254780751

254780751

ribonuclease E

GeneID in NCBI database:8209756Locus tag:CLIBASIA_03190
Protein GI in NCBI database:254780751Protein Accession:YP_003065164.1
Gene range:+(517904, 520075)Protein Length:723aa
Gene description:ribonuclease E
COG prediction:[J] Ribonucleases G and E
KEGG prediction:ribonuclease E; K08300 ribonuclease E [EC:3.1.26.12]
SEED prediction:Cytoplasmic axial filament protein CafA and Ribonuclease G (EC 3.1.4.-)
Pathway involved in KEGG:RNA degradation [PATH:las03018]
Subsystem involved in SEED:Bacterial Cell Division;
RNA processing and degradation, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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---
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRRRRRRRRPATDHHDAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTPEMESSNSSSDPIVKKTRWWKRRK
cccEEEEEEcccccEEEEEEEccEEEEEEEccccccccccEEEEEEEEEEcccccEEEEEEcccccEEEEEccccHHHHHcccccHHHHHHHHHHHHHcccccccccccccccccccccccccccHHcccccccccccccccHHHccccccccccccccccccccccHHHHHHHccccEEEEEEEEcccccccccccEEEEEcccEEEEccccccccEEEEEcccHHHHHHHHHHHHHcccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEccccHHHHHHHHHccccccEEEEccHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHccHHHHHHHHHccEEEcccccEEEEEccccEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHHHHHccccEEEEcccccccEEEEEEEcccccHHHHHccccccccccEEEEEHHHHHHHHHHHHHHHHHcccccEEEEEEcHHHHHHHHcccHHHHHHHHHHHccEEEEEEccccccccEEEEEccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccHHHEEccccccccHHHHccccccccccccccccccccccccccccccccHHcccHHHccc
ccccEEEcccccHHcEEEEEcccccEccccccccHHHHccccccccEEcccccHHHHHHHccccccccccHHHHcHHHcccccHccccccccccccccccHHHHcccccccEEEcccccHHHHHHHHHHHHccHHHcccccHHHHHHHHHHHcccccccccccccccccHHHHHHcccEEEEEEEEccccccccEEEEEEEccccEEEEcccccccccccEccccHHHHHHHHHHHHHcccccccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccHHHHHHHHHHHHccccEEEEccHHHHHHHHHHHHHHcHHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEcccccEEEEcccHHEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHHHHHHHHcccEEEccHHcHHcHHHHHHHHcccccccccccccccccccEEEcccHHHHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccccccccEEEEEEccccEcccccHHHcHHcccccHHHccEEEEcccccccccccccHEEEcccccEEcccccccHHHHHHHcccccccccccccEccHHHHHHHHcccccccccccccccccHHHcccccccccccccccccccccccccccccccHEEHcHHHHccc
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDyggnrhgflpfleihpdyyqipfsDRQALLkesniaqtdseavaddvthgdvtipndhsleevapianfsqeteEESIISAnndvvsnvedvkggspedvpkkfkRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRysvlmpntskgetisrkitnpvdrkNLKEIARglevpagmGVILRtagasrtkIEIKRDFEYLMRLWDNVRELALNSvaphlvyeEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRqyedphpiffrSGIEVQldslhqtevtlpsrgyviiNQTEALVSIdvnsgrstrehciEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCtyckgagyirsQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTghkvgsdsqapsydkniecvwqdeallpipkseslediqdnivseestgvIRKRrrrrrrrrpatdhhdagvvsdvssiqnviddsfdmymepsditnhnllengahgftenydvsippvstpemessnsssdpivkktrwwkrrk
mankmlidashveetrvvvlrdnrveeldfesehkkqikgniylakvTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTipndhsleeVAPIANFSQETEEESIISANNDVVSNVEdvkggspedvpkkfKRQYCIQEVIKNRQILLVQivkeergnkgaAVTTYLSLAGRYSVLmpntskgetisrkitnpvdrknLKEIarglevpagmgvilrtagasrtkieIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIivsgekgyrEAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVdfidmeekknnrsvekklkeslkkdrarvqvgaisnfgllemsrQRIRSSVLESTTKVCTyckgagyirsqSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPkseslediqdnivseestgvirkrrrrrrrrrpatdhhdagvvsdvssiQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTpemessnsssdpivkktrwwkrrk
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRsvekklkeslkkDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIrkrrrrrrrrrPATDHHDAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTPEMEssnsssDPIVKKTRWWKRRK
*ANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFS*************************************************************************************IQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIR*****STTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIE****************************************************************************************************************************************************KTRWWK***
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTG*******************DAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPP****************VKKTRWWKRRK
**NKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRR***************VVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPV************DPIVKKTRWWKRR*
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDxxxxxxxxxxxxxxxxxxxxxRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRRRRRRRRPATDHHDAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTPEMESSNSSSDPIVKKTRWWKRRK
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRRRRRRRRPATDHHDAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTPEMESSNSSSDPIVKKTRWWKRRK
MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRRRRRRRRPATDHHDAGVVSDVSSIQNVIDDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTPEMESSNSSSDPIVKKTRWWKRRK

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
315121914743 ribonuclease E [Candidatus Liberibacter solanacearum CL 1 0.0
110634063 868 ribonuclease E [Mesorhizobium sp. BNC1] Length = 868 1 0.0
163868350 871 ribonuclease E [Bartonella tribocorum CIP 105476] Lengt 1 0.0
319404235 861 ribonuclease E [Bartonella rochalimae ATCC BAA-1498] Le 1 0.0
319407243 860 ribonuclease E [Bartonella sp. 1-1C] Length = 860 1 0.0
319408602 864 ribonuclease E [Bartonella schoenbuchensis R1] Length = 1 0.0
319898906804 ribonuclease E [Bartonella clarridgeiae 73] Length = 80 1 0.0
319405672 865 Ribonuclease E [Bartonella sp. AR 15-3] Length = 865 1 0.0
240850605 876 ribonuclease E [Bartonella grahamii as4aup] Length = 87 1 0.0
49475635 880 ribonuclease E [Bartonella henselae str. Houston-1] Len 1 0.0
>gi|315121914|ref|YP_004062403.1| ribonuclease E [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 743 Back     alignment and organism information
 Score =  995 bits (2573), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 546/758 (72%), Positives = 606/758 (79%), Gaps = 50/758 (6%)

