Citrus Sinensis ID: 027059

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------23
Protein Sequence
MSHVFSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHccHHHHccccccccccccccccccEEEEEEEEccccccEEEEEEEcccHHHHHHHHHHHHHcHHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEc
Secondary Structure Prediction (SSPRO)
cccEEEEEccccccccEEEEccccccccccccccccccccEEccccccccccccccHHHEEHHHcccHHHHHHHHHHHHHHHHHHHHccccccEEccHHHccccccEEEEEEEEcEEEcccHcHEEEEEEEcccHHHHHHHHHHHHHcHHHHHHHHHHHHccccccEEEEEEcccccccHHHHHHHHHHHHccHHHccccccccccccccccccccccccccccEEEEc
Coil and Loop (DISEMBL)
mshvfsfnhlhtnhthqsflslplhhhypyllpitsfnsatwapkstaaihlrrsptrktvkcmanprRVKMVAKQIQRELSDMLLTDKVLQFavlpeaalgadrylsslttisdvevsaDLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLgrrmklrltpeirfiedesferGSRVIAILDRIKAEKEAAKSKnkeqfespdlpederdwegddpdediiyvk
Flexible Loop (DISEMBL)
MSHVFSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTaaihlrrsptrktvkcmanprrvKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTisdvevsadlQVVKVYVsvfgddrgkevaiaglkskakyvrsqlgrrmklrltpeirfiedesfergsrVIAILDRIKAEKEaaksknkeqfespdlpederdwegddpdediiyvk
Low Complexity Region (SEG)
MSHVFSFNHLHTNHTHQSFLSlplhhhypyllpITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIkaekeaaksknkeQFESPDLPEDERDWEGDDPDEDIIYVK
Disordered region (IsUnstruct)
****FSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRR***RKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRI****************************************
Disordered Region (DISOPRED)
***VFSFNHLHTNHTHQSFLSLPLHHHYPYLLPI**************************************VAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAI***************************************IIYVK
Disordered Region (DISEMBL)
MSHVFSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE*************************GDDPDEDIIYVK
Disordered Region (DISPRO)
*SHVFSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE****************************PDEDIIYVK
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSHVFSFNHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIxxxxxxxxxxxxxxxxxxxxxPDLPEDERDWEGDDPDEDIIYVK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	229	2.2.26 [Sep-21-2011]
O65693	215	Probable ribosome-binding	yes	no	0.925	0.986	0.713	4e-82
Q93LL7	139	Ribosome-binding factor A	yes	no	0.515	0.848	0.438	1e-23
B8HWS1	134	Ribosome-binding factor A	yes	no	0.580	0.992	0.379	3e-23
Q3M9Q8	133	Ribosome-binding factor A	yes	no	0.502	0.864	0.425	6e-23
Q8Z0M8	133	Ribosome-binding factor A	yes	no	0.502	0.864	0.425	6e-23
B0JRP8	128	Ribosome-binding factor A	yes	no	0.558	1.0	0.392	1e-22
Q5N2X2	137	Ribosome-binding factor A	yes	no	0.497	0.832	0.420	1e-21
Q31RD2	137	Ribosome-binding factor A	yes	no	0.497	0.832	0.420	1e-21
B0CDK8	138	Ribosome-binding factor A	yes	no	0.558	0.927	0.385	3e-21
Q110L1	137	Ribosome-binding factor A	yes	no	0.519	0.868	0.374	5e-21

>sp|O65693|RBFA_ARATH Probable ribosome-binding factor A, chloroplastic OS=Arabidopsis thaliana GN=At4g34730 PE=2 SV=2

 Score =  304 bits (778), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 159/223 (71%), Positives = 180/223 (80%), Gaps = 11/223 (4%)

Query: 8   NHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRS-PTRKTVKCMAN 66
           N LHTN +H  FL      H+P +  ++S   A   P+S A ++LR +   R+TV+CMAN
Sbjct: 3   NLLHTNQSHFFFL------HHPPIYTVSSKTQAFHFPQSMAPVNLRTNLSVRRTVRCMAN 56

Query: 67  PRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVK 126
           PRRVKMVAKQI RELSDMLLTD VLQ AVLPEAALGADRYLSSLTTISDVEVS DLQVVK
Sbjct: 57  PRRVKMVAKQIMRELSDMLLTDTVLQHAVLPEAALGADRYLSSLTTISDVEVSNDLQVVK 116

Query: 127 VYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186
           VYVSVFGDDRGK+VAIAGLKSKAKYVRS+LG+RMKLRLTPE+RFIEDE+ ERGSRVIAIL
Sbjct: 117 VYVSVFGDDRGKDVAIAGLKSKAKYVRSELGKRMKLRLTPEVRFIEDEAMERGSRVIAIL 176

Query: 187 DRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           D+IKAEK + + K     E  D  ED++DWE DDPDEDIIYVK
Sbjct: 177 DKIKAEKGSGEGKT----EPSDSTEDDQDWEVDDPDEDIIYVK 215

Arabidopsis thaliana (taxid: 3702)

>sp|Q93LL7|RBFA_NOSP7 Ribosome-binding factor A OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=rbfA PE=3 SV=1

 Score =  110 bits (274), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/130 (43%), Positives = 84/130 (64%), Gaps = 12/130 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV  VA+ I+RE+S MLL              +  DR  + + +++DV+VS DLQ
Sbjct: 1   MATNRRVSRVAELIKREVSQMLLN------------GIKDDRVGTGMVSVTDVDVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K+YVS++G D  K   +AGLKS   YVRS+LG R++LR TPE+ F+ED S ERG++V+
Sbjct: 49  HAKIYVSIYGTDEAKVETMAGLKSATGYVRSELGARVRLRRTPEVIFLEDRSIERGNKVL 108

Query: 184 AILDRIKAEK 193
           A+L ++  ++
Sbjct: 109 ALLSQLNHDR 118

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Nostoc punctiforme (strain ATCC 29133 / PCC 73102) (taxid: 63737)

>sp|B8HWS1|RBFA_CYAP4 Ribosome-binding factor A OS=Cyanothece sp. (strain PCC 7425 / ATCC 29141) GN=rbfA PE=3 SV=1

 Score =  108 bits (270), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 55/145 (37%), Positives = 92/145 (63%), Gaps = 12/145 (8%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV  VA+ I+RE+S ML++             +  DR  S + +++DV++S DLQ
Sbjct: 1   MATDRRVARVAELIKREISQMLMS------------GIKDDRVGSGMVSVTDVDLSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K++VS++G +  +   +AGLK+   YVRS+LG R++LR TPE+ F+ED S ERG++V+
Sbjct: 49  HAKIFVSIYGTEAARAETMAGLKAATGYVRSELGHRVRLRRTPEVVFLEDRSLERGTQVL 108

Query: 184 AILDRIKAEKEAAKSKNKEQFESPD 208
           ++L+R+  E++     ++   E P+
Sbjct: 109 SLLNRLSEERQKNADLDEMAAEEPE 133

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Cyanothece sp. (strain PCC 7425 / ATCC 29141) (taxid: 395961)

>sp|Q3M9Q8|RBFA_ANAVT Ribosome-binding factor A OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rbfA PE=3 SV=1

 Score =  107 bits (268), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 83/127 (65%), Gaps = 12/127 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV  VA+ I+RE+S ML+              +  DR  + + +++DV+VS DLQ
Sbjct: 1   MATNRRVSRVAELIKREVSQMLIN------------GIKDDRVGTGMVSVTDVDVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K+YVS++G +  K   +AGLKS   +VRS+LG R++LR TPE+ FIED S ERG++V+
Sbjct: 49  HAKIYVSIYGTEEAKAETMAGLKSATGFVRSELGARVRLRRTPEVTFIEDRSIERGTKVL 108

Query: 184 AILDRIK 190
            +L++++
Sbjct: 109 TLLNKLE 115

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Anabaena variabilis (strain ATCC 29413 / PCC 7937) (taxid: 240292)

>sp|Q8Z0M8|RBFA_NOSS1 Ribosome-binding factor A OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rbfA PE=3 SV=1

 Score =  107 bits (268), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 83/127 (65%), Gaps = 12/127 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV  VA+ I+RE+S ML+              +  DR  + + +++DV+VS DLQ
Sbjct: 1   MATNRRVSRVAELIKREVSQMLIN------------GIKDDRVGTGMVSVTDVDVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K+YVS++G +  K   +AGLKS   +VRS+LG R++LR TPE+ FIED S ERG++V+
Sbjct: 49  HAKIYVSIYGTEEAKAETMAGLKSATGFVRSELGARVRLRRTPEVTFIEDRSIERGTKVL 108

Query: 184 AILDRIK 190
            +L++++
Sbjct: 109 TLLNKLE 115

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|B0JRP8|RBFA_MICAN Ribosome-binding factor A OS=Microcystis aeruginosa (strain NIES-843) GN=rbfA PE=3 SV=1

 Score =  106 bits (265), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 55/140 (39%), Positives = 90/140 (64%), Gaps = 12/140 (8%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MAN RRV  V+  I+RE+S MLL +            +  DR  + + +++DV++S DLQ
Sbjct: 1   MANDRRVSRVSSLIKREVSQMLLME------------IKDDRVGAGMVSVTDVDLSHDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K++VS++G++  K   +AGLK+ A +VR +LG+R++LR TPE+ F+ED S ERG R++
Sbjct: 49  HAKIFVSIYGNEDAKAETMAGLKASAGFVRRELGQRIRLRRTPEVVFLEDSSLERGDRML 108

Query: 184 AILDRIKAEKEAAKSKNKEQ 203
            +LD IK ++      ++E+
Sbjct: 109 HLLDHIKTDRPPEDDDSEEE 128

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Microcystis aeruginosa (strain NIES-843) (taxid: 449447)

>sp|Q5N2X2|RBFA_SYNP6 Ribosome-binding factor A OS=Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) GN=rbfA PE=3 SV=1

 Score =  103 bits (257), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 83/126 (65%), Gaps = 12/126 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV+ VA  I+RE+S ML++             +  DR  + + +++DV VS DLQ
Sbjct: 1   MATNRRVERVASLIKREVSQMLMS------------GIKDDRVGAGMVSVTDVVVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K++VS++G    K   + GLKS A YVRS+LG+R++LR TPE+ F+ED+  ERG++VI
Sbjct: 49  HTKIFVSIYGTPEAKAETMEGLKSAASYVRSELGQRVRLRRTPEVIFVEDKGLERGTQVI 108

Query: 184 AILDRI 189
           ++L+++
Sbjct: 109 SLLEQL 114

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (taxid: 269084)

>sp|Q31RD2|RBFA_SYNE7 Ribosome-binding factor A OS=Synechococcus elongatus (strain PCC 7942) GN=rbfA PE=3 SV=1

 Score =  103 bits (257), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 83/126 (65%), Gaps = 12/126 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV+ VA  I+RE+S ML++             +  DR  + + +++DV VS DLQ
Sbjct: 1   MATNRRVERVASLIKREVSQMLMS------------GIKDDRVGAGMVSVTDVVVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K++VS++G    K   + GLKS A YVRS+LG+R++LR TPE+ F+ED+  ERG++VI
Sbjct: 49  HTKIFVSIYGTPEAKAETMEGLKSAASYVRSELGQRVRLRRTPEVIFVEDKGLERGTQVI 108

Query: 184 AILDRI 189
           ++L+++
Sbjct: 109 SLLEQL 114

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|B0CDK8|RBFA_ACAM1 Ribosome-binding factor A OS=Acaryochloris marina (strain MBIC 11017) GN=rbfA PE=3 SV=1

 Score =  102 bits (253), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 54/140 (38%), Positives = 86/140 (61%), Gaps = 12/140 (8%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RRV  VA+ I+RE+S MLL             ++  DR  S + +++ V++S DLQ
Sbjct: 1   MATGRRVSRVAELIKREVSQMLLH------------SIKDDRVGSGMISVTAVDLSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             K++VS++G D  +   +AGL+S   YVR QLG R+ LR TPE+ F ED SFE G++V+
Sbjct: 49  HAKIFVSIYGTDEARAETMAGLESATGYVRKQLGHRIHLRRTPEVIFCEDRSFEEGNQVL 108

Query: 184 AILDRIKAEKEAAKSKNKEQ 203
           ++L ++  E++   + + E+
Sbjct: 109 SLLHKLDHERQNKPAASTEK 128

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Acaryochloris marina (strain MBIC 11017) (taxid: 329726)

>sp|Q110L1|RBFA_TRIEI Ribosome-binding factor A OS=Trichodesmium erythraeum (strain IMS101) GN=rbfA PE=3 SV=1

 Score =  101 bits (251), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/131 (37%), Positives = 84/131 (64%), Gaps = 12/131 (9%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MA  RR+  +A  I++E+S MLL              +  +R    + +++DV+VS DLQ
Sbjct: 1   MAIARRISRIASLIKQEISQMLL------------HGIKDNRVGIGMVSVTDVDVSGDLQ 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
             KV+VS++G D  +   +AGL+S   YVRS+LG+R+++R TPE+ F+ED S ERG+ ++
Sbjct: 49  HAKVFVSIYGSDEVRSQTMAGLRSATGYVRSELGKRIRMRRTPEVIFVEDRSLERGTEIL 108

Query: 184 AILDRIKAEKE 194
           ++L+++  E++
Sbjct: 109 SLLNKLSQERQ 119

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA.

