254780788

254780788

transcription elongation factor NusA

GeneID in NCBI database:8209794Locus tag:CLIBASIA_03395
Protein GI in NCBI database:254780788Protein Accession:YP_003065201.1
Gene range:+(471664, 473244)Protein Length:526aa
Gene description:transcription elongation factor NusA
COG prediction:[K] Transcription elongation factor
KEGG prediction:nusA; transcription elongation factor NusA; K02600 N utilization substance protein A
SEED prediction:Transcription termination protein NusA
Pathway involved in KEGG:not defined
Subsystem involved in SEED:NusA-TFII Cluster;
Transcription factors 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------
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS
cccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccccEEEEEccccccEEEEEEEEEEccccccccEEcHHHHHHHccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEccccEEEEEcccEEEEcHHHHccccccccccEEEEEEEEEEEcccccEEEEEEccHHHHHHHHHHcccHHcccEEEEEEEEccccccEEEEEEEccccccccccEEccccHHHHHHHHHHcccEEEEEEccccHHHHHHHHccHHHccEEEEcccccEEEEEEcHHHHHHHHccccHHHHHHHHHcccEEEEEEHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHccccccHHHHHHHHHcccccHHHHHcccHHHHccccccccccHHccccccccccccHHHHHHHHHHHHHHcccccHHHcccccccccc
cccHcHHHcccccccccccccccHHHHHHHHHHHHHHHHHccccccccEEEEccccccccEEEEEEEEEcccccccccEEHHHHHHHccccccccEEEEEccccccccccHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEEcccEEEEEEccEEEEEEHHHcccccccccccEEEEEEEEEEEEccEEEEEEEcccHHHHHHHHHHHcHHHHHccEEEEEEEEEcccEEEEEEEEccccccHHHHHHccccccHHHHHHHccccEEEEEEccccHHHHHHHHcccccccEEEEEccccEEEEEEccccHHHHHcHHHHHHHHHHHHHccEEEEccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcccccHEEEEEccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHcccccHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHcccccccccccccccccHHHHHHHHHHHHHHcccccHHHHccccccccc
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRveinpetgdiSLFRLLEVVEEVENYTCQISLkvardrdpsidiggvvsdplppmdfgRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVdlgnsdgvirrdetisrenlrpgdrvksyiydvrreqrgpqvllsrthpQFMVKLFHMEVPEIYNGIVQVkavsrdpgsraklavfssdssidpvgacvgmrgSRVQAVVTELRDekidivvwspdsatFVINALRPAIVTKVvldedvgrievivpkeqLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISeiasiegfdeeTAVEIQGRAREYLEGIDITLQKKIRELGvseelcsipgidsKIKVALgengiktmedlagcsvddllgwsenkggniekfdgflsslgtpkdqVESMIIHARYKMGWIEKEKVADEEVQDAS
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQIslkvardrdpsiDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKvreaerdrqylefkdkvgeiisgtvkrveygnvivdlgnsdgvirrdetisrenlrpgdrvksyiydvrreqrgpqvllsrTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKlavfssdssidpvGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVldedvgrievivpkeqlslaigrrgqnvrlasqltgwtidIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISeiasiegfdeetAVEIQGRAREYLEGIDITLQKKIRELGVseelcsipgidsKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLevveeveNYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWtidiiteeedSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS
****NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDII*******************FMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI****************LCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWI**************
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKV*********
*VSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKV*********
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MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS
MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGNIEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDAS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target526 transcription elongation factor NusA [Candidatus Liberi
315122010536 transcription elongation factor NusA [Candidatus Liberi 1 0.0
150398625552 transcription elongation factor NusA [Sinorhizobium med 1 0.0
15963990542 transcription elongation factor NusA [Sinorhizobium mel 1 0.0
227824069536 transcription elongation factor NusA [Sinorhizobium fre 1 0.0
222084328534 N-utilization substance protein A [Agrobacterium radiob 1 0.0
86355778533 transcription elongation factor NusA [Rhizobium etli CF 1 0.0
325291533538 transcription elongation factor NusA [Agrobacterium sp. 1 0.0
209551640535 transcription elongation factor NusA [Rhizobium legumin 1 0.0
116249893533 transcription elongation factor NusA [Rhizobium legumin 1 0.0
241207071533 transcription elongation factor NusA [Rhizobium legumin 1 0.0
>gi|315122010|ref|YP_004062499.1| transcription elongation factor NusA [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 536 Back     alignment and organism information
 Score =  910 bits (2353), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 449/525 (85%), Positives = 490/525 (93%)

Query: 1   MVSANRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDI 60
           +VSANRLELLQIADAVA EKSIDRDVVLSVMA+SIQKAARSLYGT+SDIRVEIN ETG+I
Sbjct: 2   VVSANRLELLQIADAVACEKSIDRDVVLSVMAESIQKAARSLYGTLSDIRVEINRETGNI 61

Query: 61  SLFRLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQ 120
           S+ R LEVVEEVENY CQISL++ARDRDP+I+IG V+ DPLPP+DFGRVAVQSAKQVIIQ
Sbjct: 62  SICRSLEVVEEVENYACQISLQLARDRDPNINIGDVLFDPLPPIDFGRVAVQSAKQVIIQ 121

