254780275

254780275

SsrA-binding protein

GeneID in NCBI database:8209257Locus tag:CLIBASIA_00800
Protein GI in NCBI database:254780275Protein Accession:YP_003064688.1
Gene range:-(159969, 160448)Protein Length:159aa
Gene description:SsrA-binding protein
COG prediction:[O] tmRNA-binding protein
KEGG prediction:smpB; SsrA-binding protein; K03664 SsrA-binding protein
SEED prediction:tmRNA-binding protein SmpB
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Translation termination factors bacterial;
Heat shock dnaK gene cluster extended
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-------16
MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN
ccccccccccccEEEEcccEEccEEEEEEEEccEEEEccHHHHHHHcccEEEEEEEEEEccEEEEEEccccccccccEEcccccccHHHHccHHHHHHHHHHHHHcccEEEEEEEEEccccEEEEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHcc
cccHHcccccccEEEHcccccccEEEHEEEEEEEEEcccEHHHHHcccccccccEEEEccccEEEEEcccccccccccccccccccHHHHccHHHHHHHHHHHHccccEEEEHHHEEcccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHcc
mslksrgnppkkvvsdnrkarynYHIVRSFEAGIVLTGTEVKSLRVSkvnisdsyatfendeiwltnsyipeylqanrfnhyprrnRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQgkknydkretekkrdWDRQKHRILREHN
mslksrgnppkkvvsdnrkarynyhivrsfeagivltgtevkslrvskvnisdsyatfendeiwlTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYaavrrdgmtlVPMKIYFNAKGLAKIDLAlaqgkknydkretekkrdwdrqkhrilrehn
MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN
****************NRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEK*****R***RI*****
**************SDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK***************RQKHRILREHN
*********PKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRIL****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN
MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN
MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN

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
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
315122834159 SsrA-binding protein [Candidatus Liberibacter solanacea 1 3e-75
159184582160 SsrA-binding protein [Agrobacterium tumefaciens str. C5 1 5e-56
325292405160 SsrA-binding protein [Agrobacterium sp. H13-3] Length = 1 1e-55
153009967158 SsrA-binding protein [Ochrobactrum anthropi ATCC 49188] 1 2e-55
218658904156 SsrA-binding protein [Rhizobium etli IE4771] Length = 1 1 2e-55
116251269151 SsrA-binding protein [Rhizobium leguminosarum bv. vicia 1 2e-55
241203881159 SsrA-binding protein [Rhizobium leguminosarum bv. trifo 1 2e-55
304392078158 SsrA-binding protein [Ahrensia sp. R2A130] Length = 158 1 2e-55
227821395159 SsrA-binding protein [Sinorhizobium fredii NGR234] Leng 1 3e-55
239831483158 SsrA-binding protein [Ochrobactrum intermedium LMG 3301 1 3e-55
>gi|315122834|ref|YP_004063323.1| SsrA-binding protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 159 Back     alignment and organism information
 Score =  284 bits (726), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 138/157 (87%), Positives = 148/157 (94%)

Query: 1   MSLKSRGNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFEN 60
           MS KSR +   KV+S+NRKARYNYHI+RS+EAGIVLTGTEVKSLRVSKVNIS+SYAT EN
Sbjct: 1   MSSKSRSDLSLKVISENRKARYNYHILRSYEAGIVLTGTEVKSLRVSKVNISESYATVEN 60

Query: 61  DEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAK 120
           DEIWLTN+YIPEYLQANRFNH PRRNRKLLLSK+EI RL+AAVRRDGMTLVPMKIYFNAK
Sbjct: 61  DEIWLTNTYIPEYLQANRFNHSPRRNRKLLLSKKEIRRLHAAVRRDGMTLVPMKIYFNAK 120

Query: 121 GLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILRE 157
           GLAKIDLALAQGKKNYDKRETEKKRDWDRQK RI+RE
Sbjct: 121 GLAKIDLALAQGKKNYDKRETEKKRDWDRQKSRIMRE 157


