254780456

254780456

30S ribosomal protein S1

GeneID in NCBI database:8209443Locus tag:CLIBASIA_01705
Protein GI in NCBI database:254780456Protein Accession:YP_003064869.1
Gene range:-(373449, 375179)Protein Length:576aa
Gene description:30S ribosomal protein S1
COG prediction:[J] Ribosomal protein S1
KEGG prediction:rpsA; 30S ribosomal protein S1; K02945 small subunit ribosomal protein S1
SEED prediction:SSU ribosomal protein S1p
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:Cell division-ribosomal stress proteins cluster;
Ribosome SSU 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------
MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQG
cccccccHHHHHHHHHHHccccccccccEEEEEEEEEEccEEEEEEccccEEEEEHHHccccccccccccccEEEEEEEEEEccccEEEEEEEccccHHHHHHHHHHHccccEEEEEEEEEEcccEEEEEccHHHHccHHHcccccccccccccccEEEEEEEEEEccccEEEEcccHHHHHHHHHHHHHHHHccccccEEEEEEEEEEccEEEEEcccEEEEEEEEcccccccccHHHEEccccEEEEEEEEEEccccEEEEEEEccccccccccccccccccEEEEEEEEEEcccEEEEEcccEEEEEEEEEcccccEEccHHHHcccccEEEEEEEEEEccccEEEEEEEEcccccccccccccccccEEEEEEcccccccEEEEEccccEEEEEEEEcccccccccHHHEEccccEEEEEEEEEcccccEEEEEEEEcccccccccccccccccccEEEEEEEEEccccEEEEEcccccEEEEEEHHHccccccccHHHEEccccEEEEEEEEEEccccEEEEEEEEcccccHHHHHHHHccccccccHHHHHHHHHHHHcccccccccccc
cccccccHHHHHHHHHHHHHHcccccccEEEEEEEEEcccEEEEEccccccccEEHHHHcccccccEEEcccEEEEEHHHHHccccccEccHHHHHHHHHHHHHHHHHHcccEEEEEEEcEEcccEEEEcccEEEEcccccEEccccccccccccccEEEEEEEEccccccEEEEEEEEEHHccHHHHHHHHHHHHcccEEEEEEEEccccccEEEcccccccEHHcHHHHHHcccccEEEEcccEEEEEEEEEcccccEEEEcHHHcccccHHHHHHHcccccEEEEEEEEEcccccEEEEccccEEEEEEEcccccccccccccEEEEccEEEEEEEEccHHHcEEEEccHcccccHHHHHHHHcccccEEEEEEEEccccEEEEEcccccccEEEEccccccccHHHHHHHcccccEEEEEEEEcccHHHHHEccHHHcccccHHHHHHHcccccccEEEEEEEEEccccEEEEEEccccEEEEEEHHHHHHHHHHHcccEEccccEEEEEEEEEcccccEEEEEEEEccHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccccccccc
MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGlkfegriprrefmgkgqytpikvgdEVEVYVERTensfgeavfSRDKALREGVWEKIEAKFRAGERIEGVIfnqvkggmtvdlngevaflprsqidirpvrdvtplmhepqLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDlsgvdgllhvTDIAwhrilhpskvlsigqQVKVKIIRINQETHRISLGmkqleknpwddvqdkyvegskvsgvvtnLTDYGVFVELQSGIEGLAHISQISwtkknihpskilsvGQQVEVVILEVNPARKRISLGLKQALinpweefskshppgtevegevknktdfglfigldehldgmihlsdldwnrpgeKVIAEYAKGDIVKAVVLDIDVGKERISLGVkqlsgsapdvvdsvsslrkndvVSCEVISVSEGGIEVSLidhkginsfirrsdlsrdrvdqdpgrfskgqiVDACVVNvskkdgkvSLSIKALEIAEEKgavaqfgssdsgasLGDILGMALknrgndagdsndnqg
msftnpsredfATLLEEsftkkdlaenCVTKgivvglekdtvvvdvglkfegriprrefmgkgqytpikvgDEVEVYVERtensfgeavfsrdkalREGVWEKIEakfrageriegVIFNQVKGGMTVDLNGEVaflprsqidirpvrdvtplMHEPQLfeilkmdkrrgnIVVSRravleesraeqrseivqkleegqviegtvkniTDYGVFVDLSGVDGLLHVTDIAWHRILhpskvlsigqqVKVKIIRINQETHRISlgmkqleknpwdDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINpweefskshppgtevegevKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAeyakgdivKAVVLDIDVGKERISlgvkqlsgsapdvvdsvsslrkndvVSCEVIsvseggievslidhkginsfirrsdlsrdrvdqdpgrfskgqivdacvvnvskkdgkvSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALknrgndagdsndnqg
MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQG
*************L*EE**********CVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEE********IVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSR********RFSKGQIVDACVVNVSKKDGKVSLSI***********************************************
********EDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL*********EIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSK*********GEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGN**********
****NPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDS*ASLGDILGMALKNR************
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MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQG
MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQG
MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFMGKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFNQVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVLEESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKVLSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFVELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPWEEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDIVKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLIDHKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGAVAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQG

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target576 30S ribosomal protein S1 [Candidatus Liberibacter asiat
254780784699 polynucleotide phosphorylase/polyadenylase [Candid 4e-06
254780784699 polynucleotide phosphorylase/polyadenylase [Candid 0.003
254780784699 polynucleotide phosphorylase/polyadenylase [Candid 0.031
>gi|254780784|ref|YP_003065197.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str. psy62] Length = 699 Back     alignment
 Score = 44.7 bits (104), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 54/101 (53%), Gaps = 3/101 (2%)

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

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

>gi|254780784|ref|YP_003065197.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str. psy62] Length = 699 Back     alignment
 Score = 35.0 bits (79), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

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

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

>gi|254780784|ref|YP_003065197.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str. psy62] Length = 699 Back     alignment
 Score = 32.0 bits (71), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

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

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

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

IdentityAlignment graphLength Definition Round E-value
Target576 30S ribosomal protein S1 [Candidatus Liberibacter asiat
315122096576 30S ribosomal protein S1 [Candidatus Liberibacter solan 1 0.0
222084305567 ribosomal protein S1 [Agrobacterium radiobacter K84] Le 1 0.0
86355758567 30S ribosomal protein S1 [Rhizobium etli CFN 42] Length 1 0.0
190889734567 30S ribosomal protein S1 [Rhizobium etli CIAT 652] Leng 1 0.0
209551601567 30S ribosomal protein S1 [Rhizobium leguminosarum bv. t 1 0.0
116249872567 30S ribosomal protein S1 [Rhizobium leguminosarum bv. v 1 0.0
222147164573 30S ribosomal protein S1 [Agrobacterium vitis S4] Lengt 1 0.0
307306420568 ribosomal protein S1 [Sinorhizobium meliloti BL225C] Le 1 0.0
15964008568 30S ribosomal protein S1 [Sinorhizobium meliloti 1021] 1 0.0
159186030566 30S ribosomal protein S1 [Agrobacterium tumefaciens str 1 0.0
>gi|315122096|ref|YP_004062585.1| 30S ribosomal protein S1 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 576 Back     alignment and organism information
 Score = 1027 bits (2655), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 495/575 (86%), Positives = 544/575 (94%)

Query: 1   MSFTNPSREDFATLLEESFTKKDLAENCVTKGIVVGLEKDTVVVDVGLKFEGRIPRREFM 60
           MSFT PSREDFATLLE+SF+KKDLAENCV+KGIVV LEKD VVVD GLKFEGRIP +EFM
Sbjct: 1   MSFTCPSREDFATLLEDSFSKKDLAENCVSKGIVVSLEKDIVVVDAGLKFEGRIPLKEFM 60

Query: 61  GKGQYTPIKVGDEVEVYVERTENSFGEAVFSRDKALREGVWEKIEAKFRAGERIEGVIFN 120
           GKGQ   IKVGDEVEVY+ER ENSFGEAVFSRDKALREGVWEKIEAKF AGERIEGVIFN
Sbjct: 61  GKGQEATIKVGDEVEVYIERIENSFGEAVFSRDKALREGVWEKIEAKFAAGERIEGVIFN 120

Query: 121 QVKGGMTVDLNGEVAFLPRSQIDIRPVRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL 180
           QVKGG+TVDLNGE+AFLPRSQID+RP+RDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL
Sbjct: 121 QVKGGLTVDLNGEIAFLPRSQIDVRPIRDVTPLMHEPQLFEILKMDKRRGNIVVSRRAVL 180