Query: 121 KVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGD 180
           KVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLG+SDGVIRRDETISRENLR GD
Sbjct: 122 KVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGHSDGVIRRDETISRENLRLGD 181

Query: 181 RVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLA 240
           RV+SYIYDVRREQRGPQVLLSRTHPQFMVKLF++EVPEIYNGIVQ+KAVSRDPGSRAKLA
Sbjct: 182 RVRSYIYDVRREQRGPQVLLSRTHPQFMVKLFYLEVPEIYNGIVQIKAVSRDPGSRAKLA 241

Query: 241 VFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV 300
           VFSSDSSIDPVGACVGMRGSRVQAVV ELRDEKIDIVVWSPD ATFVIN+LRPAIVTKVV
Sbjct: 242 VFSSDSSIDPVGACVGMRGSRVQAVVGELRDEKIDIVVWSPDPATFVINSLRPAIVTKVV 301

Query: 301 LDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQ 360
           LDEDVGRIEV+VPK+QLSLAIGRRGQNVRLASQLTGW IDI+TEEEDS+NRQK FNERTQ
Sbjct: 302 LDEDVGRIEVVVPKDQLSLAIGRRGQNVRLASQLTGWAIDIVTEEEDSVNRQKHFNERTQ 361

Query: 361 FFMQAINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGI 420
           FFMQAINVDEII HLL AEGF+D+EELACVK+SEIASIEGFDEETA EIQGRAREY+EG+
Sbjct: 362 FFMQAINVDEIIGHLLAAEGFSDIEELACVKLSEIASIEGFDEETASEIQGRAREYMEGL 421

Query: 421 DITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENKGGN 480
           ++  ++KI+ LGVSEEL SIPG++++I VALGENGIKTMEDLAGCSVDDLLGW E K G 
Sbjct: 422 EVARREKIKGLGVSEELFSIPGMNTEIGVALGENGIKTMEDLAGCSVDDLLGWGEVKNGK 481

Query: 481 IEKFDGFLSSLGTPKDQVESMIIHARYKMGWIEKEKVADEEVQDA 525
           +E F+GFLS LG  K+Q ESMIIHARY +GWI +E +ADE V  A
Sbjct: 482 VENFEGFLSQLGVLKEQAESMIIHARYHLGWIVREDIADESVDCA 526


