254780786

254780786

ribosome-binding factor A

GeneID in NCBI database:8209792Locus tag:CLIBASIA_03385
Protein GI in NCBI database:254780786Protein Accession:YP_003065199.1
Gene range:+(476229, 476615)Protein Length:128aa
Gene description:ribosome-binding factor A
COG prediction:[J] Ribosome-binding factor A
KEGG prediction:rbfA; ribosome-binding factor A; K02834 ribosome-binding factor A
SEED prediction:Ribosome-binding factor A
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Translation initiation factors bacterial;
NusA-TFII Cluster;
RNA processing and degradation, bacterial;
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK
cccccccccHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEEEcccccEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEccHHHHHHHHHHHHHccccHHHHcc
cccccccccHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEEEEEcccccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccHHHHHcc
mknknpknsrrALRVGEEVRSALMWVILNNEFqdrlisrdvISISEVCMSVDLRVATVYIslpldvspdRVISALNCNIKFIRGRigrslrnlryvpelrfrYDTSLQSYWKLNAlmclpkipvalek
mknknpknsrralrvgeEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISlpldvspdrVISALNCNIkfirgrigrslrnlryvpeLRFRYDTSLQSYWKLNALMCLPKIPVALEK
MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK
******************VRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMC**********
***********ALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK
********SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKI******
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MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK
MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK
MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALEK

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
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
315122008132 ribosome-binding factor A [Candidatus Liberibacter sola 1 8e-50
222147150137 ribosome-binding factor A [Agrobacterium vitis S4] Leng 1 2e-27
15887440138 ribosome-binding factor A [Agrobacterium tumefaciens st 1 7e-25
325291530138 Ribosome-binding factor A [Agrobacterium sp. H13-3] Len 1 1e-24
222084325139 ribosome-binding factor A [Agrobacterium radiobacter K8 1 2e-24
227824072135 ribosome-binding factor A [Sinorhizobium fredii NGR234] 1 2e-24
239833214171 ribosome-binding factor A [Ochrobactrum intermedium LMG 1 5e-24
218682086134 ribosome-binding factor A [Rhizobium etli CIAT 894] Len 1 6e-24
17988247171 ribosome-binding factor A [Brucella melitensis bv. 1 st 1 9e-24
225853591150 ribosome-binding factor A [Brucella melitensis ATCC 234 1 9e-24
>gi|315122008|ref|YP_004062497.1| ribosome-binding factor A [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 132 Back     alignment and organism information
 Score =  199 bits (507), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 97/122 (79%), Positives = 108/122 (88%)

Query: 1   MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYI 60
           MKNK+   SRRALRVGEEVRSALMWVILNNEFQD LI RD+ISISEVCMSVDLRVATVY+
Sbjct: 1   MKNKSSVPSRRALRVGEEVRSALMWVILNNEFQDNLIHRDIISISEVCMSVDLRVATVYV 60

Query: 61  SLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLP 120
           SLP DVSPD VI AL CN KF+RGRI +SLRNL+Y+PELRFRYDTSLQ+YWK++ LMC  
Sbjct: 61  SLPPDVSPDVVIDALKCNNKFLRGRISQSLRNLKYIPELRFRYDTSLQNYWKIDTLMCSS 120