Trichodesmium erythraeum (strain IMS101) (taxid: 203124)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	229
255543903	221	Ribosome-binding factor A, putative [Ric	0.908	0.941	0.731	4e-85
30690114	215	ribosome-binding factor A [Arabidopsis t	0.925	0.986	0.713	2e-80
224080508	166	predicted protein [Populus trichocarpa]	0.724	1.0	0.873	1e-75
297798442	787	hypothetical protein ARALYDRAFT_353351 [	0.729	0.212	0.838	7e-73
359475074	215	PREDICTED: probable ribosome-binding fac	0.689	0.734	0.862	3e-70
3096942	200	putative protein [Arabidopsis thaliana]	0.777	0.89	0.714	2e-69
225427802	223	PREDICTED: probable ribosome-binding fac	0.737	0.757	0.836	1e-67
449467253	225	PREDICTED: probable ribosome-binding fac	0.973	0.991	0.648	1e-66
357467461	229	hypothetical protein MTR_3g117600 [Medic	0.812	0.812	0.663	6e-66
357110849	205	PREDICTED: probable ribosome-binding fac	0.812	0.907	0.658	1e-63

>gi|255543903|ref|XP_002513014.1| Ribosome-binding factor A, putative [Ricinus communis] gi|223548025|gb|EEF49517.1| Ribosome-binding factor A, putative [Ricinus communis]

 Score =  320 bits (819), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 161/220 (73%), Positives = 182/220 (82%), Gaps = 12/220 (5%)

Query: 10  LHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCMANPRR 69
           + T+  +   ++  LH+ +P            W PKS A+ HLR+ P   T+KCMANPRR
Sbjct: 14  VFTSQRNSPPITTILHNPFP-----------IWTPKSAASAHLRQKPFINTIKCMANPRR 62

Query: 70  VKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYV 129
           VKMVAKQIQRELSDMLLTDKVLQ+A+LPEAALGAD+YLSSLTTISDVEVS DLQVVKVYV
Sbjct: 63  VKMVAKQIQRELSDMLLTDKVLQYAILPEAALGADKYLSSLTTISDVEVSTDLQVVKVYV 122

Query: 130 SVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRI 189
           SVFGDDRGKEVAIAGLK+KAKYVRS+LGRRMKLRLTPEIRFIEDESFERGSRV+AILD+I
Sbjct: 123 SVFGDDRGKEVAIAGLKAKAKYVRSELGRRMKLRLTPEIRFIEDESFERGSRVLAILDKI 182

Query: 190 KAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           KAEKE   S++ E  ES D P+D+RDWEGDDPDE IIYVK
Sbjct: 183 KAEKENTGSED-ELSESSDSPQDDRDWEGDDPDEGIIYVK 221

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30690114|ref|NP_195199.2| ribosome-binding factor A [Arabidopsis thaliana] gi|78099793|sp|O65693.2|RBFA_ARATH RecName: Full=Probable ribosome-binding factor A, chloroplastic; Flags: Precursor gi|25082957|gb|AAN72022.1| putative protein [Arabidopsis thaliana] gi|30023650|gb|AAP13358.1| At4g34730 [Arabidopsis thaliana] gi|332661016|gb|AEE86416.1| ribosome-binding factor A [Arabidopsis thaliana]

 Score =  304 bits (778), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 159/223 (71%), Positives = 180/223 (80%), Gaps = 11/223 (4%)

Query: 8   NHLHTNHTHQSFLSLPLHHHYPYLLPITSFNSATWAPKSTAAIHLRRS-PTRKTVKCMAN 66
           N LHTN +H  FL      H+P +  ++S   A   P+S A ++LR +   R+TV+CMAN
Sbjct: 3   NLLHTNQSHFFFL------HHPPIYTVSSKTQAFHFPQSMAPVNLRTNLSVRRTVRCMAN 56

Query: 67  PRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVK 126
           PRRVKMVAKQI RELSDMLLTD VLQ AVLPEAALGADRYLSSLTTISDVEVS DLQVVK
Sbjct: 57  PRRVKMVAKQIMRELSDMLLTDTVLQHAVLPEAALGADRYLSSLTTISDVEVSNDLQVVK 116

Query: 127 VYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186
           VYVSVFGDDRGK+VAIAGLKSKAKYVRS+LG+RMKLRLTPE+RFIEDE+ ERGSRVIAIL
Sbjct: 117 VYVSVFGDDRGKDVAIAGLKSKAKYVRSELGKRMKLRLTPEVRFIEDEAMERGSRVIAIL 176

Query: 187 DRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           D+IKAEK + + K     E  D  ED++DWE DDPDEDIIYVK
Sbjct: 177 DKIKAEKGSGEGKT----EPSDSTEDDQDWEVDDPDEDIIYVK 215

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080508|ref|XP_002306146.1| predicted protein [Populus trichocarpa] gi|222849110|gb|EEE86657.1| predicted protein [Populus trichocarpa]

 Score =  288 bits (737), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 145/166 (87%), Positives = 154/166 (92%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           MANPRRVKMVAKQIQRELSDMLLTDKVLQ+AVLPEAALGAD+YLSSLTTISDVEVSADLQ
Sbjct: 1   MANPRRVKMVAKQIQRELSDMLLTDKVLQYAVLPEAALGADKYLSSLTTISDVEVSADLQ 60

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVI 183
           VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDE  ERGSRVI
Sbjct: 61  VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDEGLERGSRVI 120

Query: 184 AILDRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           AILDRIKAEK+ A+S+  E  +S +  + + DWEGDDPDEDIIYVK
Sbjct: 121 AILDRIKAEKDNAESQVDELSDSSNSIQYDEDWEGDDPDEDIIYVK 166

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798442|ref|XP_002867105.1| hypothetical protein ARALYDRAFT_353351 [Arabidopsis lyrata subsp. lyrata] gi|297312941|gb|EFH43364.1| hypothetical protein ARALYDRAFT_353351 [Arabidopsis lyrata subsp. lyrata]

 Score =  279 bits (713), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 140/167 (83%), Positives = 148/167 (88%)

Query: 63  CMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADL 122
           CMANPRRVKMVAKQI RELSDMLLTD VLQ AVLPEAALGADRYLSSLTTISDVEVS DL
Sbjct: 560 CMANPRRVKMVAKQIMRELSDMLLTDTVLQHAVLPEAALGADRYLSSLTTISDVEVSNDL 619

Query: 123 QVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRV 182
           QVVKVYVSVFGDDRGK+VAIAGLKSKAKYVRS+LG+RMKLRLTPE+RFIEDES ERGSRV
Sbjct: 620 QVVKVYVSVFGDDRGKDVAIAGLKSKAKYVRSELGKRMKLRLTPEVRFIEDESMERGSRV 679

Query: 183 IAILDRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           IAILD+IKAEK +    N+   E  DL ED +DWE DDPDEDIIYV 
Sbjct: 680 IAILDKIKAEKGSGDGVNEGLPEPSDLAEDNQDWEVDDPDEDIIYVN 726

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359475074|ref|XP_003631582.1| PREDICTED: probable ribosome-binding factor A, chloroplastic isoform 2 [Vitis vinifera]

 Score =  270 bits (690), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 138/160 (86%), Positives = 150/160 (93%), Gaps = 2/160 (1%)

Query: 60  TVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS 119
           TV+CMAN RRVKMVAKQI+RELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS
Sbjct: 54  TVRCMANQRRVKMVAKQIRRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS 113

Query: 120 ADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG 179
           ADLQVVKVYVSVFGD++GKEVAIAGLKSKAKYVRS+LGRRMKLRLTPEIRF+EDES ERG
Sbjct: 114 ADLQVVKVYVSVFGDEKGKEVAIAGLKSKAKYVRSELGRRMKLRLTPEIRFVEDESLERG 173

Query: 180 SRVIAILDRIKAEKEAAKSKNKEQFESPDLPEDERDWEGD 219
           SRVIAILDRIK EK+ A S+++   ES DLP+D+ DWEGD
Sbjct: 174 SRVIAILDRIKNEKKMAGSQDQPS-ESSDLPQDD-DWEGD 211

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3096942|emb|CAA18852.1| putative protein [Arabidopsis thaliana] gi|7270424|emb|CAB80190.1| putative protein [Arabidopsis thaliana]

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 145/203 (71%), Positives = 160/203 (78%), Gaps = 25/203 (12%)

Query: 48  AAIHLRRS-PTRKTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRY 106
           A ++LR +   R+TV+CMANPRRVKMVAKQI RELSDMLLTD VLQ AVLPEAALGADRY
Sbjct: 2   APVNLRTNLSVRRTVRCMANPRRVKMVAKQIMRELSDMLLTDTVLQHAVLPEAALGADRY 61

Query: 107 LSSLTTISDVEVSADLQ------------VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRS 154
           LSSLTTISDVEVS DLQ            VVKVYVSVFGDDRGK+VAIAGLKSKAKYVRS
Sbjct: 62  LSSLTTISDVEVSNDLQVMRNPNWKLLCNVVKVYVSVFGDDRGKDVAIAGLKSKAKYVRS 121

Query: 155 QLGRRMKLRLTPEIRFIEDESFERGSR--------VIAILDRIKAEKEAAKSKNKEQFES 206
           +LG+RMKLRLTPE+RFIEDE+ ERGSR        VIAILD+IKAEK + + K     E 
Sbjct: 122 ELGKRMKLRLTPEVRFIEDEAMERGSRKLNWRLFQVIAILDKIKAEKGSGEGKT----EP 177

Query: 207 PDLPEDERDWEGDDPDEDIIYVK 229
            D  ED++DWE DDPDEDIIYVK
Sbjct: 178 SDSTEDDQDWEVDDPDEDIIYVK 200

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427802|ref|XP_002270280.1| PREDICTED: probable ribosome-binding factor A, chloroplastic isoform 1 [Vitis vinifera]

 Score =  261 bits (668), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 143/171 (83%), Positives = 159/171 (92%), Gaps = 2/171 (1%)

Query: 60  TVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS 119
           TV+CMAN RRVKMVAKQI+RELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS
Sbjct: 54  TVRCMANQRRVKMVAKQIRRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVS 113

Query: 120 ADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG 179
           ADLQVVKVYVSVFGD++GKEVAIAGLKSKAKYVRS+LGRRMKLRLTPEIRF+EDES ERG
Sbjct: 114 ADLQVVKVYVSVFGDEKGKEVAIAGLKSKAKYVRSELGRRMKLRLTPEIRFVEDESLERG 173

Query: 180 SRVIAILDRIKAEKEAAKSKNKEQFESPDLPE-DERDWEGDDPDEDIIYVK 229
           SRVIAILDRIK EK+ A S+++   ES DLP+ D+ + +GDDPDE+IIY+K
Sbjct: 174 SRVIAILDRIKNEKKMAGSQDQPS-ESSDLPQDDDWEGDGDDPDENIIYIK 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449467253|ref|XP_004151338.1| PREDICTED: probable ribosome-binding factor A, chloroplastic-like [Cucumis sativus] gi|449529960|ref|XP_004171965.1| PREDICTED: probable ribosome-binding factor A, chloroplastic-like [Cucumis sativus]

 Score =  258 bits (660), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 146/225 (64%), Positives = 170/225 (75%), Gaps = 2/225 (0%)

Query: 7   FNHLHTNHTHQSFLSLPLH--HHYPYLLPITSFNSATWAPKSTAAIHLRRSPTRKTVKCM 64
             HL     H  F   PL      P+     +     ++P S   +         T++CM
Sbjct: 1   MTHLLLQQIHPQFYFSPLKFLQSSPFPSQFQASRPCVYSPTSVTLLPPPPVMRGATIRCM 60