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|150398625|ref|YP_001329092.1| transcription elongation factor NusA [Sinorhizobium medicae WSM419] Length = 552 Back     alignment and organism information
>gi|15963990|ref|NP_384343.1| transcription elongation factor NusA [Sinorhizobium meliloti 1021] Length = 542 Back     alignment and organism information
>gi|227824069|ref|YP_002828042.1| transcription elongation factor NusA [Sinorhizobium fredii NGR234] Length = 536 Back     alignment and organism information
>gi|222084328|ref|YP_002542857.1| N-utilization substance protein A [Agrobacterium radiobacter K84] Length = 534 Back     alignment and organism information
>gi|86355778|ref|YP_467670.1| transcription elongation factor NusA [Rhizobium etli CFN 42] Length = 533 Back     alignment and organism information
>gi|325291533|ref|YP_004277397.1| transcription elongation factor NusA [Agrobacterium sp. H13-3] Length = 538 Back     alignment and organism information
>gi|209551640|ref|YP_002283557.1| transcription elongation factor NusA [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 535 Back     alignment and organism information
>gi|116249893|ref|YP_765731.1| transcription elongation factor NusA [Rhizobium leguminosarum bv. viciae 3841] Length = 533 Back     alignment and organism information
>gi|241207071|ref|YP_002978167.1| transcription elongation factor NusA [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 533 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
Target526 transcription elongation factor NusA [Candidatus Liberi
PRK09202470 PRK09202, nusA, transcription elongation factor NusA; V 1e-180
TIGR01953341 TIGR01953, NusA, transcription termination factor NusA 1e-123
PRK12327362 PRK12327, nusA, transcription elongation factor NusA; P 1e-107
PRK12328374 PRK12328, nusA, transcription elongation factor NusA; P 7e-61
PRK12329449 PRK12329, nusA, transcription elongation factor NusA; P 5e-58
pfam08529122 pfam08529, NusA_N, NusA N-terminal domain 1e-38
cd0445567 cd04455, S1_NusA, S1_NusA: N-utilizing substance A prot 4e-19
pfam0057574 pfam00575, S1, S1 RNA binding domain 1e-04
PRK00087647 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphos 6e-04
smart0031672 smart00316, S1, Ribosomal protein S1-like RNA-binding d 0.001
PRK06299 565 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed 0.001
cd0213461 cd02134, NusA_KH, NusA_K homology RNA-binding domain (K 8e-12
cd0240968 cd02409, KH-II, KH-II (K homology RNA-binding domain, t 2e-05
smart0032269 smart00322, KH, K homology RNA-binding domain 0.001
COG1782 637 COG1782, COG1782, Predicted metal-dependent RNase, cons 0.002
TIGR0195450 TIGR01954, nusA_Cterm_rpt, transcription termination fa 7e-11
TIGR01952141 TIGR01952, nusA_arch, NusA family KH domain protein, ar 4e-05
PRK08406140 PRK08406, PRK08406, transcription elongation factor Nus 6e-05
COG0195190 COG0195, NusA, Transcription elongation factor [Transcr 3e-46
>gnl|CDD|181696 PRK09202, nusA, transcription elongation factor NusA; Validated Back     alignment and domain information
>gnl|CDD|162623 TIGR01953, NusA, transcription termination factor NusA Back     alignment and domain information
>gnl|CDD|183442 PRK12327, nusA, transcription elongation factor NusA; Provisional Back     alignment and domain information
>gnl|CDD|183443 PRK12328, nusA, transcription elongation factor NusA; Provisional Back     alignment and domain information
>gnl|CDD|183444 PRK12329, nusA, transcription elongation factor NusA; Provisional Back     alignment and domain information
>gnl|CDD|149546 pfam08529, NusA_N, NusA N-terminal domain Back     alignment and domain information
>gnl|CDD|88421 cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA), 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|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed 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|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>gnl|CDD|48407 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information
>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain Back     alignment and domain information
>gnl|CDD|31968 COG1782, COG1782, Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only] Back     alignment and domain information
>gnl|CDD|131009 TIGR01954, nusA_Cterm_rpt, transcription termination factor NusA, C-terminal duplication Back     alignment and domain information
>gnl|CDD|162622 TIGR01952, nusA_arch, NusA family KH domain protein, archaeal Back     alignment and domain information
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>gnl|CDD|30544 COG0195, NusA, Transcription elongation factor [Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 526 transcription elongation factor NusA [Candidatus Liberi
PRK09202428 nusA transcription elongation factor NusA; Validated 100.0
PRK12329457 nusA transcription elongation factor NusA; Provisional 100.0
PRK12327353 nusA transcription elongation factor NusA; Provisional 100.0
PRK12328375 nusA transcription elongation factor NusA; Provisional 100.0
TIGR01953366 NusA transcription termination factor NusA; InterPro: I 100.0
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 98.61
COG1855604 ATPase (PilT family) [General function prediction only] 93.66
COG0195190 NusA Transcription elongation factor [Transcription] 100.0
PRK11712489 ribonuclease G; Provisional 95.67
pfam08529122 NusA_N NusA N-terminal domain. This domain represents t 99.97
PRK08406142 transcription elongation factor NusA-like protein; Vali 99.92
cd02410145 archeal_CPSF_KH The archaeal cleavage and polyadenylati 94.02
KOG2190485 consensus 91.4
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein (NusA) 99.78
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 98.76
PRK07400314 30S ribosomal protein S1; Reviewed 98.59
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosoma 98.53
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 98.46
pfam0057574 S1 S1 RNA binding domain. The S1 domain occurs in a wid 98.38
PRK07400314 30S ribosomal protein S1; Reviewed 98.18
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 98.1
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.09
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protei 98.07
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Hom 98.05
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.01
PRK08059119 general stress protein 13; Validated 97.91
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans- 97.9
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is 97.89
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protei 97.81
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a transcript 97.8
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosoma 97.76
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of transla 97.76
PRK07252120 hypothetical protein; Provisional 97.7
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPa 97.69
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a tran 97.69
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protei 97.44
PRK03987262 translation initiation factor IF-2 subunit alpha; Valid 97.39
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-binding 97.38
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a tran 97.33
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protei 97.3
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protei 97.24
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a tran 97.17
PRK05807136 hypothetical protein; Provisional 97.17
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is 97.02
PRK08582139 hypothetical protein; Provisional 96.98
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RN 96.88
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 do 96.73
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea 96.7
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-l 96.69
PTZ00162170 RNA polymerase II subunit 7; Provisional 96.67
PRK08563182 DNA-directed RNA polymerase subunit E'; Provisional 96.62
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Transcrip 96.43
COG1093269 SUI2 Translation initiation factor 2, alpha subunit (eI 96.42
PRK05054 644 exoribonuclease II; Provisional 96.36
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-li 96.21
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 i 96.18
PRK04163232 exosome complex RNA-binding protein Rrp4; Provisional 96.14
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-bindi 96.13
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA 96.05
PTZ00248324 eukaryotic translation initiation factor 2 alpha subuni 95.82
pfam10246105 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This i 95.52
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-l 95.43
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is 95.43
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. 95.23
COG1097239 RRP4 RNA-binding protein Rrp4 and related proteins (con 94.89
KOG1070 1710 consensus 94.8
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a tran 94.38
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 i 94.14
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a tran 93.87
PRK09521187 exosome complex RNA-binding protein Csl4; Provisional 93.83
pfam1044772 EXOSC1 Exosome component EXOSC1/CSL4. This family of pr 93.83
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans- 93.6
KOG3409193 consensus 92.58
KOG3298170 consensus 92.28
COG1530487 CafA Ribonucleases G and E [Translation, ribosomal stru 92.04
COG1096188 Predicted RNA-binding protein (consists of S1 domain an 91.22
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). NusA i 99.65
cd0240968 KH-II KH-II (K homology RNA-binding domain, type II). K 97.89
PRK08406142 transcription elongation factor NusA-like protein; Vali 97.26
PRK11824694 polynucleotide phosphorylase/polyadenylase; Provisional 95.79