Query: 121 KI 122
           K+
Sbjct: 121 KV 122


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222147150|ref|YP_002548107.1| ribosome-binding factor A [Agrobacterium vitis S4] Length = 137 Back     alignment and organism information
>gi|15887440|ref|NP_353121.1| ribosome-binding factor A [Agrobacterium tumefaciens str. C58] Length = 138 Back     alignment and organism information
>gi|325291530|ref|YP_004277394.1| Ribosome-binding factor A [Agrobacterium sp. H13-3] Length = 138 Back     alignment and organism information
>gi|222084325|ref|YP_002542854.1| ribosome-binding factor A [Agrobacterium radiobacter K84] Length = 139 Back     alignment and organism information
>gi|227824072|ref|YP_002828045.1| ribosome-binding factor A [Sinorhizobium fredii NGR234] Length = 135 Back     alignment and organism information
>gi|239833214|ref|ZP_04681543.1| ribosome-binding factor A [Ochrobactrum intermedium LMG 3301] Length = 171 Back     alignment and organism information
>gi|218682086|ref|ZP_03529687.1| ribosome-binding factor A [Rhizobium etli CIAT 894] Length = 134 Back     alignment and organism information
>gi|17988247|ref|NP_540881.1| ribosome-binding factor A [Brucella melitensis bv. 1 str. 16M] Length = 171 Back     alignment and organism information
>gi|225853591|ref|YP_002733824.1| ribosome-binding factor A [Brucella melitensis ATCC 23457] Length = 150 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
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
PRK00521120 PRK00521, rbfA, ribosome-binding factor A; Validated 1e-20
COG0858118 COG0858, RbfA, Ribosome-binding factor A [Translation, 3e-13
TIGR00082114 TIGR00082, rbfA, ribosome-binding factor A 1e-07
PRK13817119 PRK13817, PRK13817, ribosome-binding factor A; Provisio 9e-06
PRK13816131 PRK13816, PRK13816, ribosome-binding factor A; Provisio 0.004
pfam02033104 pfam02033, RBFA, Ribosome-binding factor A 8e-17
PRK13815122 PRK13815, PRK13815, ribosome-binding factor A; Provisio 1e-06
>gnl|CDD|179054 PRK00521, rbfA, ribosome-binding factor A; Validated Back     alignment and domain information
>gnl|CDD|31199 COG0858, RbfA, Ribosome-binding factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|129191 TIGR00082, rbfA, ribosome-binding factor A Back     alignment and domain information
>gnl|CDD|139879 PRK13817, PRK13817, ribosome-binding factor A; Provisional Back     alignment and domain information
>gnl|CDD|184344 PRK13816, PRK13816, ribosome-binding factor A; Provisional Back     alignment and domain information
>gnl|CDD|145292 pfam02033, RBFA, Ribosome-binding factor A Back     alignment and domain information
>gnl|CDD|172345 PRK13815, PRK13815, ribosome-binding factor A; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 128 ribosome-binding factor A [Candidatus Liberibacter asia
PRK13816131 ribosome-binding factor A; Provisional 100.0
PRK13817119 ribosome-binding factor A; Provisional 100.0
PRK13815122 ribosome-binding factor A; Provisional 100.0
PRK13818121 ribosome-binding factor A; Provisional 100.0
PRK00521114 rbfA ribosome-binding factor A; Validated 100.0
COG0858118 RbfA Ribosome-binding factor A [Translation, ribosomal 99.97
pfam02033104 RBFA Ribosome-binding factor A. 99.96
TIGR00082121 rbfA ribosome-binding factor A; InterPro: IPR000238 Rib 99.96
KOG4700207 consensus 99.42
>PRK13816 ribosome-binding factor A; Provisional Back     alignment and domain information
>PRK13817 ribosome-binding factor A; Provisional Back     alignment and domain information
>PRK13815 ribosome-binding factor A; Provisional Back     alignment and domain information
>PRK13818 ribosome-binding factor A; Provisional Back     alignment and domain information
>PRK00521 rbfA ribosome-binding factor A; Validated Back     alignment and domain information
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam02033 RBFA Ribosome-binding factor A Back     alignment and domain information
>TIGR00082 rbfA ribosome-binding factor A; InterPro: IPR000238 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG4700 consensus 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
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
1jos_A128 Ribosome Binding Factor A(Rbfa) Length = 128 4e-21
1kkg_A108 Nmr Structure Of Ribosome-Binding Factor A (Rbfa) L 1e-19
2kzf_A106 Solution Nmr Structure Of The Thermotoga Maritima P 7e-12
1pa4_A116 Solution Structure Of A Putative Ribosome-Binding F 1e-07
2e7g_A129 Solution Structure Of Putative Ribosome-Binding Fac 4e-06
gi|33357151|pdb|1JOS|A Chain A, Ribosome Binding Factor A(Rbfa) Length = 128 Back     alignment and structure
 Score =  104 bits (260), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 32/127 (25%), Positives = 67/127 (52%), Gaps = 8/127 (6%)

Query: 5   NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPL 64
             +  +R+ RV +E++  +  ++   E +D  I   ++++S+V +S DL  A ++++   
Sbjct: 1   MAREFKRSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLF 57