Query: 1   MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVD 60
           MANKMLIDASHVEETRVVVLRDNRVE+LDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVD
Sbjct: 1   MANKMLIDASHVEETRVVVLRDNRVEDLDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVD 60

Query: 61  YGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVT-------HGDVT 113
           YGGNRHGFLPFLEIHPDYYQIPFSDRQALLK SN+ QTDS  V  DV          D+ 
Sbjct: 61  YGGNRHGFLPFLEIHPDYYQIPFSDRQALLKVSNV-QTDSGVVDSDVVITDSGVVDSDIV 119

Query: 114 IPNDHS---LEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCI 170
           I +D +   L++VA   N S E      I ++NDVV + E+V+  S E+V KK +RQYCI
Sbjct: 120 INDDVNSVELDDVASTTNLSHE------ICSSNDVVFDNENVEVDSSENVSKKLRRQYCI 173

Query: 171 QEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRK 230
           QEVIKNRQILLVQ+VKEERGNKGAAVTTYLSLAGRYSVLMPNT KGE ISRK+TNPVDR 
Sbjct: 174 QEVIKNRQILLVQVVKEERGNKGAAVTTYLSLAGRYSVLMPNTPKGEAISRKVTNPVDRN 233

Query: 231 NLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYE 290
           NLKEIAR LEVP GMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRE ALNSVAPHLVYE
Sbjct: 234 NLKEIARTLEVPPGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREFALNSVAPHLVYE 293

Query: 291 EGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRSG 350
           EG+LIKRAIRDLY KDI+EIIVSGEKGYREAKDFMKLLMPSYA+IVRQY D HPIF  SG
Sbjct: 294 EGSLIKRAIRDLYSKDITEIIVSGEKGYREAKDFMKLLMPSYAKIVRQYNDVHPIFSHSG 353

Query: 351 IEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEI 410
           IE QLD LH TEVTLPSRGY+IINQTEALV+IDVNSGRSTREH IE TA QTNLEA+EEI
Sbjct: 354 IEAQLDCLHHTEVTLPSRGYIIINQTEALVAIDVNSGRSTREHSIESTAFQTNLEASEEI 413

Query: 411 ARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQ 470
           ARQLRLRDLAGLIVVDFIDMEEK+NNR+VEKKLK+SLKKDRARVQVG+IS+FGLLEMSRQ
Sbjct: 414 ARQLRLRDLAGLIVVDFIDMEEKRNNRAVEKKLKDSLKKDRARVQVGSISHFGLLEMSRQ 473

Query: 471 RIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLY 530
           RIRSSVLESTTK+C+ CKG+GY+RSQSS+ LSILRS+EEYLL+YT HNIIVHTH D VLY
Sbjct: 474 RIRSSVLESTTKICSTCKGSGYVRSQSSITLSILRSIEEYLLEYTTHNIIVHTHPDFVLY 533

Query: 531 LLNQKRATIVEYEARFGVSINVVIGIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSY 590
           LLNQKRATIVEYE+RFGVSINVVIG+ LADKLF IEKGSPVQ  V   H V         
Sbjct: 534 LLNQKRATIVEYESRFGVSINVVIGLSLADKLFNIEKGSPVQCPVKIEHIVDFSHIQMED 593

Query: 591 DKNIECVWQDE-ALLPIPKSESLEDIQDNI---------------VSEESTG-VIRKRRR 633
           +KN+EC  +D+  LLPI   E   + QD I                 +ES+G V+RKRRR
Sbjct: 594 NKNVECSQKDQNVLLPISNLEKSGNTQDKIDDSIEQSINSRDTEGALDESSGIVVRKRRR 653

Query: 634 RRRRRRPATDHHDAGVVSDV-SSIQNVIDDSFDMY-MEPSDITNHNLLENGA------HG 685
           RRRRRRP  +H D  V SDV  SI +V+DDS  +  +E + I N NL  + +       G
Sbjct: 654 RRRRRRPVIEHSDV-VASDVLGSITHVVDDSLAIQDIESAHIQNQNLASDDSPELIAESG 712

Query: 686 FTENYDVSIPPVSTPEMESSNSSSDPIVKKTRWWKRRK 723
           F  N    +P  S    E+ N++S+P+V+K  WW+RRK
Sbjct: 713 FIPN---PLPITS----ETDNNTSEPVVRKIGWWRRRK 743