smart0032269 KH K homology RNA-binding domain. 95.39
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransferase. 94.84
KOG2193584 consensus 92.54
cd0239665 PCBP_like_KH K homology RNA-binding domain, PCBP_like. 91.99
TIGR0195452 nusA_Cterm_rpt transcription termination factor NusA, C 99.13
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 97.87
PRK04301 318 radA DNA repair and recombination protein RadA; Validat 97.4
PRK01172674 ski2-like helicase; Provisional 97.07
PTZ00035 350 Rad51; Provisional 96.7
PRK13766764 Hef nuclease; Provisional 95.78
PRK00254717 ski2-like helicase; Provisional 95.63
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 95.49
TIGR03491457 RecB family nuclease, putative, TM0106 family. Members 95.25
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 94.95
PRK02362736 ski2-like helicase; Provisional 94.55
PRK12766238 50S ribosomal protein L32e; Provisional 93.25
pfam0311862 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C t 92.6
COG2251474 Predicted nuclease (RecB family) [General function pred 92.56
TIGR0195452 nusA_Cterm_rpt transcription termination factor NusA, C 98.6
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 97.69
PTZ00035 350 Rad51; Provisional 93.0
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 98.42
PRK06299556 rpsA 30S ribosomal protein S1; Reviewed 98.37
PRK07899484 rpsA 30S ribosomal protein S1; Reviewed 98.36
PRK13806489 rpsA 30S ribosomal protein S1; Provisional 98.28
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 98.03
COG0539541 RpsA Ribosomal protein S1 [Translation, ribosomal struc 97.89
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S1; Pr 97.6
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 95.86
COG2996287 Predicted RNA-bindining protein (contains S1 and HTH do 92.24
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 98.33
PRK00087670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 R 98.21
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 98.09
TIGR00717534 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosome 97.89
TIGR03675630 arCOG00543 arCOG01782 universal archaeal KH-domain/beta 91.47
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 97.53
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 92.96
TIGR02239 317 recomb_RAD51 DNA repair protein RAD51; InterPro: IPR011 91.8
PRK01172674 ski2-like helicase; Provisional 97.17
PRK00254717 ski2-like helicase; Provisional 96.5
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 96.34
TIGR00575 706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 95.79
PRK02362736 ski2-like helicase; Provisional 94.96
PRK04301318 radA DNA repair and recombination protein RadA; Validat 96.89
PRK11642 813 exoribonuclease R; Provisional 95.92
smart00483334 POLXc DNA polymerase X family. includes vertebrate poly 93.91
PRK09202428 nusA transcription elongation factor NusA; Validated 96.71
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 96.24
cd0213461 NusA_KH NusA_K homology RNA-binding domain (KH). NusA i 95.9
TIGR02063755 RNase_R ribonuclease R; InterPro: IPR011805 This family 95.89
PRK06418167 transcription elongation factor NusA-like protein; Vali 95.54
PRK13764605 ATPase; Provisional 92.83
PRK08609 570 hypothetical protein; Provisional 94.36
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 93.77
COG2183 780 Tex Transcriptional accessory protein [Transcription] 94.24
PRK12704 455 phosphodiesterase; Provisional 93.52
PRK12705 485 hypothetical protein; Provisional 92.99
TIGR03319 514 YmdA_YtgF conserved hypothetical protein YmdA/YtgF. 92.38
PRK10811 1063 rne ribonuclease E; Reviewed 93.44
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (polynucl 92.23
TIGR03491 457 RecB family nuclease, putative, TM0106 family. Members 91.69
cd03586337 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of 91.11
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional 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
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>COG1855 ATPase (PilT family) [General function prediction only] Back     alignment and domain information
>COG0195 NusA Transcription elongation factor [Transcription] Back     alignment and domain information
>PRK11712 ribonuclease G; Provisional Back     alignment and domain information
>pfam08529 NusA_N NusA N-terminal domain Back     alignment and domain information
>PRK08406 transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH) Back     alignment and domain information
>KOG2190 consensus 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
>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
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>pfam00575 S1 S1 RNA binding domain Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>smart00316 S1 Ribosomal protein 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
>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
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK08059 general stress protein 13; Validated 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
>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
>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
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain 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
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>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
>PRK05807 hypothetical protein; Provisional 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
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain 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
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>PTZ00162 RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] 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
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain 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
>PRK04163 exosome complex RNA-binding protein Rrp4; 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
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 alpha subunit; Provisional Back     alignment and domain information
>pfam10246 MRP-S35 Mitochondrial ribosomal protein MRP-S35 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
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain 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
>KOG1070 consensus 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
>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
>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
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4 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
>KOG3409 consensus Back     alignment and domain information
>KOG3298 consensus Back     alignment and domain information
>COG1530 CafA Ribonucleases G and E [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
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information
>PRK08406 transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>smart00322 KH K homology RNA-binding domain Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>KOG2193 consensus Back     alignment and domain information
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like Back     alignment and domain information
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>PTZ00035 Rad51; Provisional Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain Back     alignment and domain information
>COG2251 Predicted nuclease (RecB family) [General function prediction only] Back     alignment and domain information
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>PTZ00035 Rad51; Provisional 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
>PRK07899 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
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] 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
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR02239 recomb_RAD51 DNA repair protein RAD51; InterPro: IPR011941 Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>PRK11642 exoribonuclease R; Provisional Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH) Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805 This family consists of an exoribonuclease, ribonuclease R, also called VacB Back     alignment and domain information
>PRK06418 transcription elongation factor NusA-like protein; Validated Back     alignment and domain information
>PRK13764 ATPase; Provisional Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PRK12704 phosphodiesterase; Provisional Back     alignment and domain information
>PRK12705 hypothetical protein; Provisional Back     alignment and domain information
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF Back     alignment and domain information
>PRK10811 rne ribonuclease E; Reviewed Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target526 transcription elongation factor NusA [Candidatus Liberi
1l2f_A369 Crystal Structure Of Nusa From Thermotoga Maritima: 1e-93
1hh2_P344 Crystal Structure Of Nusa From Thermotoga Maritima 3e-92
1k0r_A366 Crystal Structure Of Mycobacterium Tuberculosis Nus 2e-66
2asb_A251 Structure Of A Mycobacterium Tuberculosis Nusa-Rna 4e-46
2kwp_A129 Solution Structure Of The Aminoterminal Domain Of E 3e-34
2jzb_B74 Solution Structure Of The Complex Between E.Coli Nu 1e-14
1wcn_A70 Nmr Structure Of The Carboxyterminal Domains Of Esc 2e-13
1wcl_A76 Nmr Structure Of The Carboxyterminal Domains Of Esc 2e-04
1u9l_A70 Structural Basis For A Nusa- Protein N Interaction 0.002
>gi|37926540|pdb|1L2F|A Chain A, Crystal Structure Of Nusa From Thermotoga Maritima: A Structure-Based Role Of The N-Terminal Domain Length = 369 Back     alignment and structure
 Score =  348 bits (894), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 140/336 (41%), Positives = 223/336 (66%), Gaps = 1/336 (0%)