Query: 181 EESRAEQRSEIVQKLEEGQVIEGTVKNITDYGVFVDLSGVDGLLHVTDIAWHRILHPSKV 240
           EESRAEQRSEIVQKLEEGQVIEG VKNITDYG FVDLSGVDGLLHVTDIAWHRI HPSKV
Sbjct: 181 EESRAEQRSEIVQKLEEGQVIEGIVKNITDYGAFVDLSGVDGLLHVTDIAWHRIQHPSKV 240

Query: 241 LSIGQQVKVKIIRINQETHRISLGMKQLEKNPWDDVQDKYVEGSKVSGVVTNLTDYGVFV 300
           LS+GQQVKV+IIRINQETHRISLGMKQLEKNPWDD++D+YVE SKV+GVVTN+TDYG F+
Sbjct: 241 LSVGQQVKVQIIRINQETHRISLGMKQLEKNPWDDIKDRYVEESKVTGVVTNITDYGAFI 300

Query: 301 ELQSGIEGLAHISQISWTKKNIHPSKILSVGQQVEVVILEVNPARKRISLGLKQALINPW 360
           EL++GIEGLAHIS+ISWTKKNIHPSKILSVGQ+VEVVILE+NP RKRISLGLKQALINPW
Sbjct: 301 ELEAGIEGLAHISEISWTKKNIHPSKILSVGQEVEVVILEINPVRKRISLGLKQALINPW 360

Query: 361 EEFSKSHPPGTEVEGEVKNKTDFGLFIGLDEHLDGMIHLSDLDWNRPGEKVIAEYAKGDI 420
           + FS+SHPPGTEVEGE+KNKT+FGLFIGLD++LDGM+HLSDLDWNRPGE+VI EY KGD+
Sbjct: 361 KAFSESHPPGTEVEGEIKNKTEFGLFIGLDDNLDGMVHLSDLDWNRPGERVIGEYNKGDV 420

Query: 421 VKAVVLDIDVGKERISLGVKQLSGSAPDVVDSVSSLRKNDVVSCEVISVSEGGIEVSLID 480
           VKA+VLD+D+ KERISLG+KQLSGSAPD+ DS S+LRKN VVSCEVI+++EGGIEV+LID
Sbjct: 421 VKAIVLDVDIEKERISLGIKQLSGSAPDIADSASALRKNTVVSCEVIAINEGGIEVTLID 480

Query: 481 HKGINSFIRRSDLSRDRVDQDPGRFSKGQIVDACVVNVSKKDGKVSLSIKALEIAEEKGA 540
           H+GI SFIRRSDLSRDR DQDPGRFSKGQIVDA VV  S+KD KVSLSIKALEIAEE+GA
Sbjct: 481 HEGITSFIRRSDLSRDRADQDPGRFSKGQIVDARVVGTSRKDNKVSLSIKALEIAEERGA 540

Query: 541 VAQFGSSDSGASLGDILGMALKNRGNDAGDSNDNQ 575
           +AQFGSSDSGASLGDILG+ALKNRGND+ DS+ N+
Sbjct: 541 IAQFGSSDSGASLGDILGIALKNRGNDSDDSDSNK 575


