Citrus Sinensis ID: 025294

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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-------230-------240-------250-----
Protein Sequence
MLSFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHcccccccccccccccccccccccccccHHHccccccccHHHHHHcccccccccHHHHcccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccEEEEEcccccEEEEEEcccccEEEEEEccccccccccccccHHHHHHHHHHHHHHHHHccccEEEEEEEcccccccHHHHHHHHHHHcccccccccEEEEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHcccccccccHcHHccccccccccccccEEccccccccccHHHccccccEEEEEEEcccccccccccccEEEcccccccccccccccHHHHHHHcccccccccccccccEEEEEEEEccccEEEEEEEcccEEEEEEcccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHccccEEEEEEEcccccHHHHHHHHHHHHcccEEccccEEEEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
MLSFSSLRKATSLLRyngafnrplsadfagyfenekrhfcsswnvargesgrslpRVLGNLGMNLCAVSVeqnvaapyalgfrnfihstgqgddetgrssrpmdfVRGIVeedekrftgpsqfgqfprynvehssEFVHIKLMrnntfvtvtdskgnkrigassgclpelkggpkmsRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREgfansrdqnpivyiedttrrphngcrlpkkrri
Flexible Loop (DISEMBL)
MLSFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHstgqgddetgrssrPMDFVRGIVEedekrftgpsqfgqfprYNVEHSSEFVHIKLMRNNTFvtvtdskgnkrigassgclpelkggpKMSRYAAEATAEHVgrlarnmglksvvVRVKGFTYFKKKRQAIMSfregfansrdqnpivyiedttrrphngcrlpkkrri
Low Complexity Region (SEG)
MLSFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI
Disordered region (IsUnstruct)
***********SLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIH***********************************FGQFPRYNVEHSSEFVHIKLMRNNTFVTVTD******************************TAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIE******************
Disordered Region (DISOPRED)
********KATSLLRYNGAFNRPLSADFAGYFENEKRHFCS*******************LGMNLC*******************************************************************SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPE*KGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPK****
Disordered Region (DISEMBL)
MLSFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTG*********SRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI
Disordered Region (DISPRO)
**SFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIH****************DFVRGIVEE*********QFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLSFSSLRKATSLLRYNGAFNRPLSADFAGYFENEKRHFCSSWNVARGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI
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	255	2.2.26 [Sep-21-2011]
Q7NQH5	131	30S ribosomal protein S11	yes	no	0.439	0.854	0.398	2e-13
Q1LI61	133	30S ribosomal protein S11	yes	no	0.498	0.954	0.357	5e-13
B2UEJ5	133	30S ribosomal protein S11	yes	no	0.454	0.872	0.387	2e-12
Q82X71	129	30S ribosomal protein S11	yes	no	0.419	0.829	0.423	3e-12
Q0AIH3	129	30S ribosomal protein S11	yes	no	0.427	0.844	0.408	3e-12
Q8XV36	133	30S ribosomal protein S11	yes	no	0.454	0.872	0.387	3e-12
Q0VSI0	132	30S ribosomal protein S11	yes	no	0.431	0.833	0.386	3e-12
Q3J8T6	127	30S ribosomal protein S11	yes	no	0.435	0.874	0.395	4e-12
B3R7E5	132	30S ribosomal protein S11	yes	no	0.427	0.825	0.375	4e-12
Q46WG7	132	30S ribosomal protein S11	yes	no	0.427	0.825	0.375	4e-12

>sp|Q7NQH5|RS11_CHRVO 30S ribosomal protein S11 OS=Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) GN=rpsK PE=3 SV=1

 Score = 75.9 bits (185), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 49/123 (39%), Positives = 67/123 (54%), Gaps = 11/123 (8%)

Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           S   VH+    NNT +T+TD +GN    A+SG     KG  K + +AA+  AEH G++A+
Sbjct: 19  SEGIVHVHASFNNTIITITDRQGNALSWATSGGA-GFKGSRKSTPFAAQVAAEHAGKVAQ 77

Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKK 252
             G+K++ VR+KG      +  A+ +    GF        I  I D T  PHNGCR PKK
Sbjct: 78  EYGVKNLEVRIKG--PGPGRESAVRALNSLGFK-------ITSISDVTPVPHNGCRPPKK 128

Query: 253 RRI 255
           RRI
Sbjct: 129 RRI 131

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.
Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (taxid: 243365)

>sp|Q1LI61|RS11_RALME 30S ribosomal protein S11 OS=Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) GN=rpsK PE=3 SV=1

 Score = 75.1 bits (183), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 75/140 (53%), Gaps = 13/140 (9%)

Query: 119 GPSQFGQFPRYNVEH--SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKM 176
           GP+   Q  R  V+   +    H+    NNT +T+TD +GN    A++G     KG  K 
Sbjct: 4   GPNNAAQRARKKVKKNVADGIAHVHASFNNTIITITDRQGNALSWATAGGQ-GFKGSRKS 62

Query: 177 SRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVY 235
           + +AA+  AE+ GR+A++ G+K++ VR+KG    ++   A+ +    G         I  
Sbjct: 63  TPFAAQVAAENAGRVAQDQGIKNLEVRIKGPGPGRE--SAVRALNALGIK-------IAV 113

Query: 236 IEDTTRRPHNGCRLPKKRRI 255
           IED T  PHNGCR PK+RRI
Sbjct: 114 IEDVTPVPHNGCRPPKRRRI 133

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) (taxid: 266264)

>sp|B2UEJ5|RS11_RALPJ 30S ribosomal protein S11 OS=Ralstonia pickettii (strain 12J) GN=rpsK PE=3 SV=1

 Score = 72.8 bits (177), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/129 (38%), Positives = 69/129 (53%), Gaps = 13/129 (10%)

Query: 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH 187
           R NV      VH     NNT +T+TD +GN    A+SG     KG  K + +AA+  AE 
Sbjct: 17  RKNVADGIAHVHASF--NNTIITITDRQGNALSWATSGGQ-GFKGSRKSTPFAAQVAAES 73

Query: 188 VGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNG 246
            GR+A++ G+K++ VR+KG    ++   A+ +    G         I  IED T  PHNG
Sbjct: 74  AGRVAQDQGIKNLEVRIKGPGPGRE--SAVRALNNLGIK-------IQLIEDVTPVPHNG 124

Query: 247 CRLPKKRRI 255
           CR PK+RRI
Sbjct: 125 CRPPKRRRI 133

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Ralstonia pickettii (strain 12J) (taxid: 402626)

>sp|Q82X71|RS11_NITEU 30S ribosomal protein S11 OS=Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) GN=rpsK PE=3 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 50/118 (42%), Positives = 64/118 (54%), Gaps = 11/118 (9%)

Query: 139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
           HI    NNT VT++D +GN    A+SG +   KG  K + +AA+  AEH GR A   G+K
Sbjct: 22  HIHASFNNTIVTISDRQGNALSWATSGGV-GFKGSRKSTPFAAQVAAEHAGRAALEYGVK 80

Query: 199 SVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           ++ VRVKG      +  A+ +    GF        I  I D T  PHNGCR PKKRRI
Sbjct: 81  NLEVRVKG--PGPGRDSAVRALNATGFK-------ITSITDVTPIPHNGCRPPKKRRI 129

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298) (taxid: 228410)

>sp|Q0AIH3|RS11_NITEC 30S ribosomal protein S11 OS=Nitrosomonas eutropha (strain C91) GN=rpsK PE=3 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 64/120 (53%), Gaps = 11/120 (9%)

Query: 137 FVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
             HI    NNT VT++D +GN    A+SG +   KG  K + +AA+  AEH GR A   G
Sbjct: 20  VAHIHASFNNTIVTISDRQGNALSWATSGGV-GFKGSRKSTPFAAQVAAEHAGRAALEYG 78

Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           +K++ +RVKG      +  A+ +    GF        I  I D T  PHNGCR PKKRRI
Sbjct: 79  VKNLEIRVKG--PGPGRDSAVRALNATGFK-------ITSITDVTPVPHNGCRPPKKRRI 129

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Nitrosomonas eutropha (strain C91) (taxid: 335283)

>sp|Q8XV36|RS11_RALSO 30S ribosomal protein S11 OS=Ralstonia solanacearum (strain GMI1000) GN=rpsK PE=3 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 50/129 (38%), Positives = 69/129 (53%), Gaps = 13/129 (10%)

Query: 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH 187
           R NV      VH     NNT +T+TD +GN    A+SG     KG  K + +AA+  AE 
Sbjct: 17  RKNVADGIAHVHASF--NNTIITITDRQGNALSWATSGGQ-GFKGSRKSTPFAAQVAAES 73

Query: 188 VGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNG 246
            GR+A++ G+K++ VR+KG    ++   A+ +    G         I  IED T  PHNG
Sbjct: 74  AGRVAQDQGIKNLEVRIKGPGPGRE--SAVRALNNLGIK-------IQVIEDVTPVPHNG 124

Query: 247 CRLPKKRRI 255
           CR PK+RRI
Sbjct: 125 CRPPKRRRI 133

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Ralstonia solanacearum (strain GMI1000) (taxid: 267608)

>sp|Q0VSI0|RS11_ALCBS 30S ribosomal protein S11 OS=Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) GN=rpsK PE=3 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/119 (38%), Positives = 65/119 (54%), Gaps = 9/119 (7%)

Query: 137 FVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
             H+    NNT +T+TD +GN    A+SG     +G  K + +AA+  AE+ G  A++ G
Sbjct: 23  IAHVHASFNNTIITITDRQGNALSWATSGGA-GFRGSRKSTPFAAQVAAENAGNAAKDYG 81

Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           LK++ VRVKG       R++ +    G         I +IED T  PHNGCR PKKRR+
Sbjct: 82  LKNLEVRVKGPG---PGRESSIRALNGCGYK-----ITHIEDVTPIPHNGCRPPKKRRV 132

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Alcanivorax borkumensis (strain SK2 / ATCC 700651 / DSM 11573) (taxid: 393595)

>sp|Q3J8T6|RS11_NITOC 30S ribosomal protein S11 OS=Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848) GN=rpsK PE=3 SV=1

 Score = 72.0 bits (175), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 49/124 (39%), Positives = 64/124 (51%), Gaps = 13/124 (10%)

Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           S    HI    NNT VT+TD +GN    A+SG     +G  K + +AA+  AE  GR+ +
Sbjct: 15  SDGIAHIHASFNNTIVTITDRQGNTLAWATSGG-SGFRGSRKSTPFAAQVAAEKAGRIVQ 73

Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQN--PIVYIEDTTRRPHNGCRLPK 251
            MG+K++ VRVKG              RE  A S +     +  I D T  PHNGCR PK
Sbjct: 74  EMGMKNLEVRVKGPG----------PGRESAARSLNNVGFKVTNIADITPIPHNGCRPPK 123

Query: 252 KRRI 255
           KRR+
Sbjct: 124 KRRV 127

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Nitrosococcus oceani (strain ATCC 19707 / NCIMB 11848) (taxid: 323261)

>sp|B3R7E5|RS11_CUPTR 30S ribosomal protein S11 OS=Cupriavidus taiwanensis (strain R1 / LMG 19424) GN=rpsK PE=3 SV=1

 Score = 72.0 bits (175), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 45/120 (37%), Positives = 67/120 (55%), Gaps = 11/120 (9%)

Query: 137 FVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
             H+    NNT +T+TD +GN    A++G     KG  K + +AA+  AE+ GR+A++ G
Sbjct: 23  IAHVHASFNNTIITITDRQGNALSWATAGGQ-GFKGSRKSTPFAAQVAAENAGRVAQDQG 81

Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           +K++ VR+KG    ++   A+ +    G         I  IED T  PHNGCR PK+RRI
Sbjct: 82  IKNLEVRIKGPGPGRE--SAVRALNALGIK-------IAIIEDVTPIPHNGCRPPKRRRI 132

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Cupriavidus taiwanensis (strain R1 / LMG 19424) (taxid: 164546)

>sp|Q46WG7|RS11_CUPPJ 30S ribosomal protein S11 OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=rpsK PE=3 SV=1

 Score = 72.0 bits (175), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 45/120 (37%), Positives = 67/120 (55%), Gaps = 11/120 (9%)

Query: 137 FVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
             H+    NNT +T+TD +GN    A++G     KG  K + +AA+  AE+ GR+A++ G
Sbjct: 23  IAHVHASFNNTIITITDRQGNALSWATAGGQ-GFKGSRKSTPFAAQVAAENAGRVAQDQG 81

Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           +K++ VR+KG    ++   A+ +    G         I  IED T  PHNGCR PK+RRI
Sbjct: 82  IKNLEVRIKGPGPGRE--SAVRALNALGIK-------IAIIEDVTPIPHNGCRPPKRRRI 132

Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.

Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (taxid: 264198)

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	255
356559909	324	PREDICTED: uncharacterized protein LOC10	0.749	0.589	0.589	8e-55
388507998	237	unknown [Medicago truncatula]	0.694	0.746	0.609	3e-54
356530937	329	PREDICTED: uncharacterized protein LOC10	0.8	0.620	0.541	2e-53
255638431	329	unknown [Glycine max]	0.8	0.620	0.541	2e-53
357455123	247	30S ribosomal protein S11 [Medicago trun	0.721	0.744	0.587	7e-53
18398140	314	Ribosomal L.8/L5e family protein [Arabid	0.701	0.570	0.559	4e-52
12321311	235	30S ribosomal protein S11, putative [Ara	0.701	0.761	0.559	4e-52
297818906	312	hypothetical protein ARALYDRAFT_905550 [	0.701	0.573	0.568	4e-52
297851618	313	hypothetical protein ARALYDRAFT_890737 [	0.701	0.571	0.568	5e-52
255555499	226	Mitochondrial ribosomal protein S11, put	0.682	0.769	0.609	4e-50

>gi|356559909|ref|XP_003548238.1| PREDICTED: uncharacterized protein LOC100783046 [Glycine max]

 Score =  219 bits (558), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 119/202 (58%), Positives = 148/202 (73%), Gaps = 11/202 (5%)

Query: 56  RVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEK 115
           R   NLG N+ A +     A P  +  +  I+   + D ETG +SRPMDFVRGI++ED  
Sbjct: 132 RSQNNLGQNVDANAD----ALPDFMQDKENINIGSKNDAETGWNSRPMDFVRGIIDEDN- 186

Query: 116 RFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPK 175
            F   S F Q   Y  E  ++FVHIK++RNNTFVTVTDS+GN ++  S+G L +LK G K
Sbjct: 187 -FMKGSPFHQ---YQYEQDADFVHIKMLRNNTFVTVTDSQGNIKLSGSAGPLKDLKSGQK 242

Query: 176 MSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGF-ANSR-DQNPI 233
           +SRYAAEATAE VGR AR +GLKSVV++V GFT+F++KR AIMS++EGF A SR D+NPI
Sbjct: 243 LSRYAAEATAEVVGRKARGLGLKSVVMKVNGFTHFRRKRNAIMSWKEGFTAGSRGDRNPI 302

Query: 234 VYIEDTTRRPHNGCRLPKKRRI 255
           VYIEDTTR+PHNGCRLPKKRRI
Sbjct: 303 VYIEDTTRKPHNGCRLPKKRRI 324

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507998|gb|AFK42065.1| unknown [Medicago truncatula]

 Score =  218 bits (554), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 111/182 (60%), Positives = 139/182 (76%), Gaps = 5/182 (2%)

Query: 75  AAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEHS 134
           A P  L  R  I+S  + + E G +SR MDFVRG +E DEK   G   + Q   Y+ +H 
Sbjct: 60  ARPDFLRNRENINSKSENNAEIGGNSRKMDFVRGAIE-DEKSVMGGYLYNQ---YHFQHD 115

Query: 135 SEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARN 194
           ++FVHIK+ RNNTFVTVTDSKGN ++  S+G L ++K G K+SRYAAEATAE VGR +R 
Sbjct: 116 ADFVHIKMRRNNTFVTVTDSKGNVKLSGSAGSLKDMKSGQKLSRYAAEATAEVVGRRSRG 175

Query: 195 MGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCRLPKKR 253
           +GLKSVV++V GFT+F++KRQAI+S+REGF +SR D+NPIVYIEDTTRRPHNGCRLPK R
Sbjct: 176 LGLKSVVMKVNGFTHFRRKRQAILSWREGFTDSRGDKNPIVYIEDTTRRPHNGCRLPKSR 235

Query: 254 RI 255
           RI
Sbjct: 236 RI 237

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530937|ref|XP_003534035.1| PREDICTED: uncharacterized protein LOC100799648 [Glycine max]

 Score =  214 bits (546), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 123/227 (54%), Positives = 160/227 (70%), Gaps = 23/227 (10%)

Query: 42  SWNVARGESGRSLPRVLGNLGMNLCAVS---VEQNVAA-----PYALGFRNFIHSTGQGD 93
           SWN  R ++  + P  +GN   N+ + S   ++QNV A     P  +  +  I+   +  
Sbjct: 113 SWNNMR-QNVNAPPNFMGNRD-NINSRSQNNMDQNVDANADALPDFMQDKENINIGNKNY 170