Query: 65  DVSP---DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPK 121
           D      ++ +  L     +IR  +G+++R LR VPE+RF YD SL    +++ L+    
Sbjct: 58  DHDEMAIEQGMKGLEKASPYIRSLLGKAMR-LRIVPEIRFIYDQSLVEGMRMSNLVTNV- 115

Query: 122 IPVALEK 128
           +    +K
Sbjct: 116 VREDEKK 122


>gi|227968183|pdb|1KKG|A Chain A, Nmr Structure Of Ribosome-Binding Factor A (Rbfa) Length = 108 Back     alignment and structure
>gi|302565878|pdb|2KZF|A Chain A, Solution Nmr Structure Of The Thermotoga Maritima Protein Tm0855 A Putative Ribosome Binding Factor A Length = 106 Back     alignment and structure
gi|46015193|pdb|1PA4|A Chain A, Solution Structure Of A Putative Ribosome-Binding Factor From Mycoplasma Pneumoniae (Mpn156) Length = 116 Back     alignment and structure
>gi|159164340|pdb|2E7G|A Chain A, Solution Structure Of Putative Ribosome-Binding Factor A (Rbfa) From Human Mutochondrial Precursor Length = 129 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
2kzf_A106 RBFA, ribosome-binding factor A; JCSG, joint center str 6e-19
1jos_A128 RBFA, ribosome-binding factor A; RNA binding protein, s 7e-17
1pa4_A116 Probable ribosome-binding factor A; structural genomics 2e-14
2e7g_A129 Putative ribosome-binding factor A; RBFA, structural ge 2e-14
2dyj_A95 Ribosome-binding factor A; 16S rRNA processing, 17S RNA 7e-11
>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural genomics, PSI-2, protein struc initiative; NMR {Thermotoga maritima} Length = 106 Back     alignment and structure
 Score = 87.8 bits (218), Expect = 6e-19
 Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 4/102 (3%)

Query: 7   KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPLD 65
             + R   +  E++  LM  +   + +D  + +D ++ S V +S D R A VY+S L   
Sbjct: 3   NPAYRKAMLESEIQKLLMEAL--QQLRDPRLKKDFVTFSRVELSKDKRYADVYVSFLGTP 60

Query: 66  VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSL 107
                 +  LN    F R  I ++LR L   PE+RF  D  +
Sbjct: 61  EERKETVEILNRAKGFFRTFIAKNLR-LYVAPEIRFYEDKGI 101


>1jos_A RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae} SCOP: d.52.7.1 PDB: 1kkg_A Length = 128 Back     alignment and structure
>1pa4_A Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae} SCOP: d.52.7.1 Length = 116 Back     alignment and structure
>2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.52.7.1 Length = 129 Back     alignment and structure
>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8} SCOP: d.52.7.1 PDB: 2r1c_A Length = 95 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
1jos_A128 RBFA, ribosome-binding factor A; RNA binding protein, s 99.97
1pa4_A116 Probable ribosome-binding factor A; structural genomics 99.96
2kzf_A106 RBFA, ribosome-binding factor A; JCSG, joint center str 99.96
2e7g_A129 Putative ribosome-binding factor A; RBFA, structural ge 99.95
2dyj_A95 Ribosome-binding factor A; 16S rRNA processing, 17S RNA 99.92
>1jos_A RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae} SCOP: d.52.7.1 PDB: 1kkg_A Back     alignment and structure
Probab=99.97  E-value=1e-31  Score=198.16  Aligned_cols=115  Identities=26%  Similarity=0.472  Sum_probs=104.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH
Q ss_conf             8777738999999999999999951413420126516898888985875655999982798647---7899999985689
Q gi|254780786|r    5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF   81 (128)
Q Consensus         5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~   81 (128)
                      |+++++|+.||+++||++||++|.+ ++.||+++  +||||+|++|+||++|+||||++|+.++   +.++++|++++|+
T Consensus         1 M~~~~~R~~Rv~~~i~~~is~~l~~-~i~d~~l~--~vtIt~V~~S~Dl~~AkVy~s~~~~~~~~~~~~~~~~L~~~~~~   77 (128)
T 1jos_A            1 MAREFKRSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPY   77 (128)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHH-HCCCTTTC--CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9898707899999999999999998-56686668--34885999889866389999846871067799999999998999