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222084305|ref|YP_002542834.1| ribosomal protein S1 [Agrobacterium radiobacter K84] Length = 567 Back     alignment and organism information
>gi|86355758|ref|YP_467650.1| 30S ribosomal protein S1 [Rhizobium etli CFN 42] Length = 567 Back     alignment and organism information
>gi|190889734|ref|YP_001976276.1| 30S ribosomal protein S1 [Rhizobium etli CIAT 652] Length = 567 Back     alignment and organism information
>gi|209551601|ref|YP_002283518.1| 30S ribosomal protein S1 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 567 Back     alignment and organism information
>gi|116249872|ref|YP_765710.1| 30S ribosomal protein S1 [Rhizobium leguminosarum bv. viciae 3841] Length = 567 Back     alignment and organism information
>gi|222147164|ref|YP_002548121.1| 30S ribosomal protein S1 [Agrobacterium vitis S4] Length = 573 Back     alignment and organism information
>gi|307306420|ref|ZP_07586164.1| ribosomal protein S1 [Sinorhizobium meliloti BL225C] Length = 568 Back     alignment and organism information
>gi|15964008|ref|NP_384361.1| 30S ribosomal protein S1 [Sinorhizobium meliloti 1021] Length = 568 Back     alignment and organism information
>gi|159186030|ref|NP_356542.2| 30S ribosomal protein S1 [Agrobacterium tumefaciens str. C58] Length = 566 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
Target576 30S ribosomal protein S1 [Candidatus Liberibacter asiat
PRK06299565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 0.0
PRK12269863 PRK12269, PRK12269, bifunctional cytidylate kinase/ribo 3e-82
COG0539541 COG0539, RpsA, Ribosomal protein S1 [Translation, ribos 1e-151
TIGR00717516 TIGR00717, rpsA, ribosomal protein S1 1e-153
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 5e-95
PRK06676390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 2e-90
PRK07899486 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed 2e-67
PRK13806491 PRK13806, rpsA, 30S ribosomal protein S1; Provisional 5e-85
KOG1070 1710 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 5e-17
TIGR00717516 TIGR00717, rpsA, ribosomal protein S1 2e-52
KOG1070 1710 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 2e-06
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 2e-46
PRK06676390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 5e-46
PRK07899486 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed 7e-29
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 7e-37
PRK06676390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 6e-31
KOG1070 1710 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 1e-11
KOG1070 1710 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 5e-04
PRK07400318 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed 2e-27
cd0568868 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Riboso 7e-24
PRK11824693 PRK11824, PRK11824, polynucleotide phosphorylase/polyad 4e-18
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 5e-15
TIGR03591684 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyl 6e-15
pfam0057574 pfam00575, S1, S1 RNA binding domain 6e-14
COG1185692 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase 6e-14
COG2183780 COG2183, Tex, Transcriptional accessory protein [Transc 6e-13
cd0570877 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 7e-13
cd0568568 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a 3e-12
cd0569069 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Riboso 2e-11
cd0568972 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Riboso 4e-11
cd0568479 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-term 4e-11
cd0569269 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Riboso 6e-10
PRK08059123 PRK08059, PRK08059, general stress protein 13; Validate 8e-10
COG1098129 COG1098, VacB, Predicted RNA binding protein (contains 1e-09
cd0016465 cd00164, S1_like, S1_like: Ribosomal protein S1-like RN 7e-09
PRK05807136 PRK05807, PRK05807, hypothetical protein; Provisional 7e-09
cd0447268 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphory 2e-08
COG1093269 COG1093, SUI2, Translation initiation factor 2, alpha s 7e-08
PRK07252120 PRK07252, PRK07252, hypothetical protein; Provisional 4e-07
PRK03987262 PRK03987, PRK03987, translation initiation factor IF-2 4e-07
cd0446183 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7 5e-07
cd0445276 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit 5e-07
cd0569769 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 i 9e-07
cd0569173 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Riboso 1e-06
PRK08563187 PRK08563, PRK08563, DNA-directed RNA polymerase subunit 9e-06
cd0447183 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 1e-05
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 2e-05
PRK08582139 PRK08582, PRK08582, hypothetical protein; Provisional 3e-05
COG1095183 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' 5e-05
cd0568673 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-bindin 1e-04
PLN00207891 PLN00207, PLN00207, polyribonucleotide nucleotidyltrans 2e-04
cd0569870 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5 3e-04
cd0446099 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding do 3e-04
cd0570768 cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11: Rrp5 6e-04
TIGR02696719 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthet 8e-04
TIGR00448179 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), ar 0.003
cd0446567 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2 0.004
cd0568972 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Riboso 6e-21
cd0568868 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Riboso 3e-16
cd0569069 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Riboso 5e-15
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 3e-13
PRK11824693 PRK11824, PRK11824, polynucleotide phosphorylase/polyad 1e-12
pfam0057574 pfam00575, S1, S1 RNA binding domain 2e-12
COG2183780 COG2183, Tex, Transcriptional accessory protein [Transc 3e-12
cd0570877 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 2e-11
cd0568568 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a 4e-11
PRK08059123 PRK08059, PRK08059, general stress protein 13; Validate 4e-11
COG1098129 COG1098, VacB, Predicted RNA binding protein (contains 5e-11
cd0016465 cd00164, S1_like, S1_like: Ribosomal protein S1-like RN 3e-10
cd0446183 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7 1e-09
cd0569269 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Riboso 2e-09
cd0568479 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-term 7e-09
TIGR03591684 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyl 2e-08
KOG1067760 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyri 3e-08
PRK07252120 PRK07252, PRK07252, hypothetical protein; Provisional 8e-08
COG1185692 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase 9e-08
COG1093269 COG1093, SUI2, Translation initiation factor 2, alpha s 1e-06
PRK03987262 PRK03987, PRK03987, translation initiation factor IF-2 1e-06
cd0447268 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphory 5e-06
PRK05807136 PRK05807, PRK05807, hypothetical protein; Provisional 5e-06
cd0569769 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 i 1e-05
cd0445276 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit 2e-05
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 2e-05
cd0447183 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 3e-05
PLN00207891 PLN00207, PLN00207, polyribonucleotide nucleotidyltrans 4e-05
cd0569870 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5 1e-04
TIGR02696719 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthet 2e-04