Query: 65  ANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQV 124
           AN RR+KMVAKQIQRELSDMLLTDKVLQFA+LPEA+LGAD+YLSSLTTI+DVEVSADLQV
Sbjct: 61  ANSRRIKMVAKQIQRELSDMLLTDKVLQFAILPEASLGADKYLSSLTTITDVEVSADLQV 120

Query: 125 VKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIA 184
           VKVYVSVFGD+RGK+VAIAGLKSKAKYVRS LG+RMKLRLTPEIRFIEDESFERGSRVIA
Sbjct: 121 VKVYVSVFGDERGKDVAIAGLKSKAKYVRSVLGKRMKLRLTPEIRFIEDESFERGSRVIA 180

Query: 185 ILDRIKAEKEAAKSKNKEQFESPDLPEDERDWEGDDPDEDIIYVK 229
           ILDRIK +K+    ++ +Q E  D  +D+RDW+GDD DEDIIYV+
Sbjct: 181 ILDRIKDKKKDTVDEDFDQPELSDALDDDRDWKGDDADEDIIYVQ 225

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357467461|ref|XP_003604015.1| hypothetical protein MTR_3g117600 [Medicago truncatula] gi|355493063|gb|AES74266.1| hypothetical protein MTR_3g117600 [Medicago truncatula]

 Score =  256 bits (653), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 132/199 (66%), Positives = 155/199 (77%), Gaps = 13/199 (6%)

Query: 29  PYLLPITSFNSATWAPKSTAAI----HLRRSPTRKTVKCMANPRRVKMVAKQIQRELSDM 84
           P + P    N+   A  +T  I     L  + +R T+KCMANPRRVKMVAKQI+RELSDM
Sbjct: 15  PSVTPCWRCNNHRTAATATVTIFQTQRLTGNASRITIKCMANPRRVKMVAKQIRRELSDM 74

Query: 85  LLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAG 144
           L+TD VLQFAVLPEA+LGAD YLSS+TTI+DVE++ADLQV +VYVSVFGD+RGKEVA+AG
Sbjct: 75  LITDNVLQFAVLPEASLGADLYLSSVTTITDVEITADLQVARVYVSVFGDERGKEVAMAG 134

Query: 145 LKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKNKEQF 204
           LKSKAKYVR +LGRRMKLRLTPEIRF+EDESFERGSRVIAILD+IK EK +  SKN EQ 
Sbjct: 135 LKSKAKYVRGELGRRMKLRLTPEIRFLEDESFERGSRVIAILDKIKNEK-SETSKNMEQL 193

Query: 205 ESPDLPEDERDWEGDDPDE 223
           +S           GDD ++
Sbjct: 194 DSS--------VNGDDTEQ 204

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357110849|ref|XP_003557228.1| PREDICTED: probable ribosome-binding factor A, chloroplastic-like [Brachypodium distachyon]

 Score =  248 bits (633), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 127/193 (65%), Positives = 158/193 (81%), Gaps = 7/193 (3%)

Query: 44  PKSTA-AIHLRRSPTR----KTVKCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPE 98
           P++ A ++ +RR P+     + V+CMA  RRV+MVAKQIQREL+DML  D ++  AVLPE
Sbjct: 13  PRALAVSVTVRRLPSSALSLRVVRCMAKERRVRMVAKQIQRELADMLTRDPIMLRAVLPE 72

Query: 99  AALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGR 158
           AALGADRYLSSLTTI+DVE+S DLQV KVYVSVFGD+RGK+VA+AGLK K KYVRSQ+G+
Sbjct: 73  AALGADRYLSSLTTIADVELSNDLQVCKVYVSVFGDERGKKVAMAGLKDKTKYVRSQIGK 132

Query: 159 RMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKN-KEQFESPDLPEDERDWE 217
           RMKLRLTPEIRFIEDES ERGSR++ ILD++K E+E  +  + +E  E+ DL E++ DWE
Sbjct: 133 RMKLRLTPEIRFIEDESMERGSRILTILDKLKEEREKQEGNDLEEDAETSDLGEEDGDWE 192

Query: 218 GDDPD-EDIIYVK 229
           GD+PD EDIIYVK
Sbjct: 193 GDEPDEEDIIYVK 205

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	229
TAIR|locus:2139529	215	AT4G34730 "AT4G34730" [Arabido	0.925	0.986	0.681	1.7e-68
UNIPROTKB|Q81WM5	118	rbfA "Ribosome-binding factor	0.462	0.898	0.385	1.4e-14
TIGR_CMR|BA_3948	118	BA_3948 "ribosome-binding fact	0.462	0.898	0.385	1.4e-14
UNIPROTKB|Q609C1	119	rbfA "Ribosome-binding factor	0.454	0.873	0.389	5e-12
TIGR_CMR|CPS_2204	142	CPS_2204 "ribosome-binding fac	0.462	0.746	0.322	8.2e-12
TIGR_CMR|CHY_1765	125	CHY_1765 "ribosome-binding fac	0.331	0.608	0.342	2.2e-11
UNIPROTKB|Q8EHL4	147	rbfA "Ribosome-binding factor	0.598	0.931	0.301	2.8e-11
TIGR_CMR|SO_1205	147	SO_1205 "ribosome-binding fact	0.598	0.931	0.301	2.8e-11
UNIPROTKB|Q9KU79	132	rbfA "Ribosome-binding factor	0.467	0.810	0.352	5.8e-11
TIGR_CMR|VC_0644	132	VC_0644 "ribosome-binding fact	0.467	0.810	0.352	5.8e-11

TAIR|locus:2139529 AT4G34730 "AT4G34730" [Arabidopsis thaliana (taxid:3702)]

 Score = 695 (249.7 bits), Expect = 1.7e-68, P = 1.7e-68
 Identities = 152/223 (68%), Positives = 169/223 (75%)

Query:     8 NHLHTNHTHQSFLSXXXXXXXXXXXXITSFNSATWAPKSTAAIHLRRS-PTRKTVKCMAN 66
             N LHTN +H  FL             ++S   A   P+S A ++LR +   R+TV+CMAN
Sbjct:     3 NLLHTNQSHFFFLHHPPIYT------VSSKTQAFHFPQSMAPVNLRTNLSVRRTVRCMAN 56

Query:    67 PRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVK 126
             PRRVKMVAKQI RELSDMLLTD VLQ AVLPEAALGADRYLSSLTTISDVEVS DLQVVK
Sbjct:    57 PRRVKMVAKQIMRELSDMLLTDTVLQHAVLPEAALGADRYLSSLTTISDVEVSNDLQVVK 116

Query:   127 VYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186
             VYVSVFGDDRGK+VAIAGLKSKAKYVRS+LG+RMKLRLTPE+RFIEDE+ ERGSRVIAIL
Sbjct:   117 VYVSVFGDDRGKDVAIAGLKSKAKYVRSELGKRMKLRLTPEVRFIEDEAMERGSRVIAIL 176

Query:   187 DRIXXXXXXXXXXXXXQFESPDLPEDERDWEGDDPDEDIIYVK 229
             D+I               E  D  ED++DWE DDPDEDIIYVK
Sbjct:   177 DKIKAEKGSGEGKT----EPSDSTEDDQDWEVDDPDEDIIYVK 215

GO:0003723 "RNA binding" evidence=ISS

GO:0006364 "rRNA processing" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

UNIPROTKB|Q81WM5 rbfA "Ribosome-binding factor A" [Bacillus anthracis (taxid:1392)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 47/122 (38%), Positives = 74/122 (60%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R   V +Q+++EL D +++ K+       +  +G         T++DV+VS DLQ+  VY
Sbjct:     4 RANRVGEQMKKELGD-IISRKI------KDPRVG-------FVTVTDVQVSRDLQIATVY 49

Query:   129 VSVFGDDRGKEVAIAGLKSKAK-YVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             +SV GD+  KE  + GL +KAK ++RS++G+R++LR TPEI F  DES   G R+  +L 
Sbjct:    50 ISVLGDEEQKENTLKGL-AKAKGFIRSEIGQRIRLRKTPEISFEFDESIGYGHRIDTLLH 108

Query:   188 RI 189
              I
Sbjct:   109 EI 110

GO:0003674 "molecular_function" evidence=ND

TIGR_CMR|BA_3948 BA_3948 "ribosome-binding factor A" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 47/122 (38%), Positives = 74/122 (60%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R   V +Q+++EL D +++ K+       +  +G         T++DV+VS DLQ+  VY
Sbjct:     4 RANRVGEQMKKELGD-IISRKI------KDPRVG-------FVTVTDVQVSRDLQIATVY 49

Query:   129 VSVFGDDRGKEVAIAGLKSKAK-YVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             +SV GD+  KE  + GL +KAK ++RS++G+R++LR TPEI F  DES   G R+  +L 
Sbjct:    50 ISVLGDEEQKENTLKGL-AKAKGFIRSEIGQRIRLRKTPEISFEFDESIGYGHRIDTLLH 108

Query:   188 RI 189
              I
Sbjct:   109 EI 110

GO:0003674 "molecular_function" evidence=ND

GO:0006396 "RNA processing" evidence=ISS

UNIPROTKB|Q609C1 rbfA "Ribosome-binding factor A" [Methylococcus capsulatus str. Bath (taxid:243233)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 46/118 (38%), Positives = 64/118 (54%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R   V+ Q+QRE+++ L T         PE  LG       + T+SDV+VS DL V KV+
Sbjct:     7 RSDRVSAQMQREIAEFLRTG-----IDAPE--LG-------MVTVSDVDVSRDLAVAKVF 52

Query:   129 VSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186
             V+  G       A+  L   A  +R  LGRRM++R+ PEIRF  D+S ERG  +  +L
Sbjct:    53 VTFLGARLETRAAVKRLGEFAPQLRQVLGRRMRMRIIPEIRFAYDDSLERGLHMDEVL 110

GO:0003674 "molecular_function" evidence=ND

TIGR_CMR|CPS_2204 CPS_2204 "ribosome-binding factor A" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 39/121 (32%), Positives = 72/121 (59%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R   V +QIQ+E++ +L+ +       + +  L       S+TT+S VEV+ DL   K++
Sbjct:     7 RTDRVGQQIQKEIATILMRE-------IKDPRL-------SMTTVSAVEVTRDLAYAKIF 52

Query:   129 VSVFGDDRGKEVAIAGLKSKAK-YVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             V+ F D++ +  A   + ++A+ Y+RS LG+R++ R+ P +RF+ D S   G R+ A++D
Sbjct:    53 VTFFNDNQDEIKASLEVLAEAEGYIRSLLGKRLRARIMPHLRFVYDSSMSEGVRMSALVD 112

Query:   188 R 188
             +
Sbjct:   113 Q 113

GO:0006396 "RNA processing" evidence=ISS

GO:0019843 "rRNA binding" evidence=ISS

TIGR_CMR|CHY_1765 CHY_1765 "ribosome-binding factor A" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 26/76 (34%), Positives = 51/76 (67%)

Query:   112 TISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFI 171
             +++ V+++ DL   K+Y+SV+G +  K+ +   L S   +++ +L  R++LR+ PE+ F+
Sbjct:    37 SVTKVDLARDLSQAKIYISVYGSEEDKKNSFIALNSAKGFIKGELASRVRLRIMPELYFV 96

Query:   172 EDESFERGSRVIAILD 187
             ED S E G+R++ IL+
Sbjct:    97 EDPSIEYGARIMEILE 112

GO:0006396 "RNA processing" evidence=ISS

GO:0019843 "rRNA binding" evidence=ISS

UNIPROTKB|Q8EHL4 rbfA "Ribosome-binding factor A" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 47/156 (30%), Positives = 77/156 (49%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R + + +Q+Q+EL+ +L  D       + +  +G         T++DV+VS DL   KV+
Sbjct:     7 RTRRIGQQLQQELAVVLQRD-------MKDPRIG-------FVTVNDVDVSRDLSYAKVF 52

Query:   129 VSVFGDDRGK-EVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             V+ F +D+   +  +  L + A Y+R+ +  RMKLR+ PEIRF+ D S   G R+  ++ 
Sbjct:    53 VTFFEEDKDVVQEKLNALIAAAPYIRTLVAGRMKLRVMPEIRFVYDSSLVEGMRMSNLVS 112

Query:   188 RIXXXXXXXXXXXXXQFESPDLPEDERDWEGDDPDE 223
             ++             QF S D    E D E  D  E
Sbjct:   113 QVINSDKAKQQ----QFGSVDDDVIENDIEESDDTE 144