Query: 94  DETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQ---FPRYNVEHSSEFVHIKLMRNNTFVT 150
            ETG +SRPMDFVRGI++ED         FG+   + +Y  E  ++FVHIK++RNNTFVT
Sbjct: 171 AETGWNSRPMDFVRGIIDEDN--------FGRGSPYHQYQYEQDADFVHIKMLRNNTFVT 222

Query: 151 VTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYF 210
           VTDSKGN ++  S+G L +LK G K+SRYAAEATAE VGR AR +GLKSVV++V GFT+F
Sbjct: 223 VTDSKGNIKLSGSAGPLKDLKSGQKLSRYAAEATAEVVGRKARGLGLKSVVMKVNGFTHF 282

Query: 211 KKKRQAIMSFREGF-ANSR-DQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           ++KR AIMS++EGF A SR D+NPIVYIEDTTR+PHNGCRLPKKRRI
Sbjct: 283 RRKRNAIMSWKEGFTAGSRGDRNPIVYIEDTTRKPHNGCRLPKKRRI 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638431|gb|ACU19525.1| unknown [Glycine max]

 Score =  214 bits (546), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 123/227 (54%), Positives = 160/227 (70%), Gaps = 23/227 (10%)

Query: 42  SWNVARGESGRSLPRVLGNLGMNLCAVS---VEQNVAA-----PYALGFRNFIHSTGQGD 93
           SWN  R ++  + P  +GN   N+ + S   ++QNV A     P  +  +  I+   +  
Sbjct: 113 SWNNMR-QNVNAPPNFMGNRD-NINSRSQNNMDQNVDANADALPDFIQDKENINIGNKNY 170

Query: 94  DETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQ---FPRYNVEHSSEFVHIKLMRNNTFVT 150
            ETG +SRPMDFVRGI++ED         FG+   + +Y  E  ++FVHIK++RNNTFVT
Sbjct: 171 AETGWNSRPMDFVRGIIDEDN--------FGRGSPYHQYQYEQDADFVHIKMLRNNTFVT 222

Query: 151 VTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYF 210
           VTDSKGN ++  S+G L +LK G K+SRYAAEATAE VGR AR +GLKSVV++V GFT+F
Sbjct: 223 VTDSKGNIKLSGSAGPLKDLKSGQKLSRYAAEATAEVVGRKARGLGLKSVVMKVNGFTHF 282

Query: 211 KKKRQAIMSFREGF-ANSR-DQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           ++KR AIMS++EGF A SR D+NPIVYIEDTTR+PHNGCRLPKKRRI
Sbjct: 283 RRKRNAIMSWKEGFTAGSRGDRNPIVYIEDTTRKPHNGCRLPKKRRI 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455123|ref|XP_003597842.1| 30S ribosomal protein S11 [Medicago truncatula] gi|355486890|gb|AES68093.1| 30S ribosomal protein S11 [Medicago truncatula]

 Score =  213 bits (541), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 111/189 (58%), Positives = 143/189 (75%), Gaps = 5/189 (2%)

Query: 69  SVEQNVAA-PYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFP 127
           +V  N +A P  +  R  I+S  +   E G + R MDFVRG VEE+EK   G   + Q  
Sbjct: 62  NVNSNASARPNFMRDRENINSPIENKAEIGGNFRKMDFVRGSVEENEKGVMGGYLYNQ-- 119

Query: 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH 187
            Y+ +H ++FVHIK+ RNNTFVTVTDSKGN ++  S+G L ++K G K+SRYAAEATAE 
Sbjct: 120 -YHFQHDADFVHIKMRRNNTFVTVTDSKGNVKLSGSAGSLKDMKSGQKLSRYAAEATAEV 178

Query: 188 VGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNG 246
           VGR +R++GLKS V++V GFT+F++KRQAI+S+REGF++SR D+NPIVYIEDTTRRPHNG
Sbjct: 179 VGRRSRSLGLKSAVMKVNGFTHFRRKRQAILSWREGFSDSRGDKNPIVYIEDTTRRPHNG 238

Query: 247 CRLPKKRRI 255
           CRLPK RRI
Sbjct: 239 CRLPKSRRI 247

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18398140|ref|NP_564385.1| Ribosomal L.8/L5e family protein [Arabidopsis thaliana] gi|17380742|gb|AAL36201.1| putative 30S ribosomal protein S11 [Arabidopsis thaliana] gi|21436389|gb|AAM51364.1| putative 30S ribosomal protein S11 [Arabidopsis thaliana] gi|332193277|gb|AEE31398.1| Ribosomal L.8/L5e family protein [Arabidopsis thaliana]

 Score =  210 bits (535), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/184 (55%), Positives = 140/184 (76%), Gaps = 5/184 (2%)

Query: 75  AAPYALGFRNFIHSTG--QGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVE 132
           +AP    + NF  S+   + +  +G  S  +DFVR ++E++ +R  G   F  F R N+E
Sbjct: 133 SAPSLSSYENFTQSSSLLKENSRSGGKSSDLDFVREVIEDEGRRTAG--IFSHFQRPNLE 190

Query: 133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLA 192
            +++ +HIK++RNNTFVTVTDSKGN +  A+SG LP+LKGG KM+ Y A+ATAE++GR A
Sbjct: 191 TNADIIHIKMLRNNTFVTVTDSKGNVKCKATSGSLPDLKGGRKMTNYTADATAENIGRRA 250

Query: 193 RNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCRLPK 251
           + MGLKSVVV+V GFT+F KK++AI++FR+GF NSR DQNPIVYIEDTTR+ HNGCRLP+
Sbjct: 251 KAMGLKSVVVKVNGFTHFGKKKKAIIAFRDGFTNSRSDQNPIVYIEDTTRKAHNGCRLPR 310

Query: 252 KRRI 255
           KRR+
Sbjct: 311 KRRV 314

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|12321311|gb|AAG50732.1|AC079041_25 30S ribosomal protein S11, putative [Arabidopsis thaliana]

 Score =  210 bits (535), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 103/184 (55%), Positives = 140/184 (76%), Gaps = 5/184 (2%)

Query: 75  AAPYALGFRNFIHSTG--QGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVE 132
           +AP    + NF  S+   + +  +G  S  +DFVR ++E++ +R  G   F  F R N+E
Sbjct: 54  SAPSLSSYENFTQSSSLLKENSRSGGKSSDLDFVREVIEDEGRRTAG--IFSHFQRPNLE 111

Query: 133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLA 192
            +++ +HIK++RNNTFVTVTDSKGN +  A+SG LP+LKGG KM+ Y A+ATAE++GR A
Sbjct: 112 TNADIIHIKMLRNNTFVTVTDSKGNVKCKATSGSLPDLKGGRKMTNYTADATAENIGRRA 171

Query: 193 RNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCRLPK 251
           + MGLKSVVV+V GFT+F KK++AI++FR+GF NSR DQNPIVYIEDTTR+ HNGCRLP+
Sbjct: 172 KAMGLKSVVVKVNGFTHFGKKKKAIIAFRDGFTNSRSDQNPIVYIEDTTRKAHNGCRLPR 231

Query: 252 KRRI 255
           KRR+
Sbjct: 232 KRRV 235

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297818906|ref|XP_002877336.1| hypothetical protein ARALYDRAFT_905550 [Arabidopsis lyrata subsp. lyrata] gi|297323174|gb|EFH53595.1| hypothetical protein ARALYDRAFT_905550 [Arabidopsis lyrata subsp. lyrata]

 Score =  210 bits (535), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 104/183 (56%), Positives = 141/183 (77%), Gaps = 4/183 (2%)

Query: 75  AAPYALGFRNFIHSTGQGDD-ETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEH 133
           +AP    + NF  S+   ++  +G  S  +DFVR ++E++ +R +G   F  F R N+E 
Sbjct: 132 SAPSVSSYENFTQSSLLNENPRSGGKSSDLDFVREVIEDEGRRTSG--IFSHFHRPNLET 189

Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           +++ +HIK++RNNTFVTVTDSKGN +  A+SG LP+LKGG KM+ Y A+ATAE++GR A+
Sbjct: 190 NADIIHIKMLRNNTFVTVTDSKGNVKCKATSGSLPDLKGGRKMTNYTADATAENIGRRAK 249

Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCRLPKK 252
            MGLKSVVV+V GFT+F KK++AI++FR+GF NSR DQNPIVYIEDTTR+ HNGCRLPKK
Sbjct: 250 AMGLKSVVVKVNGFTHFGKKKKAIIAFRDGFTNSRSDQNPIVYIEDTTRKAHNGCRLPKK 309

Query: 253 RRI 255
           RR+
Sbjct: 310 RRV 312

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297851618|ref|XP_002893690.1| hypothetical protein ARALYDRAFT_890737 [Arabidopsis lyrata subsp. lyrata] gi|297339532|gb|EFH69949.1| hypothetical protein ARALYDRAFT_890737 [Arabidopsis lyrata subsp. lyrata]

 Score =  210 bits (534), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 104/183 (56%), Positives = 141/183 (77%), Gaps = 4/183 (2%)

Query: 75  AAPYALGFRNFIHSTGQGDDE-TGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRYNVEH 133
           +AP    + NF  S+   ++  +G  S  +DFVR ++E++ +R +G   F  F R N+E 
Sbjct: 133 SAPSVSSYENFTQSSLLNENPRSGGKSSDLDFVREVIEDEGRRTSG--IFSHFHRPNLET 190

Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           +++ +HIK++RNNTFVTVTDSKGN +  A+SG LP+LKGG KM+ Y A+ATAE++GR A+
Sbjct: 191 NADIIHIKMLRNNTFVTVTDSKGNVKCKATSGSLPDLKGGRKMTNYTADATAENIGRRAK 250

Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCRLPKK 252
            MGLKSVVV+V GFT+F KK++AI++FR+GF NSR DQNPIVYIEDTTR+ HNGCRLPKK
Sbjct: 251 AMGLKSVVVKVNGFTHFGKKKKAIIAFRDGFTNSRSDQNPIVYIEDTTRKAHNGCRLPKK 310

Query: 253 RRI 255
           RR+
Sbjct: 311 RRV 313

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555499|ref|XP_002518786.1| Mitochondrial ribosomal protein S11, putative [Ricinus communis] gi|223542167|gb|EEF43711.1| Mitochondrial ribosomal protein S11, putative [Ricinus communis]

 Score =  204 bits (518), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 114/187 (60%), Positives = 136/187 (72%), Gaps = 13/187 (6%)

Query: 70  VEQNVAAPYALGFRNFIHSTGQGDDETGRSSRPMDFVRGIVEEDEKRFTGPSQFGQFPRY 129
           +++ ++   +L   NF  S GQ D E GRS +PMDFVR  +E+D         + QF R+
Sbjct: 52  IKEALSTSNSLSSANF--SAGQRDVEMGRSYKPMDFVRRTIEQD---------YFQFSRH 100

Query: 130 NVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVG 189
           N+E + + V I L RNNTF+ V DSKGN +  A+SG      GG K++RYAAEA AE VG
Sbjct: 101 NIEQNPDIVLINLKRNNTFINVLDSKGNTKFKATSGAKAVGGGG-KVTRYAAEAAAEFVG 159

Query: 190 RLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSR-DQNPIVYIEDTTRRPHNGCR 248
           R AR MGLKSVV+RVKGFTYFKKKRQAIMSFREGF+NSR DQNPIVYIED T+RPHNGCR
Sbjct: 160 RRAREMGLKSVVMRVKGFTYFKKKRQAIMSFREGFSNSRSDQNPIVYIEDVTQRPHNGCR 219

Query: 249 LPKKRRI 255
           LPKKRRI
Sbjct: 220 LPKKRRI 226

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	255
TAIR|locus:2826195	314	NFD3 "NUCLEAR FUSION DEFECTIVE	0.807	0.656	0.514	1.5e-51
UNIPROTKB|P46746	128	RPS11 "Ribosomal protein S11,	0.474	0.945	0.386	2e-15
TIGR_CMR|CBU_0261	123	CBU_0261 "ribosomal protein S1	0.423	0.878	0.389	2.7e-13
UNIPROTKB|O06326	139	rpsK "30S ribosomal protein S1	0.450	0.827	0.388	5.6e-13
TIGR_CMR|SO_0254	130	SO_0254 "ribosomal protein S11	0.466	0.915	0.378	9.1e-13
TIGR_CMR|CPS_0624	129	CPS_0624 "ribosomal protein S1	0.419	0.829	0.389	1.2e-12
TIGR_CMR|ECH_0431	126	ECH_0431 "ribosomal protein S1	0.427	0.865	0.369	1.5e-12
UNIPROTKB|P66367	129	rpsK "30S ribosomal protein S1	0.423	0.837	0.376	2.4e-12
TIGR_CMR|VC_2573	129	VC_2573 "ribosomal protein S11	0.423	0.837	0.376	2.4e-12
TIGR_CMR|CHY_2283	129	CHY_2283 "ribosomal protein S1	0.450	0.891	0.376	3.1e-12

TAIR|locus:2826195 NFD3 "NUCLEAR FUSION DEFECTIVE 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 535 (193.4 bits), Expect = 1.5e-51, P = 1.5e-51
 Identities = 109/212 (51%), Positives = 146/212 (68%)

Query:    47 RGESGRSLPRVLGNLGMNLCAVSVEQNVAAPYALGFRNFIHSTG--QGDDETGRSSRPMD 104
             R     SLP   G     L         +AP    + NF  S+   + +  +G  S  +D
Sbjct:   106 RSRLPNSLPDQFGQTNPGLPNTG-GSGFSAPSLSSYENFTQSSSLLKENSRSGGKSSDLD 164

Query:   105 FVRGIVEEDEKRFTGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASS 164
             FVR ++E++ +R  G   F  F R N+E +++ +HIK++RNNTFVTVTDSKGN +  A+S
Sbjct:   165 FVREVIEDEGRRTAGI--FSHFQRPNLETNADIIHIKMLRNNTFVTVTDSKGNVKCKATS 222

Query:   165 GCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGF 224
             G LP+LKGG KM+ Y A+ATAE++GR A+ MGLKSVVV+V GFT+F KK++AI++FR+GF
Sbjct:   223 GSLPDLKGGRKMTNYTADATAENIGRRAKAMGLKSVVVKVNGFTHFGKKKKAIIAFRDGF 282

Query:   225 ANSR-DQNPIVYIEDTTRRPHNGCRLPKKRRI 255
              NSR DQNPIVYIEDTTR+ HNGCRLP+KRR+
Sbjct:   283 TNSRSDQNPIVYIEDTTRKAHNGCRLPRKRRV 314

GO:0003735 "structural constituent of ribosome" evidence=IEA;ISS

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

UNIPROTKB|P46746 RPS11 "Ribosomal protein S11, mitochondrial" [Prototheca wickerhamii (taxid:3111)]

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 51/132 (38%), Positives = 72/132 (54%)

Query:   125 QFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEAT 184
             Q  R  +E  S  VHI+   NNT +T+TD +GN +   S+G L   K   K + YA+ A 
Sbjct:     7 QISRKFIEKKSGIVHIQSTTNNTLITLTDLEGNTQFFVSAGTLG-FKNSRKSTVYASGAA 65

Query:   185 AEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIV-YIEDTTRRP 243
             AE +   A N G ++++V++KG  Y KK   AI     G   S   N ++  I++ T   
Sbjct:    66 AEALASKAFNEGYRTIIVKIKGLGYGKKS--AI----RGLQKS---NLVIKQIQEVTPIA 116

Query:   244 HNGCRLPKKRRI 255
             HNGCR PKKRR+
Sbjct:   117 HNGCRPPKKRRV 128

GO:0005763 "mitochondrial small ribosomal subunit" evidence=ISS

TIGR_CMR|CBU_0261 CBU_0261 "ribosomal protein S11" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 174 (66.3 bits), Expect = 2.7e-13, P = 2.7e-13
 Identities = 46/118 (38%), Positives = 63/118 (53%)

Query:   139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR-NMGL 197
             HIK   NNT ++V+D +GN     S+G     KG  K + Y A+  +E VGRLAR N  +
Sbjct:    15 HIKATFNNTMISVSDPQGNVLCFRSAGG-SGFKGSRKGTPYGAQMASEEVGRLARDNFDM 73

Query:   198 KSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
             + + VRVKG      +  AI   R           ++++ED T  PHNGCR  KKRR+
Sbjct:    74 RRIAVRVKGPG--AGRDSAIRGLRSAGLE------VIHLEDRTPLPHNGCRPRKKRRV 123

GO:0003735 "structural constituent of ribosome" evidence=ISS

UNIPROTKB|O06326 rpsK "30S ribosomal protein S11" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 171 (65.3 bits), Expect = 5.6e-13, P = 5.6e-13
 Identities = 49/126 (38%), Positives = 67/126 (53%)

Query:   130 NVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVG 189
             NV H +   HIK   NNT VT+TD +GN    ASSG +   KG  K + +AA+  AE+  
Sbjct:    25 NVPHGA--AHIKSTFNNTIVTITDPQGNVIAWASSGHVG-FKGSRKSTPFAAQLAAENAA 81

Query:   190 RLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRL 249
             R A++ G++ V V VKG      +  AI S +           +  I D T +PHNG R 
Sbjct:    82 RKAQDHGVRKVDVFVKGPG--SGRETAIRSLQAAGLE------VGAISDVTPQPHNGVRP 133

Query:   250 PKKRRI 255
             PK+RR+
Sbjct:   134 PKRRRV 139

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

TIGR_CMR|SO_0254 SO_0254 "ribosomal protein S11" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 169 (64.5 bits), Expect = 9.1e-13, P = 9.1e-13
 Identities = 50/132 (37%), Positives = 66/132 (50%)

Query:   127 PRYNVEH--SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEAT 184
             PR  V    +    HI    NNT VT+TD +GN    A+SG     +G  K + +AA+  
Sbjct:     9 PRKRVRKQVADGMAHIHASFNNTIVTITDRQGNALSWATSGG-SGFRGSRKSTPFAAQVA 67

Query:   185 AEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRP 243
             AE  G  A++ GLK++ V VKG      +  AI +    G+        I  I D T  P
Sbjct:    68 AERAGAAAQDYGLKNLEVFVKGPG--PGRESAIRALNAVGYK-------ITNITDVTPIP 118

Query:   244 HNGCRLPKKRRI 255
             HNGCR PKKRR+
Sbjct:   119 HNGCRPPKKRRV 130

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CPS_0624 CPS_0624 "ribosomal protein S11" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 46/118 (38%), Positives = 62/118 (52%)

Query:   139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
             HI    NNT VT+TD +GN    A++G     +G  K + +AA+  A+  G +A+  GLK
Sbjct:    22 HIHASFNNTIVTLTDRQGNALSWATAGG-SGFRGSRKSTPFAAQVAADRAGAVAKEFGLK 80

Query:   199 SVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
             ++ V VKG      +  AI +    GF        I  I D T  PHNGCR PKKRR+
Sbjct:    81 NIEVFVKGPG--PGRESAIRALNAAGFK-------ITNITDVTPIPHNGCRPPKKRRV 129

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

TIGR_CMR|ECH_0431 ECH_0431 "ribosomal protein S11" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 44/119 (36%), Positives = 64/119 (53%)

Query:   138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH-VGRLARNMG 196
             V+I    NN  VTVTD +G+  I  S+G     KG  K + YAA+ TA H V  +    G
Sbjct:    17 VYIHATYNNIIVTVTDQQGHSLICTSAGACG-FKGSKKATPYAAQETASHAVKTVVEQNG 75

Query:   197 LKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
             +K+V ++V G      +  AI + +    N      +  I+DTT+ PHNGC+LP +RR+
Sbjct:    76 MKTVSIKVSGPG--AGRESAIRAVQACNLN------VTSIKDTTKLPHNGCKLPGRRRV 126

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

UNIPROTKB|P66367 rpsK "30S ribosomal protein S11" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 44/117 (37%), Positives = 61/117 (52%)

Query:   139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
             HI    NNT VT+TD +GN    A++G     +G  K + +AA+  AE    +A+  GLK
Sbjct:    22 HIHASFNNTIVTITDRQGNALAWATAGG-SGFRGSRKSTPFAAQVAAERCAEMAKEYGLK 80

Query:   199 SVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
             ++ V VKG    ++     ++   GF        I  I D T  PHNGCR PKKRR+
Sbjct:    81 NLEVMVKGPGPGRESTVRALN-AAGFR-------ITNIVDATPIPHNGCRPPKKRRV 129

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_2573 VC_2573 "ribosomal protein S11" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 44/117 (37%), Positives = 61/117 (52%)

Query:   139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
             HI    NNT VT+TD +GN    A++G     +G  K + +AA+  AE    +A+  GLK
Sbjct:    22 HIHASFNNTIVTITDRQGNALAWATAGG-SGFRGSRKSTPFAAQVAAERCAEMAKEYGLK 80

Query:   199 SVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
             ++ V VKG    ++     ++   GF        I  I D T  PHNGCR PKKRR+
Sbjct:    81 NLEVMVKGPGPGRESTVRALN-AAGFR-------ITNIVDATPIPHNGCRPPKKRRV 129

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_2283 CHY_2283 "ribosomal protein S11" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 164 (62.8 bits), Expect = 3.1e-12, P = 3.1e-12
 Identities = 47/125 (37%), Positives = 66/125 (52%)

Query:   132 EHSSEFV-HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGR 190
             +H  + V HIK   NNT VT+TD +GN    AS+G +   +G  K + +AA+  AE   +
Sbjct:    14 KHVEQGVAHIKSTFNNTIVTITDPQGNTLSWASAGTVG-FEGTRKGTPFAAQLAAEKAAK 72

Query:   191 LARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP 250
              A   G+K+V V VKG      +  AI S +           +  I+D T  PHNGCR P
Sbjct:    73 EAMEFGVKTVEVYVKGPG--AGREAAIRSLQAAGLE------VSLIKDVTPIPHNGCRPP 124

Query:   251 KKRRI 255
             K+RR+
Sbjct:   125 KRRRV 129

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0042254 "ribosome biogenesis" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	255
COG0100	129	COG0100, RpsK, Ribosomal protein S11 [Translation,	2e-21
PRK05309	128	PRK05309, PRK05309, 30S ribosomal protein S11; Val	9e-21
TIGR03632	108	TIGR03632, bact_S11, 30S ribosomal protein S11	2e-19
pfam00411	109	pfam00411, Ribosomal_S11, Ribosomal protein S11	2e-19
CHL00041	116	CHL00041, rps11, ribosomal protein S11	2e-13
PRK09607	132	PRK09607, rps11p, 30S ribosomal protein S11P; Revi	1e-09
TIGR03628	114	TIGR03628, arch_S11P, archaeal ribosomal protein S	2e-07
cd00432	103	cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18	8e-04

>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]

 Score = 86.1 bits (214), Expect = 2e-21
 Identities = 51/120 (42%), Positives = 63/120 (52%), Gaps = 13/120 (10%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT VT+TD  GN  I ASSG +   KG  K + YAA+  AE   + A+  G+
Sbjct: 21  AHIHASFNNTIVTITDLTGNVIIWASSGGM-GFKGSRKSTPYAAQLAAEDAAKKAKEHGI 79

Query: 198 KSVVVRVKGFTYFKKKRQAIMS--FREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           KSV V+VKG       R+A +      G         I  IED T  PHNGCR PK+RR+
Sbjct: 80  KSVEVKVKGP---GPGREAAIRALAAAGLK-------ITRIEDVTPIPHNGCRPPKRRRV 129

Length = 129

>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated

 Score = 84.4 bits (210), Expect = 9e-21
 Identities = 47/119 (39%), Positives = 63/119 (52%), Gaps = 11/119 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT VT+TD +GN    AS+G L   KG  K + YAA+  AE   + A+  G+
Sbjct: 20  AHIHATFNNTIVTITDRQGNVISWASAGGL-GFKGSRKSTPYAAQVAAEDAAKKAKEHGM 78

Query: 198 KSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           K+V V VKG      +  AI + +  G         +  I+D T  PHNGCR PK+RR+
Sbjct: 79  KTVEVFVKGPG--SGRESAIRALQAAGLE-------VTSIKDVTPIPHNGCRPPKRRRV 128

Length = 128

>gnl|CDD|188357 TIGR03632, bact_S11, 30S ribosomal protein S11

 Score = 80.7 bits (200), Expect = 2e-19
 Identities = 44/116 (37%), Positives = 60/116 (51%), Gaps = 11/116 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT VT+TD +GN    AS+G +   KG  K + YAA+  AE   + A+  G+
Sbjct: 3   AHIHATFNNTIVTITDPQGNVLSWASAGAV-GFKGSKKSTPYAAQLAAEDAAKKAKEFGM 61

Query: 198 KSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGCRLPKK 252
           K+V V VKG      +  AI + +  G         +  I+D T  PHNGCR PK+
Sbjct: 62  KTVDVYVKGPG--AGRESAIRALQAAGLE-------VTSIKDVTPIPHNGCRPPKR 108

This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 108

>gnl|CDD|189537 pfam00411, Ribosomal_S11, Ribosomal protein S11

 Score = 80.1 bits (198), Expect = 2e-19
 Identities = 42/117 (35%), Positives = 63/117 (53%), Gaps = 11/117 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI+   NNT +T+TD  G   + +S+G     KG  K + YAA+  AE+  ++A+  G+
Sbjct: 3   AHIQASFNNTIITITDVIGRVVLWSSAGGC-GFKGSRKSTPYAAQTAAENAAKIAKEQGI 61

Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
           K++ V++KG    ++   A+ +  R G         I  I D T  PHNGCR PKKR
Sbjct: 62  KALEVKIKGPGPGRE--SALRALARSGLR-------ITRIRDVTPIPHNGCRPPKKR 109

Length = 109

>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 38/112 (33%), Positives = 54/112 (48%), Gaps = 13/112 (11%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSG-CLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
           +HI+   NNT VTVTD +G     +S+G C    KG  K + +AA+  AE+  R   + G
Sbjct: 16  IHIQASFNNTIVTVTDVRGRVISWSSAGAC--GFKGARKGTPFAAQTAAENAIRTVIDQG 73

Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFRE-GFANSRDQNPIVYIEDTTRRPHNGC 247
           +K   V +KG    +    A+ + R  G         +  I D T  PHNGC
Sbjct: 74  MKRAEVMIKGPGLGRDT--ALRAIRRSGL-------KLSSIRDVTPMPHNGC 116

Length = 116

>gnl|CDD|236588 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 40/124 (32%), Positives = 54/124 (43%), Gaps = 14/124 (11%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT +T+TD  G + I  SSG +       + S YAA   AE     A+  G+
Sbjct: 12  AHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGI 71

Query: 198 KSVVVRVKGFTYFKKK------RQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLP 250
             V ++V+      +K      + AI +  R G         I  IED T  PH+G R P
Sbjct: 72  TGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLR-------IGRIEDVTPIPHDGTRPP 124

Query: 251 KKRR 254
             RR
Sbjct: 125 GGRR 128

Length = 132

>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P

 Score = 48.2 bits (115), Expect = 2e-07
 Identities = 34/117 (29%), Positives = 49/117 (41%), Gaps = 14/117 (11%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT +T+TD  G + I  SSG +       + S YAA   A      A+  G+
Sbjct: 5   AHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGI 64

Query: 198 KSVVVRVKGFTYFKKK------RQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGC 247
             + ++V+      +K      + AI +  R G    R       IED T  PH+G 
Sbjct: 65  TGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGR-------IEDVTPIPHDGT 114

This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 114

>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit

 Score = 37.5 bits (88), Expect = 8e-04
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 145 NNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR--YAAEATAEHVGRLARNMGLKSVVV 202
            + +  + D  G+K + ++S     +KG         AA      + + A   G+K VV 
Sbjct: 21  KHIYAQIIDDSGDKTLVSASTLELAIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVF 80

Query: 203 RVKGFTYFKKKRQAIMSFREG 223
              G+ Y  + +      REG
Sbjct: 81  DRGGYRYHGRVKALAKGAREG 101

L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified. Length = 103

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	255
PRK05309	128	30S ribosomal protein S11; Validated	100.0
PRK09607	132	rps11p 30S ribosomal protein S11P; Reviewed	100.0
PF00411	110	Ribosomal_S11: Ribosomal protein S11; InterPro: IP	100.0
COG0100	129	RpsK Ribosomal protein S11 [Translation, ribosomal	100.0
TIGR03632	108	bact_S11 30S ribosomal protein S11. This model des	100.0
PTZ00129	149	40S ribosomal protein S14; Provisional	100.0
KOG0408	190	consensus Mitochondrial/chloroplast ribosomal prot	100.0
CHL00041	116	rps11 ribosomal protein S11	100.0
TIGR03628	114	arch_S11P archaeal ribosomal protein S11P. This mo	100.0
PTZ00090	233	40S ribosomal protein S11; Provisional	100.0
KOG0407	139	consensus 40S ribosomal protein S14 [Translation,	99.92
cd00432	103	Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is	97.86
PRK08569	193	rpl18p 50S ribosomal protein L18P; Reviewed	97.37
PF00861	119	Ribosomal_L18p: Ribosomal L18p/L5e family; InterPr	97.32
TIGR00060	114	L18_bact ribosomal protein L18, bacterial type. Th	97.21
CHL00139	109	rpl18 ribosomal protein L18; Validated	97.17
PRK05593	117	rplR 50S ribosomal protein L18; Reviewed	97.05
COG0256	125	RplR Ribosomal protein L18 [Translation, ribosomal	96.35
PTZ00032	211	60S ribosomal protein L18; Provisional	95.74

>PRK05309 30S ribosomal protein S11; Validated

Probab=100.00  E-value=7.1e-43  Score=288.65  Aligned_cols=114  Identities=41%  Similarity=0.550  Sum_probs=109.9

Q ss_pred             ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK  212 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~  212 (255)
                      ...+|+||++|+|||||||||.+|+++.|.|||++ ||||++|+||||||++|+.++++|+++||+.|+|+|||+|+|| 
T Consensus        15 ~~~gi~hI~~t~NNTiitlTd~~G~~~~~~S~G~~-gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr-   92 (128)
T PRK05309         15 IPSGVAHIHATFNNTIVTITDRQGNVISWASAGGL-GFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEVFVKGPGSGR-   92 (128)
T ss_pred             cceeEEEEEccCCCEEEEEEcCCCCEEEEEecCcc-EeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH-
Confidence            45699999999999999999999999999999999 9999999999999999999999999999999999999999997 


Q ss_pred             hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                       +++|++|+.      .|++|++|+|+||+|||||||||+|||
T Consensus        93 -~~air~L~~------~glkI~~I~D~TpiphNGcR~~K~RRv  128 (128)
T PRK05309         93 -ESAIRALQA------AGLEVTSIKDVTPIPHNGCRPPKRRRV  128 (128)
T ss_pred             -HHHHHHHHH------CCCEEEEEEEcCCCCCCCcCcCCCCCC
Confidence             799999975      689999999999999999999999997

>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed

Probab=100.00  E-value=3.2e-42  Score=286.47  Aligned_cols=113  Identities=31%  Similarity=0.328  Sum_probs=107.2

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc------
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG------  206 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG------  206 (255)
                      ..+|+||++|+|||||||||.+|+ ++.|.|+|.+ ||||++|+||||||.||++++++|+++||+.|+|+|||      
T Consensus         8 ~~gi~hI~as~NNTivtvTD~~G~~~~~~~S~G~~-g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~~v~v~vkG~Ggn~~   86 (132)
T PRK09607          8 KWGIAHIYASFNNTIITITDLTGAETIAKSSGGMV-VKADRDESSPYAAMQAAEKAAEDAKEKGITGVHIKVRAPGGNGQ   86 (132)
T ss_pred             eeeEEEEEcccCCeEEEEEcCCCCEEEEEecCcce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCC
Confidence            459999999999999999999996 9999999999 99999999999999999999999999999999999999      


Q ss_pred             --cCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          207 --FTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       207 --~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                        +|+||  ++||++|+.      .+++|.+|+|+||+|||||||||+||+
T Consensus        87 ~~~G~Gr--~~airal~~------~glkI~~I~DvTpiPhNGCRp~K~RR~  129 (132)
T PRK09607         87 KSPGPGA--QAAIRALAR------AGLRIGRIEDVTPIPHDGTRPPGGRRG  129 (132)
T ss_pred             cCCCCcH--HHHHHHHHH------CCCEEEEEEEcCCCCCCCCCCCCCCCC
Confidence              67775  899999975      699999999999999999999999996

>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=1.7e-42  Score=278.79  Aligned_cols=110  Identities=44%  Similarity=0.639  Sum_probs=102.9

Q ss_pred             eEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHH
Q 025294          136 EFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQ  215 (255)
Q Consensus       136 ~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~a  215 (255)
                      +|+||++|+|||||||||.+|++++|.|||++ ||||++|+|+|||+++++.++++|+++||+.|+|+|||+|+||  ++
T Consensus         1 giihI~~s~NNt~vtlTd~~G~~~~~~S~G~~-gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~ikG~g~gr--~~   77 (110)
T PF00411_consen    1 GIIHIKSSFNNTIVTLTDLKGNVLFWSSAGSL-GFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRVKIKGFGPGR--EA   77 (110)
T ss_dssp             EEEEEEEESSEEEEEEEETTSEEEEEEETTTS-STTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEEEEESSSTTH--HH
T ss_pred             CEEEEEecCCCEEEEEECCCCCEEEEEecccc-ccccccccCHHHHHHHHHHHHHHHHHcCCeEEEEEEcCCCccH--HH
Confidence            68999999999999999999999999999999 9999999999999999999999999999999999999999997  79


Q ss_pred             HHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          216 AIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       216 aIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                      +|++|+.      .+++|++|+|+||+|||||||||+||
T Consensus        78 ~lk~l~~------~gl~I~~I~D~T~iphnGcR~kK~RR  110 (110)
T PF00411_consen   78 ALKALKK------SGLKIVSITDVTPIPHNGCRPKKKRR  110 (110)
T ss_dssp             HHHHHHH------TTSEEEEEEEETT--SSSS--TTTTT
T ss_pred             HHHHHHh------cCCEEEEEEeecCCCCCCCCCCCCCC
Confidence            9999975      58999999999999999999999998

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 [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....

>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=8.6e-42  Score=282.60  Aligned_cols=114  Identities=44%  Similarity=0.566  Sum_probs=109.9

Q ss_pred             ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK  212 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~  212 (255)
                      ..++++||++|+||||||+||+.||++.|.|+|++ |||+.+|+||||||++|+.+++.++++||+.|+|+|||+|+|| 
T Consensus        16 i~~GvahI~asfNNTivtitD~~Gn~i~wassG~~-gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v~vkgpG~Gr-   93 (129)
T COG0100          16 IADGVAHIHASFNNTIVTITDLTGNVIIWASSGGM-GFKGSRKSTPYAAQLAAEDAAKKAKEHGIKSVEVKVKGPGPGR-   93 (129)
T ss_pred             cccceEEEEcccCCcEEEecCCCCCEEEEEecCCc-eEcCCCCCCHHHHHHHHHHHHHHHHHhCccEEEEEEECCCCcH-
Confidence            35699999999999999999999999999999999 9999999999999999999999999999999999999999997 


Q ss_pred             hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                       ++||++|..      .|++|.+|+|+||||||||||||+||+
T Consensus        94 -eaAiraL~~------ag~~i~~I~DvTPiphnG~Rppk~RR~  129 (129)
T COG0100          94 -EAAIRALAA------AGLKITRIEDVTPIPHNGCRPPKRRRV  129 (129)
T ss_pred             -HHHHHHHHH------ccceEEEEEEcCCCCCCCCCCCCCCCC
Confidence             899999974      699999999999999999999999996

>TIGR03632 bact_S11 30S ribosomal protein S11

Probab=100.00  E-value=1.9e-41  Score=272.45  Aligned_cols=108  Identities=40%  Similarity=0.551  Sum_probs=104.4

Q ss_pred             eEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHH
Q 025294          136 EFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQ  215 (255)
Q Consensus       136 ~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~a  215 (255)
                      +|+||++|+||||||+||++|+++.|.|||++ ||||++|+|+||||++|+.++++++++||+.|+|+|||+|+||  ++
T Consensus         1 gi~hI~~s~NNT~itlTd~~g~~~~~~S~G~~-gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v~~kG~G~gr--~~   77 (108)
T TIGR03632         1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAV-GFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDVYVKGPGAGR--ES   77 (108)
T ss_pred             CEEEEEccCCCEEEEEEcCCCCEEEEEecCce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH--HH
Confidence            58999999999999999999999999999999 9999999999999999999999999999999999999999997  79


Q ss_pred             HHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCC
Q 025294          216 AIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKK  252 (255)
Q Consensus       216 aIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~  252 (255)
                      +|++|+.      .+++|.+|+|+||+|||||||||+
T Consensus        78 ~ir~l~~------~glkI~~I~D~T~iphNGcR~~K~  108 (108)
T TIGR03632        78 AIRALQA------AGLEVTSIKDVTPIPHNGCRPPKR  108 (108)
T ss_pred             HHHHHHH------CCCEEEEEEEcCCCCCCCcCCCCC
Confidence            9999975      689999999999999999999995

This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.

>PTZ00129 40S ribosomal protein S14; Provisional

Probab=100.00  E-value=2.6e-41  Score=285.68  Aligned_cols=116  Identities=26%  Similarity=0.307  Sum_probs=109.5

Q ss_pred             ccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCC-CCchhHHHHHHHHHHHHHHHcCCcEEEEEE----
Q 025294          130 NVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGP-KMSRYAAEATAEHVGRLARNMGLKSVVVRV----  204 (255)
Q Consensus       130 ~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~r-KsT~~AAq~aae~i~~kakelGik~V~V~v----  204 (255)
                      ..+...+|+||++|+|||||||||+.|++++|.|+|.+ ||||.+ |+||||||.||+.++++|+++||+.|+|+|    
T Consensus        23 ~~~~~~Gi~hI~as~NNTiItiTD~~G~~~~w~SsG~~-gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~vr~~g  101 (149)
T PTZ00129         23 KGELVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGM-KVKADRDESSPYAAMMAAQDVAARCKELGINALHIKLRATG  101 (149)
T ss_pred             CCceeEEEEEEEcccCCeEEEEEcccCCEEEEEecCcc-eecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEecC
Confidence            34456799999999999999999999999999999999 999998 999999999999999999999999999999    


Q ss_pred             ----EccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          205 ----KGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       205 ----KG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                          +|+|+||  ++||++|+.      .+|+|.+|+|+||||||||||||+||
T Consensus       102 g~~~kg~GpGr--~~airaL~~------~glkI~~I~DvTPiPhNGcRppk~RR  147 (149)
T PTZ00129        102 GVRTKTPGPGA--QAALRALAR------AGLKIGRIEDVTPIPTDSTRRKGGRR  147 (149)
T ss_pred             CCCCCCCCCCH--HHHHHHHHH------CCCEEEEEEecCCCCCCCCCCCCCCC
Confidence                7788886  899999975      69999999999999999999999998

>KOG0408 consensus Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=9.6e-40  Score=280.05  Aligned_cols=137  Identities=32%  Similarity=0.380  Sum_probs=127.3

Q ss_pred             CCccc-ccCccccccccc-CCCCcccCCCCcccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCch
Q 025294          101 RPMDF-VRGIVEEDEKRF-TGPSQFGQFPRYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR  178 (255)
Q Consensus       101 ~~m~~-~~~~~e~d~~~~-~~g~~f~q~~~~~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~  178 (255)
                      ..|++ +-+.|++++.++ |.|++|+|+         +|+||++|+|||+|||||.+|.++.|.|||.+ ||||++|.|+
T Consensus        52 ~~i~t~I~r~p~aet~~r~~~g~~f~ei---------Pi~hIraS~NNTivtVtd~kg~vi~~~Scgte-GFrntrkgT~  121 (190)
T KOG0408|consen   52 AGIATPINRRPGAETNTRSFSGKNFREI---------PIIHIRASFNNTIVTVTDVKGEVISWSSCGTE-GFRNTRKGTP  121 (190)
T ss_pred             cccccccccCCChhhhhcccCCcccccc---------ceEEEEecCCCeEEEEEccCCcEEEEeecccc-cccccccCCc
Confidence            44444 223588777777 999999999         99999999999999999999999999999999 9999999999


Q ss_pred             hHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          179 YAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       179 ~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                      +|||.+|..+++++.++|++.|+|+|||.|+||  ++|+++|.+      .|+.|++|+|+||+|||||||+|+|||
T Consensus       122 iAaQtaavaa~~r~v~~G~~~vrV~VkGlGpGR--msa~kgl~m------~Gl~vvsItD~Tp~~~ng~RPrK~Rrl  190 (190)
T KOG0408|consen  122 IAAQTAAVAAIRRAVDQGMQTVRVRVKGLGPGR--MSALKGLRM------GGLLVVSITDNTPMPHNGCRPRKKRRL  190 (190)
T ss_pred             hhHHHHHHHHHHHHHHhcceEEEEEEecCCccH--HHHHhhhhh------cceEEEEeecCCcCCCCCCCccccccC
Confidence            999999999999999999999999999999998  899999986      599999999999999999999999996

>CHL00041 rps11 ribosomal protein S11

Probab=100.00  E-value=6.1e-38  Score=255.24  Aligned_cols=106  Identities=34%  Similarity=0.441  Sum_probs=102.2

Q ss_pred             ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK  212 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~  212 (255)
                      ...+++||++|+|||||||||++|+++.|.|||++ ||||++|+||||||++|++++++|+++||+.|+|+|||+|+|| 
T Consensus        11 ~~~gi~hI~~t~NNTiiTlTd~~G~~l~~~S~G~~-gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I~ikG~G~Gr-   88 (116)
T CHL00041         11 IPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGAC-GFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEVMIKGPGLGR-   88 (116)
T ss_pred             ceeEEEEEEcccCCEEEEEEcCCCCEEEEEecCce-eeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEECCCCcH-
Confidence            45699999999999999999999999999999999 9999999999999999999999999999999999999999997 


Q ss_pred             hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCC
Q 025294          213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC  247 (255)
Q Consensus       213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGC  247 (255)
                       +++|++|+.      .+++|.+|+|+||+|||||
T Consensus        89 -~~~ir~l~~------~glkI~~I~D~TpiphNGC  116 (116)
T CHL00041         89 -DTALRAIRR------SGLKLSSIRDVTPMPHNGC  116 (116)
T ss_pred             -HHHHHHHHH------CCCEEEEEEEcCCCCCCCC
Confidence             799999975      6999999999999999999

>TIGR03628 arch_S11P archaeal ribosomal protein S11P

Probab=100.00  E-value=4.6e-37  Score=250.14  Aligned_cols=104  Identities=28%  Similarity=0.299  Sum_probs=99.0

Q ss_pred             ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc-------
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG-------  206 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG-------  206 (255)
                      .+|+||++|+|||||||||.+|+ ++.|.|+|++ ||||++|+||||||.|+++++++|+++||+.|+|+|||       
T Consensus         2 ~gi~hI~as~NNTiitvTD~~G~~~~~~~S~G~~-g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~~v~v~ikG~gg~~~~   80 (114)
T TIGR03628         2 WGIAHIYSSFNNTIITITDITGAETIARSSGGMV-VKADRDESSPYAAMQAAGRAAEKAKERGITGLHIKVRAPGGNGQK   80 (114)
T ss_pred             cEEEEEEccCCCeEEEEEcCCCCEEEEEecCcce-EeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEEEEEecCCCCCC
Confidence            48999999999999999999995 6999999999 99999999999999999999999999999999999999       


Q ss_pred             -cCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCC
Q 025294          207 -FTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC  247 (255)
Q Consensus       207 -~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGC  247 (255)
                       +|+||  ++||++|+.      .+++|.+|+|+||+|||||
T Consensus        81 ~~G~Gr--~~air~l~~------~glkI~~I~DvTpiPhNGC  114 (114)
T TIGR03628        81 SPGPGA--QAAIRALAR------AGLRIGRIEDVTPIPHDGT  114 (114)
T ss_pred             CCCCcH--HHHHHHHHH------CCCEEEEEEEcCCCCCCCC
Confidence             67776  899999975      6999999999999999999

This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.

>PTZ00090 40S ribosomal protein S11; Provisional

Probab=100.00  E-value=5.5e-36  Score=266.01  Aligned_cols=112  Identities=19%  Similarity=0.294  Sum_probs=105.5

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCCE--EEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCc
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGNK--RIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFK  211 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gnv--l~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR  211 (255)
                      +.-.+-|++|+|||||||||..||+  ++|+|+|.+ ||||++|+||||||.||+.++++|+++||+.|+|+|||+| +|
T Consensus       117 ~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~-GFKGsKKsTpfAAQ~aae~aakka~~~GIk~V~V~vKGpG-gR  194 (233)
T PTZ00090        117 DRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNV-GFRKKLQQSERCAYRIGENIAKKCRRLGIFAVDIKFRRIM-RV  194 (233)
T ss_pred             CcEEEEEEeccCcEEEEEEeCCCCEEEEEEEccccc-CcccCccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeCCC-hH
Confidence            4567789999999999999999995  999999999 9999999999999999999999999999999999999998 44


Q ss_pred             chHHHHHHHHhcccCCCCCCCeEEEEecCCCCC---CCCCCCCCCCC
Q 025294          212 KKRQAIMSFREGFANSRDQNPIVYIEDTTRRPH---NGCRLPKKRRI  255 (255)
Q Consensus       212 ~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPh---NGCRpkK~RRv  255 (255)
                        ++||++|+.      .|++|.+|.|+||+||   |||||||+|||
T Consensus       195 --EtALRaL~~------~GLkIt~I~DvTpiPHNG~NGCRPpKKRRV  233 (233)
T PTZ00090        195 --ETVLQAFYA------NGLQVTQIIHEPRLPKCGLNAVKPRKRRRV  233 (233)
T ss_pred             --HHHHHHHHH------CCCEEEEEEECCCCCcCCCCCCCCCCCCCC
Confidence              899999986      6999999999999999   55999999997

>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]

Probab=99.92  E-value=2.4e-24  Score=175.88  Aligned_cols=121  Identities=27%  Similarity=0.310  Sum_probs=107.7

Q ss_pred             CcccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEcc
Q 025294          128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGF  207 (255)
Q Consensus       128 ~~~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~  207 (255)
                      .++.|+..+++||++|+|+|||++||+.|......-.|.++-...+..++||||++||++++.+|+++||+.+||++++.
T Consensus         9 ~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kck~~gi~alh~klrat   88 (139)
T KOG0407|consen    9 VREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKCKELGITALHIKLRAT   88 (139)
T ss_pred             hcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHHHhcCeeEEEEEEEec
Confidence            34567789999999999999999999999988888888773444568899999999999999999999999999999999


Q ss_pred             CCCcch------HHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          208 TYFKKK------RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       208 G~gR~k------~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                      |+.+.|      ++||++|.      |+|++|.+|+|+||||.+..|.|-.||
T Consensus        89 gg~ktktpgpgaqsalrala------r~gmrigriedvtpip~d~trrkggrr  135 (139)
T KOG0407|consen   89 GGTKTKTPGPGAQSALRALA------RSGMRIGRIEDVTPIPSDSTRRKGGRR  135 (139)
T ss_pred             CCcccCCCCccHHHHHHHHH------HhcceeeeecccccCCccchhhccCcc
Confidence            988776      78999985      479999999999999999999986655

>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit

Probab=97.86  E-value=0.00022  Score=56.47  Aligned_cols=89  Identities=19%  Similarity=0.246  Sum_probs=71.3

Q ss_pred             ccceEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCC
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTY  209 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~  209 (255)
                      ..++.+.|+.|.+|...+|.|.. +.++...|+-.. .+++.  ......||..+++.++++|++.|+..+.+-..|.-+
T Consensus         9 ~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~-~~~~~~~~~~n~~aA~~vG~~la~r~~~~gi~~vv~D~~~~~~   87 (103)
T cd00432           9 QERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLEL-AIKGVLGSGNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYRY   87 (103)
T ss_pred             CCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCch-hhcccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEeCCCccc
Confidence            35689999999999999999997 788999999888 87774  567788999999999999999999999888766654


Q ss_pred             CcchHHHHHHHHh
Q 025294          210 FKKKRQAIMSFRE  222 (255)
Q Consensus       210 gR~k~aaIkaL~~  222 (255)
                      +-.-.+++.++.+
T Consensus        88 ~grv~a~~~~~r~  100 (103)
T cd00432          88 HGRVKALAKGARE  100 (103)
T ss_pred             ccHHHHHHHHHHH
Confidence            3212344455554

L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.

>PRK08569 rpl18p 50S ribosomal protein L18P; Reviewed

Probab=97.37  E-value=0.0041  Score=55.51  Aligned_cols=107  Identities=19%  Similarity=0.144  Sum_probs=77.2

Q ss_pred             cCccceEEEEEccCCCeEEEEE--cCCC-CEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEE
Q 025294          131 VEHSSEFVHIKLMRNNTFVTVT--DSKG-NKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVK  205 (255)
Q Consensus       131 ~e~~~~IlhI~sT~NNTiITlT--D~~G-nvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vK  205 (255)
                      +....+-+.|+-|.+++++.|.  |..| .++.+.|+-.+ ..++-  ......||+.++..++++|++.||+.+.+=.-
T Consensus        28 ~~~~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el-~~~g~~~~~~N~~AAy~vG~llA~ral~kGi~~vvfDrG  106 (193)
T PRK08569         28 LLSGKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSREL-AKYGWKGDTGNTPAAYLTGLLAGKKALKAGVEEAVLDIG  106 (193)
T ss_pred             HhcCCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCch-hhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecC
Confidence            3445688999999999999999  5554 57777777666 55452  35667799999999999999999999887775


Q ss_pred             ccCC---CcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          206 GFTY---FKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       206 G~G~---gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                      |.=+   || -.+++++..+      .||+         +||+..|-|---|
T Consensus       107 g~~yh~gGR-V~A~akgArd------~GL~---------fPh~~~~~p~~~r  142 (193)
T PRK08569        107 LHRPTKGSR-VFAALKGAID------AGLE---------IPHGEEVLPDEDR  142 (193)
T ss_pred             CccccCCcc-HHHHHHHHHH------cCCc---------CCCCCCcCCCccc
Confidence            5443   34 2345556554      4774         6888887765433

>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.32  E-value=0.0021  Score=52.63  Aligned_cols=88  Identities=20%  Similarity=0.205  Sum_probs=68.7

Q ss_pred             cceEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC----CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG----PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT  208 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~----rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G  208 (255)
                      ..|.+-|+.|..++.+.|.|.. +.++...|+-.. .++..    ......||+.+++.++++|++.||..|.+-..|+-
T Consensus        22 ~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~-~l~~~~~~~~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr~~~~  100 (119)
T PF00861_consen   22 ERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSK-ELKKYGWKGSTKNVEAAYLVGELLAKRALEKGIAKVVFDRGGYK  100 (119)
T ss_dssp             SSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETT-TGGGTT-SSTTSSHHHHHHHHHHHHHHHHHTTSSEEEECTSTSS
T ss_pred             CCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecch-hhhhhhhccCCCCEehHHHHHHHHHHHHHHcCCcEEEEcCCCCc
Confidence            4589999999999999998766 778888888777 77752    33467899999999999999999999888877776


Q ss_pred             CCcchHHHHHHHHh
Q 025294          209 YFKKKRQAIMSFRE  222 (255)
Q Consensus       209 ~gR~k~aaIkaL~~  222 (255)
                      ++-.-.+++.++.+
T Consensus       101 y~grv~a~~~~~re  114 (119)
T PF00861_consen  101 YHGRVKALADGARE  114 (119)
T ss_dssp             SSSHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH
Confidence            65422344556665

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 [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....

>TIGR00060 L18_bact ribosomal protein L18, bacterial type

Probab=97.21  E-value=0.005  Score=50.76  Aligned_cols=71  Identities=20%  Similarity=0.182  Sum_probs=56.7

Q ss_pred             ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT  208 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G  208 (255)
                      .|-+.|+-|.+++.+.|.|..+. ++.+.|+=.. .++  ....-.||..+++.++++|++.||+.|..--.|+=
T Consensus        24 rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek-~~~--~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~~   95 (114)
T TIGR00060        24 RPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEK-KLK--YTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGYK   95 (114)
T ss_pred             CcEEEEEEeCCeEEEEEEECCCCEEEEEEecchh-hhc--CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCc
Confidence            48899999999999999977665 6666665444 666  56677899999999999999999999876644433

The archaeal and eukaryotic type rpL18 is not detectable under this model.

>CHL00139 rpl18 ribosomal protein L18; Validated

Probab=97.17  E-value=0.0058  Score=49.87  Aligned_cols=71  Identities=13%  Similarity=0.213  Sum_probs=57.9

Q ss_pred             ceEEEEEccCCCeEEEEEc-CCCCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc
Q 025294          135 SEFVHIKLMRNNTFVTVTD-SKGNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG  206 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD-~~Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG  206 (255)
                      .|.+.|+.|.+++.+.|.| .+|+++.+.|+=.. .+++.  ....-.||+.+++.++++|++.||..|..--.|
T Consensus        15 rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek-~~~~~~~~~~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg   88 (109)
T CHL00139         15 RPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEP-DVKSSLSSTSTCDASKLVGQKLAKKSLKKGITKVVFDRGG   88 (109)
T ss_pred             CCEEEEEEeCCeEEEEEEECCCCCEEEEEecCch-hhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence            4789999999999998875 56789998888666 66653  456678999999999999999999998776433

>PRK05593 rplR 50S ribosomal protein L18; Reviewed

Probab=97.05  E-value=0.0077  Score=49.66  Aligned_cols=72  Identities=18%  Similarity=0.204  Sum_probs=56.8

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCC-CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEc
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGG-PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKG  206 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~-rKsT~~AAq~aae~i~~kakelGik~V~V~vKG  206 (255)
                      ..|-+.|+.|.+++.+.|.|..+. ++.+.|+=.. .++.. +...-.||+.+++.++++|++.||+.+..--.|
T Consensus        23 ~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~-~~k~~~~~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~   96 (117)
T PRK05593         23 ERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEK-DVRAGLKGGNKEAAKKVGKLIAERAKAKGIKQVVFDRGG   96 (117)
T ss_pred             CCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcH-hHhccccCCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCC
Confidence            348999999999999999987776 6666666444 55443 367778999999999999999999997666433

>COG0256 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]

Probab=96.35  E-value=0.056  Score=45.38  Aligned_cols=77  Identities=17%  Similarity=0.179  Sum_probs=57.1

Q ss_pred             cceEEEEEccCCCeEEEEEcCCC-CEEEEEeccCcccccC--C--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccC
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKG-NKRIGASSGCLPELKG--G--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFT  208 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~G-nvl~~~SsGs~~GFKg--~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G  208 (255)
                      ..+-+-|+-|.+|.++.|.|... .++...|+=.. ..++  .  ....-.||..+++.|+++|+++||+.+.+=..|+-
T Consensus        28 ~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~-~l~~~g~~~~~~N~~aA~~vG~lia~ra~~kgi~~vVfdr~g~~  106 (125)
T COG0256          28 GRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSK-ELRKYGKKGGGGNTEAAYLVGKLIAERALAKGIEEVVFDRGGYK  106 (125)
T ss_pred             CCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchH-HHHhhcccCCCCCHHHHHHHHHHHHHHHHHcCCcEEEEcCCCCC
Confidence            44888888999999999987664 56777776553 3322  1  22346689999999999999999999997666666


Q ss_pred             CCc
Q 025294          209 YFK  211 (255)
Q Consensus       209 ~gR  211 (255)
                      ++-
T Consensus       107 yhg  109 (125)
T COG0256         107 YHG  109 (125)
T ss_pred             cch
Confidence            554

>PTZ00032 60S ribosomal protein L18; Provisional

Probab=95.74  E-value=0.09  Score=47.58  Aligned_cols=86  Identities=17%  Similarity=0.159  Sum_probs=63.6

Q ss_pred             ccceEEEEEccCCCeEEEEEcC-CCCEEEEEeccCcccccCC--------------CCCchhHHHHHHHHHHHHHHHcCC
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDS-KGNKRIGASSGCLPELKGG--------------PKMSRYAAEATAEHVGRLARNMGL  197 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~-~Gnvl~~~SsGs~~GFKg~--------------rKsT~~AAq~aae~i~~kakelGi  197 (255)
                      +..+-+-|+-|.++..+++.|. .|.++.++|+=.. .+++.              ...+-.||..+++.|+++|.++||
T Consensus       103 krrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek-~l~~~~~~~~~~~~n~~~~~g~nieaA~~VGk~IAerAl~kGI  181 (211)
T PTZ00032        103 KRRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFK-YLSHIFGTYPTKTTNRVRNNGGTIKAAYELGKLIGRKALSKGI  181 (211)
T ss_pred             CCcceEEEEecCCeEEEEEEECCCCCEEEEecCCCH-HHHhhhcccccccccccccCCCcHHHHHHHHHHHHHHHHHCCC
Confidence            3568999999999999999865 6778888777544 66542              467889999999999999999999


Q ss_pred             cEEEEEEEccCCCcchHHHHHHHHhc
Q 025294          198 KSVVVRVKGFTYFKKKRQAIMSFREG  223 (255)
Q Consensus       198 k~V~V~vKG~G~gR~k~aaIkaL~~G  223 (255)
                      +.|..==.|+=+-.    -|+||.+|
T Consensus       182 ~kVvFDRgGy~YHG----RVkALAda  203 (211)
T PTZ00032        182 SKVRFDRAHYKYAG----KVEALAEG  203 (211)
T ss_pred             CEEEEeCCCCeehh----HHHHHHHH
Confidence            98766533332221    35666544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	255
3fih_K	117	Ternary Complex-Bound E.Coli 70s Ribosome. This Ent		2e-09
1p6g_K	128	Real Space Refined Coordinates Of The 30s Subunit F		2e-09
1vs5_K	129	Crystal Structure Of The Bacterial Ribosome From Es		2e-09
2gy9_K	116	Structure Of The 30s Subunit Of A Pre-Translocation		3e-09
3bbn_K	140	Homology Model For The Spinach Chloroplast 30s Subu		6e-08
1i94_K	128	Crystal Structures Of The Small Ribosomal Subunit W		3e-05
1fjg_K	129	Structure Of The Thermus Thermophilus 30s Ribosomal		3e-05
1pns_K	119	Crystal Structure Of A Streptomycin Dependent Ribos		3e-05

>pdb|3FIH|K Chain K, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 117

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/122 (34%), Positives = 60/122 (49%), Gaps = 9/122 (7%)
Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           S    HI    NNT VT+TD +GN  +G ++      +G  K + +AA+  AE      +
Sbjct: 5   SDGVAHIHASFNNTIVTITDRQGNA-LGWATAGGSGFRGSRKSTPFAAQVAAERCADAVK 63
Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
             G+K++ V VKG    ++     ++   GF        I  I D T  PHNGCR PKKR
Sbjct: 64  EYGIKNLEVMVKGPGPGRESTIRALNA-AGFR-------ITNITDVTPIPHNGCRPPKKR 115
Query: 254 RI 255
           R+
Sbjct: 116 RV 117

>pdb|1P6G|K Chain K, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 128

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/128 (33%), Positives = 62/128 (48%), Gaps = 9/128 (7%)
Query: 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH 187
           R   + S    HI    NNT VT+TD +GN  +G ++      +G  K + +AA+  AE 
Sbjct: 10  RVRKQVSDGVAHIHASFNNTIVTITDRQGNA-LGWATAGGSGFRGSRKSTPFAAQVAAER 68
Query: 188 VGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC 247
                +  G+K++ V VKG    ++     ++   GF        I  I D T  PHNGC
Sbjct: 69  CADAVKEYGIKNLEVMVKGPGPGRESTIRALNA-AGFR-------ITNITDVTPIPHNGC 120
Query: 248 RLPKKRRI 255
           R PKKRR+
Sbjct: 121 RPPKKRRV 128

>pdb|1VS5|K Chain K, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 129

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/128 (33%), Positives = 62/128 (48%), Gaps = 9/128 (7%)
Query: 128 RYNVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEH 187
           R   + S    HI    NNT VT+TD +GN  +G ++      +G  K + +AA+  AE 
Sbjct: 11  RVRKQVSDGVAHIHASFNNTIVTITDRQGNA-LGWATAGGSGFRGSRKSTPFAAQVAAER 69
Query: 188 VGRLARNMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGC 247
                +  G+K++ V VKG    ++     ++   GF        I  I D T  PHNGC
Sbjct: 70  CADAVKEYGIKNLEVMVKGPGPGRESTIRALNA-AGFR-------ITNITDVTPIPHNGC 121
Query: 248 RLPKKRRI 255
           R PKKRR+
Sbjct: 122 RPPKKRRV 129

>pdb|2GY9|K Chain K, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 116

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/121 (34%), Positives = 59/121 (48%), Gaps = 9/121 (7%)
Query: 134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLAR 193
           S    HI    NNT VT+TD +GN  +G ++      +G  K + +AA+  AE      +
Sbjct: 5   SDGVAHIHASFNNTIVTITDRQGNA-LGWATAGGSGFRGSRKSTPFAAQVAAERCADAVK 63
Query: 194 NMGLKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
             G+K++ V VKG    ++     ++   GF        I  I D T  PHNGCR PKKR
Sbjct: 64  EYGIKNLEVMVKGPGPGRESTIRALNA-AGFR-------ITNITDVTPIPHNGCRPPKKR 115
Query: 254 R 254
           R
Sbjct: 116 R 116

>pdb|3BBN|K Chain K, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 140

Iteration: 1
 Score = 54.3 bits (129), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 9/119 (7%)
Query: 137 FVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMG 196
            +H++   NNT VTVTD +G     AS+G     +G  + + +AA+  A +  R     G
Sbjct: 31  VIHVQASFNNTIVTVTDVRGRVVSWASAGTC-GFRGTKRGTPFAAQTAAGNAIRTVVEQG 89
Query: 197 LKSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           ++   V +KG    +    A+ + R      R    + ++ D T  PHNGCR PKKRR+
Sbjct: 90  MQRAEVMIKGPGLGRD--AALRAIR------RSGILLSFVRDVTPMPHNGCRPPKKRRV 140

>pdb|1I94|K Chain K, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/115 (37%), Positives = 57/115 (49%), Gaps = 10/115 (8%)
Query: 139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
           +I    NNT VT+TD  GN  I  SSG +   KG  K + YAA+  A    + A   G++
Sbjct: 19  YIHASYNNTIVTITDPDGNP-ITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQ 77
Query: 199 SVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
           SV V V+G      + QAI + +      +       I D T  PHNGCR PKK+
Sbjct: 78  SVDVIVRGTG--AGREQAIRALQASGLQVKS------IVDDTPVPHNGCR-PKKK 123

>pdb|1FJG|K Chain K, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 129

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/115 (37%), Positives = 57/115 (49%), Gaps = 10/115 (8%)
Query: 139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
           +I    NNT VT+TD  GN  I  SSG +   KG  K + YAA+  A    + A   G++
Sbjct: 20  YIHASYNNTIVTITDPDGNP-ITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQ 78
Query: 199 SVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
           SV V V+G      + QAI + +      +       I D T  PHNGCR PKK+
Sbjct: 79  SVDVIVRGTG--AGREQAIRALQASGLQVKS------IVDDTPVPHNGCR-PKKK 124

>pdb|1PNS|K Chain K, Crystal Structure Of A Streptomycin Dependent Ribosome From E. Coli, 30s Subunit Of 70s Ribosome. This File, 1pns, Contains The 30s Subunit, Two Trnas, And One Mrna Molecule. The 50s Ribosomal Subunit Is In File 1pnu. Length = 119

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/115 (37%), Positives = 57/115 (49%), Gaps = 10/115 (8%)
Query: 139 HIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLK 198
           +I    NNT VT+TD  GN  I  SSG +   KG  K + YAA+  A    + A   G++
Sbjct: 10  YIHASYNNTIVTITDPDGNP-ITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQ 68
Query: 199 SVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKR 253
           SV V V+G      + QAI + +      +       I D T  PHNGCR PKK+
Sbjct: 69  SVDVIVRGTG--AGREQAIRALQASGLQVKS------IVDDTPVPHNGCR-PKKK 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	255
3r8n_K	117	30S ribosomal protein S11; protein biosynthesis, R	6e-26
3bbn_K	140	Ribosomal protein S11; small ribosomal subunit, sp	1e-25
3u5c_O	137	RP59A, 40S ribosomal protein S14-A; translation, r	5e-25
2vqe_K	129	30S ribosomal protein S11, 30S ribosomal protein S	5e-25
2xzm_K	151	RPS14E; ribosome, translation; 3.93A {Tetrahymena	2e-22

>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 140

 Score = 97.4 bits (243), Expect = 1e-25
 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 11/119 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
           +H++   NNT VTVTD +G     AS+G     +G  + + +AA+  A +  R     G+
Sbjct: 32  IHVQASFNNTIVTVTDVRGRVVSWASAGTC-GFRGTKRGTPFAAQTAAGNAIRTVVEQGM 90

Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           +   V +KG      +  A+ +  R G         + ++ D T  PHNGCR PKKRR+
Sbjct: 91  QRAEVMIKGPG--LGRDAALRAIRRSGI-------LLSFVRDVTPMPHNGCRPPKKRRV 140

>3u5c_O RP59A, 40S ribosomal protein S14-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_K 3o30_H 3o2z_H 3u5g_O 1s1h_K 3jyv_K* Length = 137

 Score = 95.5 bits (238), Expect = 5e-25
 Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 16/125 (12%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGG-PKMSRYAAEATAEHVGRLARNMG 196
             I    N+TFV VTD  G + I   +G + ++K    + S YAA   A+ V    + +G
Sbjct: 17  ARIYASFNDTFVHVTDLSGKETIARVTGGM-KVKADRDESSPYAAMLAAQDVAAKCKEVG 75

Query: 197 LKSVVVRVKGFTYFKKK-----RQ-AIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRL 249
           + +V V+++     + K      Q A+ +  R G         I  IED T  P +  R 
Sbjct: 76  ITAVHVKIRATGGTRTKTPGPGGQAALRALARSGL-------RIGRIEDVTPVPSDSTRK 128

Query: 250 PKKRR 254
              RR
Sbjct: 129 KGGRR 133

>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1 PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K* 1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N* 1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K* ... Length = 129

 Score = 95.0 bits (237), Expect = 5e-25
 Identities = 42/118 (35%), Positives = 55/118 (46%), Gaps = 11/118 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            +I    NNT VT+TD  GN    +S G +   KG  K + YAA+  A    + A   G+
Sbjct: 19  AYIHASYNNTIVTITDPDGNPITWSSGGVI-GYKGSRKGTPYAAQLAALDAAKKAMAYGM 77

Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254
           +SV V V+G      + QAI +    G         +  I D T  PHNGCR  KK R
Sbjct: 78  QSVDVIVRGTG--AGREQAIRALQASGLQ-------VKSIVDDTPVPHNGCRPKKKFR 126

>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K* Length = 151

 Score = 89.1 bits (221), Expect = 2e-22
 Identities = 31/125 (24%), Positives = 53/125 (42%), Gaps = 16/125 (12%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSR-YAAEATAEHVGRLARNMG 196
            HI    N+TF+ VTD  G + +   +G + ++K   + S  YAA   A  V    + + 
Sbjct: 31  CHIMATWNDTFIHVTDLSGRETLVRVTGGM-KVKADREESSPYAAMQAAIDVVNRCKELK 89

Query: 197 LKSVVVRVKGFTYFKKK-----RQ-AIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRL 249
           + ++ ++++     + K      Q A+ +  R G         I  IED T  P +  R 
Sbjct: 90  INALHIKLRAKGGVETKQPGPGAQSALRALARSGMK-------IGRIEDVTPIPTDSTRR 142

Query: 250 PKKRR 254
              RR
Sbjct: 143 EGGRR 147

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	255
3r8n_K	117	30S ribosomal protein S11; protein biosynthesis, R	100.0
2vqe_K	129	30S ribosomal protein S11, 30S ribosomal protein S	100.0
3bbn_K	140	Ribosomal protein S11; small ribosomal subunit, sp	100.0
3j20_M	137	30S ribosomal protein S11P; archaea, archaeal, KIN	100.0
3u5c_O	137	RP59A, 40S ribosomal protein S14-A; translation, r	100.0
2xzm_K	151	RPS14E; ribosome, translation; 3.93A {Tetrahymena	100.0
3r8s_O	116	50S ribosomal protein L18; protein biosynthesis, R	97.22
3v2d_S	112	50S ribosomal protein L18; ribosome associated inh	96.86
1ovy_A	120	50S ribosomal protein L18; ribosome; NMR {Geobacil	96.41
1vq8_N	187	50S ribosomal protein L18P; ribosome 50S, protein-	96.38
3j21_O	203	50S ribosomal protein L18P; archaea, archaeal, KIN	95.98
3bbo_Q	161	Ribosomal protein L18; large ribosomal subunit, sp	95.43
2zjr_L	114	50S ribosomal protein L18; ribosome, large ribosom	95.19
2zkr_n	297	60S ribosomal protein L5; protein-RNA complex, 60S	94.99
4a17_M	301	RPL5, 60S ribosomal protein L5; eukaryotic ribosom	92.81
3u5e_D	297	60S ribosomal protein L5; translation, ribosome, r	91.86
3iz5_Q	304	60S ribosomal protein L5 (L18P); eukaryotic riboso	83.34

>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: c.55.4.1 PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K* 1hr0_K 1ibk_K* 1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N* 1jgq_N* 1ml5_N* 1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K* 1xmq_K* 1xnq_K* ...

Probab=100.00  E-value=1.3e-44  Score=298.50  Aligned_cols=113  Identities=37%  Similarity=0.421  Sum_probs=109.2

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      ..+++||++|+|||||||||++|+++.|.|||++ ||||++|+||||||+||+.++++|+++||+.|+|+|||+|+||  
T Consensus        15 ~~gi~hI~as~NNTivtiTd~~G~~~~~~SaG~~-gfKg~rk~tp~AA~~aa~~~~~~~~~~Gi~~v~V~vkG~G~Gr--   91 (129)
T 2vqe_K           15 ASGRAYIHASYNNTIVTITDPDGNPITWSSGGVI-GYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGR--   91 (129)
T ss_dssp             SEEEEEEEECSSCEEEEEECTTSCEEEECCTTTT-TCCSGGGGSHHHHHHHHHHHHHHHHTTTCCEEEEEEESCCTTH--
T ss_pred             cceEEEEEecCCCEEEEEEcCCCCEEEEEeccce-eEcCCCcCCHHHHHHHHHHHHHHHHHhCCeEEEEEEECCCCCH--
Confidence            4599999999999999999999999999999999 9999999999999999999999999999999999999999997  


Q ss_pred             HHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          214 RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       214 ~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                      ++||++|+.      .|++|.+|+|+||+|||||||||+||+
T Consensus        92 e~airaL~~------~Gl~I~~I~DvTpiPhnGcRp~K~RRv  127 (129)
T 2vqe_K           92 EQAIRALQA------SGLQVKSIVDDTPVPHNGCRPKKKFRK  127 (129)
T ss_dssp             HHHHHHHHT------SSSEEEECEECCCCCSSCSCCCGGGCS
T ss_pred             HHHHHHHHH------CCCEEEEEEEcCCCCCCCCCCCCCCCC
Confidence            799999975      589999999999999999999999996

>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=100.00  E-value=5.7e-44  Score=298.32  Aligned_cols=114  Identities=32%  Similarity=0.480  Sum_probs=109.7

Q ss_pred             ccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcc
Q 025294          133 HSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKK  212 (255)
Q Consensus       133 ~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~  212 (255)
                      ..++++||++|+|||||||||++|++++|.|||++ ||||++|+||||||+||+.++++|+++||+.|+|+|||+|+|| 
T Consensus        27 ~~~gi~hI~as~NNTivtiTD~~G~~i~~~SaG~~-GfKg~rksTp~AA~~aa~~~~~~a~e~Gi~~v~V~vkG~G~GR-  104 (140)
T 3bbn_K           27 IPKGVIHVQASFNNTIVTVTDVRGRVVSWASAGTC-GFRGTKRGTPFAAQTAAGNAIRTVVEQGMQRAEVMIKGPGLGR-  104 (140)
T ss_dssp             CCCCEEEEEECSSCEEEEEECSSSCEEEEEETTTS-SCCTTSCSSHHHHHHHHTSGGGTSTTTCCCEEEEEEESCSTTS-
T ss_pred             ceeeEEEEEecCCCEEEEEEcCCCCEEEEEeccce-eEcccccCCHHHHHHHHHHHHHHHHHhCCeEEEEEEECCCCcH-
Confidence            34699999999999999999999999999999999 9999999999999999999999999999999999999999998 


Q ss_pred             hHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          213 KRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       213 k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                       ++||++|+.      .|++|.+|+|+||+|||||||||+|||
T Consensus       105 -eaairaL~~------~Gl~I~~I~DvTpiPhnGcRppK~RRv  140 (140)
T 3bbn_K          105 -DAALRAIRR------SGILLSFVRDVTPMPHNGCRPPKKRRV  140 (140)
T ss_dssp             -SHHHHHHHT------TTCEEEEEEECCCCCCSCCCCCCCCCC
T ss_pred             -HHHHHHHHH------CCCEEEEEEEcCCCCCCCCCCCCCCCC
Confidence             689999975      589999999999999999999999997

>3j20_M 30S ribosomal protein S11P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=2.6e-43  Score=293.45  Aligned_cols=113  Identities=28%  Similarity=0.283  Sum_probs=105.3

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEcc-----
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGF-----  207 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~-----  207 (255)
                      .++|+||++|+|||||||||++|+ ++.|.|+|++ ||||++|+||||||+||++++++|+++||+.|+|+|||+     
T Consensus        13 ~~gi~hI~asfNNTivtiTD~~G~~~i~~~S~G~~-gfkg~~ksTp~AA~~aa~~~~~~a~e~Gi~~v~V~vkG~gg~~~   91 (137)
T 3j20_M           13 KWGIAHIYSSFNNTIIHITDITGAETISRWSGGMV-VKADRDEPSPYAAMLAARRAAEEALEKGIVGVHIRVRAPGGSKS   91 (137)
T ss_dssp             EEEEEEEEECSSCEEEEEEESSSCSEEEEEEGGGT-CSCTTTSSSHHHHHHHHHHHHHHHHHHTEEEEEEEEECCCSSSC
T ss_pred             cceEEEEEcCCCCEEEEEEcCCCCEEEEEEcccee-eecCCccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEECCCCCCC
Confidence            679999999999999999999995 9999999999 999999999999999999999999999999999999995     


Q ss_pred             ---CCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCC---CCCCC
Q 025294          208 ---TYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP---KKRRI  255 (255)
Q Consensus       208 ---G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpk---K~RRv  255 (255)
                         |+||  ++||++|+.      .|++|.+|+|+|||||||||||   |.|||
T Consensus        92 ~~pG~Gr--esairaL~~------~Gl~I~~I~DvTpiPhnGcRp~g~rr~rrv  137 (137)
T 3j20_M           92 KTPGPGA--QAAIRALAR------AGLKIGRVEDVTPIPHDGTRPKGGRRGRRV  137 (137)
T ss_dssp             CSCCTHH--HHHHHHHHH------HTCEEEEEEECCCCCSSCCCCSCCSSSSCC
T ss_pred             cCCCCcH--HHHHHHHHh------CCCEEEEEEEcCCCCCCCCCCCCCCCCCCC
Confidence               5654  899999975      5899999999999999999999   55554

>3u5c_O RP59A, 40S ribosomal protein S14-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_K 3o30_H 3o2z_H 3u5g_O 1s1h_K 3jyv_K*

Probab=100.00  E-value=9.6e-43  Score=290.01  Aligned_cols=116  Identities=28%  Similarity=0.321  Sum_probs=108.1

Q ss_pred             ccCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCC-CCchhHHHHHHHHHHHHHHHcCCcEEEEEE----
Q 025294          130 NVEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGP-KMSRYAAEATAEHVGRLARNMGLKSVVVRV----  204 (255)
Q Consensus       130 ~~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~r-KsT~~AAq~aae~i~~kakelGik~V~V~v----  204 (255)
                      +.|..++|+||++|+|||||||||++|+++.|.|+|++ |||+.+ |+||||||+||++++++|+++||+.|+|+|    
T Consensus         9 ~~~~~~gi~hI~asfNNTivtvTD~~G~~~~~~ssG~~-gfKg~r~ksTpyAAq~aa~~~a~~a~e~Gi~~v~V~vra~g   87 (137)
T 3u5c_O            9 DNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGM-KVKADRDESSPYAAMLAAQDVAAKCKEVGITAVHVKIRATG   87 (137)
T ss_dssp             --CCCEEECCEEEETTEEEECCEETTSSSCCCCCBTTT-TSCCSTTTTCHHHHHHHHHHHHHHHHHHTCCEEECEEECSC
T ss_pred             cCceeeEEEEEEccCCCEEEEEEcCCCCEEEEEeCCCc-EEeCCcccCCHHHHHHHHHHHHHHHHHcCCeEEEEEEeccC
Confidence            34567799999999999999999999999999999999 999987 899999999999999999999999999999    


Q ss_pred             ----EccCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          205 ----KGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       205 ----KG~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                          ||+|+||  ++||++|+.      .|++|.+|+|+||||||||||||+||
T Consensus        88 g~~~kgpG~Gr--~sairaL~~------~Gl~I~~I~DvTpiPhnGcRp~K~RR  133 (137)
T 3u5c_O           88 GTRTKTPGPGG--QAALRALAR------SGLRIGRIEDVTPVPSDSTRKKGGRR  133 (137)
T ss_dssp             TTSCCSCCGGG--HHHHHHHHT------TTCEECCCEECCCCCSSCSCCTTCTT
T ss_pred             CCcccCCCcch--HHHHHHHHh------CCCEEEEEEEcCCCCCCCCCCCCCCC
Confidence                5788876  899999974      68999999999999999999999998

>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K*

Probab=100.00  E-value=2.5e-41  Score=285.38  Aligned_cols=116  Identities=24%  Similarity=0.286  Sum_probs=105.7

Q ss_pred             cCccceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCC-CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEcc--
Q 025294          131 VEHSSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGG-PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGF--  207 (255)
Q Consensus       131 ~e~~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~-rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~--  207 (255)
                      .|..++|+||++|+|||||||||.+|+++.|+|+|.+ +||+. +|+||||||+||++++++|+++||+.|+|+|||+  
T Consensus        24 ~~~~~gi~hI~asfNNTiVtiTD~~G~~~~~~ssgg~-~~k~~r~ksTpyAAq~aa~~~a~~a~e~Gi~~v~V~vkG~gg  102 (151)
T 2xzm_K           24 NENVFGVCHIMATWNDTFIHVTDLSGRETLVRVTGGM-KVKADREESSPYAAMQAAIDVVNRCKELKINALHIKLRAKGG  102 (151)
T ss_dssp             TCCCEEEEEEEBCSSCBCCEEECTTCCSEEEECCHHH-HCSSGGGGSCHHHHHHHHHHHHHHHHHHTCCEEEEEEECCCT
T ss_pred             CCeeeeEEEEEccCCCEEEEEECCCCCEEEEEecCcc-eEeCCCCcCCHHHHHHHHHHHHHHHHHcCCeEEEEEEEcCCC
Confidence            3556799999999999999999999998888888888 66665 5999999999999999999999999999999988  


Q ss_pred             ------CCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          208 ------TYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       208 ------G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                            |+||  ++||++|+.      .|++|.+|+|+||||||||||||+||+
T Consensus       103 ~~~kgpG~Gr--esairaL~~------~GlkI~~I~DvTpiPhNGcRp~K~RRv  148 (151)
T 2xzm_K          103 VETKQPGPGA--QSALRALAR------SGMKIGRIEDVTPIPTDSTRREGGRRG  148 (151)
T ss_dssp             TSCCSCCSHH--HHHHHHHHH------TSCEEEEEEECCCCCSSCCCCSSCTTC
T ss_pred             CCccCCCccH--HHHHHHHHH------CCCEEEEEEEeCCCCCCCCCCCCCCCC
Confidence                  5554  899999975      589999999999999999999999996

>3r8s_O 50S ribosomal protein L18; protein biosynthesis, RNA, tRNA, transfer RNA, 23S ribosomal subunit, ribosome recycling factor, RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_O 3j19_O 2wwq_O 3oat_O* 3oas_O* 3ofd_O 3ofc_O 3ofr_O* 3ofz_O* 3og0_O 3ofq_O 3r8t_O 3i1n_O 1p85_M 1p86_M 1vs8_O 1vs6_O 2aw4_O 2awb_O 1vt2_O ...

Probab=97.22  E-value=0.0018  Score=52.09  Aligned_cols=88  Identities=18%  Similarity=0.189  Sum_probs=65.7

Q ss_pred             cceEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCC
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYF  210 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~g  210 (255)
                      .+|-+.|+-|.+++...|.|.. |.++.+.|+-.. .+++.  ......||..+++.++++|++.||+.|..-..|+-+.
T Consensus        21 ~rpRL~V~rSnkhIyAQiidd~~g~tlasAST~e~-~~~~~~~~~~n~~AA~~vG~llA~Ral~~GI~~vvfDrgg~~yh   99 (116)
T 3r8s_O           21 GATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEK-AIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYH   99 (116)
T ss_dssp             TCCEEEEEECSSCEEEEEECTTSSCEEEECCSSSH-HHHTTCSCSSSHHHHHHHHHHHHHHHHTTTCCCCEEECTTSCSS
T ss_pred             CCCEEEEEEeCCEEEEEEEEcCCCeEEEEEeeCch-hhccccCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecCCCccc
Confidence            4588999999999999999965 568888887766 66653  3456789999999999999999999988776565443


Q ss_pred             cchHHHHHHHHh
Q 025294          211 KKKRQAIMSFRE  222 (255)
Q Consensus       211 R~k~aaIkaL~~  222 (255)
                      -.-.++..++++
T Consensus       100 GrV~Ala~~are  111 (116)
T 3r8s_O          100 GRVQALADAARE  111 (116)
T ss_dssp             SHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            211233345554

>3v2d_S 50S ribosomal protein L18; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 1vsp_M 2hgj_R 2hgq_R 2hgu_R 1vsa_M 2j03_S 2jl6_S 2jl8_S 2v47_S 2v49_S 2wdi_S 2wdj_S 2wdl_S 2wdn_S 2wh2_S 2wh4_S 2wrj_S 2wrl_S 2wro_S 2wrr_S ...

Probab=96.86  E-value=0.0061  Score=48.92  Aligned_cols=84  Identities=18%  Similarity=0.190  Sum_probs=63.3

Q ss_pred             ceEEEEEccCCCeEEEEEcCCC-CEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKG-NKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~G-nvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      .|-+.|+-|.+++...|.|..| .++.+.|+-.. .+|   .....||+.+++.++++|++.||+.|..-..|+-+.-.-
T Consensus        23 rpRL~V~rSnkhiyAQiidd~~~~tlasAsT~e~-~~k---~~n~~AA~~vG~llA~ra~~~GI~~vvfDrgg~~yhGrV   98 (112)
T 3v2d_S           23 RLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLAL-KLK---GNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRV   98 (112)
T ss_dssp             CCEEEEEECSSCEEEEEEETTTTEEEEEEETTTT-TCC---CCHHHHHHHHHHHHHHHHHTTTCCBCEEECTTSCSCSST
T ss_pred             CCEEEEEEeCCeEEEEEEecCCCeEEEEEEecch-hcc---CCCHHHHHHHHHHHHHHHHHCCCCEEEEecCCCcccHHH
Confidence            5889999999999999998665 56777777766 664   456779999999999999999999987765554433212


Q ss_pred             HHHHHHHHh
Q 025294          214 RQAIMSFRE  222 (255)
Q Consensus       214 ~aaIkaL~~  222 (255)
                      .++..++++
T Consensus        99 ~Ala~~are  107 (112)
T 3v2d_S           99 KALAEGARE  107 (112)
T ss_dssp             THHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            345556665

>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus stearothermophilus} SCOP: c.55.4.1

Probab=96.41  E-value=0.0047  Score=50.10  Aligned_cols=87  Identities=20%  Similarity=0.193  Sum_probs=62.9

Q ss_pred             ceEEEEEccCCCeEEEEEcCCC-CEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKG-NKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~G-nvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      .|-+.|+-|.+++++.|.|..| .++.+.|+=.. .++........||..+++.++++|.+.||+.|..-..|+-++-.-
T Consensus        28 rpRL~V~rSnkhIyAQiidd~~~~tl~sAsT~e~-~~~~~~~~n~~AA~~vG~llA~Ral~~GI~~vvfDrgg~~yhgrV  106 (120)
T 1ovy_A           28 RPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDK-EFGLDSTNNIEAAKKVGELVAKRALEKGIKQVVFDRGGYLYHGRV  106 (120)
T ss_dssp             CCSEEEEEETTEEEEEEECCSSCCCEEEESTTST-TTCSSCTTSHHHHHHHHHHHHHHHHHHSSSCCCCCSTTCSSCSST
T ss_pred             CCEEEEEEeCCeEEEEEEEcCCCEEEEEEecCch-hhCcCCCCcHHHHHHHHHHHHHHHHHCCCCEEEEecCCccccHHH
Confidence            4788899999999999998765 56777777655 566333567889999999999999999999876544343322212


Q ss_pred             HHHHHHHHh
Q 025294          214 RQAIMSFRE  222 (255)
Q Consensus       214 ~aaIkaL~~  222 (255)
                      .+++.++.+
T Consensus       107 ~ala~~are  115 (120)
T 1ovy_A          107 KALADAARE  115 (120)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            455556655

>1vq8_N 50S ribosomal protein L18P; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.55.4.1 PDB: 1vq4_N* 1vq5_N* 1vq6_N* 1vq7_N* 1s72_N* 1vq9_N* 1vqk_N* 1vql_N* 1vqm_N* 1vqn_N* 1vqo_N* 1vqp_N* 1yhq_N* 1yi2_N* 1yij_N* 1yit_N* 1yj9_N* 1yjn_N* 1yjw_N* 2otj_N* ...

Probab=96.38  E-value=0.027  Score=48.90  Aligned_cols=88  Identities=15%  Similarity=0.074  Sum_probs=63.1

Q ss_pred             CccceEEEEEccCCCeEEEEE--cCCCC-EEEEEeccCccccc-C--CCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEE
Q 025294          132 EHSSEFVHIKLMRNNTFVTVT--DSKGN-KRIGASSGCLPELK-G--GPKMSRYAAEATAEHVGRLARNMGLKSVVVRVK  205 (255)
Q Consensus       132 e~~~~IlhI~sT~NNTiITlT--D~~Gn-vl~~~SsGs~~GFK-g--~rKsT~~AAq~aae~i~~kakelGik~V~V~vK  205 (255)
                      ....+-+.|+.|.+++++.|.  |..|. ++.+.|+-.. . | +  .......||..++..++++|++.||+.+.+-..
T Consensus        29 ~~~rpRL~V~rSnkhIyAQII~~dd~~~~tlasAsT~e~-~-k~~~k~~~~N~~AA~~vG~llA~Ral~kGI~~vvfDrg  106 (187)
T 1vq8_N           29 KSGKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDL-A-EYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEAVLDIG  106 (187)
T ss_dssp             TTCSCEEEEEECSSCEEEEEEECCTTSCEEEEEEESGGG-G-GGTCCSCSSSHHHHHHHHHHHHHHHHHTTCCBCEEECT
T ss_pred             hcCCCEEEEEEeCCcEEEEEEEecCCCCEEEEEEEccch-h-ccccccCCCcHHHHHHHHHHHHHHHHHCCCCEEEEcCC
Confidence            345689999999999999999  66555 7777777655 3 3 2  124667889999999999999999999865554


Q ss_pred             ccC---CCcchHHHHHHHHh
Q 025294          206 GFT---YFKKKRQAIMSFRE  222 (255)
Q Consensus       206 G~G---~gR~k~aaIkaL~~  222 (255)
                      |+=   +|| -.++++++.+
T Consensus       107 g~~yh~GgR-V~Ala~gAre  125 (187)
T 1vq8_N          107 LNSPTPGSK-VFAIQEGAID  125 (187)
T ss_dssp             TSCCCTTCH-HHHHHHHHHH
T ss_pred             CceeccchH-HHHHHHHhhc
Confidence            432   133 2455556665

>3j21_O 50S ribosomal protein L18P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.98  E-value=0.015  Score=51.04  Aligned_cols=102  Identities=13%  Similarity=0.100  Sum_probs=72.9

Q ss_pred             CccceEEEEEccCCCeEEEEEc--CC-CCEEEEEeccCccccc-C--CCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEE
Q 025294          132 EHSSEFVHIKLMRNNTFVTVTD--SK-GNKRIGASSGCLPELK-G--GPKMSRYAAEATAEHVGRLARNMGLKSVVVRVK  205 (255)
Q Consensus       132 e~~~~IlhI~sT~NNTiITlTD--~~-Gnvl~~~SsGs~~GFK-g--~rKsT~~AAq~aae~i~~kakelGik~V~V~vK  205 (255)
                      .+..+-+-|+.|.+++++.|.|  .. |.++.+.|+--+ ..| +  .......||..++..++++|++.||..|.+-..
T Consensus        29 ~~~kpRL~V~rSnkhIyAQIId~d~~g~~tLasAST~El-~lk~g~~~~~~N~~AA~~vG~llA~Ral~kGI~~vvfDrg  107 (203)
T 3j21_O           29 KSGKPRLVVRKSLNHHIAQIIVYDPKGDRTLVSAHTREL-IRDFGWKGHCGNTPSAYLLGLLIGYKAKQAGIEEAILDIG  107 (203)
T ss_dssp             TTCCCEEEEEECSSCEEEEEEECCTTSCEEEEEECSTTT-SSSSSCCSCTTSHHHHHHHHHHSSSSTTSSCCCCCEEECC
T ss_pred             hcCCCEEEEEEeCCeEEEEEEEecCCCCeEEEEEEccch-hhhhcccCCCCcHHHHHHHHHHHHHHHHhCCCCEEEEecC
Confidence            3456899999999999999996  66 457777777665 322 2  234567788999999999999999999877766


Q ss_pred             ccCC---CcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCC
Q 025294          206 GFTY---FKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP  250 (255)
Q Consensus       206 G~G~---gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpk  250 (255)
                      |+-+   || -.++++++.+      .||         .+||+--|-|
T Consensus       108 g~~y~~hgR-V~Ala~gAre------~GL---------~iPhs~~~fp  139 (203)
T 3j21_O          108 LHPPVRGSS-VFAVLKGAVD------AGL---------NVPHSPEIFP  139 (203)
T ss_dssp             SSCCCTTSH-HHHHHHHHHH------HTC---------CCCCCSSCSC
T ss_pred             cceeccCcc-hhhhhhhccc------CCe---------ecccCCccCC
Confidence            6654   44 2455556665      366         4577765554

>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=95.43  E-value=0.01  Score=50.47  Aligned_cols=87  Identities=16%  Similarity=0.167  Sum_probs=61.6

Q ss_pred             ceEEEEEccCCCeEEEEEcC-CCCEEEEEeccCcccccC----CCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCC
Q 025294          135 SEFVHIKLMRNNTFVTVTDS-KGNKRIGASSGCLPELKG----GPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTY  209 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~-~Gnvl~~~SsGs~~GFKg----~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~  209 (255)
                      ++-|.|+-|.+++...|.|. .|.++...|+-.. .+++    .....-.||..+++.++++|++.||+.|..--.|+-+
T Consensus        65 rPRL~V~rSnkhIyAQvIdd~~g~tLasASTlek-~lk~~l~~g~~~n~~AA~~VG~liAeRA~e~GI~~VvFDRgg~~Y  143 (161)
T 3bbo_Q           65 RPRLCVFRSNKHLYVQVIDDSKMHTLASASTMQK-SISEELDYSSSPTIEVAKKVGEVIASACLEKGITKVAFDRGGYPY  143 (161)
T ss_dssp             CCCCEEEECSSCEEEEEECCTTSCEEEEEEHHHH-HHHHCCTTCCSSSHHHHHHHHHHSSSHHHHTSSCCCCCCCSSSCS
T ss_pred             CCEEEEEecCCeEEEEEEECCCCEEEEEEeCCcH-HHHhhccccCCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCcc
Confidence            47889999999999999865 4668888888443 3342    2356778999999999999999999998665444433


Q ss_pred             CcchHHHHHHHHh
Q 025294          210 FKKKRQAIMSFRE  222 (255)
Q Consensus       210 gR~k~aaIkaL~~  222 (255)
                      .-.-.+...++++
T Consensus       144 hGRVkAladaaRe  156 (161)
T 3bbo_Q          144 HGRVKALADAARE  156 (161)
T ss_dssp             SSTTHHHHHHHTT
T ss_pred             hHHHHHHHHHHHH
Confidence            2211333345544

>2zjr_L 50S ribosomal protein L18; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.55.4.1 PDB: 1sm1_M* 2zjp_L* 2zjq_L 1nkw_M 3cf5_L* 3dll_L* 3pio_L* 3pip_L* 1nwy_M* 1nwx_M* 1xbp_M* 1pnu_M 1pny_M 1vor_P 1vou_P 1vow_P 1voy_P 1vp0_P

Probab=95.19  E-value=0.015  Score=46.85  Aligned_cols=83  Identities=18%  Similarity=0.207  Sum_probs=58.9

Q ss_pred             ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      .|-+.|+-|.+++...|.|..|. ++.+.|+-.   +  .......||..+++.++++|++.||+.|..-..|+-++-.-
T Consensus        26 rpRL~V~rSnkhIyAQiidd~~~~tl~sAST~e---l--~~~~n~~AA~~vG~llA~Ral~~GI~~vvfDrgg~~yhgrV  100 (114)
T 2zjr_L           26 RLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAA---L--KSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRV  100 (114)
T ss_dssp             SEEECCCTTSSCCCCCEEETTTTEECCCCCSCS---C--CTTCSSSSHHHHHHHHHHHHHTTCCCCCEECCCSSCSCSHH
T ss_pred             CCEEEEEEeCCeEEEEEEEcCCCEEEEEEEchH---h--cCCCCHHHHHHHHHHHHHHHHHCCCCEEEEecCCccccHHH
Confidence            48899999999999999987766 555444432   3  23455678999999999999999999987665554433212


Q ss_pred             HHHHHHHHh
Q 025294          214 RQAIMSFRE  222 (255)
Q Consensus       214 ~aaIkaL~~  222 (255)
                      .+++.++.+
T Consensus       101 ~Ala~~are  109 (114)
T 2zjr_L          101 KALADAARE  109 (114)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            344445555

>2zkr_n 60S ribosomal protein L5; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}

Probab=94.99  E-value=0.19  Score=46.34  Aligned_cols=99  Identities=16%  Similarity=0.074  Sum_probs=68.6

Q ss_pred             ceEEEEEccCCCeEEEEEcCC--C-CEEEEEeccCcc--cccCCCCCchhHHHHHHHHHHHHHHHc--------------
Q 025294          135 SEFVHIKLMRNNTFVTVTDSK--G-NKRIGASSGCLP--ELKGGPKMSRYAAEATAEHVGRLARNM--------------  195 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~--G-nvl~~~SsGs~~--GFKg~rKsT~~AAq~aae~i~~kakel--------------  195 (255)
                      .+-+-|..|..++++.|.|..  | .++.++|+--++  |.++ ......||+.++.-++++|.+.              
T Consensus        48 kpRLvVrrSNk~I~aQII~~~~~gd~tLasAsS~El~kyg~k~-g~tN~aAAy~tGlLlArRal~k~~ld~~y~G~~e~~  126 (297)
T 2zkr_n           48 KYRMIVRVTNRDIICQIAYARIEGDMIVCARYAHELPKYGVKV-GLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVT  126 (297)
T ss_dssp             SEEEEEEEETTEEEEEEEECCSSSCEEEEEEEGGGGGGTCCCS-CSSSHHHHHHHHHHHHHHHHCCCSCCCCCSSCCSSS
T ss_pred             CceEEEEEecCcEEEEEEeccCCCCEEEEEeecCccccccccc-CCCcHHHHHHHHHHHHHHHHHhhccchhhcCccccc
Confidence            378888899999999999977  5 567777775552  2222 2355678899999999999988              


Q ss_pred             -------------CCcEEEEEEEccCC---CcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCC
Q 025294          196 -------------GLKSVVVRVKGFTY---FKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP  250 (255)
Q Consensus       196 -------------Gik~V~V~vKG~G~---gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpk  250 (255)
                                   |+..+.+=+-|.-.   || -.+++++..+      .||         .+||+-.|-|
T Consensus       127 g~~~~ve~~~~~~gi~~vvfDrGl~ryttggR-Vfa~akGArD------gGL---------~~Phs~~~fp  181 (297)
T 2zkr_n          127 GDEYNVESIDGQPGAFTCYLDAGLARTTTGNK-VFGALKGAVD------GGL---------SIPHSTKRFP  181 (297)
T ss_dssp             SCCCCCSSSCSSSCCCBEEEECTTSCCCTTCH-HHHHHHHHHH------TTC---------BCCCCGGGSC
T ss_pred             cccccccccccCCCceEEEEecCCcccCCCch-HHHHHHHHHh------cCc---------ccCCCCccCC
Confidence                         77777665544443   23 2455556655      466         3688877655

>4a17_M RPL5, 60S ribosomal protein L5; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_M 4a1c_M 4a1e_M

Probab=92.81  E-value=0.52  Score=43.55  Aligned_cols=60  Identities=18%  Similarity=-0.036  Sum_probs=46.4

Q ss_pred             ceEEEEEccCCCeEEEEEcC--CC-CEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHc
Q 025294          135 SEFVHIKLMRNNTFVTVTDS--KG-NKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNM  195 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~--~G-nvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakel  195 (255)
                      .+-+-|+-|..++++.|.|.  .| .++.++|+--+ ...+-  ......||..++..|+++|++.
T Consensus        48 kpRLvV~rSNrhIyAQIIdd~~~Gd~tLaSASS~El-~~~g~k~~~~N~~AAy~vG~LiAeRAl~k  112 (301)
T 4a17_M           48 KYRLVARATNTRIIAQIVYATLKCDRVLCAADSYEL-KRFGVSTGLASYAAAYATGLLLARRLLKQ  112 (301)
T ss_dssp             CEEEEEEECSSCEEEEEEEECSSCEEEEEEEETTHH-HHTTCCSCTTSHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCeEEEEEeecCCCCCEEEEEEeeccc-hhccccCCCCcHHHHHHHHHHHHHHHHHh
Confidence            47888889999999999986  56 67777887655 33332  2345678899999999999988

>3u5e_D 60S ribosomal protein L5; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_D 4b6a_D 3izc_Q 3izs_Q 3o58_E 3o5h_E 3jyw_E 1s1i_E

Probab=91.86  E-value=0.81  Score=42.21  Aligned_cols=60  Identities=18%  Similarity=0.055  Sum_probs=46.2

Q ss_pred             ceEEEEEccCCCeEEEEEcC--CC-CEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHc
Q 025294          135 SEFVHIKLMRNNTFVTVTDS--KG-NKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNM  195 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~--~G-nvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakel  195 (255)
                      .+-+-|+-|..++++.|.|.  .| .++.++|+--+ ...+-  ......||..++..|+++|++.
T Consensus        48 kpRLvV~rSNrhIyAQIIdd~~~Gd~tLaSASS~El-~k~g~k~~~~N~~AAy~vG~LiAeRAl~k  112 (297)
T 3u5e_D           48 KYRLVVRFTNKDIICQIISSTITGDVVLAAAYSHEL-PRYGITHGLTNWAAAYATGLLIARRTLQK  112 (297)
T ss_dssp             CCEEEEEEETTEEEEEEEECCTTCCEEEEEEEGGGG-GGGTCCSCTTSHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEcCCeEEEEEeecCCCCCEEEEEEeecch-hhcccCCCCCcHHHHHHHHHHHHHHHHHh
Confidence            47778888899999999997  45 67777887666 32332  2345678899999999999987

---

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	255
d2qalk1	117	c.55.4.1 (K:12-128) Ribosomal protein S11 {Escheri	9e-29
d2uubk1	119	c.55.4.1 (K:11-129) Ribosomal protein S11 {Thermus	1e-25

>d2qalk1 c.55.4.1 (K:12-128) Ribosomal protein S11 {Escherichia coli [TaxId: 562]} Length = 117

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein S11
species: Escherichia coli [TaxId: 562]

 Score =  103 bits (258), Expect = 9e-29
 Identities = 40/118 (33%), Positives = 56/118 (47%), Gaps = 9/118 (7%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            HI    NNT VT+TD +GN     ++      +G  K + +AA+  AE      +  G+
Sbjct: 9   AHIHASFNNTIVTITDRQGNALG-WATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGI 67

Query: 198 KSVVVRVKGFTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI 255
           K++ V VKG    ++     +    GF        I  I D T  PHNGCR PKKRR+
Sbjct: 68  KNLEVMVKGPGPGRESTIRAL-NAAGF-------RITNITDVTPIPHNGCRPPKKRRV 117

>d2uubk1 c.55.4.1 (K:11-129) Ribosomal protein S11 {Thermus thermophilus [TaxId: 274]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein S11
species: Thermus thermophilus [TaxId: 274]

 Score = 95.3 bits (237), Expect = 1e-25
 Identities = 42/118 (35%), Positives = 55/118 (46%), Gaps = 11/118 (9%)

Query: 138 VHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGL 197
            +I    NNT VT+TD  GN    +S G     KG  K + YAA+  A    + A   G+
Sbjct: 9   AYIHASYNNTIVTITDPDGNPITWSSGGV-IGYKGSRKGTPYAAQLAALDAAKKAMAYGM 67

Query: 198 KSVVVRVKGFTYFKKKRQAIMSF-REGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR 254
           +SV V V+G    ++  QAI +    G         +  I D T  PHNGCR  KK R
Sbjct: 68  QSVDVIVRGTGAGRE--QAIRALQASGL-------QVKSIVDDTPVPHNGCRPKKKFR 116

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	255
d2qalk1	117	Ribosomal protein S11 {Escherichia coli [TaxId: 56	100.0
d2uubk1	119	Ribosomal protein S11 {Thermus thermophilus [TaxId	100.0
d1vqon1	186	Ribosomal protein L18 (L18p) {Archaeon Haloarcula	97.13
d1ovya_	97	Ribosomal protein L18 (L18p) {Bacillus stearotherm	97.04
d2j01s1	86	Ribosomal protein L18 (L18p) {Thermus thermophilus	95.57
d2gycm1	113	Ribosomal protein L18 (L18p) {Escherichia coli [Ta	95.22
d2zjrl1	104	Ribosomal protein L18 (L18p) {Deinococcus radiodur	87.55

>d2qalk1 c.55.4.1 (K:12-128) Ribosomal protein S11 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein S11
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.1e-44  Score=292.11  Aligned_cols=113  Identities=37%  Similarity=0.503  Sum_probs=109.3

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      ..+|+||++|+|||||||||.+|+++.|.|||++ ||||++|+||||||++|+.++++++++||+.|+|+|+|+|+||  
T Consensus         5 ~~Gi~hI~~t~NNTiitlTD~~G~~~~~~S~G~~-gfkg~~K~t~~Aa~~~a~~~~~~~~~~gi~~v~V~~kG~G~GR--   81 (117)
T d2qalk1           5 SDGVAHIHASFNNTIVTITDRQGNALGWATAGGS-GFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGR--   81 (117)
T ss_dssp             CEEEEEEECCSSCCEEEEEETTSCEEEEEETTTS-SCCHHHHTSHHHHHHHHHHHHHHHGGGTCCEEEEEEECCSTTT--
T ss_pred             cceEEEEEecCCCEEEEEECCCCCEEEEEecccc-ccccccccchHHHHHHHHHHHHHHHHcCCcEEEEEEeCCCCch--
Confidence            4599999999999999999999999999999999 9999999999999999999999999999999999999999998  


Q ss_pred             HHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCCC
Q 025294          214 RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRRI  255 (255)
Q Consensus       214 ~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RRv  255 (255)
                      ++||++|..      .+++|++|+|+||+|||||||||+|||
T Consensus        82 ~~air~l~~------~gl~I~~I~D~TpiphnGcRp~K~RRv  117 (117)
T d2qalk1          82 ESTIRALNA------AGFRITNITDVTPIPHNGCRPPKKRRV  117 (117)
T ss_dssp             THHHHHHHH------TTCEEEEEEECCCCCSSCSCCCCCCCC
T ss_pred             HHHHHHHHh------CCCEEEEEEECCCCCCCCCCCCCCCCC
Confidence            689999975      589999999999999999999999997

>d2uubk1 c.55.4.1 (K:11-129) Ribosomal protein S11 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein S11
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=6.4e-44  Score=288.17  Aligned_cols=112  Identities=38%  Similarity=0.431  Sum_probs=108.2

Q ss_pred             cceEEEEEccCCCeEEEEEcCCCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          134 SSEFVHIKLMRNNTFVTVTDSKGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlTD~~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      ..+|+||++|+|||||||||++||++.|.|+|++ ||||++|+||||||++++.++++++++||+.|+|+|+|+|+||  
T Consensus         5 ~~GivhI~~t~NNT~itlTD~~Gn~i~~~S~G~~-gfkg~rk~t~~Aa~~~a~~~~~k~~~~g~~~v~v~~kG~G~gR--   81 (119)
T d2uubk1           5 ASGRAYIHASYNNTIVTITDPDGNPITWSSGGVI-GYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGR--   81 (119)
T ss_dssp             SEEEEEEEECSSCEEEEEECTTSCEEEEEETTTS-SCCSGGGGSHHHHHHHHHHHHHHHHTTTCCEEEEEEECCCTTH--
T ss_pred             cccEEEEEeccCCEEEEEECCCCCEEEEEecccc-eeccccccchhHHHHHHHHHHHHHHHcCCcEEEEEEEcCCCCh--
Confidence            4599999999999999999999999999999999 9999999999999999999999999999999999999999997  


Q ss_pred             HHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCCCCCC
Q 025294          214 RQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLPKKRR  254 (255)
Q Consensus       214 ~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpkK~RR  254 (255)
                      ++||++|+.      .+++|++|+|+||+|||||||||+||
T Consensus        82 ~~~ik~l~~------~g~kI~~I~D~T~iphnGcRp~K~RR  116 (119)
T d2uubk1          82 EQAIRALQA------SGLQVKSIVDDTPVPHNGCRPKKKFR  116 (119)
T ss_dssp             HHHHHHHHT------SSSEEEECEECCCCCSSCSCCCGGGC
T ss_pred             HHHHHHHHH------CCCEEEEEEECCCCCCCCCCCCCCCC
Confidence            799999974      68999999999999999999999998

>d1vqon1 c.55.4.1 (N:1-186) Ribosomal protein L18 (L18p) {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein L18 (L18p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=97.13  E-value=0.0017  Score=54.27  Aligned_cols=101  Identities=17%  Similarity=0.044  Sum_probs=70.6

Q ss_pred             cceEEEEEccCCCeEEEEE--cCCCC-EEEEEeccCcccccCCC--CCchhHHHHHHHHHHHHHHHcCCcEEEEE--EEc
Q 025294          134 SSEFVHIKLMRNNTFVTVT--DSKGN-KRIGASSGCLPELKGGP--KMSRYAAEATAEHVGRLARNMGLKSVVVR--VKG  206 (255)
Q Consensus       134 ~~~IlhI~sT~NNTiITlT--D~~Gn-vl~~~SsGs~~GFKg~r--KsT~~AAq~aae~i~~kakelGik~V~V~--vKG  206 (255)
                      ..+-+.|+.|.+|+++.|.  |..|. ++.++|+=.+ ..++.+  .....||+.++..++++|++.|++.+.+-  +.|
T Consensus        30 ~kpRLvVrrSNk~IyaQII~~d~~gd~vlaSAsS~el-~k~g~k~~~~N~~AAy~~G~liA~ra~~~gi~~vvfD~G~~~  108 (186)
T d1vqon1          30 GKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDL-AEYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEAVLDIGLNS  108 (186)
T ss_dssp             CSCEEEEEECSSCEEEEEEECCTTSCEEEEEEESGGG-GGGSCCSCSSSHHHHHHHHHHHHHHHHHTTCCBCEEECTTSC
T ss_pred             CCCeEEEEEeCCceEEEEEEecCCCCEEEEEEecchh-hhhccccCccHHHHHHHhHHHHHHHHHhhcccceEEeeCCCC
Confidence            4588999999999999999  55555 5566666554 444432  23456889999999999999999998877  446


Q ss_pred             cCCCcchHHHHHHHHhcccCCCCCCCeEEEEecCCCCCCCCCCC
Q 025294          207 FTYFKKKRQAIMSFREGFANSRDQNPIVYIEDTTRRPHNGCRLP  250 (255)
Q Consensus       207 ~G~gR~k~aaIkaL~~G~~~~r~glkI~sI~D~TpiPhNGCRpk  250 (255)
                      +-.+-.-.+++++..+      .||+         |||+-.+-|
T Consensus       109 ~~yhgRV~A~akgard------~GL~---------Iph~~~~~p  137 (186)
T d1vqon1         109 PTPGSKVFAIQEGAID------AGLD---------IPHNDDVLA  137 (186)
T ss_dssp             CCTTCHHHHHHHHHHH------TTCB---------CCCCGGGSC
T ss_pred             CCccchHHHHHHHHHh------cCcc---------CCCCCccCC
Confidence            5544322456666665      4774         577766554

>d1ovya_ c.55.4.1 (A:) Ribosomal protein L18 (L18p) {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein L18 (L18p)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.04  E-value=0.00039  Score=52.44  Aligned_cols=87  Identities=21%  Similarity=0.211  Sum_probs=62.7

Q ss_pred             ceEEEEEccCCCeEEEEEcC-CCCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEEEEEEccCCCcch
Q 025294          135 SEFVHIKLMRNNTFVTVTDS-KGNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVVVRVKGFTYFKKK  213 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~-~Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~V~vKG~G~gR~k  213 (255)
                      +|-|-|+-|.+|+.++|.|. .|.++...|+=.. -++......-.||..+++.++++|+++||+.|..--.|+-+.-.-
T Consensus         5 rpRL~V~kSnkhiyaQlIdd~~~~tl~s~St~~k-~~~~~~~~n~~aA~~vG~~~a~kak~~gi~~vvfDr~g~~yhGrv   83 (97)
T d1ovya_           5 RPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDK-EFGLDSTNNIEAAKKVGELVAKRALEKGIKQVVFDRGGYLYHGRV   83 (97)
T ss_dssp             CCSEEEEEETTEEEEEEECCSSCCCEEEESTTST-TTCSSCTTSHHHHHHHHHHHHHHHHHHSSSCCCCCSTTCSSCSST
T ss_pred             CCEEEEEEeCCeEEEEEEEcCCCeEEEEecchhh-hhcccccCcHHHHHHHHHHHHHHHHHcCCCEEEEcCCCCcchHHH
Confidence            37788999999999999966 5778887777555 555555567789999999999999999999775543333332211


Q ss_pred             HHHHHHHHh
Q 025294          214 RQAIMSFRE  222 (255)
Q Consensus       214 ~aaIkaL~~  222 (255)
                      .++..++++
T Consensus        84 ka~a~~~R~   92 (97)
T d1ovya_          84 KALADAARE   92 (97)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            344456654

>d2j01s1 c.55.4.1 (S:23-108) Ribosomal protein L18 (L18p) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein L18 (L18p)
species: Thermus thermophilus [TaxId: 274]

Probab=95.57  E-value=0.015  Score=42.71  Aligned_cols=62  Identities=19%  Similarity=0.210  Sum_probs=47.5

Q ss_pred             eEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEE
Q 025294          136 EFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVV  201 (255)
Q Consensus       136 ~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~  201 (255)
                      +-|-|+-|.+|..+.|.|.. |.++.+.|+-.. .+   +.....||..+++.++++|+++||+.|.
T Consensus         2 ~RL~V~rSnk~iyaQiIDd~~~~tl~s~St~~k-~~---k~~~~~~A~~vG~~la~~ak~~gI~~v~   64 (86)
T d2j01s1           2 LRLSVFRSLKHIYAQIIDDEKGVTLVSASSLAL-KL---KGNKTEVARQVGRALAEKALALGIKQVA   64 (86)
T ss_dssp             CEEECCBCSSCBCEEEEETTTTEEEEEECSTTT-CC---CSCHHHHHHHHHHHHHHHHHHTSCCCCB
T ss_pred             cEEEEEEcCCeEEEEEEEcCCCeEEEEEeccch-hh---cCCCHHHHHHHHHHHHHHHHHCCCCEEE
Confidence            56788999999999998766 455555554333 33   3456789999999999999999999873

>d2gycm1 c.55.4.1 (M:3-115) Ribosomal protein L18 (L18p) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein L18 (L18p)
species: Escherichia coli [TaxId: 562]

Probab=95.22  E-value=0.025  Score=43.39  Aligned_cols=66  Identities=17%  Similarity=0.130  Sum_probs=52.6

Q ss_pred             eEEEEEccCCCeEEEEEcCC-CCEEEEEeccCcccccCC--CCCchhHHHHHHHHHHHHHHHcCCcEEEE
Q 025294          136 EFVHIKLMRNNTFVTVTDSK-GNKRIGASSGCLPELKGG--PKMSRYAAEATAEHVGRLARNMGLKSVVV  202 (255)
Q Consensus       136 ~IlhI~sT~NNTiITlTD~~-Gnvl~~~SsGs~~GFKg~--rKsT~~AAq~aae~i~~kakelGik~V~V  202 (255)
                      +-|.|+-|.+|..++|.|.. |.++.+.|+=.. .+++.  ....-.||..+++.++++|++.||+.|..
T Consensus        22 pRL~V~rSnkhiyaQiIdd~~~~tl~saST~~k-~~~~~~~~~~n~~aA~~vG~~la~ra~~~gI~~vvf   90 (113)
T d2gycm1          22 TRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEK-AIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSF   90 (113)
T ss_dssp             CCCBEEECSSCEEEEEEETTTTEEEEEEETTGG-GGTSCCSCSSSHHHHHHHHHHHHHHHHHHTCCCCCC
T ss_pred             CeEEEEEeCCcEEEEEEEccCCcEEEEeeehhh-hhhhhcCCCcchHHHHHHHHHHHHHHHHCCCCEEEE
Confidence            67789999999999988766 556666666555 67765  34567899999999999999999998754

>d2zjrl1 c.55.4.1 (L:8-111) Ribosomal protein L18 (L18p) {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Translational machinery components
family: Ribosomal protein L18 and S11
domain: Ribosomal protein L18 (L18p)
species: Deinococcus radiodurans [TaxId: 1299]

Probab=87.55  E-value=0.15  Score=38.24  Aligned_cols=62  Identities=21%  Similarity=0.210  Sum_probs=46.7

Q ss_pred             ceEEEEEccCCCeEEEEEcCCCC-EEEEEeccCcccccCCCCCchhHHHHHHHHHHHHHHHcCCcEEE
Q 025294          135 SEFVHIKLMRNNTFVTVTDSKGN-KRIGASSGCLPELKGGPKMSRYAAEATAEHVGRLARNMGLKSVV  201 (255)
Q Consensus       135 ~~IlhI~sT~NNTiITlTD~~Gn-vl~~~SsGs~~GFKg~rKsT~~AAq~aae~i~~kakelGik~V~  201 (255)
                      .|-|.|+-|.+|...+|.|..+. ++.+.|+  . ..+.  .....+|..+++.+++++++.||+.|.
T Consensus        19 rpRL~V~rSnkhiyaQiIDd~~~~tl~s~St--~-~~~~--~~~~~~a~~vG~~ia~~a~~kgi~~v~   81 (104)
T d2zjrl1          19 RLRLSVYRSSKHIYAQIIDDSRGQTLAAASS--A-ALKS--GNKTDTAAAVGKALAAAAAEKGIKQVV   81 (104)
T ss_dssp             SEEECCCTTSSCCCCCEEETTTTEECCCCCS--C-SCCT--TCSSSSHHHHHHHHHHHHHTTCCCCCE
T ss_pred             CcEEEEEEccCeeEEEEEecCCCeEEEeecc--c-cccc--cchhhHHHHHHHHHHHHHHHCCCCEEE
Confidence            48899999999999999987755 4444444  3 2232  334567777999999999999999873