cd0569173 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Riboso 0.001
COG0557706 COG0557, VacB, Exoribonuclease R [Transcription] 0.001
cd0569069 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Riboso 5e-16
cd0568972 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Riboso 3e-10
pfam0057574 pfam00575, S1, S1 RNA binding domain 5e-10
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 5e-10
cd0568868 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Riboso 6e-09
cd0570877 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 1e-08
COG2183780 COG2183, Tex, Transcriptional accessory protein [Transc 5e-08
cd0568568 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a 3e-07
PRK11824693 PRK11824, PRK11824, polynucleotide phosphorylase/polyad 2e-06
cd0016465 cd00164, S1_like, S1_like: Ribosomal protein S1-like RN 3e-06
COG1185692 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase 4e-05
TIGR03591684 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyl 3e-04
PRK08059123 PRK08059, PRK08059, general stress protein 13; Validate 4e-04
cd0569269 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Riboso 5e-04
cd0447268 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphory 0.001
cd0569769 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 i 0.001
COG1098129 COG1098, VacB, Predicted RNA binding protein (contains 0.003
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 0.004
cd0446567 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2 2e-14
pfam0057574 pfam00575, S1, S1 RNA binding domain 4e-07
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 0.002
cd0569173 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Riboso 2e-12
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 2e-07
pfam0057574 pfam00575, S1, S1 RNA binding domain 6e-05
PRK06676 390 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 0.001
cd0445276 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit 0.004
KOG1067760 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyri 5e-11
PRK07400318 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed 5e-11
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 9e-11
PRK08582139 PRK08582, PRK08582, hypothetical protein; Provisional 2e-10
cd0568770 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1 8e-09
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 5e-05
pfam0057574 pfam00575, S1, S1 RNA binding domain 8e-05
PRK07400318 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed 2e-06
TIGR00717 516 TIGR00717, rpsA, ribosomal protein S1 4e-05
>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|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|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|180655 PRK06676, 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|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional 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|162009 TIGR00717, rpsA, ribosomal protein S1 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|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|180655 PRK06676, 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|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed 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|36288 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed 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|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>gnl|CDD|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain 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|32366 COG2183, Tex, Transcriptional accessory protein [Transcription] 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|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|88445 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain 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|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|88447 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated 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|88416 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|180268 PRK05807, PRK05807, hypothetical protein; Provisional 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|31290 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional 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|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|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|88452 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
>gnl|CDD|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|181471 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>gnl|CDD|88436 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>gnl|CDD|162678 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|181488 PRK08582, PRK08582, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription] 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|177797 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional 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|88426 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|88462 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
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>gnl|CDD|88430 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain 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|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain 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|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain Back     alignment and domain information
>gnl|CDD|32366 COG2183, Tex, Transcriptional accessory protein [Transcription] 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|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|181215 PRK08059, PRK08059, general stress protein 13; Validated 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|88416 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain 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|88447 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) 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|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase 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|180908 PRK07252, PRK07252, hypothetical protein; Provisional 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|31290 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] 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|88437 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|180268 PRK05807, PRK05807, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|88452 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
>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|162678 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|88436 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>gnl|CDD|177797 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase; Provisional 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|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>gnl|CDD|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|30903 COG0557, VacB, Exoribonuclease R [Transcription] 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|88444 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 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|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain 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|32366 COG2183, Tex, Transcriptional accessory protein [Transcription] 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|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional 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|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated 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|88437 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|88452 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