Query: 9   LLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEV 68
           LL+  D +  EK I ++ V+ ++  ++  A R  +G   ++ V I+  TG+I +++LLEV
Sbjct: 30  LLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEV 89

Query: 69  VEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERD 128
           VEEVE+   QISL+ A+  DP  ++G +V   L   +FGR+A Q+AKQV+IQ++RE E++
Sbjct: 90  VEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKE 149

Query: 129 RQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIYD 188
           +Q+ ++ +  G + +  V RV      + +G  +  + + E I  E ++ GD VK YI D
Sbjct: 150 KQFEKYSELKGTVTTAEVIRVXGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYIID 209

Query: 189 VRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSI 248
           V +  +GP++L+SR  P+F++ L  +E+PE+ NGIV++KA++R+PG R K+AV S+D ++
Sbjct: 210 VVKTTKGPKILVSRRVPEFVIGLXKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDPNV 269

Query: 249 DPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVL-DEDVGR 307
           DP+GAC+G  GSR+ A++ EL+ EK+D++ WS D    + NAL PA V +V + D++   
Sbjct: 270 DPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKA 329

Query: 308 IEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIIT 343
             V+VP  QLSLAIG+ GQN RLA++LTGW IDI  
Sbjct: 330 ARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKP 365


gi|16975175|pdb|1HH2|P Chain P, Crystal Structure Of Nusa From Thermotoga Maritima Length = 344 Back     alignment and structure
>gi|18158875|pdb|1K0R|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Nusa Length = 366 Back     alignment and structure
>gi|82407871|pdb|2ASB|A Chain A, Structure Of A Mycobacterium Tuberculosis Nusa-Rna Complex Length = 251 Back     alignment and structure
>gi|300508327|pdb|2KWP|A Chain A, Solution Structure Of The Aminoterminal Domain Of E. Coli Nusa Length = 129 Back     alignment and structure
>gi|228311785|pdb|2JZB|B Chain B, Solution Structure Of The Complex Between E.Coli Nusa-Ar2 And Rnap-Actd Length = 74 Back     alignment and structure
>gi|159163265|pdb|1WCN|A Chain A, Nmr Structure Of The Carboxyterminal Domains Of Escherichia Coli Nusa Length = 70 Back     alignment and structure
>gi|159163264|pdb|1WCL|A Chain A, Nmr Structure Of The Carboxyterminal Domains Of Escherichia Coli Nusa Length = 76 Back     alignment and structure
>gi|52696033|pdb|1U9L|A Chain A, Structural Basis For A Nusa- Protein N Interaction Length = 70 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target526 transcription elongation factor NusA [Candidatus Liberi
1hh2_P344 NUSA, N utilization substance protein A; transcription 1e-116
1k0r_A366 NUSA; two component arrangement, S1 domain, two K-homol 1e-106
2asb_A251 Transcription elongation protein NUSA; protein-RNA comp 2e-69
2kwp_A129 Transcription elongation protein NUSA; NMR {Escherichia 2e-33
2cxc_A144 NUSA; transcription termination, RNA binding protein, K 3e-19
2cxc_A144 NUSA; transcription termination, RNA binding protein, K 1e-05
2xr1_A 640 Cleavage and polyadenylation specificity factor 1 subun 0.002
1u9l_A70 Transcription elongation protein NUSA; escherichia coli 8e-17
1wcn_A70 Transcription elongation protein NUSA; RNA-binding prot 7e-08
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Length = 344 Back     alignment and structure
 Score =  412 bits (1061), Expect = e-116
 Identities = 141/341 (41%), Positives = 225/341 (65%), Gaps = 1/341 (0%)

