Citrus Sinensis ID: 005219

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-------71

MALSERDQPIEEPWLFQSSPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESLLPEKGSLISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKASENQHQVAISLLRSAEARANKSGKKVTLVPIKKLKSGRK

cccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccEEEEEEcccccEEEEEEEEccEEEEEEEcccccccccccEEEEEEEEEcccccEEEEcccccccccccccccccccccccccccccHHHcccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccEEEEEEEcccccccccccccccccccEEEEEEcccccccccccccHHHHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEccccHHHHHHHHccccccEEEEccHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHccccccccccEEEEcccccEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccccHHHHHHHHHHHHHHHHcccccccccccccccccHHccccccccccccccccccccEEEEEEcHHHHHHHHccccccEEEEEcccEEEEEEEcccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHHccccccEEEEEccHHHcccc

cccccccccccccHHHEccEEEEEcccccccccHccccHHHHHHHHccccccccccccccccccccccccccccEEEEEEEccHHHHHHHEEEccccEEEEEEccccccccccEEEEEEEEEEccccccEEEEcccccccHHcccccccccccccccccccccccccccHHHHcccccccccccccccHHHHHHcccccccccccccccccccccHHHHHHHHcccccEEEEEEcccHEEEEccccccccccccccccccHHHHHHHHHHHcccccccccccccccHHHHHHcccEEEEEEEccccccccHHHHHHHHHcccEEEEcccccccccEEccccHHHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccEEEEcccHHHHHHHHHHHHHHHcEEEEccHHHHHHHHHHHHHHcHHHHHHHEHcccccccccHHHHHHHHHHHHHcccccccccEEEEcccHHEEEEEccccHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHHHHHHHHHccEEEEEHHHHHcHHHHHHHccccccccccccccccccEEEEcHHHHHHHHHHccccEEEEEccHHHHHHHHHHHccccccEEEEEEccccccccccccEEEEEcccccccccccccEEEEEEEcccccccc

malserdqpieepwlfqsspillayedtvkpdmpeksnnekdeamildsdnqkfqdtesllpekgsliskdnFVSTVILINSSICTMQRIAVLEDEKLVELLLEpvksnvqcdsVYLGVVTKlvpnmggafvnignsrpslmdikhyrepfifppfrcrtkkqevngsaSAALEEHavtydndstshntedvaeadsqddlvqfehnddeehdgddfdvsEVLKNvngsiiddgepeadfedflegdhhldgesngffpsksevpddshtshpqgtkdskhtpgektwlQVQKGTKVIVQVVKEglgtkgptltaypklRSRFWILITSCdrigvsrkitgvERTRLKVIAKTlqpegfgltIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKmvvdsprtyHEVTSYLQDiapdlcdrvelydkriplfdkfNIEEEINNMlskrvplpnggslvieQTEALVSIdvngghgmfghgsskEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIdmaddsnkRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMeqkadpenpkswprfILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGftrgafevipytddkasenQHQVAISLLRSAEARAnksgkkvtlvpikklksgrk

malserdqpieepwlfqssPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESLLpekgsliskdNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPvksnvqcdSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDeehdgddfdvsEVLKNVNGSIIDDGEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTShpqgtkdskhtpgektwlqvqKGTKVIVQVvkeglgtkgptltaypklrSRFWILItscdrigvsrkitgvertrlkviaktlqpegfglTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDfidmaddsnkRLVYEEVkkaverdrsmvkvselsrhglmeitrkrammeqkadpenpksWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPytddkaseNQHQVAISLLRSaearanksgkkvtlvpikklksgrk

MALSERDQPIEEPWLFQSSPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESLLPEKGSLISKDNFVSTVILINSSICTMQRIAvledeklvelllepvKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQfehnddeehdgddfdVSEVLKNVNGSIIDDGEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRdiggiivvdfidMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKASENQHQVAISLLRSAEARANKSGKKVTLVPIKKLKSGRK

*************WLFQSSPILLAY*****************************************LISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCR*******************************************************************************************************************************TWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEV******************************************WPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTD******************************************

*******QPIEEPWLF************************************************************VILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPP********************************************************************************PEADFEDFL**********************************************VQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH************EGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGM*****SKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADPENPKSWPRFILRVDHHMCNYLTSGKRT**AVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKASENQHQ*******************VTLV***K******

*********IEEPWLFQSSPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESLLPEKGSLISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGDHHLDGESNGFFPS************************EKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRA**********PKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKASENQHQVAISLLRSAE*********VTLVPIKKLKSGRK

**LSERDQPIEEPWLFQSSPILLAYEDTVKPDM*E*SN*EKD**************TESLLPEKGSLISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTK************EEHA**********NTEDVAEA*****LVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDDGEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRA******DPENPKSWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKASENQHQVAISLLRSAEARANKSGKKVTLVPIKKL*****

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		708	2.2.26 [Sep-21-2011]
F4IV66		1001	Ribonuclease E/G-like pro	no	no	0.973	0.688	0.630	0.0
P44443		935	Ribonuclease E OS=Haemoph	yes	no	0.413	0.313	0.384	4e-57
P21513		1061	Ribonuclease E OS=Escheri	N/A	no	0.416	0.278	0.367	1e-53
Q89AH3		410	Putative truncated ribonu	yes	no	0.471	0.814	0.327	2e-51
P57429		902	Ribonuclease E OS=Buchner	yes	no	0.501	0.393	0.326	6e-49
Q8K9J9		968	Ribonuclease E OS=Buchner	yes	no	0.454	0.332	0.312	7e-49
P72656		674	Ribonuclease E homolog OS	N/A	no	0.408	0.428	0.325	1e-41
P45175		491	Ribonuclease G OS=Haemoph	no	no	0.418	0.602	0.372	2e-41
P0A9J3		489	Ribonuclease G OS=Shigell	no	no	0.484	0.701	0.328	2e-39
P0A9J0		489	Ribonuclease G OS=Escheri	N/A	no	0.484	0.701	0.328	2e-39

>sp\|F4IV66\|RNE_ARATH Ribonuclease E/G-like protein, chloroplastic OS=Arabidopsis thaliana GN=RNE PE=1 SV=1	Back alignment and function desciption

 Score =  865 bits (2236), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 474/752 (63%), Positives = 560/752 (74%), Gaps = 63/752 (8%)

Query: 3   LSERDQPIEEPWLFQSSPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESLLP 62
            S+  QPIEEPWL Q S I L +E  ++ D  +   +  D    L++D Q  Q TE+LLP
Sbjct: 264 FSDNYQPIEEPWLIQES-ITLQHERNMQTDSEQDVESCDDNENNLNTDEQNHQLTETLLP 322

Query: 63  EKGSLISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTK 122
           + G   S+   ++T ILINSSICT+QRIAVLE  KLVELLLEPVK+NVQCDSVYLGV+TK
Sbjct: 323 DGGFFQSES--IATTILINSSICTVQRIAVLEGGKLVELLLEPVKTNVQCDSVYLGVITK 380

Query: 123 LVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVTYDN 182
            VP+MGGAFVNIG++R S MDIK  REPFIFPPF   +KKQ  +GS   ++ +    ++ 
Sbjct: 381 FVPHMGGAFVNIGSARHSFMDIKSNREPFIFPPFCDGSKKQAADGSPILSMNDIPAPHEI 440

Query: 183 DSTSHNTE--DVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKN-VNGSIIDDGEPEAD 239
           +  S++ E   + + DS D    F  +DDE  + D++ VS+ L   VNG++++ G  E  
Sbjct: 441 EHASYDFEASSLLDIDSNDPGESFHDDDDEHEN-DEYHVSDHLAGLVNGTVVNHGAVEV- 498

Query: 240 FEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSK-HTPGEKTWLQVQKGTKVI 298
                       G  NG  P +     DS  S+    K SK  +  +  W+QV+KGTK+I
Sbjct: 499 ------------GSENGHIPMERGHSADSLDSNASVAKASKVMSSKDNKWIQVRKGTKII 546