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|159184582|ref|NP_354048.2| SsrA-binding protein [Agrobacterium tumefaciens str. C58] Length = 160 Back     alignment and organism information
>gi|325292405|ref|YP_004278269.1| SsrA-binding protein [Agrobacterium sp. H13-3] Length = 160 Back     alignment and organism information
>gi|153009967|ref|YP_001371182.1| SsrA-binding protein [Ochrobactrum anthropi ATCC 49188] Length = 158 Back     alignment and organism information
>gi|218658904|ref|ZP_03514834.1| SsrA-binding protein [Rhizobium etli IE4771] Length = 156 Back     alignment and organism information
>gi|116251269|ref|YP_767107.1| SsrA-binding protein [Rhizobium leguminosarum bv. viciae 3841] Length = 151 Back     alignment and organism information
>gi|241203881|ref|YP_002974977.1| SsrA-binding protein [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 159 Back     alignment and organism information
>gi|304392078|ref|ZP_07374020.1| SsrA-binding protein [Ahrensia sp. R2A130] Length = 158 Back     alignment and organism information
>gi|227821395|ref|YP_002825365.1| SsrA-binding protein [Sinorhizobium fredii NGR234] Length = 159 Back     alignment and organism information
>gi|239831483|ref|ZP_04679812.1| SsrA-binding protein [Ochrobactrum intermedium LMG 3301] Length = 158 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
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
PRK05422148 PRK05422, smpB, SsrA-binding protein; Validated 3e-63
TIGR00086144 TIGR00086, smpB, SsrA-binding protein 1e-49
COG0691153 COG0691, SmpB, tmRNA-binding protein [Posttranslational 3e-50
pfam0166868 pfam01668, SmpB, SmpB protein 4e-28
>gnl|CDD|180069 PRK05422, smpB, SsrA-binding protein; Validated Back     alignment and domain information
>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein Back     alignment and domain information
>gnl|CDD|31035 COG0691, SmpB, tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>gnl|CDD|145028 pfam01668, SmpB, SmpB protein Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 159 SsrA-binding protein [Candidatus Liberibacter asiaticus
TIGR00086145 smpB SsrA-binding protein; InterPro: IPR000037 In bacte 100.0
COG0691153 SmpB tmRNA-binding protein [Posttranslational modificat 100.0
PRK05422150 smpB SsrA-binding protein; Validated 100.0
pfam0166868 SmpB SmpB protein. 99.96
>TIGR00086 smpB SsrA-binding protein; InterPro: IPR000037 In bacteria, SsrA RNA recognises ribosomes stalled on defective messages and acts as a tRNA and mRNA to mediate the addition of a short peptide tag to the C-terminus of the partially synthesized nascent polypeptide chain Back     alignment and domain information
>COG0691 SmpB tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK05422 smpB SsrA-binding protein; Validated Back     alignment and domain information
>pfam01668 SmpB SmpB protein 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
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
3iyq_B149 Tmrna-Smpb: A Journey To The Center Of The Bacteria 2e-36
1j1h_A144 Solution Structure Of A Tmrna-Binding Protein, Smpb 2e-36
1wjx_A122 Crystal Sturucture Of Tt0801 From Thermus Thermophi 5e-34
2czj_A123 Crystal Structure Of The Trna Domain Of Tmrna From 6e-34
1p6v_A156 Crystal Structure Of The Trna Domain Of Transfer-Me 3e-33
1k8h_A133 Nmr Structure Of Small Protein B (Smpb) From Aquife 5e-29
1zc8_K130 Coordinates Of Tmrna, Smpb, Ef-Tu And H44 Fitted In 2e-27
>gi|309319903|pdb|3IYQ|B Chain B, Tmrna-Smpb: A Journey To The Center Of The Bacterial Ribosome Length = 149 Back     alignment and structure
 Score =  155 bits (392), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 71/139 (51%), Positives = 95/139 (68%)

Query: 14  VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEY 73
           V +NR+AR++Y I+ ++EAGI L GTEVKSLR  KV+ + S+A FE+ E++L N YI  Y
Sbjct: 3   VLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPY 62