Query: 7   LELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLL 66
           + LL+  D +  EK I ++ V+ ++  ++  A R  +G   ++ V I+  TG+I +++LL
Sbjct: 3   IGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLL 62

Query: 67  EVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAE 126
           EVVEEVE+   QISL+ A+  DP  ++G +V   L   +FGR+A Q+AKQV+IQ++RE E
Sbjct: 63  EVVEEVEDPATQISLEEAKKIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELE 122

Query: 127 RDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYI 186
           +++Q+ ++ +  G + +  V RV      + +G  +  + + E I  E ++ GD VK YI
Sbjct: 123 KEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRLPKKEWIPGEEIKAGDLVKVYI 182

Query: 187 YDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDS 246
            DV +  +GP++L+SR  P+F++ L  +E+PE+ NGIV++KA++R+PG R K+AV S+D 
Sbjct: 183 IDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASNDP 242

Query: 247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDV 305
           ++DP+GAC+G  GSR+ A++ EL+ EK+D++ WS D    + NAL PA V +V +LD++ 
Sbjct: 243 NVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKEN 302

Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346
               V+VP  QLSLAIG+ GQN RLA++LTGW IDI     
Sbjct: 303 KAARVLVPPTQLSLAIGKGGQNARLAAKLTGWKIDIKPIMN 343


>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 Length = 366 Back     alignment and structure
>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A Length = 251 Back     alignment and structure
>2kwp_A Transcription elongation protein NUSA; NMR {Escherichia coli} Length = 129 Back     alignment and structure
>2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A Length = 144 Back     alignment and structure
>2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A Length = 144 Back     alignment and structure
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit; hydrolase, metallo-beta-lactamase, beta-CAsp, RNA processing; 2.59A {Methanosarcina mazei} Length = 640 Back     alignment and structure
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Length = 70 Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Length = 70 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target526 transcription elongation factor NusA [Candidatus Liberi
1hh2_P344 NUSA, N utilization substance protein A; transcription 100.0
1k0r_A366 NUSA; two component arrangement, S1 domain, two K-homol 100.0
2asb_A251 Transcription elongation protein NUSA; protein-RNA comp 100.0
2kwp_A129 Transcription elongation protein NUSA; NMR {Escherichia 100.0
1wcn_A70 Transcription elongation protein NUSA; RNA-binding prot 99.64
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 96.88
1u9l_A70 Transcription elongation protein NUSA; escherichia coli 96.3
3lda_A 400 DNA repair protein RAD51; DNA binding protein, ATP-bind 96.24
1b22_A114 DNA repair protein RAD51; DNA binding, riken structural 95.94
2va8_A715 SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP 95.17
2cxc_A144 NUSA; transcription termination, RNA binding protein, K 99.63
1u9l_A70 Transcription elongation protein NUSA; escherichia coli 99.47
1pzn_A 349 RAD51, DNA repair and recombination protein RAD51, RADA 98.28
1b22_A114 DNA repair protein RAD51; DNA binding, riken structural 97.59
2z43_A 324 DNA repair and recombination protein RADA; archaea, fil 97.38
2i1q_A 322 DNA repair and recombination protein RADA; ATPase, reco 97.15
1wcn_A70 Transcription elongation protein NUSA; RNA-binding prot 97.14
3lda_A 400 DNA repair protein RAD51; DNA binding protein, ATP-bind 96.6
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 96.43
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 95.73
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 95.23
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 94.92
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein-prot 94.72
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 94.65
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 94.37
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial tran 94.28
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacterial tr 94.25
1coo_A98 RNA polymerase alpha subunit; transcription regulation, 94.0
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 93.08
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 92.87
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 92.86
1v5w_A 343 DMC1, meiotic recombination protein DMC1/LIM15 homolog; 92.67
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 92.07
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structural ge 98.31
1kl9_A182 Eukaryotic translation initiation factor 2 subunit 1; O 98.09
2a19_A175 EIF-2- alpha, eukaryotic translation initiation factor 98.07
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stress res 98.02
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zinc, zi 98.01
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprotein, 97.99
1q8k_A308 Eukaryotic translation initiation factor 2 subunit 1; N 97.99
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, phospho 97.98
3aev_A275 Translation initiation factor 2 subunit alpha; proteins 97.95
3cw2_C266 Translation initiation factor 2 subunit alpha; AIF2, in 97.74
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, struct 97.7
3go5_A285 Multidomain protein with S1 RNA-binding domains; joint 97.5
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, st 97.29
1go3_E187 DNA-directed RNA polymerase subunit E; transferase, tra 97.26
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa polype 97.25
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa polyp 97.07
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypeptide; 96.96
2waq_E180 DNA-directed RNA polymerase RPO7 subunit; multi-subunit 96.86
2je6_I251 RRP4, exosome complex RNA-binding protein 1; nuclease, 96.84
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; transcript 96.3
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SC 96.15
2nn6_G289 Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL 96.13
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding protein, 96.07
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, RNA, 95.98
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypeptide; 94.83
2rf4_A214 DNA-directed RNA polymerase I subunit RPA4; transferase 94.45
2nn6_H308 Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, 94.03
2cxc_A144 NUSA; transcription termination, RNA binding protein, K 97.66
3go5_A285 Multidomain protein with S1 RNA-binding domains; joint 97.39
2id0_A 644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA 94.21
1pzn_A 349 RAD51, DNA repair and recombination protein RAD51, RADA 97.38
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 97.37
2z0s_A235 Probable exosome complex RNA-binding protein 1; alpha/b 97.18
2ba0_A229 Archeal exosome RNA binding protein RRP4; RNAse PH, RNA 96.39
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 96.85
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-helix, b 91.12
3bzc_A 785 TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, 96.83
2jvz_A164 KH type-splicing, FAR upstream element-binding protein 96.62
2anr_A178 Neuro-oncological ventral antigen 1; protein-RNA comple 96.57
2jzx_A160 Poly(RC)-binding protein 2; PCBP2, KH domains, RNA bind 96.2
1j4w_A174 FUSE binding protein; single-stranded DNA binding prote 96.08
3krm_A163 Insulin-like growth factor 2 mRNA-binding protein 1; KH 95.58
2qnd_A144 FMR1 protein; KH domain, eukaryotic KH domains, tandem 95.53
2e3u_A219 PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RN 94.5
1tua_A191 Hypothetical protein APE0754; structural genomics, prot 94.12
2i1q_A 322 DNA repair and recombination protein RADA; ATPase, reco 96.2
2z43_A 324 DNA repair and recombination protein RADA; archaea, fil 95.66
2bx2_L517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA 96.02
3af5_A651 Putative uncharacterized protein PH1404; archaeal CPSF, 94.89
2fmp_A335 DNA polymerase beta; nucleotidyl transferase, transfera 94.58
2ihm_A360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 93.38
1dtj_A76 RNA-binding neurooncological ventral antigen 2; KH doma 92.91
1zzk_A82 Heterogeneous nuclear ribonucleoprotein K; KH domian, a 92.54
2bcq_A335 DNA polymerase lambda; misalignment, extrahelical, muta 92.43
2p2r_A76 Poly(RC)-binding protein 2; protein-DNA complex, RNA an 92.41
2va8_A 715 SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP 92.38
2opv_A85 KHSRP protein; KH domain, RNA binding protein, KSRP; NM 92.31
1wvn_A82 Poly(RC)-binding protein 1; KH domain, RNA binding doma 91.85
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA 91.38
1ec6_A87 RNA-binding protein NOVA-2; KH domain, alpha-beta fold, 91.21
1x4m_A94 FAR upstream element binding protein 1; KH domain, stru 90.93
2hh2_A107 KH-type splicing regulatory protein; KH-RNA binding dom 90.8
2hh3_A106 KH-type splicing regulatory protein; KH-RNA binding dom 90.53
2w9m_A578 Polymerase X; SAXS, DNA repair, DNA polymerase, DNA rep 94.27
1jms_A 381 Terminal deoxynucleotidyltransferase; polymerase; 2.36A 93.72
2xr1_A640 Cleavage and polyadenylation specificity factor 1 subun 90.81
2vnu_D 760 Exosome complex exonuclease RRP44; rRNA processing, RNA 90.63
>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A Back     alignment and structure
Probab=100.00  E-value=0  Score=919.56  Aligned_cols=342  Identities=41%  Similarity=0.720  Sum_probs=336.3