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|110634063|ref|YP_674271.1| ribonuclease E [Mesorhizobium sp. BNC1] Length = 868 Back     alignment and organism information
>gi|163868350|ref|YP_001609559.1| ribonuclease E [Bartonella tribocorum CIP 105476] Length = 871 Back     alignment and organism information
>gi|319404235|emb|CBI77828.1| ribonuclease E [Bartonella rochalimae ATCC BAA-1498] Length = 861 Back     alignment and organism information
>gi|319407243|emb|CBI80882.1| ribonuclease E [Bartonella sp. 1-1C] Length = 860 Back     alignment and organism information
>gi|319408602|emb|CBI82257.1| ribonuclease E [Bartonella schoenbuchensis R1] Length = 864 Back     alignment and organism information
>gi|319898906|ref|YP_004158999.1| ribonuclease E [Bartonella clarridgeiae 73] Length = 804 Back     alignment and organism information
>gi|319405672|emb|CBI79295.1| Ribonuclease E [Bartonella sp. AR 15-3] Length = 865 Back     alignment and organism information
>gi|240850605|ref|YP_002972005.1| ribonuclease E [Bartonella grahamii as4aup] Length = 876 Back     alignment and organism information
>gi|49475635|ref|YP_033676.1| ribonuclease E [Bartonella henselae str. Houston-1] Length = 880 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
TIGR00757414 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family 1e-110
pfam10150271 pfam10150, RNase_E_G, Ribonuclease E/G family 1e-103
PRK10811 1068 PRK10811, rne, ribonuclease E; Reviewed 1e-95
PRK11712489 PRK11712, PRK11712, ribonuclease G; Provisional 4e-61
COG1530487 COG1530, CafA, Ribonucleases G and E [Translation, ribo 1e-111
COG1530487 COG1530, CafA, Ribonucleases G and E [Translation, ribo 3e-22
PRK10811 1068 PRK10811, rne, ribonuclease E; Reviewed 1e-19
TIGR00757414 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family 3e-19
cd0445388 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S 2e-11
PRK11712489 PRK11712, PRK11712, ribonuclease G; Provisional 1e-08
cd0445388 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S 1e-07
>gnl|CDD|162024 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family Back     alignment and domain information
>gnl|CDD|150783 pfam10150, RNase_E_G, Ribonuclease E/G family Back     alignment and domain information
>gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed Back     alignment and domain information
>gnl|CDD|183285 PRK11712, PRK11712, ribonuclease G; Provisional Back     alignment and domain information
>gnl|CDD|31719 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|31719 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed Back     alignment and domain information
>gnl|CDD|162024 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family Back     alignment and domain information
>gnl|CDD|88419 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|183285 PRK11712, PRK11712, ribonuclease G; Provisional Back     alignment and domain information
>gnl|CDD|88419 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 723 ribonuclease E [Candidatus Liberibacter asiaticus str.
PRK10811 1063 rne ribonuclease E; Reviewed 100.0
PRK11712489 ribonuclease G; Provisional 100.0
COG1530487 CafA Ribonucleases G and E [Translation, ribosomal stru 100.0
, IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR00757">TIGR00757464 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR0046 100.0
pfam10150271 RNase_E_G Ribonuclease E/G family. Ribonuclease E and R 100.0
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA 99.95
COG1098129 VacB Predicted RNA binding protein (contains ribosomal 97.84
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 97.81
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 97.29
PRK07252120 hypothetical protein; Provisional 98.34
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protei 98.19
PRK08582139 hypothetical protein; Provisional 98.19
PRK05807136 hypothetical protein; Provisional 98.14
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of transla 98.1
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. 98.04
PRK08059119 general stress protein 13; Validated 97.98
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 97.97
pfam0057574 S1 S1 RNA binding domain. The S1 domain occurs in a wid 97.95
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea 97.87
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 97.84
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 97.83
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a tran 97.65
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 do 97.63
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Hom 97.58
PRK07400314 30S ribosomal protein S1; Reviewed 97.55
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a transcript 97.49
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protei 97.4
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 97.38
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 97.37
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is 97.36
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosoma 97.35
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protei 97.33
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 97.28
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protei 97.25
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a tran 97.21
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protei 97.17
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 97.04
PRK07400314 30S ribosomal protein S1; Reviewed 96.94
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a tran 96.94
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-binding 96.9
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 96.79
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 96.78
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 96.71
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans- 96.71
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 96.6
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 96.24
COG1093269 SUI2 Translation initiation factor 2, alpha subunit (eI 95.94
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a tran 95.57
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-li 95.49
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-l 95.24
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein (NusA) 94.98
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 94.76
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 94.57
PRK12327353 nusA transcription elongation factor NusA; Provisional 93.94
PRK08563182 DNA-directed RNA polymerase subunit E'; Provisional 93.78
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 i 92.24
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 91.82
PTZ00162170 RNA polymerase II subunit 7; Provisional 90.75
PRK03987262 translation initiation factor IF-2 subunit alpha; Valid 98.12
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 97.99
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 97.91
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 97.48
COG2183780 Tex Transcriptional accessory protein [Transcription] 95.18
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 97.46
KOG1070 1710 consensus 91.84
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 97.35
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 96.5
PTZ00248324 eukaryotic translation initiation factor 2 alpha subuni 94.18
PRK11642813 exoribonuclease R; Provisional 92.68
PRK09202428 nusA transcription elongation factor NusA; Validated 92.37
PRK00499116 rnpA ribonuclease P; Reviewed 91.88
TIGR03147126 cyt_nit_nrfF cytochrome c nitrite reductase, accessory 90.07
>PRK10811 rne ribonuclease E; Reviewed Back     alignment and domain information
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria Back     alignment and domain information
>pfam10150 RNase_E_G Ribonuclease E/G family 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
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional 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
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>pfam00575 S1 S1 RNA binding domain 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
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] 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
>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
>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
>PRK07400 30S ribosomal protein S1; Reviewed 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
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed 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
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: 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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain 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
>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
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/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
>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
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [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
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain 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
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional 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
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>PTZ00162 RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>KOG1070 consensus Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK00499 rnpA ribonuclease P; Reviewed Back     alignment and domain information
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
2vmk_A515 Crystal Structure Of E. Coli Rnase E Apoprotein - C 7e-82
2vrt_A509 Crystal Structure Of E. Coli Rnase E Possessing M1 1e-81
2bx2_L517 Catalytic Domain Of E. Coli Rnase E Length = 517 1e-81
2vmk_A515 Crystal Structure Of E. Coli Rnase E Apoprotein - C 1e-30
2vrt_A509 Crystal Structure Of E. Coli Rnase E Possessing M1 1e-30
2bx2_L517 Catalytic Domain Of E. Coli Rnase E Length = 517 2e-30
1smx_A96 Crystal Structure Of The S1 Domain Of Rnase E From 4e-15
>gi|194368574|pdb|2VMK|A Chain A, Crystal Structure Of E. Coli Rnase E Apoprotein - Catalytic Domain Length = 515 Back     alignment and structure
 Score =  309 bits (792), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 184/505 (36%), Positives = 282/505 (55%), Gaps = 8/505 (1%)