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHH
Q ss_conf             999999987521457858999738688899999985576777
Q gi|254780786|r   82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIP  123 (128)
Q Consensus        82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~  123 (128)
                      ||+.||+++ +|||+|+|+|++|++++++.+|++||++..-+
T Consensus        78 ir~~l~~~l-~lr~~P~L~F~~D~s~e~~~~I~~lL~~i~~~  118 (128)
T 1jos_A           78 IRSLLGKAM-RLRIVPEIRFIYDQSLVEGMRMSNLVTNVVRE  118 (128)
T ss_dssp             HHHHHHHHH-CCSSCCEEEEEECCCCCCCC------------
T ss_pred             HHHHHHHHC-CCEECCEEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf             999999667-88079878999789778999999999998887



>1pa4_A Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae} SCOP: d.52.7.1 Back     alignment and structure
>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural genomics, PSI-2, protein struc initiative; NMR {Thermotoga maritima} Back     alignment and structure
>2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.52.7.1 Back     alignment and structure
>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8} SCOP: d.52.7.1 PDB: 2r1c_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 128 ribosome-binding factor A [Candidatus Liberibacter asia
d1kkga_108 d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escheric 5e-16
d1josa_100 d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophi 4e-14
d2e7ga1116 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Hu 3e-13
d1pa4a_96 d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplas 3e-11
d2dyja191 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Ther 4e-10
>d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]} Length = 108 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Ribosome-binding factor A, RbfA
family: Ribosome-binding factor A, RbfA
domain: Ribosome-binding factor A, RbfA
species: Escherichia coli [TaxId: 562]
 Score = 76.8 bits (189), Expect = 5e-16
 Identities = 40/105 (38%), Positives = 55/105 (52%), Gaps = 6/105 (5%)

Query: 6   PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD 65
            K   R  RV +E++  +   IL  E +D  +   + ++S V MS DL  A VY++   D
Sbjct: 2   AKEFGRPQRVAQEMQKEIAL-ILQREIKDPRLGM-MTTVSGVEMSRDLAYAKVYVTFLND 59

Query: 66  VSPDRV---ISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSL 107
              D V   I AL     FIR  +G+++R LR VPEL F YD SL
Sbjct: 60  KDEDAVKAGIKALQEASGFIRSLLGKAMR-LRIVPELTFFYDNSL 103


>d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]} Length = 100 Back     information, alignment and structure
>d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]} Length = 116 Back     information, alignment and structure
>d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]} Length = 96 Back     information, alignment and structure
>d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]} Length = 91 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
d1kkga_108 Ribosome-binding factor A, RbfA {Escherichia coli [TaxI 99.96
d2e7ga1116 Ribosome-binding factor A, RbfA {Human (Homo sapiens) [ 99.95
d1josa_100 Ribosome-binding factor A, RbfA {Haemophilus influenzae 99.95
d1pa4a_96 Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae 99.93
d2dyja191 Ribosome-binding factor A, RbfA {Thermus thermophilus [ 99.9
>d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Ribosome-binding factor A, RbfA
family: Ribosome-binding factor A, RbfA
domain: Ribosome-binding factor A, RbfA
species: Escherichia coli [TaxId: 562]
Probab=99.96  E-value=4.8e-30  Score=187.42  Aligned_cols=105  Identities=33%  Similarity=0.473  Sum_probs=94.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH
Q ss_conf             8777738999999999999999951413420126516898888985875655999982798647---7899999985689
Q gi|254780786|r    5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF   81 (128)
Q Consensus         5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~   81 (128)
                      |++++.|+.||+++|+++||++|.+ ++.||++++ +||||+|++|+||++|+||||++++.++   ++++++||+++|+
T Consensus         1 M~~~~~R~~rv~~~i~r~is~il~~-~~~dp~l~~-~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~~~L~~~~~~   78 (108)
T d1kkga_           1 MAKEFGRPQRVAQEMQKEIALILQR-EIKDPRLGM-MTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGF   78 (108)
T ss_dssp             CCCCSSSHHHHHHHHHHHHHHHTTS-SSSSGGGTS-CCBCSCEEEETTTTEEEEEEBCSGGGCHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCCC-EEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9986727899999999999999997-563865577-06994899768813189999954772067799999999997899