>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|162678 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|88430 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 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|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) 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|144242 pfam00575, S1, S1 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|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|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] Back     alignment and domain information
>gnl|CDD|180960 PRK07400, PRK07400, 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|181488 PRK08582, PRK08582, hypothetical protein; Provisional 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|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain Back     alignment and domain information
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1 Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 576 30S ribosomal protein S1 [Candidatus Liberibacter asiat
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 100.0
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 100.0
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 100.0
KOG1070 1710 consensus 100.0
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 100.0
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 100.0
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 100.0
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 100.0
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 100.0
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 100.0
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 100.0
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 100.0
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 100.0
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 100.0
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 100.0
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 100.0
PRK07400314 30S ribosomal protein S1; Reviewed 100.0
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 100.0
PRK07400314 30S ribosomal protein S1; Reviewed 100.0
KOG1070 1710 consensus 100.0
PRK08059119 general stress protein 13; Validated 99.9
PRK08059119 general stress protein 13; Validated 99.86
PRK07252120 hypothetical protein; Provisional 99.81
PRK05807136 hypothetical protein; Provisional 99.78
COG1098129 VacB Predicted RNA binding protein (contains ribosomal 99.68
PRK08582139 hypothetical protein; Provisional 99.81
PRK07252120 hypothetical protein; Provisional 99.8
PRK05807136 hypothetical protein; Provisional 99.77
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a tran 99.74
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Hom 99.74
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of transla 99.73
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protei 99.72
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is 99.7
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 do 99.67
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protei 99.67
COG1098129 VacB Predicted RNA binding protein (contains ribosomal 99.67
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a tran 99.66
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protei 99.66
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a transcript 99.65
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protei 99.65
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a tran 99.64
PRK03987262 translation initiation factor IF-2 subunit alpha; Valid 99.62
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. 99.62
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protei 99.62
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 99.61
pfam0057574 S1 S1 RNA binding domain. The S1 domain occurs in a wid 99.61
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-l 99.37
COG1093269 SUI2 Translation initiation factor 2, alpha subunit (eI 99.36
PTZ00248324 eukaryotic translation initiation factor 2 alpha subuni 99.31
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a tran 99.29
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-binding 99.28
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a tran 99.16
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Transcrip 98.64
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans- 98.63
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 98.55
KOG2916304 consensus 98.4
PRK12327353 nusA transcription elongation factor NusA; Provisional 98.13
PRK09202428 nusA transcription elongation factor NusA; Validated 98.05
PRK09521187 exosome complex RNA-binding protein Csl4; Provisional 97.9
PRK12329457 nusA transcription elongation factor NusA; Provisional 97.85
COG1096188 Predicted RNA-binding protein (consists of S1 domain an 97.76
PRK11712489 ribonuclease G; Provisional 97.26
COG1530487 CafA Ribonucleases G and E [Translation, ribosomal stru 95.52
PRK08582139 hypothetical protein; Provisional 99.77
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protei 99.76
PRK03987262 translation initiation factor IF-2 subunit alpha; Valid 99.73
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protei 99.71
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 do 99.7
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans- 99.69
COG1093269 SUI2 Translation initiation factor 2, alpha subunit (eI 99.59
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea 99.36
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 99.27
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 i 99.23
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 i 99.09
PTZ00248324 eukaryotic translation initiation factor 2 alpha subuni 99.06
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans- 98.85
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is 98.54
PRK12328375 nusA transcription elongation factor NusA; Provisional 98.29
PRK12327353 nusA transcription elongation factor NusA; Provisional 98.28
KOG18561299 consensus 98.15
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA 98.04
PRK12329457 nusA transcription elongation factor NusA; Provisional 98.03
PRK09521187 exosome complex RNA-binding protein Csl4; Provisional 97.88
KOG2916304 consensus 97.76
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-l 97.55
KOG3409193 consensus 95.88
CHL0001078 infA translation initiation factor 1 94.51
PRK1244287 translation initiation factor IF-1; Reviewed 94.31
PRK0027672 infA translation initiation factor IF-1; Validated 93.43
cd0445164 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-li 92.46
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1 91.55
TIGR0000869 infA translation initiation factor IF-1; InterPro: IPR0 90.72
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a tran 99.75
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of transla 99.75
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Hom 99.74
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protei 99.73
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is 99.72
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans- 99.71
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a tran 99.68
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protei 99.67
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a transcript 99.66
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a tran 99.65
pfam0057574 S1 S1 RNA binding domain. The S1 domain occurs in a wid 99.63
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 99.63