Query: 74  LQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK 133
            + +  N  PRR RKLLL K E+ RL   V + G+TLVP+KIYFN +G AK+ L LA+GK
Sbjct: 63  EKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 122

Query: 134 KNYDKRETEKKRDWDRQKH 152
           K Y+KR  +KK    R   
Sbjct: 123 KAYEKRREDKKEAVRRALE 141


gi|28948412|pdb|1J1H|A Chain A, Solution Structure Of A Tmrna-Binding Protein, Smpb, From Thermus Thermophilus Length = 144 Back     alignment and structure
>gi|56966939|pdb|1WJX|A Chain A, Crystal Sturucture Of Tt0801 From Thermus Thermophilus Length = 122 Back     alignment and structure
>gi|118137454|pdb|2CZJ|A Chain A, Crystal Structure Of The Trna Domain Of Tmrna From Thermus Thermophilus Hb8 Length = 123 Back     alignment and structure
>gi|34810651|pdb|1P6V|A Chain A, Crystal Structure Of The Trna Domain Of Transfer-Messenger Rna In Complex With Smpb Length = 156 Back     alignment and structure
>gi|253722947|pdb|1K8H|A Chain A, Nmr Structure Of Small Protein B (Smpb) From Aquifex Aeolicus Length = 133 Back     alignment and structure
>gi|66361446|pdb|1ZC8|K Chain K, Coordinates Of Tmrna, Smpb, Ef-Tu And H44 Fitted Into Cryo- Em Map Of The 70s Ribosome And Tmrna Complex Length = 130 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
1j1h_A144 Small protein B; SMPB, SSRA associated protein, OB fold 3e-49
1p6v_A156 SSRA-binding protein; SMPB, tmRNA, trans-translation, p 2e-44
1wjx_A122 Small protein B, SSRA-binding protein; RNA binding prot 3e-38
>1j1h_A Small protein B; SMPB, SSRA associated protein, OB fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Thermus thermophilus} SCOP: b.111.1.1 Length = 144 Back     alignment and structure
 Score =  189 bits (481), Expect = 3e-49
 Identities = 71/143 (49%), Positives = 96/143 (67%)

Query: 12  KVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIP 71
             V +NR+AR++Y I+ ++EAGI L GTEVKSLR  KV+ + S+A FE+ E++L N YI 
Sbjct: 2   APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIA 61

Query: 72  EYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQ 131
            Y + +  N  PRR RKLLL K E+ RL   V + G+TLVP+KIYFN +G AK+ L LA+
Sbjct: 62  PYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLAR 121

Query: 132 GKKNYDKRETEKKRDWDRQKHRI 154
           GKK Y+KR  +KK    R    +
Sbjct: 122 GKKAYEKRREDKKEAVRRALEEL 144


>1p6v_A SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA complex, RNA binding protein/RNA complex; 3.20A {Aquifex aeolicus} SCOP: b.111.1.1 PDB: 2ob7_B 1k8h_A 1zc8_K Length = 156 Back     alignment and structure
>1wjx_A Small protein B, SSRA-binding protein; RNA binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.70A {Thermus thermophilus} SCOP: b.111.1.1 PDB: 2czj_A* Length = 122 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
1p6v_A156 SSRA-binding protein; SMPB, tmRNA, trans-translation, p 100.0
1j1h_A144 Small protein B; SMPB, SSRA associated protein, OB fold 100.0
1wjx_A122 Small protein B, SSRA-binding protein; RNA binding prot 100.0
>1p6v_A SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA complex, RNA binding protein/RNA complex; 3.20A {Aquifex aeolicus} SCOP: b.111.1.1 PDB: 2ob7_B 1k8h_A 1zc8_K Back     alignment and structure
Probab=100.00  E-value=0  Score=420.66  Aligned_cols=148  Identities=44%  Similarity=0.728  Sum_probs=143.9