GO:0003674 "molecular_function" evidence=ND

TIGR_CMR|SO_1205 SO_1205 "ribosome-binding factor A" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 47/156 (30%), Positives = 77/156 (49%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R + + +Q+Q+EL+ +L  D       + +  +G         T++DV+VS DL   KV+
Sbjct:     7 RTRRIGQQLQQELAVVLQRD-------MKDPRIG-------FVTVNDVDVSRDLSYAKVF 52

Query:   129 VSVFGDDRGK-EVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             V+ F +D+   +  +  L + A Y+R+ +  RMKLR+ PEIRF+ D S   G R+  ++ 
Sbjct:    53 VTFFEEDKDVVQEKLNALIAAAPYIRTLVAGRMKLRVMPEIRFVYDSSLVEGMRMSNLVS 112

Query:   188 RIXXXXXXXXXXXXXQFESPDLPEDERDWEGDDPDE 223
             ++             QF S D    E D E  D  E
Sbjct:   113 QVINSDKAKQQ----QFGSVDDDVIENDIEESDDTE 144

GO:0003674 "molecular_function" evidence=ND

GO:0006396 "RNA processing" evidence=ISS

UNIPROTKB|Q9KU79 rbfA "Ribosome-binding factor A" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 43/122 (35%), Positives = 69/122 (56%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R + VA+Q+Q+EL+ M+L  +V       ++ LG       + TISDVEVS DL   KV+
Sbjct:     7 RTQRVAQQLQKELA-MILQREVR------DSRLG-------MVTISDVEVSRDLAYAKVF 52

Query:   129 VSVFG-DDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             V+     ++  E  +A L+     +R  LG++++LRLTPEIRF  D +   G R+  ++ 
Sbjct:    53 VTFLCIGEQTPESCLAALREHEVQIRMMLGKQIRLRLTPEIRFYYDNTLVEGMRMSNLVT 112

Query:   188 RI 189
              +
Sbjct:   113 EV 114

GO:0003674 "molecular_function" evidence=ND

GO:0006396 "RNA processing" evidence=ISS

TIGR_CMR|VC_0644 VC_0644 "ribosome-binding factor A" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 152 (58.6 bits), Expect = 5.8e-11, P = 5.8e-11
 Identities = 43/122 (35%), Positives = 69/122 (56%)

Query:    69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
             R + VA+Q+Q+EL+ M+L  +V       ++ LG       + TISDVEVS DL   KV+
Sbjct:     7 RTQRVAQQLQKELA-MILQREVR------DSRLG-------MVTISDVEVSRDLAYAKVF 52

Query:   129 VSVFG-DDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
             V+     ++  E  +A L+     +R  LG++++LRLTPEIRF  D +   G R+  ++ 
Sbjct:    53 VTFLCIGEQTPESCLAALREHEVQIRMMLGKQIRLRLTPEIRFYYDNTLVEGMRMSNLVT 112

Query:   188 RI 189
              +
Sbjct:   113 EV 114

GO:0003674 "molecular_function" evidence=ND

GO:0006396 "RNA processing" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O65693	RBFA_ARATH	No assigned EC number	0.7130	0.9257	0.9860	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	229
PRK00521	120	PRK00521, rbfA, ribosome-binding factor A; Validat	1e-37
pfam02033	104	pfam02033, RBFA, Ribosome-binding factor A	2e-34
COG0858	118	COG0858, RbfA, Ribosome-binding factor A [Translat	6e-32
TIGR00082	114	TIGR00082, rbfA, ribosome-binding factor A	5e-22
PRK13815	122	PRK13815, PRK13815, ribosome-binding factor A; Pro	5e-16
PRK13816	131	PRK13816, PRK13816, ribosome-binding factor A; Pro	2e-14
PRK13817	119	PRK13817, PRK13817, ribosome-binding factor A; Pro	5e-06
PRK13818	121	PRK13818, PRK13818, ribosome-binding factor A; Pro	5e-06

>gnl|CDD|234787 PRK00521, rbfA, ribosome-binding factor A; Validated

 Score =  127 bits (321), Expect = 1e-37
 Identities = 56/135 (41%), Positives = 79/135 (58%), Gaps = 20/135 (14%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLT---DKVLQFAVLPEAALGADRYLSSLTTISDVEVSA 120
           MA  +R   VA+QIQREL+++L     D  L                    T++DVEVS 
Sbjct: 2   MAESQRALRVAEQIQRELAEILQREIKDPRLGMV-----------------TVTDVEVSP 44

Query: 121 DLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS 180
           DL   KVYV+V GD+  KE A+A LK  A ++RS+LG+R++LR  PE+RF+ DES E G+
Sbjct: 45  DLAHAKVYVTVLGDEEDKEEALAALKKAAGFLRSELGKRLRLRYVPELRFVYDESLEYGN 104

Query: 181 RVIAILDRIKAEKEA 195
           R+  +L + K E + 
Sbjct: 105 RIDELLRKAKKEDDE 119

Length = 120

>gnl|CDD|216854 pfam02033, RBFA, Ribosome-binding factor A

 Score =  118 bits (298), Expect = 2e-34
 Identities = 49/118 (41%), Positives = 73/118 (61%), Gaps = 14/118 (11%)

Query: 69  RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
           R + VA+ IQREL+++L  +       L +  LG       L T+++VEVS DL   KVY
Sbjct: 1   RTERVAELIQRELAEILQRE-------LKDPRLG-------LVTVTEVEVSPDLSHAKVY 46

Query: 129 VSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL 186
           VSV GD+  KE  +  L   A ++RS+L +R++LR TPE+RF+ D+S E G+R+  +L
Sbjct: 47  VSVLGDEEEKEETLKALNKAAGFIRSELAKRLRLRYTPELRFVYDDSLEYGARIEELL 104

Length = 104

>gnl|CDD|223927 COG0858, RbfA, Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]

 Score =  112 bits (282), Expect = 6e-32
 Identities = 50/135 (37%), Positives = 77/135 (57%), Gaps = 21/135 (15%)

Query: 64  MANPRRVKMVAKQIQRELSDML---LTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSA 120
           MA   R K VA+QIQ+EL+++L   + D  L                    T++DVEVS 
Sbjct: 1   MAKSTRAKRVAEQIQKELAEILQREIKDPRLGL-----------------VTVTDVEVSK 43

Query: 121 DLQVVKVYVSVFGDDRG-KEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG 179
           DL   KVYV+V GD+   K   +A L     ++RS+LG+R++LR TPE+ F+ D+S E G
Sbjct: 44  DLSHAKVYVTVLGDEESSKAEILAALNKAKGFIRSELGKRLRLRKTPELHFVYDDSIENG 103

Query: 180 SRVIAILDRIKAEKE 194
           +++ A+L+ +K   +
Sbjct: 104 NKIDALLNDLKKADD 118

Length = 118

>gnl|CDD|129191 TIGR00082, rbfA, ribosome-binding factor A

 Score = 86.7 bits (215), Expect = 5e-22
 Identities = 38/127 (29%), Positives = 65/127 (51%), Gaps = 20/127 (15%)

Query: 69  RVKMVAKQIQRELSDML---LTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVV 125
           R + V   I RE++ +L   + D  +                    T++ VEVS DLQ  
Sbjct: 5   RKERVESDIIREINRILIREIKDPRVGM-----------------LTVTKVEVSKDLQHA 47

Query: 126 KVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAI 185
           KV+V  +GD+   +  +  L     ++RS LG+ M+LR TPE+ F++D S ++G R+  +
Sbjct: 48  KVFVDCYGDEEAIDRVVKALNKAKGFIRSLLGQAMRLRKTPELHFVKDNSLDKGMRIENL 107

Query: 186 LDRIKAE 192
           ++ +K E
Sbjct: 108 INSLKKE 114

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'terminal helix region of 16S rRNA. Mutants lacking rbfA have a cold-sensitive phenotype [Transcription, RNA processing]. Length = 114

>gnl|CDD|172345 PRK13815, PRK13815, ribosome-binding factor A; Provisional

 Score = 71.4 bits (175), Expect = 5e-16
 Identities = 33/90 (36%), Positives = 55/90 (61%)

Query: 112 TISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFI 171
           TI+ V+V+ DL +  +Y +V GDD  K+   AGL S   ++R +LG+ +++R  PE+ F 
Sbjct: 33  TITGVKVTDDLHLATIYFTVIGDDEAKKSTEAGLNSARGFIRKELGKVLRMRYAPELIFK 92

Query: 172 EDESFERGSRVIAILDRIKAEKEAAKSKNK 201
            DES E G+R+ ++L  I  E +   S++ 
Sbjct: 93  YDESQEYGNRIDSLLKEIGTEHDGDDSEDS 122

Length = 122

>gnl|CDD|184344 PRK13816, PRK13816, ribosome-binding factor A; Provisional

 Score = 67.6 bits (165), Expect = 2e-14
 Identities = 40/142 (28%), Positives = 72/142 (50%), Gaps = 20/142 (14%)

Query: 68  RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKV 127
           +R+K +A  +QRELS+ L+  ++             D  L  L TIS V+VS DL    V
Sbjct: 3   QRLKRMADSVQRELSE-LIRQEL------------KDPRLGGLVTISSVKVSPDLGYADV 49

Query: 128 YVSVFGDDRGKEVAIAG-------LKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS 180
           YV+V G +   +            L   + ++R++L RR+K R+TP +RF  D++   G+
Sbjct: 50  YVTVMGRELSDDQNEVAHRETLDVLNKASGFLRTELSRRIKTRITPRLRFHYDKTNAYGN 109

Query: 181 RVIAILDRIKAEKEAAKSKNKE 202
            +  ++++   +    +S ++E
Sbjct: 110 YMFGLIEKAVQDLPKRESDDEE 131

Length = 131

>gnl|CDD|139879 PRK13817, PRK13817, ribosome-binding factor A; Provisional

 Score = 44.0 bits (103), Expect = 5e-06
 Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 109 SLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEI 168
           S  +++ V +S DL+  KV+ S+  +   KEV  A L     Y+R  L +   LR  P++
Sbjct: 30  SKISLTAVSISPDLKQAKVFYSLLENQNEKEVQKA-LNKATGYLRHLLAQATVLRYVPKL 88

Query: 169 RFIEDESFERGSRVIAILDRIKAEKEAAKS 198
            F+ DES ER  R+  +++R   + ++ +S
Sbjct: 89  EFVYDESIERAHRISLLIERALKKDDSDES 118

Length = 119

>gnl|CDD|184345 PRK13818, PRK13818, ribosome-binding factor A; Provisional

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 38/134 (28%), Positives = 63/134 (47%), Gaps = 17/134 (12%)

Query: 69  RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
           R+  V  +I REL+ +L  +               D  LS +T I+ VE + DL    VY
Sbjct: 4   RIGRVEGEILRELTKILRKNI-------------RDPRLSDVT-ITAVECTNDLSYATVY 49

Query: 129 VSVFGDDRGKEVAI-AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
            S+  +D  KE  +  GL+     +R  LG+ + +   PE+ F  D S   GS++  ++ 
Sbjct: 50  YSLLTEDEAKEKEVQEGLEKAKGMMRHLLGQTLTVYKVPELIFKRDNSVAYGSKIDRLIA 109

Query: 188 RIKAEKEAAKSKNK 201
            +K  K+  + +NK
Sbjct: 110 EVK--KQDQERENK 121

Length = 121

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	229
PRK13816	131	ribosome-binding factor A; Provisional	100.0
TIGR00082	114	rbfA ribosome-binding factor A. Associates with fr	100.0
PRK13815	122	ribosome-binding factor A; Provisional	100.0
PRK00521	120	rbfA ribosome-binding factor A; Validated	100.0
PRK13818	121	ribosome-binding factor A; Provisional	100.0
PRK13817	119	ribosome-binding factor A; Provisional	99.98
COG0858	118	RbfA Ribosome-binding factor A [Translation, ribos	99.97
PF02033	104	RBFA: Ribosome-binding factor A; InterPro: IPR0002	99.96
KOG4700	207	consensus Uncharacterized homolog of ribosome-bind	99.55