Query: 299 VQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAKTLQPEG 358
           VQVVKEGLGTKGPTLTAYPKLRSRFW+L+T C RIGVS+KI+GVERTRLKVIAKTLQP+G
Sbjct: 547 VQVVKEGLGTKGPTLTAYPKLRSRFWVLLTRCKRIGVSKKISGVERTRLKVIAKTLQPQG 606

Query: 359 FGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQ 418
           FGLT+RTVAAGHSLEELQKDL+GLL TWKNI + AKSAALAADEGVEGA+P LLHRAMGQ
Sbjct: 607 FGLTVRTVAAGHSLEELQKDLDGLLLTWKNITDEAKSAALAADEGVEGAIPALLHRAMGQ 666

Query: 419 TLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEE 478
           TLS+VQDYFN+KV+KMVVDSPRTYHEVT YLQD+APDLC+RVEL+DK IPLFD + IEEE
Sbjct: 667 TLSVVQDYFNDKVEKMVVDSPRTYHEVTHYLQDMAPDLCNRVELHDKGIPLFDLYEIEEE 726

Query: 479 INNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIAR 538
           I  +LSKRVPL NGGSLVIEQTEALVSIDVNGGHGMFG G+S+EKAIL+VNLAAA+QIAR
Sbjct: 727 IEGILSKRVPLSNGGSLVIEQTEALVSIDVNGGHGMFGQGNSQEKAILEVNLAAARQIAR 786

Query: 539 ELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKR- 597
           E+RLRDIGGIIVVDFIDMAD+SNKRLVYEEVKKAVERDRS+VKVSELSRHGLMEITRKR 
Sbjct: 787 EIRLRDIGGIIVVDFIDMADESNKRLVYEEVKKAVERDRSLVKVSELSRHGLMEITRKRV 846

Query: 598 ---------------------------------------AMMEQKADPENPKSWPRFILR 618
                                                  A ME++ D ENPKSWPRFILR
Sbjct: 847 RPSVTFMISEPCSCCHATGRVEALETTFSKIEQEICRQLAKMEKRGDLENPKSWPRFILR 906

Query: 619 VDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIPYTDDKA-SENQHQVA 677
           VD HM ++LT+GKRTRLA+LSSSLK WILLKVAR FTRG FEV P+ D+K  +E QHQVA
Sbjct: 907 VDSHMSSFLTTGKRTRLAILSSSLKVWILLKVARHFTRGTFEVKPFMDEKTVNERQHQVA 966

Query: 678 ISLLRSAEARANKSG-KKVTLVPIKKLKSGRK 708
           ISLL+ A+A A+ SG KK+TL+PIKK K+  K
Sbjct: 967 ISLLKKADAIADSSGKKKLTLIPIKKEKTSGK 998

Involved in intercistronic processing of primary transcripts from chloroplast operons. The endonucleolytic activity of the enzyme depends on the number of phosphates at the 5' end, is inhibited by structured RNA, and preferentially cleaves A/U-rich sequences.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: -

>sp\|P44443\|RNE_HAEIN Ribonuclease E OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=rne PE=3 SV=1	Back alignment and function description

>sp\|P21513\|RNE_ECOLI Ribonuclease E OS=Escherichia coli (strain K12) GN=rne PE=1 SV=6	Back alignment and function description

>sp\|Q89AH3\|RNE_BUCBP Putative truncated ribonuclease E OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=rne PE=3 SV=1	Back alignment and function description

>sp\|P57429\|RNE_BUCAI Ribonuclease E OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=rne PE=3 SV=1	Back alignment and function description

>sp\|Q8K9J9\|RNE_BUCAP Ribonuclease E OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN=rne PE=3 SV=1	Back alignment and function description

>sp\|P72656\|RNE_SYNY3 Ribonuclease E homolog OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rne PE=3 SV=1	Back alignment and function description

>sp\|P45175\|RNG_HAEIN Ribonuclease G OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=rng PE=3 SV=1	Back alignment and function description

>sp\|P0A9J3\|RNG_SHIFL Ribonuclease G OS=Shigella flexneri GN=rng PE=3 SV=2	Back alignment and function description

>sp\|P0A9J0\|RNG_ECOLI Ribonuclease G OS=Escherichia coli (strain K12) GN=rng PE=1 SV=2	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		708
255567240		963	hypothetical protein RCOM_1213430 [Ricin	0.995	0.732	0.685	0.0
224131900		923	predicted protein [Populus trichocarpa]	0.978	0.750	0.694	0.0
225447486		1019	PREDICTED: uncharacterized protein LOC10	0.992	0.689	0.691	0.0
356551838		983	PREDICTED: uncharacterized protein LOC10	0.960	0.691	0.669	0.0
356498920		937	PREDICTED: uncharacterized protein LOC10	0.963	0.727	0.660	0.0
449470204		992	PREDICTED: uncharacterized protein LOC10	0.980	0.699	0.643	0.0
449477847		926	PREDICTED: LOW QUALITY PROTEIN: uncharac	0.980	0.749	0.640	0.0
357490525		1009	Ribonuclease E [Medicago truncatula] gi\|	0.961	0.674	0.631	0.0
297831502		991	glycoside hydrolase starch-binding domai	0.968	0.692	0.628	0.0
27368501		818	putative endoribonuclease E [Arabidopsis	0.973	0.842	0.630	0.0

>gi\|255567240\|ref\|XP_002524601.1\| hypothetical protein RCOM_1213430 [Ricinus communis] gi\|223536154\|gb\|EEF37809.1\| hypothetical protein RCOM_1213430 [Ricinus communis]	Back alignment and taxonomy information

 Score = 1030 bits (2663), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 523/763 (68%), Positives = 602/763 (78%), Gaps = 58/763 (7%)

Query: 1   MALSERDQPIEEPWLFQSSPILLAYEDTVKPDMPEKSNNEKDEAMILDSDNQKFQDTESL 60
           + LSERDQP+EEPWL QSS I +  +D + P++ + +N   +++   D+++Q  Q  + L
Sbjct: 198 LVLSERDQPVEEPWLLQSSIIFVISKDKIMPNISKNNNIAANDSKAWDANSQHLQVKDKL 257

Query: 61  LPEKGS-LISKDNFVSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGV 119
            P  GS  I KD+ +ST+ILINSSICTMQRIAVLE+ KLVELLLEPVK+NVQCDSVYLGV
Sbjct: 258 SPADGSNFILKDDSISTIILINSSICTMQRIAVLEEGKLVELLLEPVKTNVQCDSVYLGV 317

Query: 120 VTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQEVNGSASAALEEHAVT 179
           VTK VP+MGGAFVNIG+SRPSLMDIK  REPFIFPPFR +TKK+++N S   +LEEH   
Sbjct: 318 VTKFVPHMGGAFVNIGHSRPSLMDIKQSREPFIFPPFRQKTKKEKMNDSGLDSLEEHQAA 377

Query: 180 YDNDSTSHNTE---DVAEADSQDDLVQFEHNDDEEHDGD-DFDVSEVLKNVNGSIIDDGE 235
             N+ TS + E   DVAE  SQ+DLV   HND +EH+ D DFD+SEV +NVNGSI+D G+
Sbjct: 378 DGNEHTSQDIEGIDDVAEFISQEDLVSLPHNDHDEHEADEDFDISEVKENVNGSIVDYGQ 437

Query: 236 PEADFEDFLEG-DHHLDGE-SNGFFPSKSEVPDDSHTSHPQGTKDSKHT-PGEKTWLQVQ 292
            +  FE FL G  HHL+GE  N   PS++E  + S  S PQ  KDS+H    +  W QV+
Sbjct: 438 ADPRFEHFLGGRQHHLEGEIMNRVVPSETEGSNGSKMSQPQYRKDSEHLLANDNKWTQVR 497