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protei 99.58
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 99.58
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. 99.57
COG2183780 Tex Transcriptional accessory protein [Transcription] 99.48
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 99.42
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosoma 99.42
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 99.34
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a tran 99.32
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosoma 99.3
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-binding 99.3
TIGR02063755 RNase_R ribonuclease R; InterPro: IPR011805 This family 99.26
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea 99.24
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-l 99.24
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 i 99.11
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 99.11
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 i 99.1
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a tran 99.06
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is 99.0
PRK11642813 exoribonuclease R; Provisional 98.92
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans- 98.91
KOG1067760 consensus 98.9
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans- 98.65
PRK05054644 exoribonuclease II; Provisional 98.5
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-li 98.32
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein (NusA) 98.23
KOG1856 1299 consensus 98.23
COG0557706 VacB Exoribonuclease R [Transcription] 97.88
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-bindi 97.75
TIGR02696725 pppGpp_PNP guanosine pentaphosphate synthetase I/polyri 97.74
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans- 97.36
TIGR00358684 3_prime_RNase VacB and RNase II family 3'-5' exoribonuc 94.21
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 99.63
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 99.57
COG2183780 Tex Transcriptional accessory protein [Transcription] 99.48
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 99.38
TIGR02063755 RNase_R ribonuclease R; InterPro: IPR011805 This family 99.21
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 99.2
PRK11642813 exoribonuclease R; Provisional 98.91
KOG1067760 consensus 98.78
PRK05054644 exoribonuclease II; Provisional 98.48
PRK08563182 DNA-directed RNA polymerase subunit E'; Provisional 98.43
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 98.3
COG0557706 VacB Exoribonuclease R [Transcription] 97.88
TIGR02696725 pppGpp_PNP guanosine pentaphosphate synthetase I/polyri 97.48
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans- 97.21
KOG4078173 consensus 95.58
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 99.56
COG1107 715 Archaea-specific RecJ-like exonuclease, contains DnaJ-t 98.39
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosoma 99.55
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosoma 99.42
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is 98.65
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein (NusA) 98.44
COG1107715 Archaea-specific RecJ-like exonuclease, contains DnaJ-t 97.99
PRK10811 1063 rne ribonuclease E; Reviewed 97.36
pfam10246105 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This i 97.26
COG1530487 CafA Ribonucleases G and E [Translation, ribosomal stru 96.47
TIGR00358 684 3_prime_RNase VacB and RNase II family 3'-5' exoribonuc 93.32
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 99.22
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 99.13
pfam1044772 EXOSC1 Exosome component EXOSC1/CSL4. This family of pr 97.04
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is 98.97
PRK08563182 DNA-directed RNA polymerase subunit E'; Provisional 98.46
PTZ00162170 RNA polymerase II subunit 7; Provisional 98.41
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-li 98.22
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymeras 97.11
, 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 95.81
KOG3298170 consensus 94.89
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Transcrip 98.61
PTZ00162170 RNA polymerase II subunit 7; Provisional 98.31
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymeras 96.56
KOG3298170 consensus 94.69
PRK04163232 exosome complex RNA-binding protein Rrp4; Provisional 98.55
PRK09202428 nusA transcription elongation factor NusA; Validated 98.32
PRK10811 1063 rne ribonuclease E; Reviewed 97.31
TIGR01953366 NusA transcription termination factor NusA; InterPro: I 98.19
PRK04163232 exosome complex RNA-binding protein Rrp4; Provisional 98.17
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins (con 97.73
COG1096188 Predicted RNA-binding protein (consists of S1 domain an 97.64
TIGR01953366 NusA transcription termination factor NusA; InterPro: I 98.18
PRK12328375 nusA transcription elongation factor NusA; Provisional 98.18
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins (con 97.81
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA 97.72
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-bindi 97.71
PRK11712489 ribonuclease G; Provisional 97.65
, 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 96.55
KOG3409193 consensus 96.47
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1070 consensus 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
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed 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
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PRK07899 rpsA 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
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed 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
>PRK06676 rpsA 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
>PRK07400 30S ribosomal protein S1; Reviewed 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
>KOG1070 consensus Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional 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
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PRK05807 hypothetical protein; 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
>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
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>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
>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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) 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
>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
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: 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
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain 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
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain 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
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like 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
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional Back     alignment and domain information
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain 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
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] 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
>TIGR00448 rpoE DNA-directed RNA polymerase; InterPro: IPR004519 DNA-directed RNA polymerases 2 Back     alignment and domain information
>KOG2916 consensus Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional 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
>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