>PRK13816 ribosome-binding factor A; Provisional

Probab=100.00  E-value=8e-34  Score=231.67  Aligned_cols=121  Identities=31%  Similarity=0.544  Sum_probs=108.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCc-------hhHHH
Q 027059           68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDD-------RGKEV  140 (229)
Q Consensus        68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~-------~~~~~  140 (229)
                      +|+.||+++|+++||++|+++.             .||++.++||||+|+||+||++||||||++|+.       .+++.
T Consensus         3 ~R~~Rv~~~Irreis~il~~ei-------------~dprl~~~vtVT~V~vS~DL~~AkVyvs~lg~~~~~~~~~~~~~~   69 (131)
T PRK13816          3 QRLKRMADSVQRELSELIRQEL-------------KDPRLGGLVTISSVKVSPDLGYADVYVTVMGRELSDDQNEVAHRE   69 (131)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhc-------------cCcccCCceEEeEEEECCCCCeEEEEEEecCCccccccchhHHHH
Confidence            5999999999999999997532             377776789999999999999999999999863       34567


Q ss_pred             HHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHhhhhccCc
Q 027059          141 AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEAAKSKNK  201 (229)
Q Consensus       141 vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~~~~~~~~  201 (229)
                      ++++|++++||||+.||++|+||++|+|+|++|+|++++.+|++||+++.+++++++++++
T Consensus        70 ~l~~L~~a~g~iR~~L~krl~lR~~PeL~F~~D~s~e~~~~I~~Ll~~i~~~~~~~~~~~~  130 (131)
T PRK13816         70 TLDVLNKASGFLRTELSRRIKTRITPRLRFHYDKTNAYGNYMFGLIEKAVQDLPKRESDDE  130 (131)
T ss_pred             HHHHHHHHHHHHHHHHHhhcCCeECCEEEEEECCChhHHHHHHHHHHHHHhhhhccccccc
Confidence            8999999999999999999999999999999999999999999999999988776666653

>TIGR00082 rbfA ribosome-binding factor A

Probab=100.00  E-value=2.5e-33  Score=223.62  Aligned_cols=114  Identities=35%  Similarity=0.643  Sum_probs=104.4

Q ss_pred             CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHH
Q 027059           64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIA  143 (229)
Q Consensus        64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~  143 (229)
                      |+ ++|+.||+++|+++||++|+++.             .||++ ++||||+|+||+||++||||||++|++..++.+++
T Consensus         1 m~-~~R~~Rv~~~i~~eis~il~~~i-------------~dp~~-~~vtVt~V~lS~Dl~~AkVyvs~~~~~~~~~~~l~   65 (114)
T TIGR00082         1 MA-SYRKERVESDIIREINRILIREI-------------KDPRV-GMLTVTKVEVSKDLQHAKVFVDCYGDEEAIDRVVK   65 (114)
T ss_pred             Cc-cHHHHHHHHHHHHHHHHHHHHhc-------------cCCCC-CeEEEeEEEECCCCCEEEEEEEECCChhhHHHHHH
Confidence            54 57999999999999999998642             37777 47999999999999999999999998777788999


Q ss_pred             HHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059          144 GLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE  192 (229)
Q Consensus       144 aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e  192 (229)
                      +|++++|+||+.||++|+||++|+|+|++|+++|++.+|++||+++.++
T Consensus        66 ~L~~~~g~iR~~l~k~l~lR~~P~L~F~~D~s~e~~~~i~~ll~~i~~~  114 (114)
T TIGR00082        66 ALNKAKGFIRSLLGQAMRLRKTPELHFVKDNSLDKGMRIENLINSLKKE  114 (114)
T ss_pred             HHHHHHHHHHHHHHhhCCceECCEEEEEecCcHHHHHHHHHHHHHhhhC
Confidence            9999999999999999999999999999999999999999999998753

Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'terminal helix region of 16S rRNA. Mutants lacking rbfA have a cold-sensitive phenotype.

>PRK13815 ribosome-binding factor A; Provisional

Probab=100.00  E-value=2.2e-33  Score=226.69  Aligned_cols=111  Identities=35%  Similarity=0.610  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHH
Q 027059           68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKS  147 (229)
Q Consensus        68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~  147 (229)
                      +|++||+++|+++||++|+++.             +||++ ++||||+|+||+||++||||||++|++..++.++++|++
T Consensus         3 ~R~~Rv~~~Ir~eis~il~~~i-------------~dprl-~~vtVt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~L~~   68 (122)
T PRK13815          3 KRSEKVAEAIHELISGLLVKGL-------------KDPRI-GFVTITGVKVTDDLHLATIYFTVIGDDEAKKSTEAGLNS   68 (122)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhC-------------cCCCC-CceEEeEEEECCCCCEEEEEEEECCCchhHHHHHHHHHH
Confidence            5999999999999999998542             37777 479999999999999999999999877666789999999


Q ss_pred             hhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059          148 KAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE  192 (229)
Q Consensus       148 aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e  192 (229)
                      ++|+||+.||++|+||++|+|+|++|+++|++.+|++||++++++
T Consensus        69 a~g~iR~~l~~~l~lR~~PeL~F~~D~s~e~~~~I~~lL~~i~~~  113 (122)
T PRK13815         69 ARGFIRKELGKVLRMRYAPELIFKYDESQEYGNRIDSLLKEIGTE  113 (122)
T ss_pred             HHHHHHHHHHHhCCCeECCEEEEEECCChHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999865

>PRK00521 rbfA ribosome-binding factor A; Validated

Probab=100.00  E-value=3.9e-33  Score=223.34  Aligned_cols=117  Identities=48%  Similarity=0.749  Sum_probs=108.1

Q ss_pred             cCCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHH
Q 027059           63 CMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAI  142 (229)
Q Consensus        63 ~M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl  142 (229)
                      ||+.++|++||+++|+++|+++|+++.             .||+++ .||||+|++|+||++|+||||++|++.+.+.++
T Consensus         1 ~~~~~~R~~Rv~~~i~~~is~il~~~i-------------~d~~~~-~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~   66 (120)
T PRK00521          1 MMAESQRALRVAEQIQRELAEILQREI-------------KDPRLG-MVTVTDVEVSPDLAHAKVYVTVLGDEEDKEEAL   66 (120)
T ss_pred             CCCccHHHHHHHHHHHHHHHHHHHHHc-------------cCCCCC-eeEEEEEEECCCCCEEEEEEEECCCchhHHHHH
Confidence            688899999999999999999998532             367765 799999999999999999999999777778899


Q ss_pred             HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhH
Q 027059          143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEK  193 (229)
Q Consensus       143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~  193 (229)
                      ++|++++|+||+.||++|+||++|+|+|++|++++++.+|++||+++++++
T Consensus        67 ~~L~~~~~~iR~~la~~l~lr~~P~L~F~~D~s~e~~~~i~~lL~~i~~~~  117 (120)
T PRK00521         67 AALKKAAGFLRSELGKRLRLRYVPELRFVYDESLEYGNRIDELLRKAKKED  117 (120)
T ss_pred             HHHHHhHHHHHHHHHhhCCCccCCEEEEEECCCHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999999999999999999999999998764

>PRK13818 ribosome-binding factor A; Provisional

Probab=100.00  E-value=1.4e-32  Score=221.78  Aligned_cols=114  Identities=29%  Similarity=0.452  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCch-hHHHHHHHHH
Q 027059           68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDR-GKEVAIAGLK  146 (229)
Q Consensus        68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~-~~~~vl~aL~  146 (229)
                      +|++||+++|+++||++|+++.             +||+++ +||||+|+||+||++||||||++|+++ .++.++++|+
T Consensus         3 ~R~~Rv~~~i~reis~ii~~ei-------------~Dprl~-~vtVt~V~lS~Dl~~AkVyvs~~~~~~~~~~~~~~~L~   68 (121)
T PRK13818          3 HRIGRVEGEILRELTKILRKNI-------------RDPRLS-DVTITAVECTNDLSYATVYYSLLTEDEAKEKEVQEGLE   68 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhC-------------cCCCcC-ceEEeEEEECCCCCEEEEEEEeCCCchhHHHHHHHHHH
Confidence            6999999999999999998532             478874 799999999999999999999998543 3467889999


Q ss_pred             HhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHhh
Q 027059          147 SKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKEA  195 (229)
Q Consensus       147 ~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~~  195 (229)
                      +++||||+.||++|+||++|+|+|++|+|++++.+|++||+++.+++.+
T Consensus        69 ~a~g~iR~~la~~l~lR~~P~L~F~~D~s~e~~~~I~~Ll~~i~~~~~~  117 (121)
T PRK13818         69 KAKGMMRHLLGQTLTVYKVPELIFKRDNSVAYGSKIDRLIAEVKKQDQE  117 (121)
T ss_pred             HhHHHHHHHHHhhCCCeECCEEEEEeCCChHHHHHHHHHHHHHHhhhhh
Confidence            9999999999999999999999999999999999999999999865433

>PRK13817 ribosome-binding factor A; Provisional

Probab=99.98  E-value=5.7e-32  Score=217.48  Aligned_cols=110  Identities=28%  Similarity=0.491  Sum_probs=100.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHH
Q 027059           68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKS  147 (229)
Q Consensus        68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~  147 (229)
                      +|++||+++|+++||++|+++.             .||+++ +||||+|+||+||++||||||++|+. +.+.++++|++
T Consensus         3 ~R~~Rv~~~I~reis~il~~ei-------------~dp~l~-~vtVt~V~vS~Dl~~AkVyvs~~~~~-~~~~~~~~L~~   67 (119)
T PRK13817          3 QRQQRVADLIHQQLAELLKKEV-------------RDSRLS-KISLTAVSISPDLKQAKVFYSLLENQ-NEKEVQKALNK   67 (119)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhc-------------cCCCCC-ceEEeEEEECCCCCEEEEEEEECCCc-cHHHHHHHHHH
Confidence            5999999999999999997532             377774 79999999999999999999999865 45668999999


Q ss_pred             hhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHh
Q 027059          148 KAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAE  192 (229)
Q Consensus       148 aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e  192 (229)
                      ++|+||+.||++|+||++|+|+|++|+++|++.+|++||+++.++
T Consensus        68 a~g~iR~~l~~~l~lR~~PeL~F~~D~s~e~~~~I~~Ll~~l~~~  112 (119)
T PRK13817         68 ATGYLRHLLAQATVLRYVPKLEFVYDESIERAHRISLLIERALKK  112 (119)
T ss_pred             hHHHHHHHHHHhCCCeECCEEEEEEcCchHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999754

>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]

Probab=99.97  E-value=1.4e-31  Score=215.34  Aligned_cols=116  Identities=42%  Similarity=0.714  Sum_probs=105.2

Q ss_pred             CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecC-CchhHHHHH
Q 027059           64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFG-DDRGKEVAI  142 (229)
Q Consensus        64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g-~~~~~~~vl  142 (229)
                      |+...|.+|++++|+++|+++|+++  +           +||+++. ++||+|+||+||++|+||||++| .....+.++
T Consensus         1 M~~~~R~~rv~e~i~~~l~~il~~e--i-----------kDprl~~-~~Vt~V~vS~Dl~~A~Vyvt~l~~~~~~~~~~~   66 (118)
T COG0858           1 MAKSTRAKRVAEQIQKELAEILQRE--I-----------KDPRLGL-VTVTDVEVSKDLSHAKVYVTVLGDEESSKAEIL   66 (118)
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHH--c-----------cCCCcCc-eEEEEEEEcCCCceEEEEEEecCCchhhHHHHH
Confidence            6777799999999999999999863  2           3888855 66999999999999999999999 444678889


Q ss_pred             HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhH
Q 027059          143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEK  193 (229)
Q Consensus       143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~  193 (229)
                      ++|++|+|+||+.||++++||++|+|+|++|+|++++.+|++||+++++.+
T Consensus        67 ~~L~~A~g~ir~~l~~~~~lr~~PeL~F~~D~s~~~~~ki~~Ll~~l~~~~  117 (118)
T COG0858          67 AALNKAKGFIRSELGKRLRLRKTPELHFVYDDSIENGNKIDALLNDLKKAD  117 (118)
T ss_pred             HHHHHhHHHHHHHHHHhCCeEeCCeEEEEeCcccchHHHHHHHHHHhhhcC
Confidence            999999999999999999999999999999999999999999999998654

>PF02033 RBFA: Ribosome-binding factor A; InterPro: IPR000238 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.96  E-value=1.4e-29  Score=196.74  Aligned_cols=104  Identities=40%  Similarity=0.680  Sum_probs=90.4

Q ss_pred             HHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHHh
Q 027059           69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSK  148 (229)
Q Consensus        69 R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~a  148 (229)
                      |++|++++|+++|+++|.++.             .||++ ++||||+|++|+|+++|+|||+++|++.+.+.++++|+++
T Consensus         1 R~~Rv~~~i~~~i~~il~~~~-------------~d~~l-~~vtIt~V~ls~Dl~~a~Vy~~~~~~~~~~~~~~~~L~~~   66 (104)
T PF02033_consen    1 RQQRVESLIQREISEILQREI-------------KDPRL-KLVTITRVELSPDLSHAKVYVSILGDEEEQEEVLEALNKA   66 (104)
T ss_dssp             THHHHHHHHHHHHHHHHCTCT-------------SSCGH-HCEEEEEEEECTTSSEEEEEEEESSSHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHHhhc-------------cCcCc-ceEEEEEEEECCCCCEEEEEEEEecCchhHHHHHHHHHHH
Confidence            789999999999999998652             26666 5799999999999999999999998888889999999999


Q ss_pred             hHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHH
Q 027059          149 AKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAIL  186 (229)
Q Consensus       149 ag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LL  186 (229)
                      +|+||+.||++|+||++|+|+|++|++++++.+|++||
T Consensus        67 ~~~iR~~l~~~l~lr~~P~L~F~~D~~~e~~~~i~~ll  104 (104)
T PF02033_consen   67 AGFIRHELAKRLNLRRVPELRFVYDDSIEKAARIEKLL  104 (104)
T ss_dssp             HHHHHHHHHHHTTSSSG-EEEEEESTTTSSS------S
T ss_pred             HHHHHHHHHhhcCCCcCCEEEEEECCCHHHHHHHHHhC
Confidence            99999999999999999999999999999999999986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosome-binding factor A [] (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most bacteria. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing; PDB: 2R1C_A 2DYJ_B 2KZF_A 2E7G_A 1JOS_A 1KKG_A 1PA4_A.