Query: 97  QTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVE-----D 151
           +    A+ D     D+ I +    ++ A I        E S+ +A  D  +         
Sbjct: 12  EELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLK 71

Query: 152 VKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMP 211
                          +  I++V++  Q ++VQI KEERGNKGAA+TT++SLAG Y VLMP
Sbjct: 72  EIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMP 131

Query: 212 NTSKGETISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRL 271
           N  +   ISR+I      + LKE    LE+P GMG+I+RTAG  ++   ++ D  + ++ 
Sbjct: 132 NNPRAGGISRRIEGDDRTE-LKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKH 190

Query: 272 WDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMK-LLMP 330
           W+ +++ A +  AP L+++E N+I RA RD   +DI EI++   K    A+  +  L  P
Sbjct: 191 WEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRP 250

Query: 331 SYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRST 390
            ++  ++ Y    P+F    IE Q++S  Q EV LPS G ++I+ TEAL +ID+NS R+T
Sbjct: 251 DFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARAT 310

Query: 391 REHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKD 450
           R   IE+TA  TNLEAA+EIARQLRLRDL GLIV+DFIDM   ++ R+VE +L+E++++D
Sbjct: 311 RGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQD 370

Query: 451 RARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEY 510
           RAR+Q+  IS FGLLEMSRQR+  S+ ES+  VC  C G G +R   S++LSILR +EE 
Sbjct: 371 RARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEE 430

Query: 511 LLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKLFYIEKGS 569
            L+     +       +  YLLN+KR+ +   E R  GV   +V   ++    +++ +  
Sbjct: 431 ALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVR 490

Query: 570 PVQALVNTGHKVGSDSQAPSYDKNI 594
             +      + +    +      + 
Sbjct: 491 KGEETPTLSYMLPKLHEEAMALPSE 515


>gi|194368580|pdb|2VRT|A Chain A, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain Length = 509 Back     alignment and structure
>gi|82408148|pdb|2BX2|L Chain L, Catalytic Domain Of E. Coli Rnase E Length = 517 Back     alignment and structure
>gi|194368574|pdb|2VMK|A Chain A, Crystal Structure Of E. Coli Rnase E Apoprotein - Catalytic Domain Length = 515 Back     alignment and structure
>gi|194368580|pdb|2VRT|A Chain A, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain Length = 509 Back     alignment and structure
>gi|82408148|pdb|2BX2|L Chain L, Catalytic Domain Of E. Coli Rnase E Length = 517 Back     alignment and structure
>gi|52695529|pdb|1SMX|A Chain A, Crystal Structure Of The S1 Domain Of Rnase E From E. Coli (Native) Length = 96 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
2bx2_L517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA 1e-89
2bx2_L517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA 6e-31
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 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 =  325 bits (835), Expect = 1e-89
 Identities = 172/411 (41%), Positives = 255/411 (62%), Gaps = 3/411 (0%)

Query: 159 DVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGET 218
                   +  I++V++  Q ++VQI KEERGNKGAA+TT++SLAG Y VLMPN  +   
Sbjct: 86  PANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRA-G 144

Query: 219 ISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL 278
              +     DR  LKE    LE+P GMG+I+RTAG  ++   ++ D  + ++ W+ +++ 
Sbjct: 145 GISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKA 204

Query: 279 ALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVR 337
           A +  AP L+++E N+I RA RD   +DI EI++   K    A+  +  L  P ++  ++
Sbjct: 205 AESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIK 264

Query: 338 QYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIED 397
            Y    P+F    IE Q++S  Q EV LPS G ++I+ TEAL +ID+NS R+TR   IE+
Sbjct: 265 LYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEE 324

Query: 398 TALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457
           TA  TNLEAA+EIARQLRLRDL GLIV+DFIDM   ++ R+VE +L+E++++DRAR+Q+ 
Sbjct: 325 TAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQIS 384

Query: 458 AISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAH 517
            IS FGLLEMSRQR+  S+ ES+  VC  C G G +R   S++LSILR +EE  L+    
Sbjct: 385 HISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQ 444

Query: 518 NIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKLFYIEK 567
            +       +  YLLN+KR+ +   E R  GV   +V   ++    +++ +
Sbjct: 445 EVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLR 495


>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 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

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
2bx2_L517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA 100.0
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, struct 98.24
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stress res 98.09
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, st 97.96
3aev_A275 Translation initiation factor 2 subunit alpha; proteins 97.91
1kl9_A182 Eukaryotic translation initiation factor 2 subunit 1; O 97.83
1q8k_A308 Eukaryotic translation initiation factor 2 subunit 1; N 97.74
3cw2_C266 Translation initiation factor 2 subunit alpha; AIF2, in 97.73
2a19_A175 EIF-2- alpha, eukaryotic translation initiation factor 97.7
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zinc, zi 97.63
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, phospho 97.5
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprotein, 97.28
3go5_A285 Multidomain protein with S1 RNA-binding domains; joint 96.68
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, RNA, 96.5
2waq_E180 DNA-directed RNA polymerase RPO7 subunit; multi-subunit 96.01
1go3_E187 DNA-directed RNA polymerase subunit E; transferase, tra 95.86
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nuclease, 95.18
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SC 94.98
2z0s_A235 Probable exosome complex RNA-binding protein 1; alpha/b 94.26
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH, RNA 93.77
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypeptide; 93.19
3go5_A285 Multidomain protein with S1 RNA-binding domains; joint 92.95
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa polype 92.75
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa polyp 92.5
2bh8_A101 1B11; transcription, molecular evolution, unique archit 91.85
2nn6_H308 Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, 91.02
1hh2_P344 NUSA, N utilization substance protein A; transcription 90.5
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucleotide 97.47
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA 97.43
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structural ge 97.3
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, 97.16
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 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=0  Score=1104.07  Aligned_cols=495  Identities=43%  Similarity=0.678  Sum_probs=472.4