Q ss_pred             CCEEEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHH-CCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHHHHH
Q ss_conf             8428984123331025766562241775043666762-982001115886566077740303720002332110001345
Q gi|254780275|r   10 PKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRV-SKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRK   88 (159)
Q Consensus        10 ~~~ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~-g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RK   88 (159)
                      +..+|++||||+|||+|+|+|||||||+||||||||+ |+|||+||||.+++||+||+||||+||.+++.++|||+|+||
T Consensus         5 ~~~~I~~NkKA~~~Y~i~e~~eAGivL~G~EVKSiR~~gkv~l~dsy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RK   84 (156)
T 1p6v_A            5 KIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRK   84 (156)
T ss_dssp             CEEEEEECSTTTTTSCEEEEEECCBCCCHHHHHHHHSCCCEECTTCCEECCSSCCEECCCEECCCSCC---CCCTTCCEE
T ss_pred             CCCCCEECCCCCCCEEEEEEEEEEEEEECHHHHHHHHCCCCCCCCCEEEEECCEEEEECCCCCCCCCCCCCCCCCCCHHH
T ss_conf             64265246633443358377998789812625978861862300028999999999980610354446556689762567


Q ss_pred             HHCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             5303899999998630389339999637807981999998722432110079898727888899887644
Q gi|254780275|r   89 LLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREH  158 (159)
Q Consensus        89 LLL~k~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K~~  158 (159)
                      |||||+||.+|.+.++++|+|||||++||+ +|+|||+||||+|||+|||||+||+|||+||++|+||++
T Consensus        85 LLL~K~EI~kl~~~~~~kG~TiVPl~ly~k-~g~iKveIalakGKK~~DKR~~iK~rd~~re~~R~~K~~  153 (156)
T 1p6v_A           85 LLLHKREIMRLYGKVQEKGYTIIPLKLYWK-NNKVKVLIALAKGKKLYDRRRELKEKAMKRELEREFKGK  153 (156)
T ss_dssp             BCCCHHHHHHHHHHHHHHCCEEEEEEEEEE-SSCEEEEEEEECCCCC-----------------------
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEEEEE-CCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             777599999999898548974256899990-987999999861881230567898889999999998750



>1j1h_A Small protein B; SMPB, SSRA associated protein, OB fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Thermus thermophilus} SCOP: b.111.1.1 Back     alignment and structure
>1wjx_A Small protein B, SSRA-binding protein; RNA binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.70A {Thermus thermophilus} SCOP: b.111.1.1 PDB: 2czj_A* Back     alignment and structure

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

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

IdentityAlignment graphLength Definition E-value
Target 159 SsrA-binding protein [Candidatus Liberibacter asiaticus
d1wjxa_120 b.111.1.1 (A:) Small protein B (SmpB) {Thermus thermoph 5e-38
d1p6va_128 b.111.1.1 (A:) Small protein B (SmpB) {Aquifex aeolicus 2e-34
>d1wjxa_ b.111.1.1 (A:) Small protein B (SmpB) {Thermus thermophilus [TaxId: 274]} Length = 120 Back     information, alignment and structure

class: All beta proteins
fold: Small protein B (SmpB)
superfamily: Small protein B (SmpB)
family: Small protein B (SmpB)
domain: Small protein B (SmpB)
species: Thermus thermophilus [TaxId: 274]
 Score =  150 bits (381), Expect = 5e-38
 Identities = 64/120 (53%), Positives = 86/120 (71%)

Query: 14  VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEY 73
           V +NR+AR++Y I+ ++EAGI L GTEVKSLR  KV+ + S+A FE+ E++L N YI  Y
Sbjct: 1   VLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPY 60

Query: 74  LQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK 133
            + +  N  PRR RKLLL K E+ RL   V + G+TLVP+KIYFN +G AK+ L LA+GK
Sbjct: 61  EKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK 120


>d1p6va_ b.111.1.1 (A:) Small protein B (SmpB) {Aquifex aeolicus [TaxId: 63363]} Length = 128 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
d1wjxa_120 Small protein B (SmpB) {Thermus thermophilus [TaxId: 27 100.0
d1p6va_128 Small protein B (SmpB) {Aquifex aeolicus [TaxId: 63363] 100.0
>d1wjxa_ b.111.1.1 (A:) Small protein B (SmpB) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: All beta proteins
fold: Small protein B (SmpB)
superfamily: Small protein B (SmpB)
family: Small protein B (SmpB)
domain: Small protein B (SmpB)
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=353.59  Aligned_cols=120  Identities=53%  Similarity=0.871  Sum_probs=118.1