>KOG4700 consensus Uncharacterized homolog of ribosome-binding factor A [General function prediction only]

Probab=99.55  E-value=3.2e-14  Score=122.74  Aligned_cols=116  Identities=21%  Similarity=0.271  Sum_probs=101.0

Q ss_pred             cCCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHH
Q 027059           63 CMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAI  142 (229)
Q Consensus        63 ~M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl  142 (229)
                      |--+.+|...++.++.+.|+++|+.+..- ..+           .+-.|.|++|++++|++.+.|||.+-++.+ ..++.
T Consensus        25 r~~d~~r~~~Ln~Ll~~~itdvlaTgava-~~l-----------~~l~vqiS~V~vt~dFS~~~vYWm~~~~ge-N~e~e   91 (207)
T KOG4700|consen   25 RRLDDKKVVQLNRLLEERITDVLATGAVA-EML-----------GRLQVQISRVRVTRDFSQVSVYWMCRGDGE-NSEIE   91 (207)
T ss_pred             hccchHHHHHHHHHHHHHHHHHHhchHHH-HHH-----------hhcceeEEEEEeccchhhheeEEEecCCcc-HHHHH
Confidence            44567899999999999999999974321 111           134699999999999999999999987765 56788


Q ss_pred             HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHH
Q 027059          143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKA  191 (229)
Q Consensus       143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~  191 (229)
                      +.|++.++.||+.|.+.++|+.||+|.|+-|++.--..+|++||++++-
T Consensus        92 ~~L~rs~~~~rh~l~~~~~~g~vP~IkFV~DK~~~~l~e~d~ll~~aD~  140 (207)
T KOG4700|consen   92 DFLERSKHQIRHRLEESIGIGTVPEIKFVGDKALLMLQEMDKLLREADY  140 (207)
T ss_pred             HHHHHHHHHHHHHHHHHhccccCCceEEecchHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999999999999999999999999999963

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	229
1jos_A	128	Ribosome Binding Factor A(Rbfa) Length = 128		8e-12
1kkg_A	108	Nmr Structure Of Ribosome-Binding Factor A (Rbfa) L		2e-09
2kzf_A	106	Solution Nmr Structure Of The Thermotoga Maritima P		2e-04

>pdb|1JOS|A Chain A, Ribosome Binding Factor A(Rbfa) Length = 128

Iteration: 1
 Score = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 41/117 (35%), Positives = 68/117 (58%), Gaps = 16/117 (13%)
Query: 68  RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKV 127
           +R   VA++IQ+E++ +L  +       + +  +G       + T+SDVEVS+DL   K+
Sbjct: 6   KRSDRVAQEIQKEIAVILQRE-------VKDPRIG-------MVTVSDVEVSSDLSYAKI 51
Query: 128 YVSVF--GDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRV 182
           +V+     D+   E  + GL+  + Y+RS LG+ M+LR+ PEIRFI D+S   G R+
Sbjct: 52  FVTFLFDHDEMAIEQGMKGLEKASPYIRSLLGKAMRLRIVPEIRFIYDQSLVEGMRM 108

>pdb|1KKG|A Chain A, Nmr Structure Of Ribosome-Binding Factor A (Rbfa) Length = 108

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 41/123 (33%), Positives = 69/123 (56%), Gaps = 20/123 (16%)
Query: 62  KCMANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSAD 121
           K    P+RV   A+++Q+E++ ++L  ++             D  L  +TT+S VE+S D
Sbjct: 3   KEFGRPQRV---AQEMQKEIA-LILQREI------------KDPRLGMMTTVSGVEMSRD 46
Query: 122 LQVVKVYVSVFGDDRGKEVAIAGLKS---KAKYVRSQLGRRMKLRLTPEIRFIEDESFER 178
           L   KVYV+ F +D+ ++   AG+K+    + ++RS LG+ M+LR+ PE+ F  D S   
Sbjct: 47  LAYAKVYVT-FLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVE 105
Query: 179 GSR 181
           G R
Sbjct: 106 GMR 108

>pdb|2KZF|A Chain A, Solution Nmr Structure Of The Thermotoga Maritima Protein Tm0855 A Putative Ribosome Binding Factor A Length = 106

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 35/68 (51%)
Query: 110 LTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIR 169
             T S VE+S D +   VYVS  G    ++  +  L     + R+ + + ++L + PEIR
Sbjct: 35  FVTFSRVELSKDKRYADVYVSFLGTPEERKETVEILNRAKGFFRTFIAKNLRLYVAPEIR 94
Query: 170 FIEDESFE 177
           F ED+  E
Sbjct: 95  FYEDKGIE 102
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
2kzf_A	106	RBFA, ribosome-binding factor A; JCSG, joint cente	5e-37
1jos_A	128	RBFA, ribosome-binding factor A; RNA binding prote	2e-35
1pa4_A	116	Probable ribosome-binding factor A; structural gen	2e-34
2e7g_A	129	Putative ribosome-binding factor A; RBFA, structur	5e-32
2dyj_A	95	Ribosome-binding factor A; 16S rRNA processing, 17	5e-26

>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural genomics, PSI-biology, protein structure initiative; NMR {Thermotoga maritima} Length = 106

 Score =  124 bits (314), Expect = 5e-37
 Identities = 30/118 (25%), Positives = 49/118 (41%), Gaps = 13/118 (11%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQ 123
           M    R  M+  +IQ+ L + L   +               R      T S VE+S D +
Sbjct: 2   MNPAYRKAMLESEIQKLLMEALQQLR-------------DPRLKKDFVTFSRVELSKDKR 48

Query: 124 VVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSR 181
              VYVS  G    ++  +  L     + R+ + + ++L + PEIRF ED+  E   +
Sbjct: 49  YADVYVSFLGTPEERKETVEILNRAKGFFRTFIAKNLRLYVAPEIRFYEDKGIEASVK 106

>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

 Score =  121 bits (305), Expect = 2e-35
 Identities = 45/144 (31%), Positives = 72/144 (50%), Gaps = 23/144 (15%)

Query: 64  MANP-RRVKMVAKQIQRELSDMLLT---DKVLQFAVLPEAALGADRYLSSLTTISDVEVS 119
           MA   +R   VA++IQ+E++ +L     D  +                    T+SDVEVS
Sbjct: 1   MAREFKRSDRVAQEIQKEIAVILQREVKDPRIGM-----------------VTVSDVEVS 43

Query: 120 ADLQVVKVYVSVFG--DDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFE 177
           +DL   K++V+     D+   E  + GL+  + Y+RS LG+ M+LR+ PEIRFI D+S  
Sbjct: 44  SDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPYIRSLLGKAMRLRIVPEIRFIYDQSLV 103

Query: 178 RGSRVIAILDRIKAEKEAAKSKNK 201
            G R+  ++  +  E E    +  
Sbjct: 104 EGMRMSNLVTNVVREDEKKHVEES 127

>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

 Score =  118 bits (298), Expect = 2e-34
 Identities = 21/134 (15%), Positives = 54/134 (40%), Gaps = 22/134 (16%)

Query: 64  MANPRRVKMVAKQIQRELSDMLLT---DKVLQFAVLPEAALGADRYLSSLTTISDVEVSA 120
           MA+  + + +   I R ++  ++    ++ ++                    ++ V++S 
Sbjct: 1   MAS-YKKERLENDIIRLINRTVIHEIYNETVKTG-----------------HVTHVKLSD 42

Query: 121 DLQVVKVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS 180
           DL  V VY+  +  ++   V +             L   + L    +I F++D++ +   
Sbjct: 43  DLLHVTVYLDCYNREQIDRV-VGAFNQAKGVFSRVLAHNLYLAKAVQIHFVKDKAIDNAM 101

Query: 181 RVIAILDRIKAEKE 194
           R+ +I++ +K  K 
Sbjct: 102 RIESIINSLKKSKP 115

>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

 Score =  112 bits (282), Expect = 5e-32
 Identities = 22/124 (17%), Positives = 46/124 (37%), Gaps = 12/124 (9%)

Query: 66  NPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVV 125
           +  R++ +   + + L+D+L T +V            +         +S V ++ D    
Sbjct: 11  DHARLRALNGLLYKALTDLLCTPEV------------SQELYDLNVELSKVSLTPDFSAC 58

Query: 126 KVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAI 185
           + Y              A L+  A ++R  L  +  LR  P I F++D+     + +  +
Sbjct: 59  RAYWKTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQTLRNVPPIVFVQDKGNAALAELDQL 118

Query: 186 LDRI 189
           L   
Sbjct: 119 LAVA 122

>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain; 1.84A {Thermus thermophilus} SCOP: d.52.7.1 PDB: 2r1c_A Length = 95

 Score = 96.1 bits (240), Expect = 5e-26
 Identities = 24/110 (21%), Positives = 45/110 (40%), Gaps = 22/110 (20%)

Query: 68  RRVKMVAKQIQRELSDML--LTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVV 125
                +  Q++R L++ +  L D  L                    T+  V +S D  V+
Sbjct: 3   YGKAHLEAQLKRALAEEIQALEDPRLFLL-----------------TVEAVRLSKDGSVL 45

Query: 126 KVYVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDES 175
            VYV  F ++   E A+  L    + + + L RR+++R  P + F+   +
Sbjct: 46  SVYVEAFREE---EGALRALSRAERRLVAALARRVRMRRLPRLEFLPWRA 92

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
1jos_A	128	RBFA, ribosome-binding factor A; RNA binding prote	100.0
1pa4_A	116	Probable ribosome-binding factor A; structural gen	99.98
2e7g_A	129	Putative ribosome-binding factor A; RBFA, structur	99.97
2kzf_A	106	RBFA, ribosome-binding factor A; JCSG, joint cente	99.97
2dyj_A	95	Ribosome-binding factor A; 16S rRNA processing, 17	99.96

>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

Probab=100.00  E-value=3.7e-34  Score=230.92  Aligned_cols=117  Identities=38%  Similarity=0.628  Sum_probs=91.4

Q ss_pred             CCC-hHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecC--CchhHHH
Q 027059           64 MAN-PRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFG--DDRGKEV  140 (229)
Q Consensus        64 M~~-~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g--~~~~~~~  140 (229)
                      |+. ..|+.||+++|+++|+++|+++.             +||+++ +||||+|+||+||++||||||++|  ++.+.+.
T Consensus         1 M~~~~~R~~Rv~~~i~~~ls~il~~ei-------------kDprl~-~vtVt~V~vS~Dl~~AkVyvs~~g~~~~~~~~~   66 (128)
T 1jos_A            1 MAREFKRSDRVAQEIQKEIAVILQREV-------------KDPRIG-MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQ   66 (128)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHC-------------CCTTTC-CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHH
T ss_pred             CCCcchHHHHHHHHHHHHHHHHHHHHc-------------cCCccC-ceEEeEEEECCCCCEEEEEEEeCCCCchhhHHH
Confidence            664 35999999999999999997531             478875 799999999999999999999998  6667788