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCEEEEEEEEEEECCCCCCCCEECHHHHH
Q ss_conf             89999999999862399999999999999999996136874535999749988399999988517677875323489998
Q gi|254780788|r    6 RLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEVVEEVENYTCQISLKVAR   85 (526)
Q Consensus         6 ~~ell~vie~va~EK~I~~e~i~~aie~Al~~a~kK~~~~~~~i~V~iD~~tG~i~i~~~~~VVedved~~~eI~l~~A~   85 (526)
                      |.+|+.+++++|+||||+++.+++|+|+||.+||+|+||++.+++|.||++||++++|+.|.||++++|+..||+|++|+
T Consensus         2 n~ell~al~~ia~EKgI~~e~vi~aie~Al~~A~kK~~g~~~~i~V~ID~~tGei~v~~~k~VVeev~d~~~eI~l~eAk   81 (344)
T 1hh2_P            2 NIGLLEALDQLEEEKGISKEEVIPILEKALVSAYRKNFGNSKNVEVVIDRNTGNIKVYQLLEVVEEVEDPATQISLEEAK   81 (344)
T ss_dssp             CCSSCSSTTTTSSSSCCCHHHHHHHHHHHHHHHHHTTTCSSSCEEEECCSTTCCCEEEEEEEEESSCSCTTSCEEHHHHH
T ss_pred             CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCCCHHHHHHHH
T ss_conf             88999999999987297999999999999999996543996857999988998699999988616777864110277766