Q ss_pred             EEEECCEEEEEEEEEEEECCEEEEEHHHHHHHHCCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHHHHHHHCCH
Q ss_conf             98412333102576656224177504366676298200111588656607774030372000233211000134553038
Q gi|254780275|r   14 VSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRRNRKLLLSK   93 (159)
Q Consensus        14 i~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RKLLL~k   93 (159)
                      |++||||+|||+|+|+|||||||+||||||||+|++||.||||.+++||+||.||||+||.+++.++|||+|+|||||||
T Consensus         1 I~~NkkA~~dY~i~e~~eAGivL~G~EVKSiR~g~~~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R~RKLLL~k   80 (120)
T d1wjxa_           1 VLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHK   80 (120)
T ss_dssp             CEECHHHHHHEEEEEEEEEEECCCTTHHHHHHTTCEECTTCEEEEETTEEEEESCEECC--------CCTTCCEEEECCH
T ss_pred             CCCCCCCCCCEEEEEEEEEEEEEEEHHHHHHHHCCCCCCCEEEEEECCCEEEEEEEECCHHCCCCCCCCCCCCHHHHCCH
T ss_conf             96576232204673779987899107079898577883740799975938999412346001565456765324221559


Q ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCC
Q ss_conf             9999999863038933999963780798199999872243
Q gi|254780275|r   94 REIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGK  133 (159)
Q Consensus        94 ~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGK  133 (159)
                      +||.+|.+.++++|+|||||++||+++|+|||+|||||||
T Consensus        81 ~EI~kl~~~~~~kG~TiVPl~ly~~~~g~iKveIaLakGK  120 (120)
T d1wjxa_          81 HELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK  120 (120)
T ss_dssp             HHHHHHTTTSSCTTEEEEEEEEEECTTCCEEEEEEEEEEC
T ss_pred             HHHHHHHHHHHCCCEEEEEHHHHCCCCCEEEEEEEEECCC
T ss_conf             9999999898559879998358084799899999986289



>d1p6va_ b.111.1.1 (A:) Small protein B (SmpB) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 159 SsrA-binding protein [Candidatus Liberibacter asia
1j1h_A_144 (A:) Small protein B; SMPB, SSRA associated protei 7e-53
1p6v_A_156 (A:) SSRA-binding protein; SMPB, tmRNA, trans-tran 7e-52
1wjx_A_122 (A:) Small protein B, SSRA-binding protein; RNA bi 5e-46
>1j1h_A (A:) Small protein B; SMPB, SSRA associated protein, OB fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Thermus thermophilus}Length = 144 Back     alignment and structure
 Score =  200 bits (511), Expect = 7e-53
 Identities = 71/143 (49%), Positives = 96/143 (67%)

Query: 12  KVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRVSKVNISDSYATFENDEIWLTNSYIP 71
             V +NR+AR++Y I+ ++EAGI L GTEVKSLR  KV+ + S+A FE+ E++L N YI 
Sbjct: 2   APVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIA 61

Query: 72  EYLQANRFNHYPRRNRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQ 131
            Y + +  N  PRR RKLLL K E+ RL   V + G+TLVP+KIYFN +G AK+ L LA+
Sbjct: 62  PYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLAR 121