Q ss_pred             HHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhHh
Q 027059          141 AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEKE  194 (229)
Q Consensus       141 vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~~  194 (229)
                      ++++|++++||||++||++++||++|+|+|++|++++++.+|++||++++++++
T Consensus        67 ~~~~L~~a~g~iR~~l~~~l~lr~~PeL~F~~D~s~e~~~~i~~Ll~~~~~~~~  120 (128)
T 1jos_A           67 GMKGLEKASPYIRSLLGKAMRLRIVPEIRFIYDQSLVEGMRMSNLVTNVVREDE  120 (128)
T ss_dssp             HHHHHHHTHHHHHHHHHHHHCCSSCCEEEEEECCCCCCCC--------------
T ss_pred             HHHHHHHHHHHHHHHHHhhcCCCcCCeEEEEEcCcHHHHHHHHHHHHHHHhcch
Confidence            999999999999999999999999999999999999999999999999987654

>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

Probab=99.98  E-value=6e-34  Score=226.10  Aligned_cols=114  Identities=18%  Similarity=0.359  Sum_probs=89.0

Q ss_pred             CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHH
Q 027059           64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIA  143 (229)
Q Consensus        64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~  143 (229)
                      |+ ++|++||+++|+++||++|+++.             +||+++ +||||+|+||+||++||||||++|++. .+.+++
T Consensus         1 M~-~~R~~Rv~~~i~~~ls~il~~ei-------------kDprl~-~vtVt~V~vs~Dl~~AkVyvs~~~~~~-~~~~~~   64 (116)
T 1pa4_A            1 MA-SYKKERLENDIIRLINRTVIHEI-------------YNETVK-TGHVTHVKLSDDLLHVTVYLDCYNREQ-IDRVVG   64 (116)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCS-------------SSSCHH-HHCCSCCEEETTTTEEEECCCCSSSSS-HHHHHH
T ss_pred             Cc-cHHHHHHHHHHHHHHHHHHHHhc-------------cCcccC-ceEEeEEEECCCCCEEEEEEEeCCchh-HHHHHH
Confidence            66 47999999999999999997532             377775 799999999999999999999998764 677999


Q ss_pred             HHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHHhH
Q 027059          144 GLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKAEK  193 (229)
Q Consensus       144 aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~e~  193 (229)
                      +|++|+||||++||++++||++|+|+|++|+|++++.+|++||+++++++
T Consensus        65 ~L~~a~g~iR~~l~~~l~lr~~PeL~F~~D~s~e~~~~i~~Ll~~~~~~~  114 (116)
T 1pa4_A           65 AFNQAKGVFSRVLAHNLYLAKAVQIHFVKDKAIDNAMRIESIINSLKKSK  114 (116)
T ss_dssp             HHHHTHHHHHHHHHTTCCCGGGCCCEECSSSTTSSCC-------------
T ss_pred             HHHHhHHHHHHHHHhhcCCccCCeEEEEECCcHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999999999999999999999999987653

>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

Probab=99.97  E-value=8.8e-33  Score=222.97  Aligned_cols=113  Identities=19%  Similarity=0.243  Sum_probs=98.8

Q ss_pred             ChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCC-CceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHH
Q 027059           66 NPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLS-SLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAG  144 (229)
Q Consensus        66 ~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~-~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~a  144 (229)
                      +++|+.||+++|+++|+++|+++.             .||++. .+||||+|+||+||++||||||+++++.+.+.++++
T Consensus        11 ~s~R~~Rv~~~i~~~ls~il~~~~-------------~dp~l~~~~vtVt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~~   77 (129)
T 2e7g_A           11 DHARLRALNGLLYKALTDLLCTPE-------------VSQELYDLNVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAV   77 (129)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCTT-------------TCHHHHHHTCCEEEEEECTTSCCEEEEECCCSCHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhcc-------------cCccccCCeeEEEEEEECCCCcEEEEEEEecCChhhHHHHHHH
Confidence            478999999999999999998531             123221 169999999999999999999966566666778999


Q ss_pred             HHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHHHH
Q 027059          145 LKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRIKA  191 (229)
Q Consensus       145 L~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i~~  191 (229)
                      |++|+||||++||++++||++|+|+|++|++++++.+|++||++++.
T Consensus        78 L~~a~g~iR~~l~~~l~lr~~PeL~F~~D~s~e~~~~i~~LL~~~~~  124 (129)
T 2e7g_A           78 LQRSAAHMRHLLMSQQTLRNVPPIVFVQDKGNAALAELDQLLAVADS  124 (129)
T ss_dssp             HHHTHHHHHHHHHTCTTCSCCCCEEEEETTCCCCCCCCCCCSCCCCC
T ss_pred             HHHhHHHHHHHHHhhcCCccCCeEEEEEcCCHHHHHHHHHHHHhhhc
Confidence            99999999999999999999999999999999999999999988753

>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural genomics, PSI-biology, protein structure initiative; NMR {Thermotoga maritima}

Probab=99.97  E-value=2.8e-31  Score=207.79  Aligned_cols=102  Identities=29%  Similarity=0.464  Sum_probs=93.0

Q ss_pred             CCChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCC-CceEEEEEEEcCCcceEEEEEEecCCchhHHHHH
Q 027059           64 MANPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLS-SLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAI  142 (229)
Q Consensus        64 M~~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~-~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl  142 (229)
                      |+ ++|++||+++|+++|+++ +.+.             +||++. ++||||+|+||+||++||||||++|++.+.+.++
T Consensus         3 M~-~~R~~Rv~~~i~~~ls~i-~~ei-------------kDprl~~~~vtVt~V~vs~Dl~~AkVyvs~~g~~~~~~~~~   67 (106)
T 2kzf_A            3 NP-AYRKAMLESEIQKLLMEA-LQQL-------------RDPRLKKDFVTFSRVELSKDKRYADVYVSFLGTPEERKETV   67 (106)
T ss_dssp             SC-CTTTHHHHHHHHHHHHHH-HHTT-------------CCSSCCGGGCCEEEEEECTTSCEEEEEECCSSCHHHHHHHH
T ss_pred             cH-HHHHHHHHHHHHHHHHHH-HHhc-------------cCccccCCceEEEEEEECCCCCEEEEEEEeCCChhhHHHHH
Confidence            55 689999999999999999 6542             488884 5899999999999999999999999777778899


Q ss_pred             HHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHH
Q 027059          143 AGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS  180 (229)
Q Consensus       143 ~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~  180 (229)
                      ++|++|+||||++||++++||++|+|+|++|+++|++.
T Consensus        68 ~~L~~a~g~iR~~l~~~l~lr~~P~L~F~~D~s~e~~~  105 (106)
T 2kzf_A           68 EILNRAKGFFRTFIAKNLRLYVAPEIRFYEDKGIEASV  105 (106)
T ss_dssp             HHHHHHHHHHHHHHHHHSCSSSCCEEEEESSCCCTTCC
T ss_pred             HHHHHhHHHHHHHHHhhcCCccCCeEEEEECCchhhhc
Confidence            99999999999999999999999999999999999874

>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain; 1.84A {Thermus thermophilus} SCOP: d.52.7.1 PDB: 2r1c_A

Probab=99.96  E-value=4.3e-29  Score=192.31  Aligned_cols=92  Identities=26%  Similarity=0.395  Sum_probs=84.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHH
Q 027059           68 RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKS  147 (229)
Q Consensus        68 ~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~  147 (229)
                      +|++|++++|+++|+++| ++.             +||+++ +||||+|+||+||++||||||++|+   .+.++++|++
T Consensus         3 ~R~~Rv~~~i~~~ls~il-~ei-------------~Dprl~-~vtVt~V~vs~Dl~~AkVyvs~~~~---~~~~~~~L~~   64 (95)
T 2dyj_A            3 YGKAHLEAQLKRALAEEI-QAL-------------EDPRLF-LLTVEAVRLSKDGSVLSVYVEAFRE---EEGALRALSR   64 (95)
T ss_dssp             -CHHHHHHHHHHHHHHHH-HTC-------------CCGGGT-TCEEEEEEECTTSSEEEEEEECSSC---HHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHH-HHh-------------cCcccC-cEEEEEEEECCCCCEEEEEEEeCCC---HHHHHHHHHH
Confidence            699999999999999999 542             478774 7999999999999999999999987   4678999999


Q ss_pred             hhHHHHHHHHhccCCcccceEEEEEcCchh
Q 027059          148 KAKYVRSQLGRRMKLRLTPEIRFIEDESFE  177 (229)
Q Consensus       148 aag~IR~~LakrL~lR~vPeL~Fv~D~S~E  177 (229)
                      ++||||++||++++||++|+|+|++|+++|
T Consensus        65 a~g~iR~~l~~~l~lr~~P~L~F~~D~s~e   94 (95)
T 2dyj_A           65 AERRLVAALARRVRMRRLPRLEFLPWRASP   94 (95)
T ss_dssp             THHHHHHHHHTTSCCSSCCEEEEEEGGGCC
T ss_pred             hHHHHHHHHHhhcCCccCCeEEEEEcCCCC
Confidence            999999999999999999999999999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	229
d1kkga_	108	d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Esc	7e-25
d2e7ga1	116	d.52.7.1 (A:86-201) Ribosome-binding factor A, Rbf	6e-23
d1josa_	100	d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Hae	2e-22
d1pa4a_	96	d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Myc	2e-18
d2dyja1	91	d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA	2e-16

>d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]} Length = 108

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 = 92.2 bits (229), Expect = 7e-25
 Identities = 40/121 (33%), Positives = 61/121 (50%), Gaps = 16/121 (13%)

Query: 64  MANP-RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADL 122
           MA    R + VA+++Q+E++ +L  +               D  L  +TT+S VE+S DL
Sbjct: 1   MAKEFGRPQRVAQEMQKEIALILQRE-------------IKDPRLGMMTTVSGVEMSRDL 47

Query: 123 QVVKVYVSVFGDDRGKEV--AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS 180
              KVYV+   D     V   I  L+  + ++RS LG+ M+LR+ PE+ F  D S   G 
Sbjct: 48  AYAKVYVTFLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGM 107

Query: 181 R 181
           R
Sbjct: 108 R 108

>d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]} Length = 116

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: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.6 bits (217), Expect = 6e-23
 Identities = 22/122 (18%), Positives = 45/122 (36%), Gaps = 12/122 (9%)

Query: 68  RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKV 127
            R++ +   + + L+D+L T +V            +         +S V ++ D    + 
Sbjct: 6   ARLRALNGLLYKALTDLLCTPEV------------SQELYDLNVELSKVSLTPDFSACRA 53

Query: 128 YVSVFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILD 187
           Y              A L+  A ++R  L  +  LR  P I F++D+     + +  +L 
Sbjct: 54  YWKTTLSAEQNAHMEAVLQRSAAHMRHLLMSQQTLRNVPPIVFVQDKGNAALAELDQLLA 113

Query: 188 RI 189
             
Sbjct: 114 VA 115

>d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]} Length = 100

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: Haemophilus influenzae [TaxId: 727]

 Score = 85.7 bits (212), Expect = 2e-22
 Identities = 40/113 (35%), Positives = 65/113 (57%), Gaps = 16/113 (14%)

Query: 69  RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVY 128
           R   VA++IQ+E++ +L  +       + +  +G       + T+SDVEVS+DL   K++
Sbjct: 1   RSDRVAQEIQKEIAVILQRE-------VKDPRIG-------MVTVSDVEVSSDLSYAKIF 46

Query: 129 VSVFGD--DRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG 179
           V+   D  +   E  + GL+  + Y+RS LG+ M+LR+ PEIRFI D+S   G
Sbjct: 47  VTFLFDHDEMAIEQGMKGLEKASPYIRSLLGKAMRLRIVPEIRFIYDQSLVEG 99

>d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]} Length = 96

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: Mycoplasma pneumoniae [TaxId: 2104]

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 16/107 (14%), Positives = 39/107 (36%), Gaps = 15/107 (14%)

Query: 73  VAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVF 132
           +   I R ++  ++ +       +    +           ++ V++S DL  V VY+  +
Sbjct: 4   LENDIIRLINRTVIHE-------IYNETVK-------TGHVTHVKLSDDLLHVTVYLDCY 49

Query: 133 GDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG 179
             ++   V  A            L   + L    +I F++D++ +  
Sbjct: 50  NREQIDRVVGA-FNQAKGVFSRVLAHNLYLAKAVQIHFVKDKAIDNA 95

