RP  LRP+NLLT+R
Sbjct: 730 IVKGKNFAQVKHIAISLEAESGGVLVSVDRTPKGYAIIVYRGKNYQRPHALRPKNLLTKR 789

Query: 768 QALARSVELQRRTKTSH 784
           QALARS+ELQR     H
Sbjct: 790 QALARSIELQRHEALKH 806

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297738658\|emb\|CBI27903.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255546121\|ref\|XP_002514120.1\| conserved hypothetical protein [Ricinus communis] gi\|223546576\|gb\|EEF48074.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|224091282\|ref\|XP_002309217.1\| predicted protein [Populus trichocarpa] gi\|222855193\|gb\|EEE92740.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449452735\|ref\|XP_004144114.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449529423\|ref\|XP_004171699.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356564786\|ref\|XP_003550629.1\| PREDICTED: chloroplastic group IIA intron splicing facilitator CRS1, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|334187011\|ref\|NP_194704.2\| CRS1 / YhbY (CRM) domain-containing protein [Arabidopsis thaliana] gi\|332660271\|gb\|AEE85671.1\| CRS1 / YhbY (CRM) domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|242044486\|ref\|XP_002460114.1\| hypothetical protein SORBIDRAFT_02g022940 [Sorghum bicolor] gi\|241923491\|gb\|EER96635.1\| hypothetical protein SORBIDRAFT_02g022940 [Sorghum bicolor]	Back alignment and taxonomy information

>gi\|115478793\|ref\|NP_001062990.1\| Os09g0363100 [Oryza sativa Japonica Group] gi\|48716728\|dbj\|BAD23409.1\| putative CRS1 [Oryza sativa Japonica Group] gi\|50726191\|dbj\|BAD33710.1\| putative CRS1 [Oryza sativa Japonica Group] gi\|113631223\|dbj\|BAF24904.1\| Os09g0363100 [Oryza sativa Japonica Group] gi\|125591023\|gb\|EAZ31373.1\| hypothetical protein OsJ_15500 [Oryza sativa Japonica Group]	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		791
TAIR\|locus:2094558		881	CFM3A "CRM family member 3A" [	0.680	0.610	0.485	7.1e-132
TAIR\|locus:2094997		848	EMB1865 "embryo defective 1865	0.682	0.636	0.433	1e-109
TAIR\|locus:2096662		1011	CFM2 "CRM family member 2" [Ar	0.690	0.540	0.423	2.4e-108
TAIR\|locus:2181372		720	CRS1 "ortholog of maize chloro	0.476	0.523	0.416	4e-83
TAIR\|locus:2094438		444	LOH1 "LAG One Homologue 1" [Ar	0.156	0.279	0.426	8.3e-19
TAIR\|locus:2056558		372	AT2G28480 [Arabidopsis thalian	0.150	0.319	0.436	4.8e-17
TAIR\|locus:2123276		343	AT4G13070 [Arabidopsis thalian	0.149	0.344	0.414	7e-17
TAIR\|locus:2091458		491	AT3G27550 [Arabidopsis thalian	0.152	0.246	0.362	6.1e-15
TAIR\|locus:2061604		701	CAF1 [Arabidopsis thaliana (ta	0.174	0.196	0.286	1.5e-11
TAIR\|locus:2028100		564	CAF2 [Arabidopsis thaliana (ta	0.175	0.246	0.267	1.3e-08

TAIR\|locus:2094558 CFM3A "CRM family member 3A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1293 (460.2 bits), Expect = 7.1e-132, P = 7.1e-132
 Identities = 268/552 (48%), Positives = 363/552 (65%)

Query:   238 RRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLK 297
             ++ +   LAE  +PE EL+RLRN++ R   + ++   G+TQ  VD+I EKWK  E+V+LK
Sbjct:   209 KKENRYSLAEMTLPESELRRLRNLTFRTASKMRIRGGGVTQVAVDAIKEKWKSAEIVRLK 268

Query:   298 FEEPHSLQMKRTHEILERRTGGLVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDV 357
              E   +L M++ HEILE++TGGLVIWRSG+S+ L+RG++Y+LP      K N  ++ +  
Sbjct:   269 IEGASALNMRKMHEILEKKTGGLVIWRSGTSISLYRGVSYELPS----GKWNKQRREETP 324

Query:   358 TNEVMRNVGEHPP---RSAMESYVPDSANNLENLSKEELMDLC-----ELNYLLDELGPR 409
                V+ N  E      +S  + ++P       ++ K++          EL+ LLD+LGPR
Sbjct:   325 PEAVIENHDETTTMVDKSDEKVHLPQLEQETTSVEKKDQTSPVVEYEDELDELLDDLGPR 384

Query:   410 FKDWPGREXXXXXXXXXXXXXXXYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFAL 469
             F DWPG                 Y+PP R+LPYG++  L   E T  RRLAR  PPHFAL
Sbjct:   385 FMDWPGDNPLPVDADLLPGAIPDYEPPFRVLPYGVRSSLGPKEATALRRLARSIPPHFAL 444

Query:   470 GRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIV 529
             GR+R+LQGLA AMV+LWEKS +AKIAIKR V +T +ERMAE+LKKLTGG +L RNKD++V
Sbjct:   445 GRSRQLQGLATAMVRLWEKSMLAKIAIKRGVQSTTSERMAEDLKKLTGGIMLSRNKDFLV 504

Query:   530 FYRGNDFLPPVVTDAVKERSKLTDIRQDEEERARHVASALIELKAKGFVGSLV-AGTLAE 588
             FYRG +FL   V DA+ E+ +     QDEEE+AR   S+ + + +      LV AGTL E
Sbjct:   505 FYRGKNFLSREVADALVEQERFVRTLQDEEEQARLRGSSALIVPSTEPANKLVSAGTLGE 564

Query:   589 TLAATSRWGRQPSYED-VEKMMRDSTLSRHASLLRYXXXXXXXXXXXXXXXXXXXXXVQE 647
             TL AT +WG+    +D  +++ ++  + RH +L+R                      V+ 
Sbjct:   565 TLDATGKWGKNLDDDDHSDEVKQEVEILRHENLVRKLERKLAFAERKLLKAERGLAKVEV 624

Query:   648 SLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKI 707
              L PAE   D E+IT+EERF+ RK+GL MK +LLLGRRG++DGT+ENMHLHWKYRELVKI
Sbjct:   625 CLKPAEQREDPESITDEERFMFRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKYRELVKI 684

Query:   708 IVKGKSFAQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRR 767
             IVK K+F  VK++A++LEAESGG+LVS+DK  KG AIIVYRG++Y RP  LRP+NLLT+R
Sbjct:   685 IVKAKTFDGVKKVALALEAESGGILVSIDKVTKGYAIIVYRGQDYKRPTMLRPKNLLTKR 744

Query:   768 QALARSVELQRR 779
             +ALARS+ELQRR
Sbjct:   745 KALARSIELQRR 756

GO:0003723 "RNA binding" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0000373 "Group II intron splicing" evidence=IMP

GO:0048316 "seed development" evidence=IGI

TAIR\|locus:2094997 EMB1865 "embryo defective 1865" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2096662 CFM2 "CRM family member 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2181372 CRS1 "ortholog of maize chloroplast splicing factor CRS1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2094438 LOH1 "LAG One Homologue 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2056558 AT2G28480 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2123276 AT4G13070 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2091458 AT3G27550 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2061604 CAF1 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2028100 CAF2 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		791
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	3e-21
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	2e-20
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	3e-17
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	6e-16
smart01103		84	smart01103, CRS1_YhbY, Escherichia coli YhbY is as	1e-14
pfam01985		84	pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	5e-13

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

 Score = 88.3 bits (220), Expect = 3e-21
 Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 4/88 (4%)

Query: 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQI 720
           +T +++  LR +   +KP + +G+ G+ +G +E +    +  EL+K+ V G      K+I
Sbjct: 1   LTGKQKRYLRSLAHHLKPVVQIGKNGLTEGVLEEIDEALEKHELIKVKVLGNDREDRKEI 60

Query: 721 AISLEAESGGVLVSLDKTPKGIAIIVYR 748
           A  L  E+G  LV +     G  I++YR
Sbjct: 61  AEELAEETGAELVQV----IGKTIVLYR 84

GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

>gnl\|CDD\|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly	Back alignment and domain information

>gnl\|CDD\|190184 pfam01985, CRS1_YhbY, CRS1 / YhbY (CRM) domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		791
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	100.0
PRK10343		97	RNA-binding protein YhbY; Provisional	99.93
TIGR00253		95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.93
PF01985		84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.92
PRK10343		97	RNA-binding protein YhbY; Provisional	99.92
TIGR00253		95	RNA_bind_YhbY putative RNA-binding protein, YhbY f	99.91
COG1534		97	Predicted RNA-binding protein containing KH domain	99.91
PF01985		84	CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR	99.9
COG1534		97	Predicted RNA-binding protein containing KH domain	99.88
KOG1990		564	consensus Poly(A)-specific exoribonuclease PARN [R	98.7