Query: 132 GKKNYDKRETEKKRDWDRQKHRI 154
           GKK Y+KR  +KK    R    +
Sbjct: 122 GKKAYEKRREDKKEAVRRALEEL 144


>1p6v_A (A:) SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA complex, RNA binding protein/RNA complex; 3.20A {Aquifex aeolicus}Length = 156 Back     alignment and structure
>1wjx_A (A:) Small protein B, SSRA-binding protein; RNA binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.70A {Thermus thermophilus}Length = 122 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target159 SsrA-binding protein [Candidatus Liberibacter asiaticus
1p6v_A_156 SSRA-binding protein; SMPB, tmRNA, trans-translati 100.0
1j1h_A_144 Small protein B; SMPB, SSRA associated protein, OB 100.0
1wjx_A_122 Small protein B, SSRA-binding protein; RNA binding 100.0
>1p6v_A (A:) SSRA-binding protein; SMPB, tmRNA, trans-translation, protein-RNA complex, RNA binding protein/RNA complex; 3.20A {Aquifex aeolicus} Back     alignment and structure
Probab=100.00  E-value=0  Score=433.90  Aligned_cols=152  Identities=43%  Similarity=0.701  Sum_probs=148.0

Q ss_pred             CCCCCEEEEEECCEEEEEEEEEEEECCEEEEEHHHHHHHH-CCCEEEEEEEEEECCEEEEEECCCCCHHCCCCCCCCCHH
Q ss_conf             7898428984123331025766562241775043666762-982001115886566077740303720002332110001
Q gi|254780275|r    7 GNPPKKVVSDNRKARYNYHIVRSFEAGIVLTGTEVKSLRV-SKVNISDSYATFENDEIWLTNSYIPEYLQANRFNHYPRR   85 (159)
Q Consensus         7 ~~~~~~ii~~NkkA~~~Y~i~e~~eAGIvL~G~EVKSiR~-g~v~l~~sy~~~~~~E~~L~n~~I~~y~~~~~~~~~p~R   85 (159)
                      ++++.++|++||||+|||+|+|+|||||||+||||||||+ |+|||.||||.+++||+||+||||+||.+++.++|||+|
T Consensus         2 k~~~~~~i~~NkkA~~~Y~i~e~~EAGIvL~G~EVKSiR~~gk~~l~dsy~~~~~~E~~L~n~~I~~y~~~~~~nh~p~R   81 (156)
T 1p6v_A            2 KSDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLR   81 (156)
T ss_dssp             -CCCEEEEEECSTTTTTSCEEEEEECCBCCCHHHHHHHHSCCCEECTTCCEECCSSCCEECCCEECCCSCC---CCCTTC
T ss_pred             CCCCCCEEEECCCCCCCEEEEEEEEEEEEEECHHHHHHHHCCCCCCCCCEEEEECCEEEEEECEECCCCCCCCCCCCCCC
T ss_conf             98773263246634443358377998789912625978861863300028999999999980630464446555689872


Q ss_pred             HHHHHCCHHHHHHHHHHHHCCCCEEEEEEEEEECCCEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             34553038999999986303893399996378079819999987224321100798987278888998876449
Q gi|254780275|r   86 NRKLLLSKREIHRLYAAVRRDGMTLVPMKIYFNAKGLAKIDLALAQGKKNYDKRETEKKRDWDRQKHRILREHN  159 (159)
Q Consensus        86 ~RKLLL~k~EI~kl~~~~~~kG~TiVPlkly~~~~g~~Kv~IalaKGKK~~DKR~~iK~rd~~re~~R~~K~~n  159 (159)
                      +|||||||+||.+|.+.++++|+|||||++||+ +|||||+||||+|||.|||||+||+|||+||++|+||+++
T Consensus        82 ~RKLLLhk~EI~kL~~~~~~kG~TiVPl~~y~k-~g~iKveIalakGKk~~DKR~~iK~rd~~Re~~r~lk~~~  154 (156)
T 1p6v_A           82 KRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWK-NNKVKVLIALAKGKKLYDRRRELKEKAMKRELEREFKGKI  154 (156)
T ss_dssp             CEEBCCCHHHHHHHHHHHHHHCCEEEEEEEEEE-SSCEEEEEEEECCCCC------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEE-CCEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             466665399999999887448961677788892-8878999999608812305678888899999999987522



>1j1h_A (A:) Small protein B; SMPB, SSRA associated protein, OB fold, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Thermus thermophilus} Back     alignment and structure
>1wjx_A (A:) Small protein B, SSRA-binding protein; RNA binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.70A {Thermus thermophilus} Back     alignment and structure