>d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]} Length = 91

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: Thermus thermophilus [TaxId: 274]

 Score = 69.4 bits (170), Expect = 2e-16
 Identities = 24/105 (22%), Positives = 45/105 (42%), Gaps = 22/105 (20%)

Query: 73  VAKQIQRELSDML--LTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVS 130
           +  Q++R L++ +  L D  L                    T+  V +S D  V+ VYV 
Sbjct: 5   LEAQLKRALAEEIQALEDPRLFL-----------------LTVEAVRLSKDGSVLSVYVE 47

Query: 131 VFGDDRGKEVAIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDES 175
            F ++   E A+  L    + + + L RR+++R  P + F+   +
Sbjct: 48  AFREE---EGALRALSRAERRLVAALARRVRMRRLPRLEFLPWRA 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	229
d1kkga_	108	Ribosome-binding factor A, RbfA {Escherichia coli	99.95
d2e7ga1	116	Ribosome-binding factor A, RbfA {Human (Homo sapie	99.95
d1josa_	100	Ribosome-binding factor A, RbfA {Haemophilus influ	99.95
d1pa4a_	96	Ribosome-binding factor A, RbfA {Mycoplasma pneumo	99.93
d2dyja1	91	Ribosome-binding factor A, RbfA {Thermus thermophi	99.91

>d1kkga_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Escherichia coli [TaxId: 562]}

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=99.95  E-value=1.2e-29  Score=197.07  Aligned_cols=104  Identities=37%  Similarity=0.586  Sum_probs=92.0

Q ss_pred             CCCh-HHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchh--HHH
Q 027059           64 MANP-RRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRG--KEV  140 (229)
Q Consensus        64 M~~~-~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~--~~~  140 (229)
                      |+.+ .|+.||+++|+++||++|.++.             +||+++++||||+|++|+||++|+||||++|+..+  .+.
T Consensus         1 M~~~~~R~~rv~~~i~r~is~il~~~~-------------~dp~l~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~   67 (108)
T d1kkga_           1 MAKEFGRPQRVAQEMQKEIALILQREI-------------KDPRLGMMTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKA   67 (108)
T ss_dssp             CCCCSSSHHHHHHHHHHHHHHHTTSSS-------------SSGGGTSCCBCSCEEEETTTTEEEEEEBCSGGGCHHHHHH
T ss_pred             CCCcCcHHHHHHHHHHHHHHHHHHHhc-------------cCcccCCeeEEeEEEEcCCcceEEEEEEecCCchhHHHHH
Confidence            6643 4999999999999999998652             36777777899999999999999999999987543  356


Q ss_pred             HHHHHHHhhHHHHHHHHhccCCcccceEEEEEcCchhHHH
Q 027059          141 AIAGLKSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGS  180 (229)
Q Consensus       141 vl~aL~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~  180 (229)
                      ++++|++++|+||+.||++|+||++|+|.|++|+|+|+|.
T Consensus        68 ~~~~L~~~~~~ir~~l~~~l~lr~~P~L~F~~D~s~e~a~  107 (108)
T d1kkga_          68 GIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGM  107 (108)
T ss_dssp             HHHHHHHTHHHHHHHHHHHTTCSCCCEEEEEECCTTSSSC
T ss_pred             HHHHHHHHHHHHHHHHHhhCCCeECCEEEEEecCchhhhc
Confidence            7899999999999999999999999999999999999875

>d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]}

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: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.4e-30  Score=202.88  Aligned_cols=112  Identities=20%  Similarity=0.245  Sum_probs=99.3

Q ss_pred             ChHHHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHH
Q 027059           66 NPRRVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGL  145 (229)
Q Consensus        66 ~~~R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL  145 (229)
                      ++.|+.|++++|+++|+++|+++..-            |+..+..||||+|+||+||++|+|||+++|+++..+.++++|
T Consensus         4 ~s~R~~kv~~li~k~is~il~~~~~~------------~~l~~~~ItIt~V~vS~Dl~~AkVy~s~~~~~~~~~~~~~~L   71 (116)
T d2e7ga1           4 DHARLRALNGLLYKALTDLLCTPEVS------------QELYDLNVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAVL   71 (116)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCTTTC------------HHHHHHTCCEEEEEECTTSCCEEEEECCCSCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhcCcC------------ccccCceEEEEEEEEcCCCcEEEEEEEeCCchhhHHHHHHHH
Confidence            36899999999999999999874321            222234699999999999999999999999877778888999


Q ss_pred             HHhhHHHHHHHHhccCCcccceEEEEEcCchhHHHHHHHHHHHH
Q 027059          146 KSKAKYVRSQLGRRMKLRLTPEIRFIEDESFERGSRVIAILDRI  189 (229)
Q Consensus       146 ~~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a~rId~LLd~i  189 (229)
                      ++++|+||+.|+++++||++|+|+|++|++++++.+|++||+++
T Consensus        72 ~~~~~~ir~~l~~~l~lr~~P~L~F~~D~s~~~~~~i~~ll~~~  115 (116)
T d2e7ga1          72 QRSAAHMRHLLMSQQTLRNVPPIVFVQDKGNAALAELDQLLAVA  115 (116)
T ss_dssp             HHTHHHHHHHHHTCTTCSCCCCEEEEETTCCCCCCCCCCCSCCC
T ss_pred             HHHHHHHHHHHHHHhCccccceEEEEeCCCHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999998764

>d1josa_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Haemophilus influenzae [TaxId: 727]}

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: Haemophilus influenzae [TaxId: 727]

Probab=99.95  E-value=2.2e-28  Score=187.05  Aligned_cols=97  Identities=41%  Similarity=0.673  Sum_probs=87.4

Q ss_pred             HHHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCc--hhHHHHHHHHH
Q 027059           69 RVKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDD--RGKEVAIAGLK  146 (229)
Q Consensus        69 R~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~--~~~~~vl~aL~  146 (229)
                      |+.||+++|+++||++|.++.             .||++ ++||||+|++|+||++|+||||++|+.  ...+.++++|+
T Consensus         1 R~~rv~~~i~~~is~il~~~i-------------~d~~l-~~vtIt~V~~S~Dl~~A~Vy~s~~~~~~~~~~~~~~~~L~   66 (100)
T d1josa_           1 RSDRVAQEIQKEIAVILQREV-------------KDPRI-GMVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLE   66 (100)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHC-------------CCTTT-CCEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHhc-------------cCccc-CceEEEEEEEcCCcceEEEEEEecCcchhhhHHHHHHHHH
Confidence            789999999999999998642             36776 469999999999999999999999864  34567899999


Q ss_pred             HhhHHHHHHHHhccCCcccceEEEEEcCchhHH
Q 027059          147 SKAKYVRSQLGRRMKLRLTPEIRFIEDESFERG  179 (229)
Q Consensus       147 ~aag~IR~~LakrL~lR~vPeL~Fv~D~S~E~a  179 (229)
                      +++|+||++||++++||++|+|.|++|+|+|+|
T Consensus        67 ~~~~~ir~~la~~l~~r~~P~L~F~~D~s~e~g   99 (100)
T d1josa_          67 KASPYIRSLLGKAMRLRIVPEIRFIYDQSLVEG   99 (100)
T ss_dssp             HTHHHHHHHHHHHHCCSSCCEEEEEECCCCCCC
T ss_pred             HHHHHHHHHHHHhcCCccCCeEEEEecCchhcc
Confidence            999999999999999999999999999999986

>d1pa4a_ d.52.7.1 (A:) Ribosome-binding factor A, RbfA {Mycoplasma pneumoniae [TaxId: 2104]}

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: Mycoplasma pneumoniae [TaxId: 2104]

Probab=99.93  E-value=1e-27  Score=183.12  Aligned_cols=95  Identities=15%  Similarity=0.324  Sum_probs=85.1

Q ss_pred             HHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHHhh
Q 027059           70 VKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKA  149 (229)
Q Consensus        70 ~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~aa  149 (229)
                      ++|++++|+++||++|.++.             .||+++ +||||+|++|+||++|+||||++++++ .+.++++|++++
T Consensus         1 ~eR~~~~i~r~is~~l~~ei-------------~d~~l~-~vtIt~V~vS~Dl~~AkVy~s~~~~~~-~~~~~~~L~~~~   65 (96)
T d1pa4a_           1 KERLENDIIRLINRTVIHEI-------------YNETVK-TGHVTHVKLSDDLLHVTVYLDCYNREQ-IDRVVGAFNQAK   65 (96)
T ss_dssp             CCHHHHHHHHHHHHHHTTCS-------------SSSCHH-HHCCSCCEEETTTTEEEECCCCSSSSS-HHHHHHHHHHTH
T ss_pred             ChHHHHHHHHHHHHHHHHhC-------------CCcccC-ceEEEEEEECCCCcEEEEEEEeCCccc-hHHHHHHHHHHH
Confidence            36999999999999998642             366664 699999999999999999999997654 456899999999


Q ss_pred             HHHHHHHHhccCCcccceEEEEEcCchhHH
Q 027059          150 KYVRSQLGRRMKLRLTPEIRFIEDESFERG  179 (229)
Q Consensus       150 g~IR~~LakrL~lR~vPeL~Fv~D~S~E~a  179 (229)
                      |+||++||++++||++|+|+|++|+|+|+|
T Consensus        66 g~ir~~l~~~l~lr~~P~L~F~~D~s~e~~   95 (96)
T d1pa4a_          66 GVFSRVLAHNLYLAKAVQIHFVKDKAIDNA   95 (96)
T ss_dssp             HHHHHHHHTTCCCGGGCCCEECSSSTTSSC
T ss_pred             HHHHHHHHHhcCCccCCeEEEEeCCchhcc
Confidence            999999999999999999999999999986

>d2dyja1 d.52.7.1 (A:4-94) Ribosome-binding factor A, RbfA {Thermus thermophilus [TaxId: 274]}

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: Thermus thermophilus [TaxId: 274]

Probab=99.91  E-value=1.9e-24  Score=163.05  Aligned_cols=89  Identities=28%  Similarity=0.446  Sum_probs=79.2

Q ss_pred             HHHHHHHHHHHHHHHHhcChhhhhhhchhhhcccccCCCCceEEEEEEEcCCcceEEEEEEecCCchhHHHHHHHHHHhh
Q 027059           70 VKMVAKQIQRELSDMLLTDKVLQFAVLPEAALGADRYLSSLTTISDVEVSADLQVVKVYVSVFGDDRGKEVAIAGLKSKA  149 (229)
Q Consensus        70 ~~RVas~IqreLS~iL~~Dp~l~~~i~~~~~~g~Dp~l~~lVTVT~VevS~DLs~AKVYvSi~g~~~~~~~vl~aL~~aa  149 (229)
                      ..||+++|+++||++|..   +           .||++ ++||||+|++|+||++|+|||++++++   +.++++|++++
T Consensus         2 k~rle~~i~r~is~il~~---~-----------~d~~~-~~vtIt~V~~S~Dl~~akVyvs~~~~~---~~~~~~L~~~~   63 (91)
T d2dyja1           2 KAHLEAQLKRALAEEIQA---L-----------EDPRL-FLLTVEAVRLSKDGSVLSVYVEAFREE---EGALRALSRAE   63 (91)
T ss_dssp             HHHHHHHHHHHHHHHHHT---C-----------CCGGG-TTCEEEEEEECTTSSEEEEEEECSSCH---HHHHHHHHHTH
T ss_pred             hHHHHHHHHHHHHHHHHH---c-----------cCccc-CceEEEEEEECCCcccEEEEEEeccch---HHHHHHHHHHH
Confidence            479999999999999963   1           25555 479999999999999999999999864   46889999999


Q ss_pred             HHHHHHHHhccCCcccceEEEEEcCch
Q 027059          150 KYVRSQLGRRMKLRLTPEIRFIEDESF  176 (229)
Q Consensus       150 g~IR~~LakrL~lR~vPeL~Fv~D~S~  176 (229)
                      |+||+.|+++++||++|+|+|++|+|-
T Consensus        64 ~~ir~~l~~~l~~r~~P~L~F~~D~s~   90 (91)
T d2dyja1          64 RRLVAALARRVRMRRLPRLEFLPWRAS   90 (91)
T ss_dssp             HHHHHHHHTTSCCSSCCEEEEEEGGGC
T ss_pred             HHHHHHHHhhCCCccCCEEEEEeCCCC
Confidence            999999999999999999999999873