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCHHHHHH
Q ss_conf             9999999875214578589997386888999
Q gi|254780786|r   82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWK  112 (128)
Q Consensus        82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~  112 (128)
                      ||++||++| ++||||+|+|++|+++|++.+
T Consensus        79 ir~~l~~~l-~lr~~P~L~F~~D~s~e~a~R  108 (108)
T d1kkga_          79 IRSLLGKAM-RLRIVPELTFFYDNSLVEGMR  108 (108)
T ss_dssp             HHHHHHHHT-TCSCCCEEEEEECCTTSSSCC
T ss_pred             HHHHHHHHC-CCEECCEEEEEECCCHHHHCC
T ss_conf             999998447-980898889996595530057



>d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]} Back     information, alignment and structure
>d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 128 ribosome-binding factor A [Candidatus Liberibacter
2e7g_A_129 (A:) Putative ribosome-binding factor A; RBFA, str 2e-21
1pa4_A_116 (A:) Probable ribosome-binding factor A; structura 6e-18
1jos_A_128 (A:) RBFA, ribosome-binding factor A; RNA binding 1e-17
2dyj_A_95 (A:) Ribosome-binding factor A; 16S rRNA processin 1e-16
>2e7g_A (A:) Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}Length = 129 Back     alignment and structure
 Score = 95.6 bits (238), Expect = 2e-21
 Identities = 19/117 (16%), Positives = 40/117 (34%), Gaps = 3/117 (2%)

Query: 1   MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYI 60
             +   ++  R   +   +  AL  ++   E    L     + +S+V ++ D      Y 
Sbjct: 4   GSSGRKEDHARLRALNGLLYKALTDLLCTPEVSQELYDL-NVELSKVSLTPDFSACRAYW 62

Query: 61  S-LPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
                      + + L  +   +R  +      LR VP + F  D    +  +L+ L
Sbjct: 63  KTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQT-LRNVPPIVFVQDKGNAALAELDQL 118


>1pa4_A (A:) Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae}Length = 116 Back     alignment and structure
>1jos_A (A:) RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae}Length = 128 Back     alignment and structure
>2dyj_A (A:) Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8}Length = 95 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target128 ribosome-binding factor A [Candidatus Liberibacter asia
1jos_A_128 RBFA, ribosome-binding factor A; RNA binding prote 99.97
2e7g_A_129 Putative ribosome-binding factor A; RBFA, structur 99.96
1pa4_A_116 Probable ribosome-binding factor A; structural gen 99.96
2dyj_A_95 Ribosome-binding factor A; 16S rRNA processing, 17 99.92
>1jos_A (A:) RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae} Back     alignment and structure
Probab=99.97  E-value=4.9e-31  Score=195.22  Aligned_cols=118  Identities=25%  Similarity=0.446  Sum_probs=106.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH
Q ss_conf             8777738999999999999999951413420126516898888985875655999982798647---7899999985689
Q gi|254780786|r    5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF   81 (128)
Q Consensus         5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~   81 (128)
                      |+++|.|+.|++++|+++||++|.+ ++.||++.  +||||+|++|+|+++|+||||++|+.++   +.++++|++++|+
T Consensus         1 M~~~s~R~~rv~~~i~~~is~il~~-ei~d~~~~--~vtIt~V~vs~Dl~~akVy~s~~~~~~~~~~~~~~~~L~~~~g~   77 (128)
T 1jos_A            1 MAREFKRSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPY   77 (128)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHH-HCCCTTTC--CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9898717899999999999999997-56576668--15897999768855179999956871056799999999998999


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHHHH
Q ss_conf             999999987521457858999738688899999985576777764
Q gi|254780786|r   82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVAL  126 (128)
Q Consensus        82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~d~  126 (128)
                      ||+.||+++ .||++|+|+|++|++++++.+|++||++.+.+...
T Consensus        78 iR~~l~~~l-~lr~~P~L~F~~D~~~~~~~~i~~ll~~~~~~~~~  121 (128)
T 1jos_A           78 IRSLLGKAM-RLRIVPEIRFIYDQSLVEGMRMSNLVTNVVREDEK  121 (128)
T ss_dssp             HHHHHHHHH-CCSSCCEEEEEECCCCCCCC---------------
T ss_pred             HHHHHHHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999667-88079878999789778999999999998887663



>2e7g_A (A:) Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1pa4_A (A:) Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae} Back     alignment and structure
>2dyj_A (A:) Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8} Back     alignment and structure