Query: 293 KGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGVERTRLKVIAK 352
           KGTK++VQVVKEGLGTKGPTLTAYPKLRSRFWIL   CDRIG+S+KI+G+ERTRL+VIAK
Sbjct: 498 KGTKIVVQVVKEGLGTKGPTLTAYPKLRSRFWILHARCDRIGISKKISGIERTRLRVIAK 557

Query: 353 TLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILL 412
           TLQP GFGLT RTVA GHSLEELQKDLEGLLSTWKNI+EHAKSAALAADEG+EGA+P++L
Sbjct: 558 TLQPPGFGLTARTVAGGHSLEELQKDLEGLLSTWKNILEHAKSAALAADEGIEGAIPVIL 617

Query: 413 HRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK 472
           H AMGQTLS+VQDYF+EKVKKMVVDSPRTYHEVT+YLQ+IAPDLCDRVELYDKRIPLFD+
Sbjct: 618 HTAMGQTLSVVQDYFSEKVKKMVVDSPRTYHEVTNYLQEIAPDLCDRVELYDKRIPLFDE 677

Query: 473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAA 532
           + IEEEINN+LSKRVPLP GGSLVIEQTEALVSIDVNGGH MFG G+S+EKAILDVNL A
Sbjct: 678 YKIEEEINNILSKRVPLPRGGSLVIEQTEALVSIDVNGGHVMFGQGNSQEKAILDVNLEA 737

Query: 533 AKQIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLME 592
           AK+IARELRLRDIGGIIVVDFIDMADDSNKRLVYEE+K AVE DRSMVKVSELS+HGLME
Sbjct: 738 AKRIARELRLRDIGGIIVVDFIDMADDSNKRLVYEEMKTAVEGDRSMVKVSELSKHGLME 797

Query: 593 ITRKR----------------------------------------AMMEQKADPENPKSW 612
           ITRKR                                        AMM+QKA PENPK+W
Sbjct: 798 ITRKRVRPSVSFMISEPCTCCHATGRVEALETSFSKIEQEICRLLAMMDQKAYPENPKTW 857

Query: 613 PRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLK----------VARGFTRGAFEVI 662
           PRF+LRVDHHMCNYLTSGKRTRLA+LSSSLK WILLK          VARGFTRGAFEV 
Sbjct: 858 PRFLLRVDHHMCNYLTSGKRTRLAILSSSLKVWILLKMLITRALTPQVARGFTRGAFEVQ 917

Query: 663 PYTDDKASENQHQVAISLLRSAEARANKSGKKVTLVPIKKLKS 705
           P+ DD+A+ENQHQVAIS+LR  E R   SGKKVTLVP+K  +S
Sbjct: 918 PFADDQANENQHQVAISVLRQTETRTINSGKKVTLVPVKTCRS 960

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224131900\|ref\|XP_002321206.1\| predicted protein [Populus trichocarpa] gi\|222861979\|gb\|EEE99521.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225447486\|ref\|XP_002267175.1\| PREDICTED: uncharacterized protein LOC100256290 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356551838\|ref\|XP_003544280.1\| PREDICTED: uncharacterized protein LOC100809907 [Glycine max]	Back alignment and taxonomy information

>gi\|356498920\|ref\|XP_003518294.1\| PREDICTED: uncharacterized protein LOC100795436 [Glycine max]	Back alignment and taxonomy information

>gi\|449470204\|ref\|XP_004152808.1\| PREDICTED: uncharacterized protein LOC101204095 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449477847\|ref\|XP_004155141.1\| PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein LOC101228180, partial [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357490525\|ref\|XP_003615550.1\| Ribonuclease E [Medicago truncatula] gi\|355516885\|gb\|AES98508.1\| Ribonuclease E [Medicago truncatula]	Back alignment and taxonomy information

>gi\|297831502\|ref\|XP_002883633.1\| glycoside hydrolase starch-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297329473\|gb\|EFH59892.1\| glycoside hydrolase starch-binding domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|27368501\|emb\|CAD48421.1\| putative endoribonuclease E [Arabidopsis thaliana]	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		708
TIGR_CMR\|GSU_3239		500	GSU_3239 "ribonuclease G" [Geo	0.416	0.59	0.347	2.5e-52
UNIPROTKB\|Q4KFS6		1071	rne "Ribonuclease E" [Pseudomo	0.416	0.275	0.359	2.8e-52
UNIPROTKB\|Q9KQG8		1052	VC_2030 "Ribonuclease E" [Vibr	0.460	0.309	0.354	3.3e-52
TIGR_CMR\|VC_2030		1052	VC_2030 "ribonuclease E" [Vibr	0.460	0.309	0.354	3.3e-52
TIGR_CMR\|CBU_0486		720	CBU_0486 "ribonuclease, Rne/Rn	0.460	0.452	0.341	8.5e-51
UNIPROTKB\|Q3IHD2		1071	rne "RNase E: endoribonuclease	0.416	0.275	0.372	4e-50
TIGR_CMR\|SO_2785		1088	SO_2785 "ribonuclease E" [Shew	0.460	0.299	0.363	5.7e-50
TIGR_CMR\|CPS_2289		1004	CPS_2289 "ribonuclease E" [Col	0.460	0.324	0.334	3e-49
TIGR_CMR\|SO_4094		502	SO_4094 "ribonuclease G" [Shew	0.415	0.585	0.353	2.3e-47
UNIPROTKB\|Q4KIA2		485	rng "Ribonuclease G" [Pseudomo	0.416	0.608	0.329	4.5e-45

TIGR_CMR\|GSU_3239 GSU_3239 "ribonuclease G" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

 Score = 471 (170.9 bits), Expect = 2.5e-52, Sum P(3) = 2.5e-52
 Identities = 107/308 (34%), Positives = 171/308 (55%)

Query:   291 VQKGTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKV 349
             +Q+G +++VQV KE +GTKG  +T++  L  R  + + + D +GVSR+I    ER RLK 
Sbjct:   108 LQEGQEILVQVSKEPIGTKGARITSHVSLPGRHLVYMPTVDHVGVSRRIEDEPERERLKE 167

Query:   350 IAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVP 409
             I    +P G G  +RT A G + E+L  D+  L   W+ ++   + A            P
Sbjct:   168 IVGKAKPAGGGFIVRTAAEGKTEEDLVADMNYLTKLWEEVVRRNEKAH----------AP 217

Query:   410 ILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPL 469
              L+H  +  T  +++D   E V ++VVDS   + ++  ++    P +   +ELYD   P+
Sbjct:   218 CLIHADLDVTQKVIRDILTENVSRIVVDSRHEHDKIVQFISTFMPKMKYSMELYDDEEPI 277

Query:   470 FDKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVN 529
             FD F +E EI+  L ++V L +GG ++IEQTEAL +IDVN G  +  H  + E  IL  N
Sbjct:   278 FDHFGLEVEISRALGRKVWLKSGGYIIIEQTEALTAIDVNTGRFVGKH--NLEDTILKTN 335

Query:   530 LAAAKQIARELRLRXXXXXXXXXXXXMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHG 589
             L A K+IA +LRLR            M  + N+  V+  +++A++ D+S   + ++S  G
Sbjct:   336 LEAVKEIAYQLRLRNIGGIIIIDFIDMEKEVNREKVFTALEEAMKADKSKTNILKISDLG 395

Query:   590 LMEITRKR 597
             L+E+TRKR
Sbjct:   396 LVEMTRKR 403

GO:0000910 "cytokinesis" evidence=ISS

GO:0004540 "ribonuclease activity" evidence=ISS

GO:0006396 "RNA processing" evidence=ISS

UNIPROTKB\|Q4KFS6 rne "Ribonuclease E" [Pseudomonas protegens Pf-5 (taxid:220664)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9KQG8 VC_2030 "Ribonuclease E" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]	Back alignment and assigned GO terms

TIGR_CMR\|VC_2030 VC_2030 "ribonuclease E" [Vibrio cholerae O1 biovar El Tor (taxid:686)]	Back alignment and assigned GO terms