Q ss_pred             CCCEEEEECCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCC
Q ss_conf             98526896528960799999899899999607334604287879899783638823135327897713022213712102
Q gi|254780751|r    1 MANKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQ   80 (723)
Q Consensus         1 M~k~~lI~~~~~~e~Rvav~e~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~   80 (723)
                      | |+||||+++|+|||||+++||+|+||++|+.+..+++||||+|||+||+|||||||||||.+|+||||++||+|+||+
T Consensus         8 M-k~ilI~~~~~~e~RvAlle~g~l~e~~ie~~~~~~~vGnIY~GrV~~v~pgl~AAFVdiG~~k~gFL~~~di~~~~~~   86 (517)
T 2bx2_L            8 M-KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFP   86 (517)
T ss_dssp             C-EEEEEECSCTTCEEEEEEETTEEEEEEEECSSSCCCTTCEEEEEEEEEETTTTEEEEESSSSSCEEEEGGGSCGGGCC
T ss_pred             C-CCEEEECCCCCEEEEEEEECCEEEEEEEECCCCCCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEEHHHCCHHHCC
T ss_conf             1-014887589971899999999999999942888888798899999423798866999618997148886884845415


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             89889999999888631111100000001112233444334454222233445543322223432112211121100001
Q gi|254780751|r   81 IPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDV  160 (723)
Q Consensus        81 ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (723)
                      .+.                                                                             
T Consensus        87 ~~~-----------------------------------------------------------------------------   89 (517)
T 2bx2_L           87 ANY-----------------------------------------------------------------------------   89 (517)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCC-----------------------------------------------------------------------------
T ss_conf             552-----------------------------------------------------------------------------


Q ss_pred             CCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             22344442133106888579998403332345641012334576523442278875124204688689999999998630
Q gi|254780751|r  161 PKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLE  240 (723)
Q Consensus       161 ~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~  240 (723)
                        ...++++|+++|++||.|||||+|||+++|||+||++|||+|||+||||+.+ ++++|+||.+.++|++|+.++..+.
T Consensus        90 --~~~~~~~I~~~l~~Gq~ilVQV~ke~~~~Kg~~lT~~Isl~GrylVl~P~~~-~i~~sski~~~~er~~l~~~l~~~~  166 (517)
T 2bx2_L           90 --SAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNP-RAGGISRRIEGDDRTELKEALASLE  166 (517)
T ss_dssp             ------CCCGGGTCCTTCEEEEEEEECCCTTCCCEEESSCCEECSSEEEETTCT-TCCEECTTCC------HHHHHTTSC
T ss_pred             --CCCCCCCHHHCCCCCCEEEEEECCCCCCCCCCCEECEEEECCCCEEECCCCC-CCCEECCCCCHHHHHHHHHHHHHHC
T ss_conf             --2245655544078999899997246767777655240640787468745788-6111504477588999999998635


Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEECCCCCHHHH
Q ss_conf             02587169985045575799999999999999987764201432212345645888888752376631111035320366
Q gi|254780751|r  241 VPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYRE  320 (723)
Q Consensus       241 ~~~~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~li~~~~~~~~~~ird~~~~~~~~i~vd~~~~~~~  320 (723)
                      .|+++|+|+||+|++++.++|..|+.+|..+|+.|.+.+...++|+|||++.+++.+++||+++.++..|+||+...|..
T Consensus       167 ~pe~~G~IiRT~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~P~ll~~~~~~~~r~lrd~~~~~~~~i~vd~~~~~~~  246 (517)
T 2bx2_L          167 LPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLEL  246 (517)
T ss_dssp             CCTTCEEEECGGGGGCCHHHHHHHHHHHHHHHHHHHHHHHTSCSCEEEECCCCHHHHHHHHHCCTTEEEEEESCHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHCCHHHHCCCCCCHHHHHH
T ss_conf             89884389987556999999999999999999888875424898637862874999999986360332233676889999


Q ss_pred             HHHHHHH-HHHCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHH
Q ss_conf             7888987-631012112201344203567769999999842221436786499832880699982375544455511479
Q gi|254780751|r  321 AKDFMKL-LMPSYARIVRQYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTA  399 (723)
Q Consensus       321 ~~~~~~~-~~p~~~~~v~~~~~~~~lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~  399 (723)
                      +++|+.. .+|++..++++|.+..|||+.|+|+.||+.+|+++||||||||||||+||||||||||||+++++++.++|+
T Consensus       247 ~~~~~~~~~~~~~~~~v~~y~~~~~lF~~y~Ie~~I~~ll~~~V~L~sGG~ivIe~TEALt~IDVNSG~~~~~~~~eet~  326 (517)
T 2bx2_L          247 ARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETA  326 (517)
T ss_dssp             HHHHHHHTTCHHHHTTEEECCCSSCHHHHTTCHHHHHHTTCSEEECTTSCEEEEEECSSCEEEEEECCC----CCHHHHH
T ss_pred             HHHHHHHCCCCCCCCEEEEECCCCCHHHHHCCHHHHHHHHCCCEECCCCCEEEEECCCEEEEEEECCCCCCCCCCHHHHH
T ss_conf             87531101586311648996699896776361999998643654338886899970440489870476645677778889


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHH
Q ss_conf             99999999999998731036863896033479888899999999997312787289986048614898515666301121
Q gi|254780751|r  400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLES  479 (723)
Q Consensus       400 l~tNleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~  479 (723)
                      |+||||||+||||||||||||||||||||||++.+|++.|++.|+++|++|+++|+|++||+||||||||||.|+||.++
T Consensus       327 l~tNleAa~EIaRQLRLRnigGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~~T~lGLvEmTRkR~r~sl~~~  406 (517)
T 2bx2_L          327 FNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGES  406 (517)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCEEEEEECCCCSSHHHHHHHHHHHHHHTTTCSSCEEEEEECTTSEEEEEECCCSCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEECCCCCCCHHHH
T ss_conf             99999999999999874478752999725767587899999999999841998503356677640899626668772322


Q ss_pred             HCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCHHHHHHHHHHH-HCCEEEEEECCCC
Q ss_conf             002367546537860611468998878899973036431013576999998730237999999998-4887999847877
Q gi|254780751|r  480 TTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVLYLLNQKRATIVEYEAR-FGVSINVVIGIEL  558 (723)
Q Consensus       480 ~~~~c~~c~g~g~~~~~~~~~~~~~r~i~~~~~~~~~~~i~v~~~~~va~~lln~kr~~l~~lE~~-~~~~I~i~~d~~l  558 (723)
                      ++++||+|+|+|+|+|.++++++|+|.|++.+.+.+.+.+.+.+||+|+.||+|+++.+|.++|.+ ++++|.|.+|++|
T Consensus       407 ~~~~Cp~C~G~G~v~s~~~~~~~i~r~i~~~~~~~~~~~i~i~~~~~v~~~l~~~~~~~l~~~e~~~~~~~i~i~~~~~l  486 (517)
T 2bx2_L          407 SHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQM  486 (517)
T ss_dssp             HCCCCSSSSSSSCCCCHHHHHHHHHHHHHHHHHSTTEEEEEEEECHHHHHHHTTTTHHHHHHHHHHTTTCEEEEEECTTC
T ss_pred             CCCCCCCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHCCHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             14348986886798788999999999999998766885799998999999998422999999999875917999847888


Q ss_pred             CCCCEEEEECCCCCCCCC
Q ss_conf             886338971554433333
Q gi|254780751|r  559 ADKLFYIEKGSPVQALVN  576 (723)
Q Consensus       559 ~~~~f~Ier~~~~~~~~~  576 (723)
                      +.++|.|.+.+..+....
T Consensus       487 ~~~~~~i~~~~~~~~~~~  504 (517)
T 2bx2_L          487 ETPHYHVLRVRKGEETPT  504 (517)
T ss_dssp             CTTCCEEEEEETTCCCCC
T ss_pred             CCCCEEEEECCCCCCCCC
T ss_conf             777529998568985565



>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
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} 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
>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
>1kl9_A Eukaryotic translation initiation factor 2 subunit 1; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 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
>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 Back     alignment and structure
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha subunit; transferase, protein biosynthesis, protein synthesis/transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A 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
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; joint center for structural genomics, protein structure initiative, PSI-2; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} 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
>2waq_E DNA-directed RNA polymerase RPO7 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_E 2pmz_E 3hkz_E 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
>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
>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
>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
>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
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; joint center for structural genomics, protein structure initiative, PSI-2; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} 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
>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
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, activator, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 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
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A 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
>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
>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

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 723 ribonuclease E [Candidatus Liberibacter asiaticus str.
d1smxa_87 b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia 1e-10
d1smxa_87 b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia 3e-08
>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 = 62.3 bits (151), Expect = 1e-10
 Identities = 29/66 (43%), Positives = 38/66 (57%)

Query: 41  NIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDS 100
           NIY  K+TR+EPSL+AAFVDYG  RHGFLP  EI  +Y+   +S       +  + +   
Sbjct: 2   NIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQE 61

Query: 101 EAVADD 106
             V  D
Sbjct: 62  VIVQID 67


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

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [TaxId: 5 99.95
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {H 97.67
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharomyces 97.11
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosphoryla 98.16
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1, ECR 97.95
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1, ECR 97.95
d2je6i187 S1-domain of exosome complex RNA-binding protein 1, ECR 97.86
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} 97.8
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, RRP4 { 97.68
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP7 (Rp 97.66
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N-termi 97.61
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N-termi 97.43
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (Homo s 97.12
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosphoryla 97.0
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP7 (Rp 95.26
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} 94.83
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} 94.25
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP7 (Rp 94.21
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1 92.65
d2nn6i1125 Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxI 95.03
>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=99.95  E-value=5.5e-29  Score=217.33  Aligned_cols=87  Identities=55%  Similarity=0.888  Sum_probs=77.9

Q ss_pred             CCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             87879899783638823135327897713022213712102898899999998886311111000000011122334443
Q gi|254780751|r   40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHS  119 (723)
Q Consensus        40 GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (723)
                      .|||+|+|+||+|||||||||||.+|+||||++|++++||+.+                                     
T Consensus         1 ~NIY~G~V~~V~pgl~AAFVDiG~~k~gFL~~~di~~~~~~~~-------------------------------------   43 (87)
T d1smxa_           1 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPAN-------------------------------------   43 (87)
T ss_dssp             CCCEEEEEEEEEGGGTEEEEESSSSSCEEEEGGGSCGGGCSSC-------------------------------------
T ss_pred             CCCEEEEEEEECCCCEEEEEEECCCCCCEEEECCCCEEEECCC-------------------------------------
T ss_conf             9757999978167850899970887644157032003420136-------------------------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCCCCCCCC
Q ss_conf             34454222233445543322223432112211121100001223444421331068885799984033323456410123
Q gi|254780751|r  120 LEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTY  199 (723)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lk~gq~ilVQV~ke~~~~Kga~lT~~  199 (723)
                                                                ......++|+++|++||.|||||+|||+++|||+||++
T Consensus        44 ------------------------------------------~~~~~~~~i~~~l~~G~~ilVQV~Ke~~~~KGprlT~~   81 (87)
T d1smxa_          44 ------------------------------------------YSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTF   81 (87)
T ss_dssp             ------------------------------------------CCSSSCCCGGGTCCTTCEEEEEEEECCBTTBCCEEESC
T ss_pred             ------------------------------------------CCCCCCCCHHHHCCCCCEEEEEEEECCCCCCCCEEEEE
T ss_conf             ------------------------------------------43233322343203797389998443667888458877


Q ss_pred             CCCCCC
Q ss_conf             345765
Q gi|254780751|r  200 LSLAGR  205 (723)
Q Consensus       200 isl~Gr  205 (723)
                      |||||-
T Consensus        82 Isl~G~   87 (87)
T d1smxa_          82 ISLAGS   87 (87)
T ss_dssp             CCCTTC
T ss_pred             EECCCC
T ss_conf             973789



>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {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
>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
>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
>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
>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
>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
>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
>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
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 723 ribonuclease E [Candidatus Liberibacter asiaticus
2bx2_L_273-410138 (L:273-410) Ribonuclease E, RNAse E; RNA-binding, 2e-52
2bx2_L_127-20882 (L:127-208) Ribonuclease E, RNAse E; RNA-binding, 8e-19
2bx2_L_411-517107 (L:411-517) Ribonuclease E, RNAse E; RNA-binding, 4e-14
2bx2_L_1-42_219-27296 (L:1-42,L:219-272) Ribonuclease E, RNAse E; RNA-bi 6e-11
2bx2_L_1-42_219-27296 (L:1-42,L:219-272) Ribonuclease E, RNAse E; RNA-bi 4e-09
2bx2_L_43-126_209-21894 (L:43-126,L:209-218) Ribonuclease E, RNAse E; RNA- 8e-09
>2bx2_L (L:273-410) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 138 Back     alignment and structure
 Score =  201 bits (514), Expect = 2e-52
 Identities = 79/142 (55%), Positives = 104/142 (73%), Gaps = 4/142 (2%)

Query: 346 FFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLE 405
           F    IE Q++S  Q EV LPS G ++I+ TEAL +ID+NS R+TR   IE+TA  TNLE
Sbjct: 1   FSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLE 60

Query: 406 AAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLL 465
           AA+EIARQLRLRDL GLIV+DFIDM   ++ R+VE +L+E++++DRAR+Q+  IS FGLL
Sbjct: 61  AADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLL 120

Query: 466 EMSRQRIRSSVLESTTKVCTYC 487
           EMSRQR+  S+ ES      + 
Sbjct: 121 EMSRQRLSPSLGES----SHHV 138


>2bx2_L (L:127-208) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 82 Back     alignment and structure
>2bx2_L (L:411-517) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 107 Back     alignment and structure
>2bx2_L (L:1-42,L:219-272) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 96 Back     alignment and structure
>2bx2_L (L:1-42,L:219-272) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 96 Back     alignment and structure
>2bx2_L (L:43-126,L:209-218) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_ALength = 94 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target723 ribonuclease E [Candidatus Liberibacter asiaticus str.
2bx2_L_273-410138 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 100.0
2bx2_L_411-517107 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 99.77
2bx2_L_127-20882 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 99.72
2bx2_L_1-42_219-27296 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 99.46
2bx2_L_43-126_209-21894 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 99.44
2khi_A_115 30S ribosomal protein S1; acetylation, phosphoprot 98.19
1wi5_A_119 RRP5 protein homolog; S1 domain, OB-fold, structur 98.08
2khj_A_109 30S ribosomal protein S1; OB fold, acetylation, ph 97.89
2cqo_A_119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 97.84
3cw2_C_1-8585 Translation initiation factor 2 subunit alpha; AIF 97.75
2nn6_I_76-16994 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 97.58
3bzc_A_642-785144 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 97.46
2b8k_G_83-215133 B16, DNA-directed RNA polymerase II 19 kDa polypep 97.12
2ckz_B_81-218138 C25, DNA-directed RNA polymerase III 25 KD polypep 97.03
2je6_I_71-15585 RRP4, exosome complex RNA-binding protein 1; nucle 98.07
2z0s_A_1-147147 Probable exosome complex RNA-binding protein 1; al 98.01
2ba0_A_54-13582 Archeal exosome RNA binding protein RRP4; RNAse PH 98.0
2nn6_H_92-18392 Exosome complex exonuclease RRP4; RNA, exosome, PM 97.98
2ja9_A_1-9090 Exosome complex exonuclease RRP40; RNA-binding pro 97.9
1go3_E_81-187107 DNA-directed RNA polymerase subunit E; transferase 97.78
2nn6_G_123-20987 Exosome complex exonuclease RRP40; RNA, exosome, P 97.75
3go5_A_65-13571 Multidomain protein with S1 RNA-binding domains; s 97.68
2k52_A_80 Uncharacterized protein MJ1198; metal-binding, zin 97.67
2a19_A_1-8888 EIF-2- alpha, eukaryotic translation initiation fa 97.58
2eqs_A_103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 97.49
1yz6_A_1-8383 Probable translation initiation factor 2 alpha sub 97.49
3cdi_A_151-239_464-723349 Polynucleotide phosphorylase; mRNA turnover, RNAse 97.45
1kl9_A_1-8888 Eukaryotic translation initiation factor 2 subunit 97.42
1y14_B_83-17189 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 97.42
2id0_A_559-64486 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 97.39
2waq_E_81-180100 DNA-directed RNA polymerase RPO7 subunit; multi-su 97.33
1q8k_A_1-8686 Eukaryotic translation initiation factor 2 subunit 97.3
1hh2_P_129-21587 NUSA, N utilization substance protein A; transcrip 97.26
3h0g_G_84-17289 DNA-directed RNA polymerase II subunit RPB7; trans 97.1
1e3p_A_592-757166 Guanosine pentaphosphate synthetase; polyribonucle 97.04
2ba1_A_54-14592 Archaeal exosome RNA binding protein CSL4; RNAse P 96.93
2c35_B_81-17292 Human RPB7, DNA-directed RNA polymerase II 19 kDa 96.92
1luz_A_88 Protein K3, protein K2; stranded anti-parallel bet 96.56
3go5_A_136-21984 Multidomain protein with S1 RNA-binding domains; s 96.5
2k4k_A_130 GSP13, general stress protein 13; cytoplasm, stres 97.98
>2bx2_L (L:273-410) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 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=0  Score=401.17  Aligned_cols=138  Identities=56%  Similarity=0.814  Sum_probs=135.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             56776999999984222143678649983288069998237554445551147999999999999998731036863896
Q gi|254780751|r  346 FFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEEIARQLRLRDLAGLIVV  425 (723)
Q Consensus       346 f~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~~e~t~l~tNleAA~EIaRQlRLRnlgGiIvI  425 (723)
                      |+.|+|+.+|+.+++++||||||||||||+|||||+||||||+++++++.++|+++||+|||+|||||||||||||||||
T Consensus         1 F~~~~i~~~i~~~~~~~V~L~~Gg~lvIe~TEALt~IDVNsG~~~~~~~~~~~~~~~N~eAa~eIarqlrLRnigGiIvI   80 (138)
T 2bx2_L            1 FSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVI   80 (138)
T ss_dssp             HHHTTCHHHHHHTTCSEEECTTSCEEEEEECSSCEEEEEECCC----CCHHHHHHHHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHCHHHHHHHHHHCCEECCCCEEEEEECCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             78718499999986304544788089993154058985046654567777788999989999999987657516864997


Q ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCCCCCCC
Q ss_conf             03347988889999999999731278728998604861489851566630112100236754
Q gi|254780751|r  426 DFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYC  487 (723)
Q Consensus       426 DFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~~c~~c  487 (723)
                      |||||+++++++.|++.|+++|++|+++++|++||+||||||||||.|+||.    ++||+|
T Consensus        81 DFI~m~~~~~~~~v~~~l~~~~~~D~~~~~v~~~t~lGL~EitRkR~~~sl~----e~cp~C  138 (138)
T 2bx2_L           81 DFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLG----ESSHHV  138 (138)
T ss_dssp             ECCCCSSHHHHHHHHHHHHHHTTTCSSCEEEEEECTTSEEEEEECCCSCCHH----HHHCCC
T ss_pred             ECCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCEEEEECCCCCCCHH----HHHCCC
T ss_conf             2566666789999999999998516865057456666338886144556601----220433



>2bx2_L (L:411-517) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Back     alignment and structure
>2bx2_L (L:127-208) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Back     alignment and structure
>2bx2_L (L:1-42,L:219-272) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Back     alignment and structure
>2bx2_L (L:43-126,L:209-218) Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Back     alignment and structure
>2khi_A (A:) 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>1wi5_A (A:) RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} Back     alignment and structure
>2khj_A (A:) 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>2cqo_A (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
>3cw2_C (C:1-85) 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 Back     alignment and structure
>2nn6_I (I:76-169) 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} Back     alignment and structure
>3bzc_A (A:642-785) TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} Back     alignment and structure
>2b8k_G (G:83-215) B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} Back     alignment and structure
>2ckz_B (B:81-218) C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
>2je6_I (I:71-155) RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} Back     alignment and structure
>2z0s_A (A:1-147) Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} Back     alignment and structure
>2ba0_A (A:54-135) Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} Back     alignment and structure
>2nn6_H (H:92-183) Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} Back     alignment and structure
>2ja9_A (A:1-90) Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} Back     alignment and structure
>1go3_E (E:81-187) DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} Back     alignment and structure
>2nn6_G (G:123-209) Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} Back     alignment and structure
>3go5_A (A:65-135) Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} Back     alignment and structure
>2k52_A (A:) Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>2a19_A (A:1-88) EIF-2- alpha, eukaryotic translation initiation factor 2 alpha subunit; transferase, protein biosynthesis, protein synthesis/transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A Back     alignment and structure
>2eqs_A (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
>1yz6_A (A:1-83) Probable translation initiation factor 2 alpha subunit; beta barrel, helical domain and alpha beta domain; 3.37A {Pyrococcus abyssi} Back     alignment and structure
>3cdi_A (A:151-239,A:464-723) Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>1kl9_A (A:1-88) Eukaryotic translation initiation factor 2 subunit 1; OB fold, helical domain; 1.90A {Homo sapiens} Back     alignment and structure
>1y14_B (B:83-171) B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>2id0_A (A:559-644) Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli K12} Back     alignment and structure
>2waq_E (E:81-180) DNA-directed RNA polymerase RPO7 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_E 2pmz_E 3hkz_E Back     alignment and structure
>1q8k_A (A:1-86) Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} Back     alignment and structure
>1hh2_P (P:129-215) NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} Back     alignment and structure
>3h0g_G (G:84-172) DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1e3p_A (A:592-757) Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} Back     alignment and structure
>2ba1_A (A:54-145) Archaeal exosome RNA binding protein CSL4; RNAse PH, RNA degradation, exoribonuclease, RNA binding, S1 domain, Zn-ribbon, phosphorolytic; 2.70A {Archaeoglobus fulgidus} Back     alignment and structure
>2c35_B (B:81-172) Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} Back     alignment and structure
>1luz_A (A:) Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus WR} Back     alignment and structure
>3go5_A (A:136-219) Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae TIGR4} Back     alignment and structure
>2k4k_A (A:) GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Back     alignment and structure