Q ss_pred             HHCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCEEEE
Q ss_conf             62889864737998508456207999999999999999999887799998520838999998405763899957935874
Q gi|254780788|r   86 DRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI  165 (526)
Q Consensus        86 ~~~~~~~iGD~i~~~i~~~~fgRiaAq~AKQvI~QkireaEr~~i~~ef~~r~Geiv~G~V~r~e~~~iiVdlg~~ea~L  165 (526)
                      +++|++++||++.++++|.+|||+|||+|||+|.||||++||+.+|++|++|+|+||+|+|+|+++++++||+|+++|+|
T Consensus        82 ~i~~~~~iGD~i~~~i~~~~fgRiaaqtAKQvi~QkIre~Ere~i~~ef~~k~GeIVtG~V~r~~~~~~~vdlg~~ea~L  161 (344)
T 1hh2_P           82 KIDPLAEVGSIVKKELNVKNFGRIAAQTAKQVLIQRIRELEKEKQFEKYSELKGTVTTAEVIRVMGEWADIRIGKLETRL  161 (344)
T ss_dssp             HHCTTCCTTCEEEEECCCCCSSSCSGGGHHHHHHHHHHHHTTCCSSCCTTCCTTCEEEEEEEEECSSEEEEEETTEEEEE
T ss_pred             HHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCEEEECCCCCCCC
T ss_conf             30113566865886567553078999999999999999999999999999856916888899985240378427645648


Q ss_pred             EHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCEEEEEEEECC
Q ss_conf             47874887511527669999976113587028987159889999999976677755808785663167750349999408
Q gi|254780788|r  166 RRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSD  245 (526)
Q Consensus       166 p~~e~ip~E~~~~Gdrika~i~~V~~~~rgpqi~lSRt~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RsKIAV~s~d  245 (526)
                      |++||+|||+|++|||+||||.+|+.++|||||+||||||+||++||++|||||++|+|+||+|||+||+||||||+|+|
T Consensus       162 P~~eqip~E~y~~Gdrik~~i~~V~~~~kgp~IilSRt~p~~v~~Lfe~EVPEI~dG~VeIk~IaRepG~RtKvAV~s~d  241 (344)
T 1hh2_P          162 PKKEWIPGEEIKAGDLVKVYIIDVVKTTKGPKILVSRRVPEFVIGLMKLEIPEVENGIVEIKAIAREPGVRTKVAVASND  241 (344)
T ss_dssp             EGGGSCTTCCCCTTCEEEEEEEEEEEETTEEEEEEESSSHHHHHHHHHHHCHHHHHSSEEEEEEEEETTTEEEEEEEESS
T ss_pred             CHHHCCCCCCCCCCCEEEEEEEEEEECCCCCEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCEEEEEEECC
T ss_conf             97884975458999989999999875588965899459889999999976589738828999953578772469999348


Q ss_pred             CCCCCEEEEECCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCCCEEE-ECCCCCEEEEEECCCCCCCCCCCC
Q ss_conf             9988127655488621788998627782679955987899999762866542489-875678799998534221102544
Q gi|254780788|r  246 SSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVV-LDEDVGRIEVIVPKEQLSLAIGRR  324 (526)
Q Consensus       246 ~~iDpVGAcVG~rGsRiq~I~~EL~gEkIDii~ws~d~~~fi~nAl~PA~v~~v~-~de~~~~~~v~v~~~qls~AIGk~  324 (526)
                      ++|||||||||+||||||+|++||+|||||||+||+||++||+|||+||+|.+|. +|++++++.|+||++|||+||||+
T Consensus       242 ~~iDpvGa~vG~~G~ri~~i~~el~ge~idii~~s~d~~~fi~nal~Pa~v~~v~~~~~~~~~~~v~v~~~~~~~aIGk~  321 (344)
T 1hh2_P          242 PNVDPIGACIGEGGSRIAAILKELKGEKLDVLKWSDDPKQLIANALAPATVIEVEILDKENKAARVLVPPTQLSLAIGKG  321 (344)
T ss_dssp             TTSCHHHHHHCTTSTTHHHHHHHTTTCEEEEEECCSSHHHHHHHHTCSSCCSEEEEEETTTTEEEEEECTTSHHHHHCGG
T ss_pred             CCCCCCEEEECCCCCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEEEEECCCCCEEEEEECHHHHHHHHCCC
T ss_conf             87551014565897179999998579935899668999999998449563018999738887799998802402641798


Q ss_pred             HHHHHHHHHHHCCEEEEEECCCH
Q ss_conf             27899999861674578552200
Q gi|254780788|r  325 GQNVRLASQLTGWTIDIITEEED  347 (526)
Q Consensus       325 GqNvrLas~Ltg~~idi~~~~~~  347 (526)
                      ||||||||+||||+|||++..+.
T Consensus       322 G~Nv~la~~l~~~~idi~~~~~~  344 (344)
T 1hh2_P          322 GQNARLAAKLTGWKIDIKPIMNL  344 (344)
T ss_dssp             GHHHHHHHHHHSCEEEEEECCCC
T ss_pred             CHHHHHHHHHHCCEEEEEECCCC
T ss_conf             72599999987987522770229



>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 Back     alignment and structure
>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A Back     alignment and structure
>2kwp_A Transcription elongation protein NUSA; NMR {Escherichia coli} Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Back     alignment and structure
>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A* Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-binding, nucleotide-binding; 2.30A {Sulfolobus solfataricus} Back     alignment and structure
>2cxc_A NUSA; transcription termination, RNA binding protein, KH domain, structural genomics, NPPSFA; 2.00A {Aeropyrum pernix K1} PDB: 2cy1_A Back     alignment and structure
>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A Back     alignment and structure
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 Back     alignment and structure