TIGR_CMR\|CBU_0486 CBU_0486 "ribonuclease, Rne/Rng family" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3IHD2 rne "RNase E: endoribonuclease for rRNA processing and mRNA degradation; member of the degradosome; involved in the production of deoxyribonucleotides via the formation of NDPs" [Pseudoalteromonas haloplanktis TAC125 (taxid:326442)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_2785 SO_2785 "ribonuclease E" [Shewanella oneidensis MR-1 (taxid:211586)]	Back alignment and assigned GO terms

TIGR_CMR\|CPS_2289 CPS_2289 "ribonuclease E" [Colwellia psychrerythraea 34H (taxid:167879)]	Back alignment and assigned GO terms

TIGR_CMR\|SO_4094 SO_4094 "ribonuclease G" [Shewanella oneidensis MR-1 (taxid:211586)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4KIA2 rng "Ribonuclease G" [Pseudomonas protegens Pf-5 (taxid:220664)]	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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.12	0.737
3rd Layer	3.1.26	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.XIV.3873.1	hypothetical protein (923 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		708
pfam10150		271	pfam10150, RNase_E_G, Ribonuclease E/G family	1e-112
TIGR00757		414	TIGR00757, RNaseEG, ribonuclease, Rne/Rng family	3e-96
COG1530		487	COG1530, CafA, Ribonucleases G and E [Translation,	6e-82
PRK11712		489	PRK11712, PRK11712, ribonuclease G; Provisional	1e-65
PRK10811		1068	PRK10811, rne, ribonuclease E; Reviewed	5e-48
cd04453		88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	9e-09
cd04453		88	cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase	1e-07
COG1530		487	COG1530, CafA, Ribonucleases G and E [Translation,	3e-06
TIGR00757		414	TIGR00757, RNaseEG, ribonuclease, Rne/Rng family	4e-05

>gnl\|CDD\|220602 pfam10150, RNase_E_G, Ribonuclease E/G family	Back alignment and domain information

 Score =  340 bits (874), Expect = e-112
 Identities = 127/280 (45%), Positives = 180/280 (64%), Gaps = 13/280 (4%)

Query: 319 LRSRFWILITSCDRIGVSRKITG-VERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQK 377
           L  R+ +L+ +   IG+SRKI    ER RLK I ++L+PEG GL IRT A G S EEL  
Sbjct: 2   LPGRYLVLMPNSPGIGISRKIEDEEERKRLKEILESLKPEGMGLIIRTAAEGASEEELAA 61

Query: 378 DLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVD 437
           DLE LL  W+ I++ AKSA            P LL+  +   L  ++D  N  V +++VD
Sbjct: 62  DLEYLLKLWEEILKKAKSAK----------APSLLYEELDLVLRALRDLLNPDVDEIIVD 111

Query: 438 SPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVPLPNGGSLVI 497
               Y ++  +L++ AP+L  +VELY+   PLFD + IEE+I   LS++V L +GG LVI
Sbjct: 112 DREAYEKLKEFLKEFAPELAKKVELYEGERPLFDLYGIEEQIEKALSRKVWLKSGGYLVI 171

Query: 498 EQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVDFIDMA 557
           EQTEAL +IDVN G    G  +  E+  L  NL AAK+IAR+LRLR++GGIIV+DFIDM 
Sbjct: 172 EQTEALTAIDVNSG-KFTGKRNL-EETALKTNLEAAKEIARQLRLRNLGGIIVIDFIDME 229

Query: 558 DDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKR 597
           D+ ++R V   +K+A++RDR+  ++  ++  GL+E+TRKR
Sbjct: 230 DEEHRRQVLRALKEALKRDRAKTQILGITELGLVEMTRKR 269

Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs. Length = 271

>gnl\|CDD\|233116 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family	Back alignment and domain information

>gnl\|CDD\|224447 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|183285 PRK11712, PRK11712, ribonuclease G; Provisional	Back alignment and domain information

>gnl\|CDD\|236766 PRK10811, rne, ribonuclease E; Reviewed	Back alignment and domain information

>gnl\|CDD\|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain	Back alignment and domain information

>gnl\|CDD\|224447 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|233116 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		708
PRK11712		489	ribonuclease G; Provisional	100.0
PRK10811		1068	rne ribonuclease E; Reviewed	100.0
TIGR00757		414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	100.0
COG1530		487	CafA Ribonucleases G and E [Translation, ribosomal	100.0
PF10150		271	RNase_E_G: Ribonuclease E/G family; InterPro: IPR0	100.0
cd04453		88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	99.62
PF00575		74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	97.63
cd04472		68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	97.31
COG1098		129	VacB Predicted RNA binding protein (contains ribos	97.09
cd05704		72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	97.04
cd05692		69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	96.94
smart00316		72	S1 Ribosomal protein S1-like RNA-binding domain.	96.93
cd05698		70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	96.61
cd05685		68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	96.54
cd04461		83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	96.44
PRK07252		120	hypothetical protein; Provisional	96.43
PTZ00248		319	eukaryotic translation initiation factor 2 subunit	96.38
cd05707		68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	96.27
PRK08059		123	general stress protein 13; Validated	96.21
cd05684		79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	96.19
cd05687		70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	96.17
cd05706		73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	96.04
cd05697		69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	95.81
cd05686		73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	95.77
cd04452		76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	95.57
cd05691		73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	95.54
PRK08582		139	hypothetical protein; Provisional	95.47
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	95.46
cd05696		71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	95.37
cd05688		68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	95.13
cd05789		86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	95.09
TIGR02696		719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	94.7
TIGR03591		684	polynuc_phos polyribonucleotide nucleotidyltransfe	94.67
PRK05807		136	hypothetical protein; Provisional	94.62
cd05705		74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	94.49
PRK03987		262	translation initiation factor IF-2 subunit alpha;	94.4
cd05694		74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	94.36
cd05708		77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	94.29
cd04454		82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	94.16
PRK11824		693	polynucleotide phosphorylase/polyadenylase; Provis	94.12
cd04455		67	S1_NusA S1_NusA: N-utilizing substance A protein (	94.09
PRK09521		189	exosome complex RNA-binding protein Csl4; Provisio	93.63
cd00164		65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	93.55
PRK04163		235	exosome complex RNA-binding protein Rrp4; Provisio	93.06
PLN00207		891	polyribonucleotide nucleotidyltransferase; Provisi	92.37
cd05690		69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	90.8
PRK14865		116	rnpA ribonuclease P; Provisional	90.63
cd05689		72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	90.39
PRK07400		318	30S ribosomal protein S1; Reviewed	90.35
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	90.15
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	89.67
PRK07400		318	30S ribosomal protein S1; Reviewed	89.0
PRK00588		118	rnpA ribonuclease P; Reviewed	88.78
TIGR01953		341	NusA transcription termination factor NusA. This m	88.24
cd05702		70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	87.84
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	87.8
PRK13806		491	rpsA 30S ribosomal protein S1; Provisional	87.62
cd04471		83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	87.2
cd04465		67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	86.98
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	86.3
COG0539		541	RpsA Ribosomal protein S1 [Translation, ribosomal	86.19
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	86.13
PRK00396		130	rnpA ribonuclease P; Reviewed	86.12
PRK03459		122	rnpA ribonuclease P; Reviewed	85.84
cd04473		77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	84.72
PRK06299		565	rpsA 30S ribosomal protein S1; Reviewed	84.56
PRK07899		486	rpsA 30S ribosomal protein S1; Reviewed	84.17
PRK12269		863	bifunctional cytidylate kinase/ribosomal protein S	83.8
PRK00499		114	rnpA ribonuclease P; Reviewed	83.21
PRK06676		390	rpsA 30S ribosomal protein S1; Reviewed	83.1
TIGR00717		516	rpsA ribosomal protein S1. This model provides tru	83.06
PRK04390		120	rnpA ribonuclease P; Reviewed	82.89
PRK09202		470	nusA transcription elongation factor NusA; Validat	82.41
PRK01313		129	rnpA ribonuclease P; Reviewed	82.15

>PRK11712 ribonuclease G; Provisional	Back alignment and domain information

Probab=100.00  E-value=8.4e-122  Score=1017.32  Aligned_cols=457  Identities=30%  Similarity=0.500  Sum_probs=416.4

Q ss_pred             CceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcC
Q 005219           74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF  153 (708)
Q Consensus        74 m~keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~  153 (708)
                      |+++||||+.+ .++|+|++|||+|+||++|+.+...++||||+|+|+||+|||||||||||.+|+||||++|..+++.+
T Consensus         1 M~~~i~i~~~~-~e~r~Alledg~l~e~~iE~~~~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~   79 (489)
T PRK11712          1 MTAELLVNVTP-SETRVALIEGGILQEIHIEREAKRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTEC   79 (489)
T ss_pred             CceEEEEecCC-CeEEEEEEECCEEEEEEEecCCcccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhh
Confidence            88999999987 69999999999999999999999999999999999999999999999999999999999986321100


Q ss_pred             CcccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 005219          154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD  233 (708)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (708)
                      ..      .                                               ++.             .       
T Consensus        80 ~~------~-----------------------------------------------~~~-------------~-------   86 (489)
T PRK11712         80 VA------G-----------------------------------------------EEQ-------------K-------   86 (489)
T ss_pred             cc------c-----------------------------------------------ccc-------------c-------
Confidence            00      0                                               000             0       


Q ss_pred             CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCcee
Q 005219          234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL  313 (708)
Q Consensus       234 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprL  313 (708)
                                                      . ..              ..++...|++||+|||||+|||+|+|||+|
T Consensus        87 --------------------------------~-~~--------------~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~l  119 (489)
T PRK11712         87 --------------------------------Q-FV--------------VRDISELVRQGQDIMVQVVKDPLGTKGARL  119 (489)
T ss_pred             --------------------------------c-cc--------------cccHHHhccCCCEEEEEEEeCCcCCCCCeE
Confidence                                            0 00              012346799999999999999999999999


Q ss_pred             eecceecceeEEEeeCCCceeeecCCChH-HHHHHHHHHHhhCCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 005219          314 TAYPKLRSRFWILITSCDRIGVSRKITGV-ERTRLKVIAKTLQPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEH  392 (708)
Q Consensus       314 Tt~IsL~GRylVl~P~~~~igiSrKI~~~-eR~rLk~i~~~l~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~~  392 (708)
                      |++|||||||+||||+++++||||||+++ +|+||+.++..+.++++|+||||+|+++++++|.+|+++|.++|++|.++
T Consensus       120 T~~Isl~GrylVl~P~~~~vgiSrKI~de~~R~rLk~i~~~~~~~~~GvIiRT~A~~a~~eel~~dl~~L~~~w~~i~~~  199 (489)
T PRK11712        120 TTDITLPSRYLVFMPGASHVGVSQRIESEEERERLKKIVAPYCDEQGGFIIRTAAEGVGEEELAQDAAFLKRLWTKVMER  199 (489)
T ss_pred             EEEEEeccceEEEECCCCCeeEecCCCChHHHHHHHHHHHhhCCCCceEEEEccCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999886 69999999999988889999999999999999999999999999999999


Q ss_pred             HHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhhCCCcCCceeeccCCCCcccc
Q 005219          393 AKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIAPDLCDRVELYDKRIPLFDK  472 (708)
Q Consensus       393 ~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~~p~~~~~v~~y~~~~plF~~  472 (708)
                      ++.+          ++|+|||++.+++.+++||++++++++|+||+++.|+++++|+..++|+...++++|++..|||+.
T Consensus       200 ~~~~----------~~p~ll~~e~~~~~~~lrD~~~~~~~~IivD~~~~~~~i~~~~~~~~p~~~~~v~~y~~~~plF~~  269 (489)
T PRK11712        200 KKRY----------QTRYQLYGELALAQRVLRDFVGAELDRIRVDSRLTYEELKEFTSEYIPEMTDKLEHYSGRQPIFDL  269 (489)
T ss_pred             HhcC----------CCCeEEEcCCcHHHHHHHHhccCCCCEEEECCHHHHHHHHHHHHHhCccccceeEEecCCCChhHh
Confidence            9875          589999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             cCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEEEE
Q 005219          473 FNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIVVD  552 (708)
Q Consensus       473 y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIVID  552 (708)
                      |||+.+|+++++++||||||||||||+||||||||||||++  .|+.++++|+++||+|||+||||||||||||||||||
T Consensus       270 y~ie~~i~~~l~~~V~L~sGg~lvIe~TeAlt~IDVnsGk~--~~~~~~eet~~~tN~eAa~eiarqlrLR~igGiIviD  347 (489)
T PRK11712        270 YDVENEIQRALERKVELKSGGYLIIDQTEAMTTVDINTGAF--VGHRNLEETIFNTNIEATQAIARQLRLRNLGGIIIID  347 (489)
T ss_pred             cCHHHHHHHHhcCcEEcCCCcEEEEeccccEEEEEecCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEEE
Confidence            99999999999999999999999999999999999999984  5677899999999999999999999999999999999


Q ss_pred             cCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccccCC--CCCC--------------------
Q 005219          553 FIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQKADP--ENPK--------------------  610 (708)
Q Consensus       553 FIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~~~~--~~~~--------------------  610 (708)
                      ||||+++++|++|+++|+++|++|+++++|+|||+||||||||||.+.++....  .||+                    
T Consensus       348 FidM~~~~~r~~v~~~l~~~l~~D~~k~~v~~~T~lGLvEmTRkR~r~sl~~~l~~~Cp~C~G~G~v~s~e~~~~~i~r~  427 (489)
T PRK11712        348 FIDMNNEDHRRRVLHSLEQALSKDRVKTNINGFSQLGLVEMTRKRTRESLEHVLCGECPTCHGRGTVKTVETVCYEIMRE  427 (489)
T ss_pred             CCCCCCHHHHHHHHHHHHHHhhcCCCCceEcccCCCceEEEEecccCCChHHHhcCCCCCCCCCCCcCCHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999876543222  2332                    


Q ss_pred             --------CCCeEEEEECHHHHHHHHcCchhhHHHHHhhcCCeEEEEeCCCCCCcCeEEEE
Q 005219          611 --------SWPRFILRVDHHMCNYLTSGKRTRLAVLSSSLKAWILLKVARGFTRGAFEVIP  663 (708)
Q Consensus       611 --------~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~~~~I~i~~d~~l~~~~~~i~~  663 (708)
                              ..+.+++++||.|++||.+.++.++..|+.++|.++.|.+++.+++++|+|..
T Consensus       428 i~~~~~~~~~~~~~~~~~p~v~~~l~~~~~~~~~~le~~~g~~i~i~~~~~~~~~~~~i~~  488 (489)
T PRK11712        428 IVRVHHAYDSDRFLVYASPAVAEALKGEESHALAELEIFVGKQVKVQIEPLYNQEQFDVVM  488 (489)
T ss_pred             HHHHHhhCCCceEEEEECHHHHHHHHccchHHHHHHHHHhCCeEEEEECCCCCccceEEEe
Confidence                    13458999999999999998888999999999999999999999999999864

>PRK10811 rne ribonuclease E; Reviewed	Back alignment and domain information

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family	Back alignment and domain information

>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF10150 RNase_E_G: Ribonuclease E/G family; InterPro: IPR019307 Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs []	Back alignment and domain information

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain	Back alignment and domain information

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms	Back alignment and domain information

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain	Back alignment and domain information

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa	Back alignment and domain information

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains	Back alignment and domain information

>PRK07252 hypothetical protein; Provisional	Back alignment and domain information

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional	Back alignment and domain information

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>PRK08059 general stress protein 13; Validated	Back alignment and domain information

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide	Back alignment and domain information

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain	Back alignment and domain information

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain	Back alignment and domain information

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>PRK08582 hypothetical protein; Provisional	Back alignment and domain information

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain	Back alignment and domain information

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase	Back alignment and domain information

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase	Back alignment and domain information

>PRK05807 hypothetical protein; Provisional	Back alignment and domain information

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated	Back alignment and domain information

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain	Back alignment and domain information

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional	Back alignment and domain information

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain	Back alignment and domain information

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional	Back alignment and domain information

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain	Back alignment and domain information

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional	Back alignment and domain information

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional	Back alignment and domain information

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>PRK14865 rnpA ribonuclease P; Provisional	Back alignment and domain information

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>PRK07400 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK13806 rpsA 30S ribosomal protein S1; Provisional	Back alignment and domain information

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK07400 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK00588 rnpA ribonuclease P; Reviewed	Back alignment and domain information

>TIGR01953 NusA transcription termination factor NusA	Back alignment and domain information

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits	Back alignment and domain information

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK13806 rpsA 30S ribosomal protein S1; Provisional	Back alignment and domain information

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain	Back alignment and domain information

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain	Back alignment and domain information

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>PRK00396 rnpA ribonuclease P; Reviewed	Back alignment and domain information

>PRK03459 rnpA ribonuclease P; Reviewed	Back alignment and domain information

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease	Back alignment and domain information

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional	Back alignment and domain information

>PRK00499 rnpA ribonuclease P; Reviewed	Back alignment and domain information

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed	Back alignment and domain information

>TIGR00717 rpsA ribosomal protein S1	Back alignment and domain information

>PRK04390 rnpA ribonuclease P; Reviewed	Back alignment and domain information

>PRK09202 nusA transcription elongation factor NusA; Validated	Back alignment and domain information

>PRK01313 rnpA ribonuclease P; Reviewed	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		708
2vmk_A		515	Crystal Structure Of E. Coli Rnase E Apoprotein - C		6e-46
2bx2_L		517	Catalytic Domain Of E. Coli Rnase E Length = 517		6e-46
2vrt_A		509	Crystal Structure Of E. Coli Rnase E Possessing M1		7e-46

>pdb|2VMK|A Chain A, Crystal Structure Of E. Coli Rnase E Apoprotein - Catalytic Domain Length = 515

Back alignment and structure

Iteration: 1

Score = 182 bits (462), Expect = 6e-46, Method: Compositional matrix adjust. Identities = 119/367 (32%), Positives = 190/367 (51%), Gaps = 35/367 (9%) Query: 237 EADFEDFLEGDHHLDGESNGFFPSKS---EVPDDSHTSHPQGTKDSKHTPGEKTWLQVQK 293 EA F D+ E +GF P K E ++++H + P K L+ + Sbjct: 54 EAAFVDY-------GAERHGFLPLKEIAREYFPANYSAHGR--------PNIKDVLR--E 96 Query: 294 GTKVIVQVVKEGLGTKGPTLTAYPKLRSRFWILITSCDRIG-VSRKITGVERTRLKVIAK 352 G +VIVQ+ KE G KG LT + L + +L+ + R G +SR+I G +RT LK Sbjct: 97 GQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALA 156 Query: 353 TLQ-PEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPIL 411 +L+ PEG GL +RT G S E LQ DL L W+ I + A+S P L Sbjct: 157 SLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRP----------APFL 206 Query: 412 LHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDIA-PDLCDRVELYDKRIPLF 470 +H+ + +DY + + ++++D+P+ ++ + PD +++LY IPLF Sbjct: 207 IHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLF 266 Query: 471 DKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNL 530 + IE +I + + V LP+GGS+VI+ TEAL +ID+N G E+ + NL Sbjct: 267 SHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARAT--RGGDIEETAFNTNL 324 Query: 531 AAAKQIARELRLRXXXXXXXXXXXXMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGL 590 AA +IAR+LRLR M ++R V +++AV +DR+ +++S +SR GL Sbjct: 325 EAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGL 384 Query: 591 MEITRKR 597 +E++R+R Sbjct: 385 LEMSRQR 391

PyMOL of 2vmk

>pdb|2BX2|L Chain L, Catalytic Domain Of E. Coli Rnase E Length = 517

Back alignment and structure

>pdb|2VRT|A Chain A, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain Length = 509

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		708
2bx2_L		517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	1e-109
2bx2_L		517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	9e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-08

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Length = 517	Back alignment and structure

 Score =  338 bits (870), Expect = e-109
 Identities = 119/349 (34%), Positives = 192/349 (55%), Gaps = 22/349 (6%)

Query: 252 GESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGP 311
            E +GF P    + + +    P           +     +++G +VIVQ+ KE  G KG 
Sbjct: 69  AERHGFLP----LKEIAREYFPANYSAHGRPNIKDV---LREGQEVIVQIDKEERGNKGA 121

Query: 312 TLTAYPKLRSRFWILITSCDRI-GVSRKITGVERTRLKVIAKTLQ-PEGFGLTIRTVAAG 369
            LT +  L   + +L+ +  R  G+SR+I G +RT LK    +L+ PEG GL +RT   G
Sbjct: 122 ALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVG 181

Query: 370 HSLEELQKDLEGLLSTWKNIMEHAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNE 429
            S E LQ DL   L  W+ I + A+S             P L+H+     +   +DY  +
Sbjct: 182 KSAEALQWDLSFRLKHWEAIKKAAESRP----------APFLIHQESNVIVRAFRDYLRQ 231

Query: 430 KVKKMVVDSPRTYHEVTSYLQDIA-PDLCDRVELYDKRIPLFDKFNIEEEINNMLSKRVP 488
            + ++++D+P+       ++  +  PD   +++LY   IPLF  + IE +I +   + V 
Sbjct: 232 DIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVR 291

Query: 489 LPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGI 548
           LP+GGS+VI+ TEAL +ID+N        G   E+   + NL AA +IAR+LRLRD+GG+
Sbjct: 292 LPSGGSIVIDSTEALTAIDINSAR--ATRGGDIEETAFNTNLEAADEIARQLRLRDLGGL 349

Query: 549 IVVDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKR 597
           IV+DFIDM    ++R V   +++AV +DR+ +++S +SR GL+E++R+R
Sbjct: 350 IVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQR 398

PyMOL of 2bx2

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Length = 517	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

>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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		708
2bx2_L		517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	100.0
3cw2_C		266	Translation initiation factor 2 subunit alpha; AIF	98.62
1q8k_A		308	Eukaryotic translation initiation factor 2 subunit	98.22
2eqs_A		103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	97.59
2k52_A		80	Uncharacterized protein MJ1198; metal-binding, zin	97.51
2khj_A		109	30S ribosomal protein S1; OB fold, acetylation, ph	97.46
2k4k_A		130	GSP13, general stress protein 13; cytoplasm, stres	97.44
2cqo_A		119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	97.43
2khi_A		115	30S ribosomal protein S1; acetylation, phosphoprot	97.34
3m7n_A		179	Putative uncharacterized protein AF_0206; exosome,	96.31
1kl9_A		182	Eukaryotic translation initiation factor 2 subuni;	96.3
3aev_A		275	Translation initiation factor 2 subunit alpha; pro	96.22
1y14_B		171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	96.1
1go3_E		187	DNA-directed RNA polymerase subunit E; transferase	95.99
2a19_A		175	EIF-2- alpha, eukaryotic translation initiation fa	95.82
2b8k_G		215	B16, DNA-directed RNA polymerase II 19 kDa polypep	95.47
1wi5_A		119	RRP5 protein homolog; S1 domain, OB-fold, structur	94.81
2ba0_A		229	Archeal exosome RNA binding protein RRP4; RNAse PH	94.37
2c35_B		172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	94.36
2z0s_A		235	Probable exosome complex RNA-binding protein 1; al	93.34
2nn6_I		209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	92.97
3h0g_G		172	DNA-directed RNA polymerase II subunit RPB7; trans	92.38
3cdi_A		723	Polynucleotide phosphorylase; mRNA turnover, RNAse	92.35
2je6_I		251	RRP4, exosome complex RNA-binding protein 1; nucle	92.33
3psi_A		1219	Transcription elongation factor SPT6; nucleus; 3.3	92.28
1luz_A		88	Protein K3, protein K2; stranded anti-parallel bet	91.7
3bzc_A		785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	91.48
1hh2_P		344	NUSA, N utilization substance protein A; transcrip	90.93
1a6f_A		119	RNAse P protein, ribonuclease P protein; endonucle	90.88
4ayb_E		180	DNA-directed RNA polymerase; transferase, multi-su	89.69
4aid_A		726	Polyribonucleotide nucleotidyltransferase; transfe	89.47
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	88.32
1k0r_A		366	NUSA; two component arrangement, S1 domain, two K-	86.83
1d6t_A		117	Ribonuclease P, RNAse P protein; endonuclease, sub	86.58
3psf_A		1030	Transcription elongation factor SPT6; nucleus; 2.5	86.47
2ljp_A		119	Ribonuclease P protein component; rnasep, ribozyme	85.44
2asb_A		251	Transcription elongation protein NUSA; protein-RNA	81.94
3go5_A		285	Multidomain protein with S1 RNA-binding domains; s	80.14

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A	Back alignment and structure

Probab=100.00  E-value=1.4e-123  Score=1035.61  Aligned_cols=461  Identities=30%  Similarity=0.535  Sum_probs=413.0

Q ss_pred             CceEEEEEecCCCeEEEEEEECCEEEEEEeecCCCCcccCCeEEEEEeeecCCcceEEecccCCcceeeEeccCCCCCcC
Q 005219           74 VSTVILINSSICTMQRIAVLEDEKLVELLLEPVKSNVQCDSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIF  153 (708)
Q Consensus        74 m~keilIn~~~~~e~RvAvlEdgkL~El~iE~~~~~~~vGnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~~~~~~  153 (708)
                      |+++||||+++++++|||++|||+|+||++|+......+||||+|+|+||+|+|||||||||.+++||||++++...++ 
T Consensus         7 ~M~~ilI~~~~~ee~rvAl~e~~~L~el~iE~~~~~~~vGnIY~GkV~rv~p~~~aAFVdiG~gk~gfLhisei~~~~~-   85 (517)
T 2bx2_L            7 HMKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYF-   85 (517)
T ss_dssp             SCEEEEEECSCTTCEEEEEEETTEEEEEEEECSSSCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGC-
T ss_pred             chheEEEEcCCCCeEEEEEEeCCEEEEEEEecCCCcCCCCCEEEEEEEEeccCCceEEEEeCCCcEEEEEHHHcChhhh-
Confidence            6678999998668999999999999999999999999999999999999999999999999999999999998621110 


Q ss_pred             CcccccchhhhccccchhhhhhhhcccCCCCCCCCcchhhhcccccccccccCCCCCCCCCCCcchhhhhhccCCcccCC
Q 005219          154 PPFRCRTKKQEVNGSASAALEEHAVTYDNDSTSHNTEDVAEADSQDDLVQFEHNDDEEHDGDDFDVSEVLKNVNGSIIDD  233 (708)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (708)
                          .   .                                               . .        .   .        
T Consensus        86 ----~---~-----------------------------------------------~-~--------~---~--------   91 (517)
T 2bx2_L           86 ----P---A-----------------------------------------------N-Y--------S---A--------   91 (517)
T ss_dssp             ----C---------------------------------------------------------------------------
T ss_pred             ----c---c-----------------------------------------------c-c--------c---c--------
Confidence                0   0                                               0 0        0   0        


Q ss_pred             CCCCccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccCCCEEEEEEEecCCCCCCcee
Q 005219          234 GEPEADFEDFLEGDHHLDGESNGFFPSKSEVPDDSHTSHPQGTKDSKHTPGEKTWLQVQKGTKVIVQVVKEGLGTKGPTL  313 (708)
Q Consensus       234 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~lk~Gq~ILVQV~KE~~gtKGprL  313 (708)
                                                                      ....++.+.|++||+|+|||+|+|+|+|||+|
T Consensus        92 ------------------------------------------------~~~~~i~d~lk~Gq~VlVQV~Ke~~g~KGa~l  123 (517)
T 2bx2_L           92 ------------------------------------------------HGRPNIKDVLREGQEVIVQIDKEERGNKGAAL  123 (517)
T ss_dssp             --------------------------------------------------CCCGGGTCCTTCEEEEEEEECCCTTCCCEE
T ss_pred             ------------------------------------------------ccccchhhhccCCCEEEEEEEeeccccCCceE
Confidence                                                            00012346799999999999999999999999


Q ss_pred             eecceecceeEEEeeCCCce-eeecCCChHHHHHHHHHHHhh-CCCCeeEEEeecCCCCCHHHHHHHHHHHHHHHHHHHH
Q 005219          314 TAYPKLRSRFWILITSCDRI-GVSRKITGVERTRLKVIAKTL-QPEGFGLTIRTVAAGHSLEELQKDLEGLLSTWKNIME  391 (708)
Q Consensus       314 Tt~IsL~GRylVl~P~~~~i-giSrKI~~~eR~rLk~i~~~l-~p~~~GvIiRTaA~g~~~eeL~~Dl~~L~~~W~~I~~  391 (708)
                      |++||||||||||||+++++ ||||||++++|+|||+++..+ .|+++|+||||+|+|+++++|.+|+++|.++|+.|++
T Consensus       124 Tt~isl~GRylVl~P~~~~~~giSrkI~~~eR~rLk~~~~~~~~~~~~G~IvRT~a~g~~~eel~~dl~~L~~~w~~I~~  203 (517)
T 2bx2_L          124 TTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKK  203 (517)
T ss_dssp             ESSCCEECSSEEEETTCTTCCEECTTCC------HHHHHTTSCCCTTCEEEECGGGGGCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             EeeEEeccceEEEeCCCCCcCcccccCChHHHHHHHHHHHhhcCCCCceEEEEcccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999987 899999988899999999988 5889999999999999999999999999999999999


Q ss_pred             HHHHhhhhhccCCCCCCceeeeecCCchhhhhhhhcCCCccEEEEcCHHHHHHHHHHHHhh-CCCcCCceeeccCCCCcc
Q 005219          392 HAKSAALAADEGVEGAVPILLHRAMGQTLSIVQDYFNEKVKKMVVDSPRTYHEVTSYLQDI-APDLCDRVELYDKRIPLF  470 (708)
Q Consensus       392 ~~~~~~~~~~~g~~~~~P~LLy~e~~~~~r~lRD~~~~~v~~IiVDd~~~y~~i~~~l~~~-~p~~~~~v~~y~~~~plF  470 (708)
                      +++.+          ++|+|||++.+++.+++|||+++++++|+||+++.|+++++|++.+ +|+...+|++|+++.|||
T Consensus       204 ~~~~~----------~~P~ll~~e~~~~~r~lRD~~~~~~~~I~vd~~~~~~~~~~~~~~~~~p~~~~~v~~y~~~~plF  273 (517)
T 2bx2_L          204 AAESR----------PAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLF  273 (517)
T ss_dssp             HHHTS----------CSCEEEECCCCHHHHHHHHHCCTTEEEEEESCHHHHHHHHHHHHHTTCHHHHTTEEECCCSSCHH
T ss_pred             HHhcC----------CCCEEEEecCcHHHHHHHHHccCCCCEEEECCHHHHHHHHHHHHHhcCccccceEEEEeCCCChh
Confidence            98765          5899999999999999999999999999999999999999999999 999999999999999999


Q ss_pred             cccCHHHHHHHHhCCceeCCCCcEEEEecccceEEEEecCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcccCCCcEE
Q 005219          471 DKFNIEEEINNMLSKRVPLPNGGSLVIEQTEALVSIDVNGGHGMFGHGSSKEKAILDVNLAAAKQIARELRLRDIGGIIV  550 (708)
Q Consensus       471 ~~y~Ie~qIe~al~r~V~L~sGG~LVIE~TEALtvIDVNSGk~~~~~~~~~eet~lktNLEAA~EIARQLRLRnIGGIIV  550 (708)
                      +.|+|++||++||+++||||||||||||+||||||||||||++  +++.++++|+++||||||+||||||||||||||||
T Consensus       274 ~~y~ie~~i~~al~~~V~L~sGGylvIe~TEALt~IDVNsG~~--~~~~~~eet~~~tNleAA~EIaRQLRLRnlgGiIv  351 (517)
T 2bx2_L          274 SHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARA--TRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIV  351 (517)
T ss_dssp             HHTTCHHHHHHTTCSEEECTTSCEEEEEECSSCEEEEEECCC------CCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             HhcCHHHHHHHHhCCeEEcCCCeEEEEecCcceEEEEccCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHhhcCCCcEEE
Confidence            9999999999999999999999999999999999999999985  56679999999999999999999999999999999


Q ss_pred             EEcCCCCChhhHHHHHHHHHHHHhcCCCCcEEeccCCceeEEEeecCCCcccc--cCCCCCC------------------
Q 005219          551 VDFIDMADDSNKRLVYEEVKKAVERDRSMVKVSELSRHGLMEITRKRAMMEQK--ADPENPK------------------  610 (708)
Q Consensus       551 IDFIDM~~~~~r~~V~~~Lk~alk~Dr~k~~V~~iT~lGLvEmTRkR~~~~~~--~~~~~~~------------------  610 (708)
                      ||||||++++||++|++.|+++|++|+++++|++||+||||||||||.+.++.  .+..||+                  
T Consensus       352 IDFIdM~~~~~r~~v~~~l~~al~~Dr~k~~v~~~S~lGLvEmTRkR~r~sL~e~~~~~Cp~C~G~G~v~s~~~~~~~i~  431 (517)
T 2bx2_L          352 IDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSIL  431 (517)
T ss_dssp             EECCCCSSHHHHHHHHHHHHHHTTTCSSCEEEEEECTTSEEEEEECCCSCCHHHHHCCCCSSSSSSSCCCCHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHHHHHHhcCCCCcEEeccCCCceEEEeecCcCcChhhhhcCcCCCcCCceeECCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999877542  1222332                  


Q ss_pred             ----------CCCeEEEEECHHHHHHHHcCchhhHHHHHhhc-CCeEEEEeCCCCCCcCeEEEEeecCcc
Q 005219          611 ----------SWPRFILRVDHHMCNYLTSGKRTRLAVLSSSL-KAWILLKVARGFTRGAFEVIPYTDDKA  669 (708)
Q Consensus       611 ----------~~~~~~l~v~p~v~~~l~~~~~~~l~~Le~~~-~~~I~i~~d~~l~~~~~~i~~~~~~~~  669 (708)
                                ....+.+.+||+|++||.++++..+..||.++ |++|.|.++++|++++|+|..+++++.
T Consensus       432 R~i~~~~~~~~~~~~~~~~~~~va~~l~~~~~~~l~~le~~~~~~~i~i~~~~~~~~~~y~i~~~~~~~~  501 (517)
T 2bx2_L          432 RLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEE  501 (517)
T ss_dssp             HHHHHHHHSTTEEEEEEEECHHHHHHHTTTTHHHHHHHHHHTTTCEEEEEECTTCCTTCCEEEEEETTCC
T ss_pred             HHHHHHHhhcCCceEEEEECHHHHHHHHhcchHHHHHHHHHcCCceEEEEECCCCCCCceEEEEccCCcc
Confidence                      12469999999999999999999999999999 999999999999999999999887664

PyMOL of 2bx2

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*	Back alignment and structure

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1	Back alignment and structure

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}	Back alignment and structure

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}	Back alignment and structure

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}	Back alignment and structure

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A	Back alignment and structure

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5	Back alignment and structure

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A	Back alignment and structure

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...	Back alignment and structure

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1	Back alignment and structure

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A	Back alignment and structure

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1	Back alignment and structure

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5	Back alignment and structure

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1	Back alignment and structure

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1	Back alignment and structure

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1	Back alignment and structure

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2	Back alignment and structure

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}	Back alignment and structure

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A	Back alignment and structure

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C	Back alignment and structure

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}	Back alignment and structure

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5	Back alignment and structure

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A	Back alignment and structure

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A	Back alignment and structure

>1a6f_A RNAse P protein, ribonuclease P protein; endonuclease, subunit; 2.60A {Bacillus subtilis} SCOP: d.14.1.2	Back alignment and structure

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E	Back alignment and structure

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A	Back alignment and structure

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}	Back alignment and structure

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1	Back alignment and structure

>1d6t_A Ribonuclease P, RNAse P protein; endonuclease, subunit, hydrolase; NMR {Staphylococcus aureus} SCOP: d.14.1.2	Back alignment and structure

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}	Back alignment and structure

>2ljp_A Ribonuclease P protein component; rnasep, ribozyme, hydrolase; NMR {Escherichia coli}	Back alignment and structure

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A	Back alignment and structure

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}	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		708
d1smxa_		87	b.40.4.5 (A:) S1-domain of Ribonuclease E {Escheri	6e-07
d1smxa_		87	b.40.4.5 (A:) S1-domain of Ribonuclease E {Escheri	9e-05
d3bzka4		94	b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas ae	0.002

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Length = 87	Back information, alignment and structure


class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

 Score = 45.7 bits (108), Expect = 6e-07
 Identities = 10/49 (20%), Positives = 22/49 (44%)

Query: 115 VYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYREPFIFPPFRCRTKKQ 163
           +Y G +T++ P++  AFV+ G  R   + +K     +    +    +  
Sbjct: 3   IYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPN 51

PyMOL of d1smxa_

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Length = 87	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 94	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		708
d1smxa_		87	S1-domain of Ribonuclease E {Escherichia coli [Tax	99.94
d1sroa_		76	S1 RNA-binding domain of polyribonucleotide phosph	97.66
d2ba0a1		83	S1-domain of exosome complex RNA-binding protein 1	97.46
d2z0sa1		88	S1-domain of exosome complex RNA-binding protein 1	97.4
d2je6i1		87	S1-domain of exosome complex RNA-binding protein 1	97.27
d3bzka4		94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	96.71
d2nn6g1		88	S1-domain of exosome component 3 (RRP40) {Human (H	96.51
d1kl9a2		86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	96.37
d2ja9a1		90	S1-domain of exosome component 3 (RRP40) {Saccharo	96.24
d1wi5a_		119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	96.1
d2ahob2		84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	95.93
d1go3e1		106	C-terminal domain of RNA polymerase II subunit RBP	95.78
d2nn6h1		95	S1-domain of Ribosomal RNA-processing protein 4, R	95.71
d1e3pa2		62	S1 RNA-binding domain of polyribonucleotide phosph	92.04
d1y14b1		91	C-terminal domain of RNA polymerase II subunit RBP	91.49
d1hh2p1		72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	87.27

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=6.8e-28  Score=209.41  Aligned_cols=36  Identities=28%  Similarity=0.635  Sum_probs=34.1

Q ss_pred             CCeEEEEEeeecCCcceEEecccCCcceeeEeccCC
Q 005219          113 DSVYLGVVTKLVPNMGGAFVNIGNSRPSLMDIKHYR  148 (708)
Q Consensus       113 GnIY~GrV~kV~PgmqAAFVDIG~~k~aFL~~~d~~  148 (708)
                      -|||+|||+||+|||||||||||.+|+||||++|..
T Consensus         1 ~NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~   36 (87)
T d1smxa_           1 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA   36 (87)
T ss_dssp             CCCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSC
T ss_pred             CCcEEEEEEEecCCceEEEEEeCCCccceeEecccc
Confidence            399999999999999999999999999999999863

PyMOL of d1smxa_

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}	Back information, alignment and structure

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}	Back information, alignment and structure

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure