254780784

254780784

polynucleotide phosphorylase/polyadenylase

GeneID in NCBI database:8209790Locus tag:CLIBASIA_03375
Protein GI in NCBI database:254780784Protein Accession:YP_003065197.1
Gene range:+(477223, 479322)Protein Length:699aa
Gene description:polynucleotide phosphorylase/polyadenylase
COG prediction:[J] Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase)
KEGG prediction:pnp; polynucleotide phosphorylase/polyadenylase; K00962 polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]
SEED prediction:Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
RNA degradation [PATH:las03018]
Subsystem involved in SEED:Bacterial RNA-metabolizing Zn-dependent hydrolases
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
TOPPRED3 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-------70
MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV
ccccEEEEEEEccEEEEEEEcccccccccEEEEEEcccEEEEEEEEccccccccccEEEEEEEccccHHcccccccccEEccccccHHHHHHHHHHccHHHcccccccccEEEEEEEEEEccccccHHHHHHHHHHHHHHccccccccEEEEEEEEEccEEEEcccHHHHHccccEEEEEcccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEEcccccccEEEEEEEccEEEEEEEEEcccccccccccccccccEEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHccHHHcccEEEEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHccEEEEEEEEEEccccEEEEEccccccccccccEEEEEEccccEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHccEEEEEEEcHHHHHHHHccccHHHHHHHHHcccEEEEccccEEEEEEEHHHHHHHHHHHHHHHHHccccccEEEEEEEEEEcccEEEEcccccEEEEEEEEccccccccHHHHcccccEEEEEEEEEcccccEEEEHHHcccccccccc
cccccEEEEEEcccEEEEEccHEEEEcccEEEEEcccEEEEEEEEEccccccccccccEEEEEEEEEEcccccccccEccccccccccHHHHHccccccccccccccccEEEEEEEEEEcccccccHHHHHHHHHHHHHHcccccccccccEEEEEEccEEEEcccHHHHHccccEEEcccHHHEEEEHccHccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEcEEEEcEcccccccccccccccEEEEEEEcccHHHHHHHHHccccccccEEEEEcccccccccccccccccccEcccHHHHHHHHHHccccHHHccEEEEEEEEEEccccccccccccHHHHHHHHccccccccHHHEEHHEEEccccEEEEEccccccHccccccEEEEcccccEEEEEEHEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHcccEEEEEccHHHHHHHccccHHHHHHHHHHcccEEEEccccEEEEEEccHHHHHHHHHHHHHHHccccccEEEEEEEEEEEEccHHHEccccccccEEHHHHHHHHHHHHHHHHccccEEEEEEEEEcccccEEEEHHHHccccccccc
MFDVHTVEIewagrplkletgriarqsdgaVLATYGETVVLATVVYdrslkdgqdffpltvnyqertyavgkipggylrresrpteNEILISRMIDrsirplfskcykNETQVIINVMQhdlessphVVSMVAASAALMLsglpfegpvvgaqvdyingqyvlnprldedqgsldlfvsGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCakepividskDFSKLEEEMSQMIKEDLrvscfipekyvrckQIDDLKKKMVSYFSSehsswnegeiVSVFEDIQAKVVRTVMLDkkvrmdgrdsetVRDISAQVGLlqrthgsslfirgdTQAIVVVTLGtredeqyvdslsgtqrndfmmhynflpcatgevsrmgapsrreighgrlarraihpvlpqtaqfpytLRIVSEitesdgsssmatvcgsslalmdagvpiskpvaGIAMGlvkdgddfiilsdisgdedhlghmdfkvagtdsgITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRlqlgeftprveimaippdqirnVIGMGGKVIRGIVEQtgakvnidddgtvKIASSSLAEIEAAREMIRSItdvpevnkiyKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKtsdvvkegdTVWVKLldfddrgkiKLSMKVVdqntgkpiv
mfdvhtveiewagrplkletgriaRQSDGAVLATYGETVVLATVVYDRSLKDGQDFFpltvnyqertyavgkipggylrresrptenEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKedlrvscfipekyvrckqiDDLKKKMVSYFSSehsswnegeivSVFEDIQAKVVRTVMldkkvrmdgrdsetvrdisaqvgllqrthgsslfirgdtQAIVVVTLgtredeqyvDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRlarraihpvlpqtaqfpYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGeftprveimaippdqirNVIGMGGKVIRGIVEQTgakvnidddgtvKIASSSLAEIEAAREMIrsitdvpevnKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLstervaktsdvvkegdtvwvklldfddrgkiklsmkvvdqntgkpiv
MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHvvsmvaasaalmlsGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKiassslaeieaaREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV
****HTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS**RLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVV*********
MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEIT*********TVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV
*FDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ*******
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MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV
MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV
MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPIV

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target699 polynucleotide phosphorylase/polyadenylase [Candidatus
254780630242 ribonuclease PH [Candidatus Liberibacter asiaticus 1e-06
254780456 576 30S ribosomal protein S1 [Candidatus Liberibacter 5e-06
254780456 576 30S ribosomal protein S1 [Candidatus Liberibacter 0.004
254780456 576 30S ribosomal protein S1 [Candidatus Liberibacter 0.039
>gi|254780630|ref|YP_003065043.1| ribonuclease PH [Candidatus Liberibacter asiaticus str. psy62] Length = 242 Back     alignment
 Score = 47.0 bits (110), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/144 (26%), Positives = 65/144 (45%), Gaps = 8/144 (5%)

Query: 312 VRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQR 371
           +R+ GR    +R+IS    + +   GS L   GDT  +   TL    +E+    +  T+ 
Sbjct: 1   MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATL----EEKVPMWIRNTKH 56

Query: 372 NDFMMHYNFLPCATGEVSRMGAPSRREIGHG----RLARRAIHPVLPQTAQFPYTLRIVS 427
                 Y  LP +TG   +  A S R+ G      R+  RA+  V+  +A     + I  
Sbjct: 57  GWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116

Query: 428 EITESDGSSSMATVCGSSLALMDA 451
           ++ ++DG +  A + G+ +AL D 
Sbjct: 117 DVIQADGGTRTAAITGAWVALHDC 140

>gi|254780456|ref|YP_003064869.1| 30S ribosomal protein S1 [Candidatus Liberibacter asiaticus str. psy62] Length = 576 Back     alignment
 Score = 44.7 bits (104), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 3/101 (2%)

Query: 595 IASSSLAEIEAAREMIRS-ITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS 653
           I  S  A +E +R   RS I    E  ++ +G V  + D+G FV   G  DGL+H++ ++
Sbjct: 172 IVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGV-DGLLHVTDIA 230

Query: 654 TERVAKTSDVVKEGDTVWVKLLDFD-DRGKIKLSMKVVDQN 693
             R+   S V+  G  V VK++  + +  +I L MK +++N
Sbjct: 231 WHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKN 271

>gi|254780456|ref|YP_003064869.1| 30S ribosomal protein S1 [Candidatus Liberibacter asiaticus str. psy62] Length = 576 Back     alignment
 Score = 35.0 bits (79), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 625 GQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDFDD-RGK 682
           G V  + D+G FV      +GL HISQ+S T++    S ++  G  V V +L+ +  R +
Sbjct: 288 GVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKR 347

Query: 683 IKLSMK 688
           I L +K
Sbjct: 348 ISLGLK 353

>gi|254780456|ref|YP_003064869.1| 30S ribosomal protein S1 [Candidatus Liberibacter asiaticus str. psy62] Length = 576 Back     alignment
 Score = 32.0 bits (71), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 624 KGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKE---GDTVWVKLLDFDDR 680
           +G+V    DFG F+      DG++H+S L   R  +   V+ E   GD V   +LD  D 
Sbjct: 374 EGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEK--VIAEYAKGDIVKAVVLDI-DV 430

Query: 681 GKIKLSMKV 689
           GK ++S+ V
Sbjct: 431 GKERISLGV 439

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

IdentityAlignment graphLength Definition Round E-value
Target699 polynucleotide phosphorylase/polyadenylase [Candidatus
315122006699 polynucleotide phosphorylase/polyadenylase [Candidatus 1 0.0
227824076717 polynucleotide phosphorylase/polyadenylase [Sinorhizobi 1 0.0
257096719712 RecName: Full=Polyribonucleotide nucleotidyltransferase 1 0.0
325291527715 polynucleotide phosphorylase [Agrobacterium sp. H13-3] 1 0.0
222084321710 polyribonucleotide nucleotidyltransferase protein [Agro 1 0.0
150398632714 polynucleotide phosphorylase/polyadenylase [Sinorhizobi 1 0.0
15887437713 polynucleotide phosphorylase/polyadenylase [Agrobacteri 1 0.0
15963997717 polynucleotide phosphorylase/polyadenylase [Sinorhizobi 1 0.0
116249886712 polynucleotide phosphorylase/polyadenylase [Rhizobium l 1 0.0
241207064712 polynucleotide phosphorylase/polyadenylase [Rhizobium l 1 0.0
>gi|315122006|ref|YP_004062495.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 699 Back     alignment and organism information
 Score = 1222 bits (3163), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 590/698 (84%), Positives = 641/698 (91%)

Query: 1   MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60
           MFDVHTVE++WAGRPLKLETGRIA+QSDGAVLATYGETVVLATVV+DR+LK  QDFFPLT
Sbjct: 1   MFDVHTVEVDWAGRPLKLETGRIAQQSDGAVLATYGETVVLATVVFDRNLKKDQDFFPLT 60

Query: 61  VNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQH 120
           VNYQERTYAVGKIPGGYLRRESRPTENE+LISRMIDRSIRPLF K YKNETQVIINVMQH
Sbjct: 61  VNYQERTYAVGKIPGGYLRRESRPTENEVLISRMIDRSIRPLFPKHYKNETQVIINVMQH 120

Query: 121 DLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSG 180
           DLE+ PHVVSMVA SAALMLSGLPFEGP+ GAQVDY++ +YVLNP LD ++GSLDLFVSG
Sbjct: 121 DLENDPHVVSMVAVSAALMLSGLPFEGPIAGAQVDYVDDKYVLNPPLDGEKGSLDLFVSG 180

Query: 181 TQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKL 240
           T+DAVLMVELEANQLSEDVVLDAI+FGH ECKPVIEAISKL KMCAKEPI  DSKD SKL
Sbjct: 181 TRDAVLMVELEANQLSEDVVLDAIMFGHAECKPVIEAISKLVKMCAKEPIFFDSKDLSKL 240

Query: 241 EEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQA 300
           EEEM  M   DLR S FIPEK VRC+ I+D+K+K+ S+F +E SSW E E+ SVFED+ A
Sbjct: 241 EEEMFHMFGADLRNSSFIPEKSVRCEAINDIKEKVFSHFCTEDSSWTEEEVSSVFEDMHA 300

Query: 301 KVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDE 360
           KVVR  +++ K+RMDGRD ETVRDISAQVGLLQRTHGSS F RG TQAIVVVTLGT+EDE
Sbjct: 301 KVVRASIVENKIRMDGRDVETVRDISAQVGLLQRTHGSSFFSRGSTQAIVVVTLGTKEDE 360

Query: 361 QYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFP 420
           QYVDSL+GTQRNDFMMHYNF P + GEV R+GAPSRREIGHGRLARRAIHP+LPQ AQFP
Sbjct: 361 QYVDSLAGTQRNDFMMHYNFFPFSVGEVGRIGAPSRREIGHGRLARRAIHPILPQAAQFP 420

Query: 421 YTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDIS 480
           YTLRIVSEIT S+GSSSMATVCG+SLALMDAGVPISKPVAGIAMGLVK+ D F++LSDIS
Sbjct: 421 YTLRIVSEITGSNGSSSMATVCGASLALMDAGVPISKPVAGIAMGLVKEDDQFVVLSDIS 480

Query: 481 GDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS 540
           G+EDH GHMDFKV+GTDSGITAMQMDMKI GIS++I+++ALQQ KRGRLHILNEMSKV+S
Sbjct: 481 GEEDHFGHMDFKVSGTDSGITAMQMDMKIRGISKDIIMVALQQGKRGRLHILNEMSKVIS 540

Query: 541 ESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSL 600
           ESRLQLGEFTPRVEIM IPPDQIRNVIG+GGKVIR IVE+TGAKVNIDDDGT+KIASSS 
Sbjct: 541 ESRLQLGEFTPRVEIMVIPPDQIRNVIGVGGKVIRNIVEKTGAKVNIDDDGTIKIASSSP 600

Query: 601 AEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKT 660
           AEIEAA EMIR ITDVPEVNKIYKG VVKVMDFGAFV+FCGARDGLVHIS LSTERVAKT
Sbjct: 601 AEIEAACEMIRLITDVPEVNKIYKGHVVKVMDFGAFVNFCGARDGLVHISHLSTERVAKT 660

Query: 661 SDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQNTGKPI 698
           SD+VKEGD VWVKLLDFDDRGKIKLSMKVVDQNTGKPI
Sbjct: 661 SDIVKEGDVVWVKLLDFDDRGKIKLSMKVVDQNTGKPI 698


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227824076|ref|YP_002828049.1| polynucleotide phosphorylase/polyadenylase [Sinorhizobium fredii NGR234] Length = 717 Back     alignment and organism information
>gi|257096719|sp|B3PXD7|PNP_RHIE6 RecName: Full=Polyribonucleotide nucleotidyltransferase; AltName: Full=Polynucleotide phosphorylase; Short=PNPase Length = 712 Back     alignment and organism information
>gi|325291527|ref|YP_004277391.1| polynucleotide phosphorylase [Agrobacterium sp. H13-3] Length = 715 Back     alignment and organism information
>gi|222084321|ref|YP_002542850.1| polyribonucleotide nucleotidyltransferase protein [Agrobacterium radiobacter K84] Length = 710 Back     alignment and organism information
>gi|150398632|ref|YP_001329099.1| polynucleotide phosphorylase/polyadenylase [Sinorhizobium medicae WSM419] Length = 714 Back     alignment and organism information
>gi|15887437|ref|NP_353118.1| polynucleotide phosphorylase/polyadenylase [Agrobacterium tumefaciens str. C58] Length = 713 Back     alignment and organism information
>gi|15963997|ref|NP_384350.1| polynucleotide phosphorylase/polyadenylase [Sinorhizobium meliloti 1021] Length = 717 Back     alignment and organism information
>gi|116249886|ref|YP_765724.1| polynucleotide phosphorylase/polyadenylase [Rhizobium leguminosarum bv. viciae 3841] Length = 712 Back     alignment and organism information
>gi|241207064|ref|YP_002978160.1| polynucleotide phosphorylase/polyadenylase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 712 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
Target699 polynucleotide phosphorylase/polyadenylase [Candidatus
PRK11824693 PRK11824, PRK11824, polynucleotide phosphorylase/polyad 0.0
TIGR03591684 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyl 0.0
PLN00207891 PLN00207, PLN00207, polyribonucleotide nucleotidyltrans 1e-172
KOG1067760 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyri 1e-164
TIGR02696719 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthet 1e-160
COG1185692 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase 0.0
pfam01138128 pfam01138, RNase_PH, 3' exoribonuclease family, domain 5e-28
TIGR02065230 TIGR02065, ECX1, archaeal exosome-like complex exonucle 1e-07
pfam01138128 pfam01138, RNase_PH, 3' exoribonuclease family, domain 3e-26
PRK03983244 PRK03983, PRK03983, exosome complex exonuclease Rrp41; 3e-24
TIGR02065230 TIGR02065, ECX1, archaeal exosome-like complex exonucle 5e-23
COG0689230 COG0689, Rph, RNase PH [Translation, ribosomal structur 2e-20
KOG1068245 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclea 4e-12
KOG1069217 KOG1069, KOG1069, KOG1069, Exosomal 3'-5' exoribonuclea 8e-07
COG2123272 COG2123, COG2123, RNase PH-related exoribonuclease [Tra 3e-06
cd0447268 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphory 3e-22
cd0568479 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-term 4e-17
PRK06676 390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 1e-16
PRK06676390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 2e-14
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 2e-14
cd0569269 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Riboso 4e-14
COG1098129 COG1098, VacB, Predicted RNA binding protein (contains 6e-14
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 6e-14
cd0568673 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-bindin 2e-13
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 8e-13
PRK06299 565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 2e-12
PRK13806 491 PRK13806, rpsA, 30S ribosomal protein S1; Provisional 6e-12
COG0539 541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 1e-11
PRK13806 491 PRK13806, rpsA, 30S ribosomal protein S1; Provisional 6e-11
PRK05807136 PRK05807, PRK05807, hypothetical protein; Provisional 6e-11
pfam0057574 pfam00575, S1, S1 RNA binding domain 9e-11
cd0568868 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Riboso 1e-10
COG2183780 COG2183, Tex, Transcriptional accessory protein [Transc 1e-10
PRK08059123 PRK08059, PRK08059, general stress protein 13; Validate 1e-10
PRK07899 486 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed 2e-10
PRK07899 486 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed 3e-10
TIGR00717 516 TIGR00717, rpsA, ribosomal protein S1 3e-10
COG1093 269 COG1093, SUI2, Translation initiation factor 2, alpha s 4e-10
PRK08582139 PRK08582, PRK08582, hypothetical protein; Provisional 4e-10
PRK06299 565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 2e-09
TIGR00717 516 TIGR00717, rpsA, ribosomal protein S1 2e-09
PRK06299 565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 3e-09
PRK06299565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 5e-09
PRK12269 863 PRK12269, PRK12269, bifunctional cytidylate kinase/ribo 5e-09
cd0568568 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a 7e-09
cd0016465 cd00164, S1_like, S1_like: Ribosomal protein S1-like RN 1e-08
PRK03987 262 PRK03987, PRK03987, translation initiation factor IF-2 5e-08
cd0445276 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit 7e-08
PRK06676 390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 8e-08
TIGR00717516 TIGR00717, rpsA, ribosomal protein S1 8e-08
cd0446183 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7 9e-08
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase subunit 1e-07
cd0570877 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 8e-07
COG0539541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 7e-06
TIGR00717516 TIGR00717, rpsA, ribosomal protein S1 1e-05
PRK07252120 PRK07252, PRK07252, hypothetical protein; Provisional 1e-05
cd0569069 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Riboso 2e-05
PRK07400318 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed 5e-05
cd0447377 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of t 6e-05
cd0569870 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5 8e-05
cd0568770 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1 1e-04
COG0539541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 2e-04
cd0446099 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding do 2e-04
KOG1070 1710 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 3e-04
PRK12269 863 PRK12269, PRK12269, bifunctional cytidylate kinase/ribo 3e-04
KOG2916 304 KOG2916, KOG2916, KOG2916, Translation initiation facto 4e-04
cd0568972 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Riboso 0.001
COG0539 541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 0.003
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' 0.003
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 0.003
COG0557706 COG0557, VacB, Exoribonuclease R [Transcription] 0.004
cd0239361 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPas 2e-17
pfam0001357 pfam00013, KH_1, KH domain 9e-09
smart0032269 smart00322, KH, K homology RNA-binding domain 5e-07
cd0010564 cd00105, KH-I, K homology RNA-binding domain, type I 2e-05
PRK13763181 PRK13763, PRK13763, putative RNA-processing protein; Pr 1e-04
TIGR03665172 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH 0.002
cd0239462 cd02394, vigilin_like_KH, K homology RNA-binding domain 0.003
COG0539 541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 5e-12
PRK00087 647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 3e-05
TIGR01966236 TIGR01966, RNasePH, ribonuclease PH 9e-10
COG0689230 COG0689, Rph, RNase PH [Translation, ribosomal structur 2e-08
PRK03983244 PRK03983, PRK03983, exosome complex exonuclease Rrp41; 4e-08
COG2123272 COG2123, COG2123, RNase PH-related exoribonuclease [Tra 0.002
pfam0372680 pfam03726, PNPase, Polyribonucleotide nucleotidyltransf 6e-07
pfam0372567 pfam03725, RNase_PH_C, 3' exoribonuclease family, domai 8e-07
pfam0372567 pfam03725, RNase_PH_C, 3' exoribonuclease family, domai 3e-04
KOG1676 600 KOG1676, KOG1676, KOG1676, K-homology type RNA binding 0.002
PRK04282271 PRK04282, PRK04282, exosome complex RNA-binding protein 0.002
>gnl|CDD|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>gnl|CDD|177797 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] Back     alignment and domain information
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1 Back     alignment and domain information
>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1 Back     alignment and domain information
>gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1 Back     alignment and domain information
>gnl|CDD|179695 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional Back     alignment and domain information
>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1 Back     alignment and domain information
>gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|36286 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|36287 KOG1069, KOG1069, KOG1069, Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|88437 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|88439 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
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|88447 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|31295 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|88441 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional Back     alignment and domain information
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional Back     alignment and domain information
>gnl|CDD|180268 PRK05807, PRK05807, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain Back     alignment and domain information
>gnl|CDD|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|32366 COG2183, Tex, Transcriptional accessory protein [Transcription] Back     alignment and domain information
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated Back     alignment and domain information
>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1 Back     alignment and domain information
>gnl|CDD|31290 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|181488 PRK08582, PRK08582, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1 Back     alignment and domain information
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>gnl|CDD|88440 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
>gnl|CDD|88416 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|179696 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>gnl|CDD|88418 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
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1 Back     alignment and domain information
>gnl|CDD|88427 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
>gnl|CDD|181471 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>gnl|CDD|88463 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
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1 Back     alignment and domain information
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|88445 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|88438 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>gnl|CDD|88453 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
>gnl|CDD|88442 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|88426 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|36288 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>gnl|CDD|38127 KOG2916, KOG2916, KOG2916, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|88444 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>gnl|CDD|162678 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|30903 COG0557, VacB, Exoribonuclease R [Transcription] Back     alignment and domain information
>gnl|CDD|29003 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH) Back     alignment and domain information
>gnl|CDD|143804 pfam00013, KH_1, KH domain Back     alignment and domain information
>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain Back     alignment and domain information
>gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I Back     alignment and domain information
>gnl|CDD|184310 PRK13763, PRK13763, putative RNA-processing protein; Provisional Back     alignment and domain information
>gnl|CDD|132704 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain protein Back     alignment and domain information
>gnl|CDD|29004 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like Back     alignment and domain information
>gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH Back     alignment and domain information
>gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|179695 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional Back     alignment and domain information
>gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|146390 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA binding domain Back     alignment and domain information
>gnl|CDD|146389 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2 Back     alignment and domain information
>gnl|CDD|146389 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2 Back     alignment and domain information
>gnl|CDD|36889 KOG1676, KOG1676, KOG1676, K-homology type RNA binding proteins [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|179808 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 699 polynucleotide phosphorylase/polyadenylase [Candidatus
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 100.0
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 100.0
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 100.0
KOG1067760 consensus 100.0
TIGR02696725 pppGpp_PNP guanosine pentaphosphate synthetase I/polyri 100.0
PRK00173237 rph ribonuclease PH; Reviewed 100.0
TIGR02065231 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 100.0
PRK03983243 exosome complex exonuclease Rrp41; Provisional 100.0
PRK04282271 exosome complex RNA-binding protein Rrp42; Provisional 100.0
COG0689230 Rph RNase PH [Translation, ribosomal structure and biog 100.0
TIGR01966237 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryoti 99.97
KOG1068245 consensus 99.92
COG2123272 RNase PH-related exoribonuclease [Translation, ribosoma 99.6
KOG1069217 consensus 99.54
KOG1614291 consensus 98.71
KOG1612288 consensus 98.68
KOG1613298 consensus 98.34
PRK00173237 rph ribonuclease PH; Reviewed 99.97
PRK03983243 exosome complex exonuclease Rrp41; Provisional 99.95
TIGR02065231 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 99.78
TIGR01966237 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryoti 99.74
PRK04282271 exosome complex RNA-binding protein Rrp42; Provisional 99.68
COG0689230 Rph RNase PH [Translation, ribosomal structure and biog 99.67
KOG1067760 consensus 99.64
COG2123272 RNase PH-related exoribonuclease [Translation, ribosoma 99.46
KOG1068245 consensus 98.92
KOG1069217 consensus 98.91
TIGR02696725 pppGpp_PNP guanosine pentaphosphate synthetase I/polyri 98.7
KOG1614291 consensus 98.59
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 99.87
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 99.86
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 99.64
pfam01138128 RNase_PH 3' exoribonuclease family, domain 1. This fami 99.82
PRK08582139 hypothetical protein; Provisional 99.79
PRK05807136 hypothetical protein; Provisional 99.78
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. 99.77
PRK07899 484 rpsA 30S ribosomal protein S1; Reviewed 99.75
PRK07252120 hypothetical protein; Provisional 99.72
PRK07400314 30S ribosomal protein S1; Reviewed 99.71
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 99.71
PRK00087 670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 99.7
COG1098129 VacB Predicted RNA binding protein (contains ribosomal 99.7
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 do 99.69
PRK13806 489 rpsA 30S ribosomal protein S1; Provisional 99.69
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of transla 99.69
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protei 99.69
PRK08059119 general stress protein 13; Validated 99.68
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 99.68
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 99.67
PRK06299 556 rpsA 30S ribosomal protein S1; Reviewed 99.66
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 99.65
PRK13806 489 rpsA 30S ribosomal protein S1; Provisional 99.63
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a tran 99.6
PRK03987 262 translation initiation factor IF-2 subunit alpha; Valid 99.6
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea 99.57
TIGR00717 534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 99.5
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protei 99.5
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protei 99.49
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a transcript 99.49
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protei 99.48
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protei 99.45
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is 99.44
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Hom 99.41
pfam0057574 S1 S1 RNA binding domain. The S1 domain occurs in a wid 99.4
COG1093 269 SUI2 Translation initiation factor 2, alpha subunit (eI 99.39
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a tran 99.38
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a tran 99.37
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans- 99.34
COG2183780 Tex Transcriptional accessory protein [Transcription] 99.21
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosoma 99.13
PTZ00248 324 eukaryotic translation initiation factor 2 alpha subuni 99.02
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-l 99.01
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-binding 98.97
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.83
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 i 98.83
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 98.81
PRK11642813 exoribonuclease R; Provisional 98.69
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a tran 98.47
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a tran 98.36
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA 98.32
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-li 98.31
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosoma 98.19
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans- 98.1
PRK05054644 exoribonuclease II; Provisional 98.08
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Transcrip 97.96
KOG2916 304 consensus 97.95
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 i 97.95
PRK08563182 DNA-directed RNA polymerase subunit E'; Provisional 97.92
PTZ00162170 RNA polymerase II subunit 7; Provisional 97.68
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-bindi 97.4
KOG1070 1710 consensus 97.39
PRK04163232 exosome complex RNA-binding protein Rrp4; Provisional 97.38
PRK09521187 exosome complex RNA-binding protein Csl4; Provisional 97.19
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins (con 97.08
COG1096188 Predicted RNA-binding protein (consists of S1 domain an 96.74
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-l 96.6
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is 96.59
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 95.89
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is 95.56
, 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">TIGR00757 464 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR0046 95.43
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein (NusA) 95.35
TIGR01953 366 NusA transcription termination factor NusA; InterPro: I 95.2
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans- 95.13
KOG1856 1299 consensus 94.81
PRK1244287 translation initiation factor IF-1; Reviewed 92.97
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans- 92.13
TIGR00358684 3_prime_RNase VacB and RNase II family 3'-5' exoribonuc 91.01
pfam1044772 EXOSC1 Exosome component EXOSC1/CSL4. This family of pr 90.71
cd0445164 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-li 90.39
CHL0001078 infA translation initiation factor 1 90.32
PRK0027672 infA translation initiation factor IF-1; Validated 90.14
PRK07899 484 rpsA 30S ribosomal protein S1; Reviewed 99.74
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 99.66
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 99.62
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 99.59
PRK07400 314 30S ribosomal protein S1; Reviewed 99.02
KOG1070 1710 consensus 98.01
COG2996 287 Predicted RNA-bindining protein (contains S1 and HTH do 92.37
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 99.66
TIGR00717 534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 99.63
pfam01138128 RNase_PH 3' exoribonuclease family, domain 1. This fami 99.63
KOG1613298 consensus 96.79
KOG1612288 consensus 95.17
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 99.61
TIGR02063755 RNase_R ribonuclease R; InterPro: IPR011805 This family 98.93
COG0557706 VacB Exoribonuclease R [Transcription] 98.01
cd0239361 PNPase_KH Polynucleotide phosphorylase (PNPase) K homol 99.54
TIGR03665172 arCOG04150 arCOG04150 universal archaeal KH domain prot 98.34
pfam0001357 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoan 98.13
smart0032269 KH K homology RNA-binding domain. 98.05
cd0010564 KH-I K homology RNA-binding domain, type I. KH binds si 98.01
cd0239462 vigilin_like_KH K homology RNA-binding domain_vigilin_l 97.95
cd0239665 PCBP_like_KH K homology RNA-binding domain, PCBP_like. 97.84
PRK13763185 putative RNA-processing protein; Provisional 97.81
PRK04163232 exosome complex RNA-binding protein Rrp4; Provisional 97.67
PRK11712489 ribonuclease G; Provisional 97.66
cd02395120 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-bind 97.54
PRK12704 455 phosphodiesterase; Provisional 97.41
COG1094194 Predicted RNA-binding protein (contains KH domains) [Ge 97.4
KOG2190485 consensus 97.23
TIGR03665172 arCOG04150 arCOG04150 universal archaeal KH domain prot 97.16
COG1094194 Predicted RNA-binding protein (contains KH domains) [Ge 96.8
KOG1588259 consensus 96.79
PRK13763185 putative RNA-processing protein; Provisional 96.69
KOG2193584 consensus 96.57
COG5176269 MSL5 Splicing factor (branch point binding protein) [RN 96.5
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins (con 95.84
KOG2193584 consensus 95.55
KOG2814 345 consensus 94.53
KOG2192390 consensus 94.35
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). NusA i 92.14
pfam0372680 PNPase Polyribonucleotide nucleotidyltransferase, RNA b 99.26
pfam0372567 RNase_PH_C 3' exoribonuclease family, domain 2. This fa 98.9
KOG2191402 consensus 95.32
KOG1676 600 consensus 98.19
KOG1676 600 consensus 97.64
KOG2191 402 consensus 97.36
KOG2192 390 consensus 93.5
COG1847208 Jag Predicted RNA-binding protein [General function pre 90.18
KOG0119 554 consensus 98.04
KOG2190 485 consensus 95.26
100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to Escherichia coli RpoE.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR00448">TIGR00448184 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 D 97.9
COG1107715 Archaea-specific RecJ-like exonuclease, contains DnaJ-t 97.54
PRK10811 1063 rne ribonuclease E; Reviewed 97.41
TIGR03319514 YmdA_YtgF conserved hypothetical protein YmdA/YtgF. 97.31
PRK12705485 hypothetical protein; Provisional 96.88
PRK00106535 hypothetical protein; Provisional 96.83
pfam0372567 RNase_PH_C 3' exoribonuclease family, domain 2. This fa 97.08
KOG0336629 consensus 96.3
PRK13764605 ATPase; Provisional 97.05
COG1855604 ATPase (PilT family) [General function prediction only] 95.54
PRK12327353 nusA transcription elongation factor NusA; Provisional 96.78
PRK09202428 nusA transcription elongation factor NusA; Validated 96.38
PRK12328375 nusA transcription elongation factor NusA; Provisional 95.74
COG1530487 CafA Ribonucleases G and E [Translation, ribosomal stru 96.34
PRK12329457 nusA transcription elongation factor NusA; Provisional 94.89
PRK08406142 transcription elongation factor NusA-like protein; Vali 93.7
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1067 consensus Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented Back     alignment and domain information
>PRK00173 rph ribonuclease PH; Reviewed Back     alignment and domain information
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function Back     alignment and domain information
>PRK03983 exosome complex exonuclease Rrp41; Provisional Back     alignment and domain information
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional Back     alignment and domain information
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2 Back     alignment and domain information
>KOG1068 consensus Back     alignment and domain information
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1069 consensus Back     alignment and domain information
>KOG1614 consensus Back     alignment and domain information
>KOG1612 consensus Back     alignment and domain information
>KOG1613 consensus Back     alignment and domain information
>PRK00173 rph ribonuclease PH; Reviewed Back     alignment and domain information
>PRK03983 exosome complex exonuclease Rrp41; Provisional Back     alignment and domain information
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function Back     alignment and domain information
>TIGR01966 RNasePH ribonuclease PH; InterPro: IPR002381 Prokaryotic ribonuclease PH (2 Back     alignment and domain information
>PRK04282 exosome complex RNA-binding protein Rrp42; Provisional Back     alignment and domain information
>COG0689 Rph RNase PH [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1067 consensus Back     alignment and domain information
>COG2123 RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1068 consensus Back     alignment and domain information
>KOG1069 consensus Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase; InterPro: IPR014069 The of the characterization of two proteins from Streptomyces coelicolor ahs been presented Back     alignment and domain information
>KOG1614 consensus Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam01138 RNase_PH 3' exoribonuclease family, domain 1 Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed 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
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed 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
>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
>PRK13806 rpsA 30S ribosomal protein S1; 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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) 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
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] 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
>PRK13806 rpsA 30S ribosomal protein S1; Provisional 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
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated 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
>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
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) 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
>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
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) 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
>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
>pfam00575 S1 S1 RNA binding domain 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
>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
>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
>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
>COG2183 Tex Transcriptional accessory protein [Transcription] 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
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain 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
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional 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
>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
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding 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
>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
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>KOG2916 consensus Back     alignment and domain information
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>PTZ00162 RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>KOG1070 consensus Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: 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
>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
>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
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation substance protein A, a bacterial transcription termination factor Back     alignment and domain information
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>KOG1856 consensus Back     alignment and domain information
>PRK12442 translation initiation factor IF-1; Reviewed Back     alignment and domain information
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476 This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria Back     alignment and domain information
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4 Back     alignment and domain information
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain Back     alignment and domain information
>CHL00010 infA translation initiation factor 1 Back     alignment and domain information
>PRK00276 infA translation initiation factor IF-1; Validated Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back