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=2.6e-71  Score=623.01  Aligned_cols=504  Identities=45%  Similarity=0.634  Sum_probs=466.6

Q ss_pred             cccchhhhhcCCCCHHHHHHHHHhhccCCCeEEeCCCCCCHHHHHHHHHHhhhCCeEEEEecCCChHhHHHHHHHHHHHh
Q 003851          238 RRRSNTELAEKMIPEHELQRLRNISLRMLERTKVGSAGITQALVDSIHEKWKLDEVVKLKFEEPHSLQMKRTHEILERRT  317 (791)
Q Consensus       238 ~~~~~~~lae~tLT~kErr~LRklAh~LkpvV~IGK~GVTd~VVeeIh~awk~hELVKVK~~~~~~~dm~~~~e~LEekT  317 (791)
                      +..+ +.+|++++.+.++.+||..|..+...+  +++|+|+++++.|++.|+.+|+++++|....+.+|.+.+++++..|
T Consensus         3 ~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~   79 (564)
T KOG1990|consen    3 NFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST   79 (564)
T ss_pred             cccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence            4556 999999999999999999999998887  9999999999999999999999999999999999999999999999


Q ss_pred             CC-eEEEEEccEEEEeecCCCCCCCcccccccccccccccccchhhcccCCCCCCCccccCCCCcccccccchHHHHhhH
Q 003851          318 GG-LVIWRSGSSVVLFRGMAYKLPCVQSFTKHNHTQQTQDVTNEVMRNVGEHPPRSAMESYVPDSANNLENLSKEELMDL  396 (791)
Q Consensus       318 Gg-~VVqrIG~viVLYRG~NY~~p~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ee~~~~  396 (791)
                      || .+||+.|.....|++..|..|..-....                          .+        ....+..  ....
T Consensus        80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~--------------------------~~--------~~~~~~~--~~~~  123 (564)
T KOG1990|consen   80 GGNFVVWSRGDSISSPEFLCQRSPVDFVARQ--------------------------QE--------NQAGKWP--SELE  123 (564)
T ss_pred             CCceeeeecCccccCCccceeecchhhhhhh--------------------------ch--------hhhhhhH--HHHH
Confidence            99 9999999999999999999884311000                          00        0000101  1236


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCChHHHHHHHHhhhcCCCeEEecccchhh
Q 003851          397 CELNYLLDELGPRFKDWPGREPLPVDADLLPPVVPDYKPPLRLLPYGIKPGLRDCETTEFRRLARKTPPHFALGRNRELQ  476 (791)
Q Consensus       397 ~E~n~LLD~LGPRf~dW~g~~PlPVDaDLLP~vvPgy~~PfRllP~gv~~~Ls~~E~t~LRk~a~~lpph~aLGRn~~~~  476 (791)
                      ++.+.++|++||+|.|||+.+|+|+|+||+|++||+|.+|||.+|+|++++|+..|++.+|++|..+||||++|+++.++
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~  203 (564)
T KOG1990|consen  124 KEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQ  203 (564)
T ss_pred             HHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhCceeEEeecCCCCCCcHHHHHHHH--hhccCcEEEeeeCCeEEEEecCCCCChhhhhHHHHhhhhhhh
Q 003851          477 GLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEEL--KKLTGGTLLCRNKDYIVFYRGNDFLPPVVTDAVKERSKLTDI  554 (791)
Q Consensus       477 gLa~aI~~~wek~~lakI~~K~gv~~T~~~~m~~eL--k~LTGgvLLSRnk~~IVlYRGkdf~p~~Va~al~ERe~~~~~  554 (791)
                      |++.+|+.+|++|+++++.|++|++.+..+.||.+|  ..+||++|++||+.++|+|||++|++ .|.++|.++......
T Consensus       204 ~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~~~~  282 (564)
T KOG1990|consen  204 GLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDSSSM  282 (564)
T ss_pred             cchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhhhhh
Confidence            999999999999999999999999999999999999  99999999999999999999999999 999999999999888


Q ss_pred             hhhHHHHhhhhhhHHHHhhccccccccccchhHHHHHHhhhccCCCChhHHH-HHHHhhhHHHHHHHHHHHHHHHHHHHH
Q 003851          555 RQDEEERARHVASALIELKAKGFVGSLVAGTLAETLAATSRWGRQPSYEDVE-KMMRDSTLSRHASLLRYLEQKLALAKR  633 (791)
Q Consensus       555 ~q~eEE~aR~~~~~~~~~~~~~~~~~~~aGtl~E~~~a~~~wg~~~~~~~~~-~~~~e~~~~~~~~~~k~~e~kL~~a~~  633 (791)
                      .++.++.+|....+   +    ......+||+.|+..+.++|+......+.. .+..+......+...+.+.++++.+..
T Consensus       283 fp~~~~~~~~~~~~---~----~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~  355 (564)
T KOG1990|consen  283 FPNIEDTKRLAKLS---E----YQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKK  355 (564)
T ss_pred             hhhhHHHHHhhccc---c----ccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhh
Confidence            89999999966511   1    112357899999999999999999877653 678888999999999999999999999


Q ss_pred             HHHHHHHHHHhhcccCCCCCCCCCcCCCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCC
Q 003851          634 KLKMADKALAKVQESLDPAELPSDLETITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKS  713 (791)
Q Consensus       634 K~~rae~~LaKl~~~~~P~e~~~d~E~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~  713 (791)
                      |+..++..|++++.+..|.+..+|++.+|.+++.+++++|.+|++++.+|++|+++|++.++|.||++||++|++|+...
T Consensus       356 ~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~  435 (564)
T KOG1990|consen  356 KLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKN  435 (564)
T ss_pred             hccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeecccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             H-HHHHHHHHHHHHHhCCeEEeeeecCCCcEEEEeccCCCCCCCccCCcccccHHHHHHHHHHHHhhhhhhhcccc
Q 003851          714 F-AQVKQIAISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKLRPQNLLTRRQALARSVELQRRTKTSHLGLT  788 (791)
Q Consensus       714 ~-ed~keia~~Le~~SGg~LVqVIk~~iG~~iILYRgkNy~rP~illP~nlLtKrkAL~rSie~QR~esl~~h~l~  788 (791)
                      . .+++..|..++.++|+++|+++++..|++|+.|||+||++|..+.|.|+|+||+|+.+|+++|+.+||++|+-.
T Consensus       436 ~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~  511 (564)
T KOG1990|consen  436 LPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRKEALKSHISD  511 (564)
T ss_pred             ccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHHHHHhhhcch
Confidence            6 99999999999999999999999999999999999999999999999999999999999999999999999853

>PRK10343 RNA-binding protein YhbY; Provisional	Back alignment and domain information

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family	Back alignment and domain information

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain	Back alignment and domain information

>PRK10343 RNA-binding protein YhbY; Provisional	Back alignment and domain information

>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family	Back alignment and domain information

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain	Back alignment and domain information

>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		791
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	1e-12
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	4e-08
1rq8_A		104	Conserved hypothetical protein; structural genomic	8e-12
1rq8_A		104	Conserved hypothetical protein; structural genomic	2e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98	Back alignment and structure

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 18/89 (20%), Positives = 42/89 (47%), Gaps = 4/89 (4%)

Query: 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQ 719
           T++ +++  L+ +   + P ++LG  G+ +G +  +     + EL+K+ V G      + 
Sbjct: 2   TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAGADRETKQL 61

Query: 720 IAISLEAESGGVLVSLDKTPKGIAIIVYR 748
           I  ++  E+    V       G  +++YR
Sbjct: 62  IINAIVRETKAAQVQT----IGHILVLYR 86

PyMOL of 1jo0

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A Length = 98	Back alignment and structure

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104	Back alignment and structure

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1 Length = 104	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

 Score = 58.7 bits (141), Expect = 7e-09
 Identities = 99/696 (14%), Positives = 204/696 (29%), Gaps = 231/696 (33%)

Query: 125 PWIHGTDSKEIKFDSPQTKITTKK-EDI---GDD--------GLLGSFEKTVVHSAVKEK 172
            ++   D K+++ D P++ ++ ++ + I    D           L S ++ +V   V+E 
Sbjct: 28  AFVDNFDCKDVQ-DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV 86

Query: 173 TVIELDKEGDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWK 232
               L    +Y   L +    I     + S      +   ++         +D  V   K
Sbjct: 87  ----LRI--NYK-FLMS---PIKTEQRQPSMMTRMYIEQRDRLY-------NDNQVFA-K 128

Query: 233 RNTDRRRRSNTELAEKMIPEHELQRLRNISLR-M-------LERTKVGSAGITQALVDSI 284
            N   R +   +L + ++   EL+  +N+ +  +       +      S  +   +   I
Sbjct: 129 YNV-SRLQPYLKLRQALL---ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184

Query: 285 HEKW-----------------KLDEVVKLKFEEP--HSLQMKRTHEILERRTGGLVIWRS 325
              W                 KL   +   +     HS  +K     ++     L+  + 
Sbjct: 185 F--WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242

Query: 326 G--SSVVL--------FRGMAYKLPCVQSFTKHNHTQQTQD--VTNEVMRNVGEHPPRSA 373
                +VL        +   A+ L C    T       T+   VT+ +      H     
Sbjct: 243 YENCLLVLLNVQNAKAWN--AFNLSCKILLT-------TRFKQVTDFLSAATTTHIS--- 290

Query: 374 MESYVPDSANNLENLSKEELMDLCELNYLLDELGPRFKDWPGRE-----PLPVDADLLPP 428
           ++       ++   L+ +E+  L     LL  L  R +D P RE     P  +   ++  
Sbjct: 291 LD-------HHSMTLTPDEVKSL-----LLKYLDCRPQDLP-REVLTTNPRRLS--IIAE 335

Query: 429 VVPDYKPPLRLLPY----------GIKPGLRDCETTEFRRLAR---------KTPPHFAL 469
            + D         +           I+  L   E  E+R++             P     
Sbjct: 336 SIRDG--LATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT---- 389

Query: 470 GRNRELQGLAKAMVKLWEKSAIAKIAIKRDVMNTRNERMAEELKKLTGGTLLCRNKDYIV 529
                       +  +W         IK DV       +  +L K     +  + K+  +
Sbjct: 390 ----------ILLSLIWFDV------IKSDV-----MVVVNKLHKY--SLVEKQPKESTI 426

Query: 530 FYRGNDFLPPVVTDAVKERSKLTDIR-QDEEERARHVASALIE--LKAKGFVGSLVAGTL 586
                                  +++ + E E A H   ++++     K F         
Sbjct: 427 SIPSIYL----------------ELKVKLENEYALH--RSIVDHYNIPKTF--------- 459

Query: 587 AETLAATSRWGRQPSYED------VEKMMRDSTLSRHASLLRYLEQKLALAKRKLKMADK 640
                        P Y D      +   +++       +L R +       ++K++    
Sbjct: 460 -------DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDST 512

Query: 641 ALAKVQESLDPAELPSDLET----ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMH 696
           A       L+       L+     I + +    R +  ++  +L           IE   
Sbjct: 513 AWNASGSILN---TLQQLKFYKPYICDNDPKYERLVN-AILDFLP---------KIEENL 559

Query: 697 LHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVL 732
           +  KY +L+             +IA  L AE   + 
Sbjct: 560 ICSKYTDLL-------------RIA--LMAEDEAIF 580

PyMOL of 1vt4

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		791
1rq8_A		104	Conserved hypothetical protein; structural genomic	99.94
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	99.94
1rq8_A		104	Conserved hypothetical protein; structural genomic	99.94
1jo0_A		98	Hypothetical protein HI1333; structural genomics,	99.94

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1	Back alignment and structure

Probab=99.94  E-value=4.2e-27  Score=214.23  Aligned_cols=96  Identities=25%  Similarity=0.427  Sum_probs=92.8

Q ss_pred             CCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeecC
Q 003851          660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP  739 (791)
Q Consensus       660 ~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~~  739 (791)
                      |||++||++||++||+|+|+|+|||+|||++|+++|++||++||||||+|.+++.++++++|+.|++.|||++||+|   
T Consensus         1 mLt~kqr~~LR~~ah~Lkpvv~IGK~GlTe~vi~ei~~aL~~hELIKVkvl~~~~~d~~e~a~~la~~t~a~vVq~I---   77 (104)
T 1rq8_A            1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVI---   77 (104)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEE---
T ss_pred             CCCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCHHHHHHHHHHHHHHhCCEEEEEE---
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999987   


Q ss_pred             CCcEEEEeccCCCCCCCccCC
Q 003851          740 KGIAIIVYRGKNYVRPLKLRP  760 (791)
Q Consensus       740 iG~~iILYRgkNy~rP~illP  760 (791)
                       |+++||||+++ ..|.+.+|
T Consensus        78 -G~~~VLYR~~~-~~~~i~~~   96 (104)
T 1rq8_A           78 -GSMIVIYRESK-ENKEIELP   96 (104)
T ss_dssp             -TTEEEEEECCC-SCCSCCCC
T ss_pred             -CCEEEEEeCCC-CCCceecc
Confidence             99999999987 55888888

PyMOL of 1rq8

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_A	Back alignment and structure

>1rq8_A Conserved hypothetical protein; structural genomics, SAV1595, YHBY, UPF0044, unknown function; NMR {Staphylococcus aureus} SCOP: d.68.4.1	Back alignment and structure

>1jo0_A Hypothetical protein HI1333; structural genomics, YHBY_HAEI structure 2 function project, S2F, unknown function; 1.37A {Haemophilus influenzae} SCOP: d.68.4.1 PDB: 1ln4_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		791
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	6e-21
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	7e-17
d1rq8a_		96	d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphy	5e-14
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	8e-21
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	3e-14
d1jo0a_		97	d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus i	2e-13

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

 Score = 85.9 bits (213), Expect = 6e-21
 Identities = 24/98 (24%), Positives = 50/98 (51%), Gaps = 4/98 (4%)

Query: 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQI 720
           +T +++  LR +  ++ P   +G+ GI +  I+ +    + REL+K+ V   +F   K++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 721 AISLEAESGGVLVSLDKTPKGIAIIVYRGKNYVRPLKL 758
           A +L   +   LV +     G  I++YR     + ++L
Sbjct: 62  AETLSEATRSELVQV----IGSMIVIYRESKENKEIEL 95

PyMOL of d1rq8a_

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]} Length = 96	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]} Length = 97	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		791
d1rq8a_		96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.94
d1jo0a_		97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.94
d1rq8a_		96	Hypothetical protein SAV1595 {Staphylococcus aureu	99.93
d1jo0a_		97	YhbY homologue HI1333 {Haemophilus influenzae [Tax	99.93

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: YhbY-like
family: YhbY-like
domain: Hypothetical protein SAV1595
species: Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]

Probab=99.94  E-value=5.2e-27  Score=208.10  Aligned_cols=96  Identities=25%  Similarity=0.425  Sum_probs=92.5

Q ss_pred             CCCHHHHHHHHHccCCCCceEeeCCCCCCHHHHHHHHHHHHhcceEEEEecCCCHHHHHHHHHHHHHHhCCeEEeeeecC
Q 003851          660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQIAISLEAESGGVLVSLDKTP  739 (791)
Q Consensus       660 ~LT~eERk~LRklGhkLKPvV~IGK~GVtdgVIeeI~~ALk~hELVKIkv~~~~~ed~keia~~Le~~SGg~LVqVIk~~  739 (791)
                      |||++||++||++||+|+|+|+||++|||++|+.+|+.||+.||||||+|.+++.+++++++++||+.|||++||+|   
T Consensus         1 mLt~kqr~~LR~~ah~l~p~v~IGk~Glt~~vi~ei~~~l~~~ELIKvk~~~~~~~~~~~~~~~l~~~t~a~~V~~i---   77 (96)
T d1rq8a_           1 MLTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKELAETLSEATRSELVQVI---   77 (96)
T ss_dssp             CCCHHHHHHHHHHTTSSCCSCEECSSSCCHHHHHHHHHHHHHSSEEEEEECCCCHHHHHHHHHHHHHHHTEEEEEEE---
T ss_pred             CcCHHHHHHHHHHhcCCCCEEEECCCCCCHHHHHHHHHHHHhCCeeEEEecCCCHHHHHHHHHHHHHHhCCEEEEEE---
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999987   


Q ss_pred             CCcEEEEeccCCCCCCCccCC
Q 003851          740 KGIAIIVYRGKNYVRPLKLRP  760 (791)
Q Consensus       740 iG~~iILYRgkNy~rP~illP  760 (791)
                       |+++||||++++ .|++.||
T Consensus        78 -G~~~vlyR~~~~-~~ki~LP   96 (96)
T d1rq8a_          78 -GSMIVIYRESKE-NKEIELP   96 (96)
T ss_dssp             -TTEEEEEECCCS-CCSCCCC
T ss_pred             -CCEEEEEeCCCC-CCCCCCC
Confidence             999999998765 4888888

PyMOL of d1rq8a_

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1rq8a_ d.68.4.1 (A:) Hypothetical protein SAV1595 {Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280]}	Back information, alignment and structure

>d1jo0a_ d.68.4.1 (A:) YhbY homologue HI1333 {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure