Citrus Sinensis ID: 029135

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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-------20
Protein Sequence
MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSFA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHHHcccccccccccEEEEcccccEEEEEEEcccccEEEEEcccHHHHHccccccccHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHcccEEccccc
Secondary Structure Prediction (SSPRO)
cccEccccHHEEccccHccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHHHHHcccccccccEEEEEccccEEEEEEEcccccEEEEEccccHHHHcccccccHHHHHHHHHHHHHHHHHHcHEEEccccccccHHHHHHHHHHHHcccccEEccEEccccccHHHHHHHHHHHHHHccEEEcccc
Coil and Loop (DISEMBL)
MSLTKAAAALQFNacdffgtkakpfnllpsqtqrrsfILKPLVVEARANARTESAKIRNRRIQkkfngtptkprlsvfcsdkQLYAMLVDDqnkkclffgSTLQqsirgngnppcstifpLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVvvreckplrfqypvmascnKDRLSFLLFLTVSLChakfrltsfa
Flexible Loop (DISEMBL)
MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEAranartesakirnrriqkkfngtptkprlsvFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSFA
Low Complexity Region (SEG)
MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPlsrkllsvlvkslsrlvlHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSFA
Disordered region (IsUnstruct)
*******AALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEA***************************RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRL****
Disordered Region (DISOPRED)
*************ACDF******************************************RRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQ***************PLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSF*
Disordered Region (DISEMBL)
MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSFA
Disordered Region (DISPRO)
***TKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSF*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHLMIVMAPVVVRECKPLRFQYPVMASCNKDRLSFLLFLTVSLCHAKFRLTSFA
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	198	2.2.26 [Sep-21-2011]
Q9SX68	170	50S ribosomal protein L18	no	no	0.535	0.623	0.336	1e-09
B7KI02	120	50S ribosomal protein L18	yes	no	0.545	0.9	0.318	2e-09
Q8SAY0	170	50S ribosomal protein L18	no	no	0.505	0.588	0.358	2e-08
B1IGD8	119	50S ribosomal protein L18	yes	no	0.550	0.915	0.327	5e-08
A9FGF8	119	50S ribosomal protein L18	yes	no	0.267	0.445	0.490	6e-08
Q7NEG8	120	50S ribosomal protein L18	yes	no	0.333	0.55	0.352	6e-08
Q3MFA6	120	50S ribosomal protein L18	yes	no	0.545	0.9	0.292	1e-07
B7K233	120	50S ribosomal protein L18	yes	no	0.277	0.458	0.454	2e-07
C3KVN5	119	50S ribosomal protein L18	yes	no	0.550	0.915	0.318	2e-07
B1KSK9	119	50S ribosomal protein L18	yes	no	0.560	0.932	0.313	2e-07

>sp|Q9SX68|RK18_ARATH 50S ribosomal protein L18, chloroplastic OS=Arabidopsis thaliana GN=RPL18 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/116 (33%), Positives = 57/116 (49%), Gaps = 10/116 (8%)

Query: 27  LLPSQTQRRSFILKP----------LVVEARANARTESAKIRNRRIQKKFNGTPTKPRLS 76
            L +  Q R+  LKP          +VVEA+    +E    R+ RI+KK NGT  +PRL 
Sbjct: 19  FLGNGLQHRAVFLKPWSSSSLQSRSMVVEAKTKTSSEDRIARHSRIRKKVNGTTERPRLC 78

Query: 77  VFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKS 132
           VF S+K LY  ++DD     L   ST Q+ I    +        +++K+  V+ KS
Sbjct: 79  VFRSNKHLYVQVIDDTKMHTLASASTKQKPISEEFDYTSGPTIEVAKKVGEVIAKS 134

Binds 5S rRNA, forms part of the central protuberance of the 50S subunit.
Arabidopsis thaliana (taxid: 3702)

>sp|B7KI02|RL18_CYAP7 50S ribosomal protein L18 OS=Cyanothece sp. (strain PCC 7424) GN=rplR PE=3 SV=1

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 59/113 (52%), Gaps = 5/113 (4%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG- 109
           RTES + R+ RI++K  GTP++PRL+VF S+  +YA ++DD  +  L   STL + ++G 
Sbjct: 5   RTESVQRRHSRIRRKVEGTPSRPRLAVFRSNNHIYAQVIDDVAQHTLVAASTLDKDLKGE 64

Query: 110 -NGNPPCSTIFPLSRKLLS--VLVKSLSRLVLHLTLRKFHLMIVMAPVVVREC 159
            +    C     +  KL++   L K + ++V       +H  I       RE 
Sbjct: 65  FSSGATCEASEAVG-KLVAQRALAKGIEKVVFDRGGNLYHGRIRALAQAAREA 116

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Cyanothece sp. (strain PCC 7424) (taxid: 65393)

>sp|Q8SAY0|RK18_ORYSJ 50S ribosomal protein L18, chloroplastic OS=Oryza sativa subsp. japonica GN=RPL18 PE=2 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 58/106 (54%), Gaps = 6/106 (5%)

Query: 29  PSQTQRRSFILKPLVVEARANARTESAK--IRNRRIQKKFNGTPTKPRLSVFCSDKQLYA 86
           PSQ +RR+     LVV A+    T  A    R+ R++KK +GT  +PRLSVF S+K LYA
Sbjct: 33  PSQARRRA----SLVVVAKVKVSTPQADRIARHVRLRKKVSGTTERPRLSVFRSNKHLYA 88

Query: 87  MLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKS 132
            ++DD     L   ST+ +S+  +          +++K+  V+ KS
Sbjct: 89  QVIDDTKSCTLVSASTMHKSLSKDLEYSAGPTVEVAQKIGEVIAKS 134

Binds 5S rRNA, forms part of the central protuberance of the 50S subunit.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|B1IGD8|RL18_CLOBK 50S ribosomal protein L18 OS=Clostridium botulinum (strain Okra / Type B1) GN=rplR PE=3 SV=1

 Score = 57.8 bits (138), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 57/113 (50%), Gaps = 4/113 (3%)

Query: 49  NARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIR 108
           N R++S + R+ R++KK  GT  +PRLSV+ S+K +YA L+DD   K L   S+ +Q   
Sbjct: 5   NDRSQSRERRHMRVRKKIFGTAERPRLSVYRSEKHIYAQLIDDVEGKTLVAASSAEQGFD 64

Query: 109 GNGNPPCSTIFPLSRKLLS--VLVKSLSRLVLHLTLRKFHLMIVMAPVVVREC 159
           G G+        L  K+++   L K L ++V       +H  I       RE 
Sbjct: 65  GVGSNKEGA--KLVGKMVAEKALEKGLKKVVFDRGGFIYHGRIKELAEGAREA 115

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Clostridium botulinum (strain Okra / Type B1) (taxid: 498213)

>sp|A9FGF8|RL18_SORC5 50S ribosomal protein L18 OS=Sorangium cellulosum (strain So ce56) GN=rplR PE=3 SV=1

 Score = 57.4 bits (137), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 36/53 (67%)

Query: 58  RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           R  RI+KK  GTP +PRLSVF S K +YA ++DD + K L   STL + ++G+
Sbjct: 11  RKLRIRKKVEGTPERPRLSVFRSSKHIYAQVIDDVSGKTLAHASTLSKDLKGS 63

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Sorangium cellulosum (strain So ce56) (taxid: 448385)

>sp|Q7NEG8|RL18_GLOVI 50S ribosomal protein L18 OS=Gloeobacter violaceus (strain PCC 7421) GN=rplR PE=3 SV=1

 Score = 57.4 bits (137), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 2/68 (2%)

Query: 58  RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN--GNPPC 115
           R++RI++K  GTP +PRL+V+ S++ +YA ++DD +++ L   STL+  +R    G   C
Sbjct: 12  RHQRIRRKIAGTPEQPRLAVYRSNRHIYAQVIDDVHQRTLVAASTLEAPLRSGEEGTATC 71

Query: 116 STIFPLSR 123
                + R
Sbjct: 72  EAATAVGR 79

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Gloeobacter violaceus (strain PCC 7421) (taxid: 251221)

>sp|Q3MFA6|RL18_ANAVT 50S ribosomal protein L18 OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rplR PE=3 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 58/113 (51%), Gaps = 5/113 (4%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           R ES + R+RR++ K  G+P +PRL+VF S++ +YA ++DD     L   ST++  ++ +
Sbjct: 5   RRESKQRRHRRVRGKVQGSPERPRLAVFRSNEHIYAQVIDDTQHHTLVSASTVEPEVKSS 64

Query: 111 --GNPPCSTIFPLSRKLLSV--LVKSLSRLVLHLTLRKFHLMIVMAPVVVREC 159
                 C     +  KL++V  L K ++++V       +H  I       RE 
Sbjct: 65  LASGANCEASSQIG-KLIAVRSLEKGITKVVFDRGGNLYHGRIKALAEAAREA 116

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

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

>sp|B7K233|RL18_CYAP8 50S ribosomal protein L18 OS=Cyanothece sp. (strain PCC 8801) GN=rplR PE=3 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 38/55 (69%)

Query: 50  ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQ 104
           +R ES + R+RRI+KK NGTP  PRL+VF S+  +YA ++DD  +  +   ST++
Sbjct: 4   SRKESVQRRHRRIRKKVNGTPNCPRLAVFRSNLHIYAQIIDDVGQHTIAAASTVE 58

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Cyanothece sp. (strain PCC 8801) (taxid: 41431)

>sp|C3KVN5|RL18_CLOB6 50S ribosomal protein L18 OS=Clostridium botulinum (strain 657 / Type Ba4) GN=rplR PE=3 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 57/113 (50%), Gaps = 4/113 (3%)

Query: 49  NARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIR 108
           N R++S + R+ R++KK  GT  +PRLSV+ S+K +YA L+DD   K L   S+ ++   
Sbjct: 5   NDRSQSRERRHMRVRKKIFGTAERPRLSVYRSEKHIYAQLIDDIEGKTLVAASSAEKGFD 64

Query: 109 GNGNPPCSTIFPLSRKLLS--VLVKSLSRLVLHLTLRKFHLMIVMAPVVVREC 159
           G G+        L  K+++   L K L ++V       +H  I       RE 
Sbjct: 65  GVGSNKEGA--KLVGKMVAEKALEKGLKKVVFDRGGFIYHGRIKELAEGAREA 115

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Clostridium botulinum (strain 657 / Type Ba4) (taxid: 515621)

>sp|B1KSK9|RL18_CLOBM 50S ribosomal protein L18 OS=Clostridium botulinum (strain Loch Maree / Type A3) GN=rplR PE=3 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 58/115 (50%), Gaps = 4/115 (3%)

Query: 47  RANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQS 106
           + N R++S + R+ R++KK  GT  +PRLSV+ S+K +YA L+DD   K L   S+ ++ 
Sbjct: 3   KKNDRSQSRERRHMRVRKKIFGTAERPRLSVYRSEKHIYAQLIDDVEGKTLVAASSSEKG 62

Query: 107 IRGNGNPPCSTIFPLSRKLLS--VLVKSLSRLVLHLTLRKFHLMIVMAPVVVREC 159
             G G+        L  K+++   L K L ++V       +H  I       RE 
Sbjct: 63  FDGVGSNKEGA--KLVGKMIAEKALEKGLKKVVFDRGGFIYHGRIKELAEGAREA 115

This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.

Clostridium botulinum (strain Loch Maree / Type A3) (taxid: 498214)

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	198
357487053	189	50S ribosomal protein L18 [Medicago trun	0.595	0.624	0.642	1e-33
388499264	164	unknown [Lotus japonicus]	0.646	0.780	0.601	2e-33
224101357	165	predicted protein [Populus trichocarpa]	0.575	0.690	0.652	4e-32
225448091	177	PREDICTED: 50S ribosomal protein L18-lik	0.570	0.638	0.623	3e-31
297844324	221	ribosomal protein L18 family protein [Ar	0.676	0.606	0.528	3e-31
449434778	180	PREDICTED: 50S ribosomal protein L18, ch	0.590	0.65	0.581	3e-31
255562882	164	50S ribosomal protein L18, chloroplast p	0.535	0.646	0.654	4e-31
356499819	170	PREDICTED: 50S ribosomal protein L18, ch	0.661	0.770	0.572	4e-31
298204602	164	unnamed protein product [Vitis vinifera]	0.570	0.689	0.623	5e-31
334182569	165	Ribosomal L.8/L5e family protein [Arabid	0.646	0.775	0.537	8e-31

>gi|357487053|ref|XP_003613814.1| 50S ribosomal protein L18 [Medicago truncatula] gi|355515149|gb|AES96772.1| 50S ribosomal protein L18 [Medicago truncatula]

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 79/123 (64%), Positives = 91/123 (73%), Gaps = 5/123 (4%)

Query: 10  LQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGT 69
            QFN   FFG   KPF  +  Q Q  S I K LV +A+ANAR ESAKIRNR++QKKFNGT
Sbjct: 11  FQFNTSSFFGVIPKPF--ISFQPQTTSLIKKSLVTKAKANARKESAKIRNRKMQKKFNGT 68

Query: 70  PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL 129
            T PRLSVFCSDKQLYAMLVDDQNKKCLF+GSTLQ+  R   NPPCSTI   ++++   L
Sbjct: 69  ATHPRLSVFCSDKQLYAMLVDDQNKKCLFYGSTLQKLFR--ENPPCSTI-EAAQRVGEAL 125

Query: 130 VKS 132
           VK+
Sbjct: 126 VKA 128

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388499264|gb|AFK37698.1| unknown [Lotus japonicus]

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 80/133 (60%), Positives = 94/133 (70%), Gaps = 5/133 (3%)

Query: 7   AAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKF 66
           A AL F +   FG   K F     Q Q R  I KPLVVEARAN RTES KIRNRR+QKKF
Sbjct: 6   APALHFKSSSVFGINPKSFIYF--QGQSRCLIKKPLVVEARANTRTESPKIRNRRMQKKF 63

Query: 67  NGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLL 126
           NGT   PRLSVFCSDKQLYAMLVDD+NKKCLF+GSTL +S R   NPPCST+   ++++ 
Sbjct: 64  NGTARHPRLSVFCSDKQLYAMLVDDKNKKCLFYGSTLHKSFR--ENPPCSTV-EAAQRVG 120

Query: 127 SVLVKSLSRLVLH 139
             LVK+ + L ++
Sbjct: 121 EALVKACTDLKIN 133

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101357|ref|XP_002312248.1| predicted protein [Populus trichocarpa] gi|222852068|gb|EEE89615.1| predicted protein [Populus trichocarpa]

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 77/118 (65%), Positives = 88/118 (74%), Gaps = 4/118 (3%)

Query: 1   MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNR 60
           M++    +AL F  CD FG   KPFN LP QT  R+F  K LV + RAN RTESAKIRNR
Sbjct: 1   MAVRSVPSALPFKTCDVFGNPLKPFNFLPIQT--RNFQTKTLVAKRRANTRTESAKIRNR 58

Query: 61  RIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTI 118
           R  KKFNGT TKPRLSVFCS KQLYAMLVDDQ+KKCLF+GSTLQ+ +  +G+ P STI
Sbjct: 59  RTLKKFNGTRTKPRLSVFCSTKQLYAMLVDDQSKKCLFYGSTLQKPL--SGDLPRSTI 114

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448091|ref|XP_002276553.1| PREDICTED: 50S ribosomal protein L18-like [Vitis vinifera]

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 73/117 (62%), Positives = 86/117 (73%), Gaps = 4/117 (3%)

Query: 7   AAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKF 66
           A  LQF +   FGT +   + L S     SF  K +V+EARANA+ +SAKIRNRR+Q+KF
Sbjct: 19  APTLQFKSSGLFGTHSNSISFL-SMPITNSFT-KAMVIEARANAKKDSAKIRNRRLQRKF 76

Query: 67  NGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSR 123
           NG+PTKPRLSVFCS KQLYAMLVDDQNK+CLF+GSTLQ+SI GN   PCS I    R
Sbjct: 77  NGSPTKPRLSVFCSAKQLYAMLVDDQNKRCLFYGSTLQKSIHGNN--PCSAIEAAER 131

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844324|ref|XP_002890043.1| ribosomal protein L18 family protein [Arabidopsis lyrata subsp. lyrata] gi|297335885|gb|EFH66302.1| ribosomal protein L18 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 73/138 (52%), Positives = 92/138 (66%), Gaps = 4/138 (2%)

Query: 1   MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNR 60
           M+   + + +QF   D  GT+ KP+   P +    S  +KP V+EAR N+R ES K RNR
Sbjct: 1   MAALSSLSFVQFRVSDILGTRLKPYPQFPIRITNMS--VKPFVIEARGNSRVESPKTRNR 58

Query: 61  RIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFP 120
           R +KKFNGT TKPRLSVFCSDKQLYAMLVDD NKKCLF+ STLQ+SIR  G+PPC+ I  
Sbjct: 59  RSRKKFNGTQTKPRLSVFCSDKQLYAMLVDDFNKKCLFYASTLQKSIR--GDPPCTVIHL 116

Query: 121 LSRKLLSVLVKSLSRLVL 138
           +    +   V S+  +V 
Sbjct: 117 VGVCFVVYAVYSIGGIVF 134

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434778|ref|XP_004135173.1| PREDICTED: 50S ribosomal protein L18, chloroplastic-like [Cucumis sativus] gi|449478396|ref|XP_004155307.1| PREDICTED: 50S ribosomal protein L18, chloroplastic-like [Cucumis sativus]

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 71/122 (58%), Positives = 93/122 (76%), Gaps = 5/122 (4%)

Query: 18  FGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSV 77
           FG ++KPF+    +T+     +KPL ++AR N++TESAK+RNRR+QKK+NGTPT+PRLSV
Sbjct: 34  FGLQSKPFDFRSLKTKHCD--VKPLTIQARGNSKTESAKVRNRRMQKKYNGTPTRPRLSV 91

Query: 78  FCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLV 137
           FCSDKQLYAMLVDDQNKKCLF+GSTLQ+S+R    P C+TI   ++ +   LVK    L 
Sbjct: 92  FCSDKQLYAMLVDDQNKKCLFYGSTLQKSMR--PTPSCTTI-EAAQHVGEELVKVCMDLN 148

Query: 138 LH 139
           +H
Sbjct: 149 IH 150

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562882|ref|XP_002522446.1| 50S ribosomal protein L18, chloroplast precursor, putative [Ricinus communis] gi|223538331|gb|EEF39938.1| 50S ribosomal protein L18, chloroplast precursor, putative [Ricinus communis]

 Score =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 72/110 (65%), Positives = 83/110 (75%), Gaps = 4/110 (3%)

Query: 9   ALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKFNG 68
           ALQF  CDFFG ++K F  LP QT   +F    ++   RAN +TESAK  N R +KKFNG
Sbjct: 8   ALQFKNCDFFGNRSKAFTFLPLQTT--NFQAMTVMASKRANTKTESAKTINIRRRKKFNG 65

Query: 69  TPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTI 118
           TP KPRLSVFCS KQLYAMLVDDQNKKCLF+GSTLQ+S+R  G+PPCS I
Sbjct: 66  TPIKPRLSVFCSTKQLYAMLVDDQNKKCLFYGSTLQKSLR--GSPPCSKI 113

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499819|ref|XP_003518734.1| PREDICTED: 50S ribosomal protein L18, chloroplastic-like [Glycine max]

 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/138 (57%), Positives = 97/138 (70%), Gaps = 7/138 (5%)

Query: 7   AAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARA--NARTESAKIRNRRIQK 64
           A  LQF     FG +  P + +  QTQ RS   KPLV+EARA  N R ES KIRNRR+ K
Sbjct: 9   APMLQFKNSALFGIQ--PNSFVCFQTQSRSITKKPLVIEARARANTRKESGKIRNRRMLK 66

Query: 65  KFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRK 124
           K+NGT T PRLSVFCSDKQLYAMLVDD+NKKCLF+GSTLQ+SIR   +PPCST+   +++
Sbjct: 67  KYNGTATHPRLSVFCSDKQLYAMLVDDKNKKCLFYGSTLQKSIR--QDPPCSTL-EAAQR 123

Query: 125 LLSVLVKSLSRLVLHLTL 142
           +   LVK+   L ++  L
Sbjct: 124 VGEALVKACVDLNINEIL 141

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204602|emb|CBI23877.3| unnamed protein product [Vitis vinifera]

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 73/117 (62%), Positives = 86/117 (73%), Gaps = 4/117 (3%)

Query: 7   AAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKF 66
           A  LQF +   FGT +   + L S     SF  K +V+EARANA+ +SAKIRNRR+Q+KF
Sbjct: 6   APTLQFKSSGLFGTHSNSISFL-SMPITNSFT-KAMVIEARANAKKDSAKIRNRRLQRKF 63

Query: 67  NGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSR 123
           NG+PTKPRLSVFCS KQLYAMLVDDQNK+CLF+GSTLQ+SI GN   PCS I    R
Sbjct: 64  NGSPTKPRLSVFCSAKQLYAMLVDDQNKRCLFYGSTLQKSIHGNN--PCSAIEAAER 118

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334182569|ref|NP_683305.2| Ribosomal L.8/L5e family protein [Arabidopsis thaliana] gi|332191001|gb|AEE29122.1| Ribosomal L.8/L5e family protein [Arabidopsis thaliana]

 Score =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 71/132 (53%), Positives = 92/132 (69%), Gaps = 4/132 (3%)

Query: 1   MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNR 60
           M+   + + +QF   D  GT+ KP+   P +    S ++KP V+EAR N R ES K RNR
Sbjct: 1   MAALTSLSTVQFRVSDILGTRLKPYPQFPIRITTMS-VVKPFVIEARGNTRVESPKTRNR 59

Query: 61  RIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFP 120
           R +KKF GT TKPRLSVFCSDKQLYAMLVDD NKKCLF+ STLQ+SIR  G+PPC T+  
Sbjct: 60  RSRKKFTGTQTKPRLSVFCSDKQLYAMLVDDFNKKCLFYASTLQKSIR--GDPPC-TVIE 116

Query: 121 LSRKLLSVLVKS 132
            ++++   L+K+
Sbjct: 117 AAKRVGEELIKA 128

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	198
TAIR|locus:2007690	170	EMB3105 "EMBRYO DEFECTIVE 3105	0.505	0.588	0.364	3.6e-09
TIGR_CMR|CHY_2293	122	CHY_2293 "ribosomal protein L1	0.297	0.483	0.423	3.3e-08
TIGR_CMR|BA_0126	120	BA_0126 "ribosomal protein L18	0.338	0.558	0.371	2.9e-07
TIGR_CMR|DET_0490	121	DET_0490 "ribosomal protein L1	0.272	0.446	0.409	1.1e-05
TIGR_CMR|GSU_2841	122	GSU_2841 "ribosomal protein L1	0.242	0.393	0.416	1.1e-05
UNIPROTKB|P66076	122	rplR "50S ribosomal protein L1	0.262	0.426	0.346	0.00028

TAIR|locus:2007690 EMB3105 "EMBRYO DEFECTIVE 3105" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 3.6e-09, P = 3.6e-09
 Identities = 39/107 (36%), Positives = 53/107 (49%)

Query:     1 MSLTKAAAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNR 60
             +SL    +A   N         KP++   S  Q RS     +VVEA+    +E    R+ 
Sbjct:    10 VSLITNRSAFLGNGLQHRAVFLKPWS--SSSLQSRS-----MVVEAKTKTSSEDRIARHS 62

Query:    61 RIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSI 107
             RI+KK NGT  +PRL VF S+K LY  ++DD     L   ST Q+ I
Sbjct:    63 RIRKKVNGTTERPRLCVFRSNKHLYVQVIDDTKMHTLASASTKQKPI 109

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0042254 "ribosome biogenesis" evidence=ISS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0007389 "pattern specification process" evidence=RCA

GO:0008361 "regulation of cell size" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0009832 "plant-type cell wall biogenesis" evidence=RCA

GO:0009926 "auxin polar transport" evidence=RCA

GO:0010015 "root morphogenesis" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0040007 "growth" evidence=RCA

GO:0048653 "anther development" evidence=RCA

TIGR_CMR|CHY_2293 CHY_2293 "ribosomal protein L18" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query:    51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
             R    K R+ R++KK +GTP +PRL+V+ S K +YA ++DD + + L   STL   +RG
Sbjct:     7 RNLERKRRHLRVRKKIHGTPERPRLNVYRSLKHIYAQIIDDVSGRTLVAASTLDPELRG 65

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|BA_0126 BA_0126 "ribosomal protein L18" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 117 (46.2 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 26/70 (37%), Positives = 42/70 (60%)

Query:    42 LVVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGS 101
             ++ +A  NA   + K R+ R++ K  GT  +PRL+VF S++ +YA ++DD N   L   S
Sbjct:     1 MITKADKNA---TRKKRHARVRAKLTGTAERPRLNVFRSNQHIYAQVIDDVNGVTLVSAS 57

Query:   102 TLQQSIRGNG 111
             TL + +  NG
Sbjct:    58 TLDKDLALNG 67

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|DET_0490 DET_0490 "ribosomal protein L18" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 103 (41.3 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 25/61 (40%), Positives = 39/61 (63%)

Query:    46 ARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQ 105
             A+ NAR E+  +R+ R++KK +GT  +PRL VF S + +Y  +++D    C   GSTL Q
Sbjct:     2 AKVNAR-EARIVRHERLRKKVSGTEARPRLCVFRSIENIYTQVINDN---C---GSTLVQ 54

Query:   106 S 106
             +
Sbjct:    55 A 55

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

GO:0006412 "translation" evidence=ISS

GO:0015934 "large ribosomal subunit" evidence=ISS

TIGR_CMR|GSU_2841 GSU_2841 "ribosomal protein L18" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 103 (41.3 bits), Expect = 1.1e-05, P = 1.1e-05
 Identities = 20/48 (41%), Positives = 30/48 (62%)

Query:    58 RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQ 105
             R  R++KK  GT  +PRL+VF S + +YA ++DD     L   ST+Q+
Sbjct:    14 RKTRVRKKIRGTTERPRLNVFKSAQHIYAQIIDDTTGTTLVSASTVQK 61

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

GO:0006412 "translation" evidence=ISS

GO:0042254 "ribosome biogenesis" evidence=ISS

UNIPROTKB|P66076 rplR "50S ribosomal protein L18" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 91 (37.1 bits), Expect = 0.00028, P = 0.00028
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query:    58 RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
             R+ R++KK +GT  +PRL V  S + ++  LV+D N   +   S+++  +RG
Sbjct:    16 RHTRLRKKLSGTAERPRLVVHRSARHIHVQLVNDLNGTTVAAASSIEADVRG 67


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.328   0.137   0.413    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      198       180   0.00092  109 3  11 22  0.45    31
                                                     31  0.39    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  574 (61 KB)
  Total size of DFA:  141 KB (2087 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  14.54u 0.13s 14.67t   Elapsed:  00:00:01
  Total cpu time:  14.54u 0.13s 14.67t   Elapsed:  00:00:01
  Start:  Fri May 10 07:10:19 2013   End:  Fri May 10 07:10:20 2013

GO:0040007 "growth" evidence=IMP

---

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	198
CHL00139	109	CHL00139, rpl18, ribosomal protein L18; Validated	3e-11
cd00432	103	cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18	3e-10
PRK05593	117	PRK05593, rplR, 50S ribosomal protein L18; Reviewe	1e-09
COG0256	125	COG0256, RplR, Ribosomal protein L18 [Translation,	1e-07
pfam00861	119	pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e fami	1e-07
TIGR00060	114	TIGR00060, L18_bact, ribosomal protein L18, bacter	2e-06

>gnl|CDD|214373 CHL00139, rpl18, ribosomal protein L18; Validated

 Score = 57.3 bits (139), Expect = 3e-11
 Identities = 23/55 (41%), Positives = 36/55 (65%)

Query: 58  RNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGN 112
           +  R++KK  GT  +PRLSVF S+K +YA ++DD N K L   STL+  ++ + +
Sbjct: 1   KRERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLS 55

Length = 109

>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 = 54.5 bits (132), Expect = 3e-10
 Identities = 20/48 (41%), Positives = 30/48 (62%)

Query: 62  IQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
            ++K  GT  +PRL V  S+K +YA ++DD   K L   STL+ +I+G
Sbjct: 1   RRRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKG 48

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

>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed

 Score = 53.6 bits (130), Expect = 1e-09
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
           + E+   R+RR++KK +GT  +PRLSVF S++ +YA ++DD   K L   STL++ +R 
Sbjct: 3   KKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRA 61

Length = 117

>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 23/61 (37%), Positives = 32/61 (52%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           R      R  RI+KK  GT  +PRL V  S++ +YA ++DD     L   STL + +R  
Sbjct: 8   RRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKY 67

Query: 111 G 111
           G
Sbjct: 68  G 68

Length = 125

>gnl|CDD|216159 pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e family

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 50  ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
            +    + +  R+++K  GT  +PRL V  S+K +YA ++DD     L   STL + ++ 
Sbjct: 1   GKRRRRRRKRLRVRRKLKGTAERPRLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKK 60

Query: 110 NG 111
            G
Sbjct: 61  YG 62

This family includes ribosomal proteins from the large subunit. This family includes L18 from bacteria and L5 from eukaryotes. It has been shown that the amino terminal 93 amino acids of rat Rpl5 are necessary and sufficient to bind 5S rRNA in vitro. Suggesting that the entire family has a function in rRNA binding. Length = 119

>gnl|CDD|213499 TIGR00060, L18_bact, ribosomal protein L18, bacterial type

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 2/64 (3%)

Query: 51  RTESAKIRNRRIQKKFNGT--PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIR 108
           +  +   R++RI++K   T    +PRL VF S++ +YA ++DD   + L   STL++ ++
Sbjct: 1   KKSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK 60

Query: 109 GNGN 112
             GN
Sbjct: 61  YTGN 64

The archaeal and eukaryotic type rpL18 is not detectable under this model [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 114

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	198
PRK05593	117	rplR 50S ribosomal protein L18; Reviewed	100.0
TIGR00060	114	L18_bact ribosomal protein L18, bacterial type. Th	100.0
CHL00139	109	rpl18 ribosomal protein L18; Validated	100.0
COG0256	125	RplR Ribosomal protein L18 [Translation, ribosomal	100.0
PF00861	119	Ribosomal_L18p: Ribosomal L18p/L5e family; InterPr	99.96
PTZ00032	211	60S ribosomal protein L18; Provisional	99.94
cd00432	103	Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is	99.94
PRK08569	193	rpl18p 50S ribosomal protein L18P; Reviewed	99.93
PTZ00069	300	60S ribosomal protein L5; Provisional	99.2
KOG3333	188	consensus Mitochondrial/chloroplast ribosomal prot	98.29
PF00411	110	Ribosomal_S11: Ribosomal protein S11; InterPro: IP	96.26
PTZ00090	233	40S ribosomal protein S11; Provisional	95.82
TIGR03632	108	bact_S11 30S ribosomal protein S11. This model des	95.59
CHL00041	116	rps11 ribosomal protein S11	94.87
PRK05309	128	30S ribosomal protein S11; Validated	94.49
KOG0875	264	consensus 60S ribosomal protein L5 [Translation, r	94.38
PRK09607	132	rps11p 30S ribosomal protein S11P; Reviewed	94.14
TIGR03628	114	arch_S11P archaeal ribosomal protein S11P. This mo	93.76
PTZ00129	149	40S ribosomal protein S14; Provisional	90.31
COG0100	129	RpsK Ribosomal protein S11 [Translation, ribosomal	82.18

>PRK05593 rplR 50S ribosomal protein L18; Reviewed

Probab=100.00  E-value=7.9e-35  Score=229.12  Aligned_cols=106  Identities=28%  Similarity=0.400  Sum_probs=99.4

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL  129 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL  129 (198)
                      ++++.|.+|++|+|+||.||+++|||+||+||+|||||||||++++||+|+||+|++++..+ . ++|++||+ .||++|
T Consensus         2 ~~~~~r~~r~~r~r~ki~g~~~rpRL~V~~SnkhiyAQvidd~~~~tl~saST~e~~~k~~~-~-~~n~~aa~-~vG~~l   78 (117)
T PRK05593          2 DKKEARLRRHRRVRKKISGTAERPRLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVRAGL-K-GGNKEAAK-KVGKLI   78 (117)
T ss_pred             chHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEECCCCEEEEEEecCcHhHhccc-c-CCCHHHHH-HHHHHH
Confidence            56778899999999999999999999999999999999999999999999999999986533 2 79999999 999999


Q ss_pred             HHHHHhcChhHHH-----Hhhhheeehhhhhhhc
Q 029135          130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVRE  158 (198)
Q Consensus       130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~  158 (198)
                      |++|+++||++++     ++|||+|..+++-+|+
T Consensus        79 a~ra~~~gi~~vvfDrg~~~yhGrV~a~a~~are  112 (117)
T PRK05593         79 AERAKAKGIKQVVFDRGGYKYHGRVKALADAARE  112 (117)
T ss_pred             HHHHHHCCCCEEEEcCCCCcccHHHHHHHHHHHH
Confidence            9999999999998     8999999999999887

>TIGR00060 L18_bact ribosomal protein L18, bacterial type

Probab=100.00  E-value=7.2e-35  Score=229.23  Aligned_cols=102  Identities=25%  Similarity=0.376  Sum_probs=95.7

Q ss_pred             HHHHHHHHHHHHhhhcCCC--CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135           52 TESAKIRNRRIQKKFNGTP--TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL  129 (198)
Q Consensus        52 ~e~R~rR~rRiRkKI~GTa--~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL  129 (198)
                      ++.|.+|+.|+|+||.||+  ++|||+||+||+|||||||||++++||+|+||+|++++     +++|+++|+ +||++|
T Consensus         2 ~~~r~~r~~r~r~ki~gt~~~~rpRL~V~rSnk~iyaQiIdd~~~~tlasaST~ek~~~-----~~~n~~aA~-~vG~~l   75 (114)
T TIGR00060         2 KSARIRRHKRIRRKLRETGEANRPRLVVFRSNRHIYAQVIDDSKSEVLASASTLEKKLK-----YTGNKDAAK-KVGKLV   75 (114)
T ss_pred             cHHHHHHHHHHHHHhcCCCCCCCcEEEEEEeCCeEEEEEEECCCCEEEEEEecchhhhc-----CCCCHHHHH-HHHHHH
Confidence            3567789999999999999  89999999999999999999999999999999999975     348999999 999999


Q ss_pred             HHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ||+|+++||+.++     ++|||+|..+++-+||-
T Consensus        76 a~ra~~~gi~~vvfDrgg~~YhGrv~A~a~~aRe~  110 (114)
T TIGR00060        76 AERLKEKGIKDVVFDRGGYKYHGRVAALAEAAREA  110 (114)
T ss_pred             HHHHHHCCCCEEEEeCCCCcchHHHHHHHHHHHHh
Confidence            9999999999999     89999999999999974

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

>CHL00139 rpl18 ribosomal protein L18; Validated

Probab=100.00  E-value=1.6e-34  Score=225.13  Aligned_cols=99  Identities=31%  Similarity=0.403  Sum_probs=94.7

Q ss_pred             HHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcCh
Q 029135           59 NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVL  138 (198)
Q Consensus        59 ~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI  138 (198)
                      ++|+|+||.||+++|||+||+||+|||||||||.+|+||+|+||+|+++++|+ ++++|+++|+ .||++|||+|+++||
T Consensus         2 ~~r~r~ki~g~~~rpRL~V~rSnkhiyaQvidd~~g~tlasaST~ek~~~~~~-~~~~n~~aA~-~vG~lla~ra~~~gi   79 (109)
T CHL00139          2 RERVRKKIKGTAERPRLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSL-SSTSTCDASK-LVGQKLAKKSLKKGI   79 (109)
T ss_pred             CeeeeeeecCCCCCCEEEEEEeCCeEEEEEEECCCCCEEEEEecCchhhhccc-cCCCCHHHHH-HHHHHHHHHHHHCCC
Confidence            57899999999999999999999999999999999999999999999999987 6789999999 999999999999999


Q ss_pred             hHHH-----Hhhhheeehhhhhhhcc
Q 029135          139 HLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       139 ~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ++++     ++|||+|..+++-.|+-
T Consensus        80 ~~vvfDrgg~~yhGrV~a~a~~are~  105 (109)
T CHL00139         80 TKVVFDRGGKLYHGRIKALAEAAREA  105 (109)
T ss_pred             CEEEEcCCCCccchHHHHHHHHHHHh
Confidence            9999     89999999999999873

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

Probab=100.00  E-value=1.7e-33  Score=225.04  Aligned_cols=109  Identities=24%  Similarity=0.255  Sum_probs=101.4

Q ss_pred             hcchHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcC--CCCCCCCCHHHHHHHH
Q 029135           48 ANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG--NGNPPCSTIFPLSRKL  125 (198)
Q Consensus        48 ~~~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~--~l~~~~~NieAA~~~V  125 (198)
                      +..|++++.+|+.|+|+||.|++++|||+|||||+|||||||||..+.||+++||++++++.  |. ..++|+++|+ +|
T Consensus         5 ~~~rr~~~~kr~~r~R~kl~g~~~rpRL~V~rSnkhi~aQiId~~~~~tla~aSt~~~~l~~~g~~-~~~~N~~aA~-~v   82 (125)
T COG0256           5 VKFRRRRRGKRAYRIRKKLLGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKK-GGGGNTEAAY-LV   82 (125)
T ss_pred             hhhHHHHHHhHHHHHHHhhccCCCCcEEEEEEeCCcEEEEEEEcCCCceEEEEEcchHHHHhhccc-CCCCCHHHHH-HH
Confidence            34677888999999999999999999999999999999999999999999999999999954  54 4578999999 99


Q ss_pred             HHHHHHHHHhcChhHHH-----Hhhhheeehhhhhhhc
Q 029135          126 LSVLVKSLSRLVLHLTL-----RKFHLMIVMAPVVVRE  158 (198)
Q Consensus       126 GklLAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~  158 (198)
                      |++||++|+++||+++|     ++|||||..+++-.||
T Consensus        83 G~lia~ra~~kgi~~vVfdr~g~~yhgRV~Ala~~Are  120 (125)
T COG0256          83 GKLIAERALAKGIEEVVFDRGGYKYHGRVAALADGARE  120 (125)
T ss_pred             HHHHHHHHHHcCCcEEEEcCCCCCcchHHHHHHHHHHH
Confidence            99999999999999999     9999999999998876

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

Probab=99.96  E-value=3.4e-30  Score=201.51  Aligned_cols=107  Identities=25%  Similarity=0.322  Sum_probs=98.6

Q ss_pred             hHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcC--CCCCCCCCHHHHHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG--NGNPPCSTIFPLSRKLLSV  128 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~--~l~~~~~NieAA~~~VGkl  128 (198)
                      |++.+.+|+.++|+++.+++++|||+||+||+|||||||||..+.||+++||++++++.  |. .+++|+++|+ .||++
T Consensus         2 k~~~~~~r~~~~r~~~~~~~~~~RL~V~~Snk~i~aQii~~~~~~~l~~aSt~~~~l~~~~~~-~~~~n~~aa~-~vG~l   79 (119)
T PF00861_consen    2 KKRRRRRRKLRIRRKIKGTAERPRLVVFRSNKHIYAQIIDDSKGGTLASASTLSKELKKYGWK-GSTKNVEAAY-LVGEL   79 (119)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEEECTTTEEEEEEEEETTTGGGTT-S-STTSSHHHHH-HHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCCCCEEEEEeccCeEEEEEEeeCCCCeEEEEEecchhhhhhhhc-cCCCCEehHH-HHHHH
Confidence            45677889999999999999999999999999999999999999999999999999985  33 5678999999 99999


Q ss_pred             HHHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          129 LVKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       129 LAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ||++|+++||..++     ++|||+|..+++-+|+.
T Consensus        80 la~ra~~~gi~~v~fdr~~~~y~grv~a~~~~~re~  115 (119)
T PF00861_consen   80 LAKRALEKGIAKVVFDRGGYKYHGRVKALADGAREG  115 (119)
T ss_dssp             HHHHHHHTTSSEEEECTSTSSSSSHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCcEEEEcCCCCcccHHHHHHHHHHHHc
Confidence            99999999998888     89999999999998875

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 ....

>PTZ00032 60S ribosomal protein L18; Provisional

Probab=99.94  E-value=5.8e-28  Score=206.74  Aligned_cols=89  Identities=19%  Similarity=0.170  Sum_probs=82.1

Q ss_pred             CCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCC-----------CCCCCHHHHHHHHHHHHHHHHHhcCh
Q 029135           70 PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGN-----------PPCSTIFPLSRKLLSVLVKSLSRLVL  138 (198)
Q Consensus        70 a~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~-----------~~~~NieAA~~~VGklLAerAkeaGI  138 (198)
                      ..||||+|||||+|||||||||.+|+||+|+||+++++++.++           ..++|+++|+ .||++|||+|+++||
T Consensus       103 krrPRLsV~RSnkHIYAQIIDD~~~~TLasaSTlek~l~~~~~~~~~~~~n~~~~~g~nieaA~-~VGk~IAerAl~kGI  181 (211)
T PTZ00032        103 KRRPRLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAY-ELGKLIGRKALSKGI  181 (211)
T ss_pred             CCcceEEEEecCCeEEEEEEECCCCCEEEEecCCCHHHHhhhcccccccccccccCCCcHHHHH-HHHHHHHHHHHHCCC
Confidence            3699999999999999999999999999999999999976431           1478999999 999999999999999


Q ss_pred             hHHH-----Hhhhheeehhhhhhhcc
Q 029135          139 HLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       139 ~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ++++     ++|||||..++|-.||-
T Consensus       182 ~kVvFDRgGy~YHGRVkALAdaARe~  207 (211)
T PTZ00032        182 SKVRFDRAHYKYAGKVEALAEGARAV  207 (211)
T ss_pred             CEEEEeCCCCeehhHHHHHHHHHHHc
Confidence            9999     99999999999999984

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

Probab=99.94  E-value=2.3e-27  Score=179.70  Aligned_cols=95  Identities=26%  Similarity=0.297  Sum_probs=88.0

Q ss_pred             HhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           63 QKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        63 RkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      ++++.|+..+|||+|++||+|||||||||.+++||+++||+|+++++++ ++++|++||+ .||++||++|+++||++++
T Consensus         2 ~~~~~~~~~~~RL~v~~Sn~~i~aqvi~~~~~~vl~sast~e~~~~~~~-~~~~n~~aA~-~vG~~la~r~~~~gi~~vv   79 (103)
T cd00432           2 RRKRLGTQERPRLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIKGVL-GSGNNVEAAY-LVGRLLAKRALEKGIKKVV   79 (103)
T ss_pred             ceEecCcCCCCEEEEEEeCCEEEEEEEEeCcCeEEEEEecCchhhcccc-cCCCcHHHHH-HHHHHHHHHHHHCCCCEEE
Confidence            3455677789999999999999999999999999999999999999877 6789999999 9999999999999999998


Q ss_pred             -----Hhhhheeehhhhhhhcc
Q 029135          143 -----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       143 -----~kyHg~i~~~~~~~~~~  159 (198)
                           ++|||+|..+.+-+|+.
T Consensus        80 ~D~~~~~~~grv~a~~~~~r~~  101 (103)
T cd00432          80 FDRGGYRYHGRVKALAKGAREG  101 (103)
T ss_pred             EeCCCcccccHHHHHHHHHHHc
Confidence                 99999999999988874

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=99.93  E-value=1.7e-26  Score=195.79  Aligned_cols=105  Identities=15%  Similarity=0.075  Sum_probs=97.1

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLS  127 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGk  127 (198)
                      .|.|.++.+++|.|....   ++|||+||+||+|||||||  ||++|+||+||||+|++.++|. .+++|++||+ +||.
T Consensus        13 RrRegkTdY~~R~rl~~~---~kpRLvV~rSNkhIyaQiI~~dd~gd~tLaSAsS~el~~~g~~-~~~~N~~AAy-~vG~   87 (193)
T PRK08569         13 RRREGKTDYRKRLKLLLS---GKPRLVVRKTNKHVIAQIVKYDPKGDRTLASAHSRELAKYGWK-GDTGNTPAAY-LTGL   87 (193)
T ss_pred             ccccccccHHHHHHHHhc---CCCEEEEEEeCCeEEEEEEEccCCCCEEEEEEecCchhhcccc-CCCCCHHHHH-HHHH
Confidence            467888899999887654   7999999999999999999  9999999999999999999987 5789999999 9999


Q ss_pred             HHHHHHHhcChhHHH-----Hhhh--heeehhhhhhhcc
Q 029135          128 VLVKSLSRLVLHLTL-----RKFH--LMIVMAPVVVREC  159 (198)
Q Consensus       128 lLAerAkeaGI~~~v-----~kyH--g~i~~~~~~~~~~  159 (198)
                      +||++|+++||+++|     ++||  |||.-+++-.|+.
T Consensus        88 llA~ral~kGi~~vvfDrGg~~yh~gGRV~A~akgArd~  126 (193)
T PRK08569         88 LAGKKALKAGVEEAVLDIGLHRPTKGSRVFAALKGAIDA  126 (193)
T ss_pred             HHHHHHHHCCCCEEEEecCCccccCCccHHHHHHHHHHc
Confidence            999999999999998     9999  9999999999975

>PTZ00069 60S ribosomal protein L5; Provisional

Probab=99.20  E-value=7e-11  Score=106.40  Aligned_cols=85  Identities=16%  Similarity=0.053  Sum_probs=74.4

Q ss_pred             chHHHHHHHHHHHHhhhcCC----CCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGT----PTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSR  123 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GT----a~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~  123 (198)
                      -|.|.++.+++|.|.-+.+.    +-+|||+|..||++|.|||+  +.+++++|++|.|.|+.-+||. .+.+|.+||+ 
T Consensus        22 RRREGKTdY~~R~rLi~q~knKynspK~RlVVR~TN~~ii~Qiv~~~~~GD~vl~sA~S~eL~kyG~k-~gl~N~~AAY-   99 (300)
T PTZ00069         22 RRREGKTDYYARRRLILQDKNKYNSPKYRLVVRITNKDIICQIVYATIVGDKVLAAAYSHELPRFGIP-VGLTNYAAAY-   99 (300)
T ss_pred             hhhcccccHHHHHHHHHccccccCCCCceEEEEEECCcEEEEEEEeecCCCEEEEEeehhhHhhcCcC-CCCccHHHHH-
Confidence            36677788888888777652    24899999999999999999  5789999999999999878887 6789999999 


Q ss_pred             HHHHHHHHHHHhc
Q 029135          124 KLLSVLVKSLSRL  136 (198)
Q Consensus       124 ~VGklLAerAkea  136 (198)
                      ++|.++|.|++++
T Consensus       100 ~TGlL~arR~L~k  112 (300)
T PTZ00069        100 ATGLLLARRLLKK  112 (300)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999999987

>KOG3333 consensus Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis]

Probab=98.29  E-value=9.7e-07  Score=74.77  Aligned_cols=67  Identities=15%  Similarity=0.126  Sum_probs=61.5

Q ss_pred             CeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        73 PRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      .||.|-++..|+-+-|.. .+|.+++||||.|+.|+..+ .++.|+.|+. .+|.+||+||++.||+..+
T Consensus        61 h~lev~~~~~hveg~v~H-~~~gvvvSAST~EwaIk~qL-Yst~dtsA~~-niGRVLAqRCLqsGI~fm~  127 (188)
T KOG3333|consen   61 HRLEVIRTQHHVEGLVEH-QNGGVVVSASTREWAIKKQL-YSTRDTSACE-NIGRVLAQRCLQSGINFMV  127 (188)
T ss_pred             eEEEEeecccceeeeeeE-ecCCEEEEecccchHHHHHH-hhccchHHHH-HHHHHHHHHHHHhCcceec
Confidence            489999999999999886 66778899999999999877 7889999999 9999999999999999877

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

Probab=96.26  E-value=0.027  Score=43.79  Aligned_cols=63  Identities=17%  Similarity=0.191  Sum_probs=53.0

Q ss_pred             EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      +-|+-|.+++.+.+.| ..|+++.+.|+-...+++.   ..++..||+ .+++.++++|++.||..+.
T Consensus         3 ihI~~s~NNt~vtlTd-~~G~~~~~~S~G~~gfK~~---rk~t~~Aa~-~~a~~~~~~~~~~gi~~v~   65 (110)
T PF00411_consen    3 IHIKSSFNNTIVTLTD-LKGNVLFWSSAGSLGFKGA---RKSTPYAAQ-QAAEKIAKKAKELGIKTVR   65 (110)
T ss_dssp             EEEEEESSEEEEEEEE-TTSEEEEEEETTTSSTTTT---CGSSHHHHH-HHHHHHHHHHHCTTEEEEE
T ss_pred             EEEEecCCCEEEEEEC-CCCCEEEEEeccccccccc---cccCHHHHH-HHHHHHHHHHHHcCCeEEE
Confidence            6788999999999987 6688999999987777763   347889999 9999999999999987544

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 ....

>PTZ00090 40S ribosomal protein S11; Provisional

Probab=95.82  E-value=0.029  Score=49.81  Aligned_cols=73  Identities=15%  Similarity=0.052  Sum_probs=57.5

Q ss_pred             CCCeEEEEeccceEEEEEEecCCCe-EEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135           71 TKPRLSVFCSDKQLYAMLVDDQNKK-CLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL  147 (198)
Q Consensus        71 ~RPRLsVfRSNKHIYAQIIDD~~gk-TLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg  147 (198)
                      ++-+++|.-|-+++.++|.|..+.. ||+-+|+-...+++..   .++--||+ .+++.+|++|++.||..+-=.++|
T Consensus       117 ~~f~~vI~aSfNNTIVTlTD~~GNv~tl~WSSAG~~GFKGsK---KsTpfAAQ-~aae~aakka~~~GIk~V~V~vKG  190 (233)
T PTZ00090        117 DRFMLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKL---QQSERCAY-RIGENIAKKCRRLGIFAVDIKFRR  190 (233)
T ss_pred             CcEEEEEEeccCcEEEEEEeCCCCEEEEEEEcccccCcccCc---cCCHHHHH-HHHHHHHHHHHHcCCeEEEEEEeC
Confidence            4668999999999999999866664 6888888777777643   35667777 999999999999998766533443

>TIGR03632 bact_S11 30S ribosomal protein S11

Probab=95.59  E-value=0.064  Score=41.79  Aligned_cols=63  Identities=11%  Similarity=0.072  Sum_probs=51.6

Q ss_pred             EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      +-|+.|.+++.+.+.|. .|++++.+|+-...+++.   ..++.-||. .+++.+++++++.||..+.
T Consensus         3 ~hI~~s~NNT~itlTd~-~g~~~~~~S~G~~gfkg~---rk~t~~Aa~-~~a~~~~~~~~~~gi~~v~   65 (108)
T TIGR03632         3 AHIHATFNNTIVTITDP-QGNVLSWASAGAVGFKGS---KKSTPYAAQ-LAAEDAAKKAKEFGMKTVD   65 (108)
T ss_pred             EEEEccCCCEEEEEEcC-CCCEEEEEecCceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEE
Confidence            56899999999999986 566888888877777763   346778888 9999999999999987654

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.

>CHL00041 rps11 ribosomal protein S11

Probab=94.87  E-value=0.14  Score=40.52  Aligned_cols=65  Identities=9%  Similarity=0.058  Sum_probs=54.1

Q ss_pred             CeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           73 PRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        73 PRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      =-+-|+.|-+++.+.+-|. .|++|+.+|.-...+++.   ..++..||. .+++.++++|++.|+..+-
T Consensus        14 gi~hI~~t~NNTiiTlTd~-~G~~l~~~S~G~~gfKg~---rK~T~~Aa~-~~a~~~~~~~~~~gi~~v~   78 (116)
T CHL00041         14 GVIHIQASFNNTIVTVTDV-RGRVISWSSAGACGFKGA---RKGTPFAAQ-TAAENAIRTVIDQGMKRAE   78 (116)
T ss_pred             EEEEEEcccCCEEEEEEcC-CCCEEEEEecCceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEE
Confidence            3788999999999999985 578999999877777763   246778888 9999999999999987754

>PRK05309 30S ribosomal protein S11; Validated

Probab=94.49  E-value=0.21  Score=40.27  Aligned_cols=65  Identities=9%  Similarity=0.053  Sum_probs=53.6

Q ss_pred             CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135           72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT  141 (198)
Q Consensus        72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~  141 (198)
                      .-.+-|+-|.+++.+.+-| ..|++++..|.-...+++.   ..++..||. .+++.+++.|++.||..+
T Consensus        17 ~gi~hI~~t~NNTiitlTd-~~G~~~~~~S~G~~gfKg~---rK~T~~Aa~-~aa~~~~~~~~~~gi~~v   81 (128)
T PRK05309         17 SGVAHIHATFNNTIVTITD-RQGNVISWASAGGLGFKGS---RKSTPYAAQ-VAAEDAAKKAKEHGMKTV   81 (128)
T ss_pred             eeEEEEEccCCCEEEEEEc-CCCCEEEEEecCccEeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEE
Confidence            4589999999999999998 5678898888866667663   346778888 999999999999998643

>KOG0875 consensus 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis]

Probab=94.38  E-value=0.075  Score=47.97  Aligned_cols=76  Identities=9%  Similarity=-0.039  Sum_probs=58.1

Q ss_pred             CCCeEEEEeccceEEEEEEe--cCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHh-cChhHHHHhhhh
Q 029135           71 TKPRLSVFCSDKQLYAMLVD--DQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSR-LVLHLTLRKFHL  147 (198)
Q Consensus        71 ~RPRLsVfRSNKHIYAQIID--D~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAke-aGI~~~v~kyHg  147 (198)
                      .+.|+.|..+|+.|.+||+-  -+++.+++++-+-|..-++.. ..-.|-.||+ ..|-+||.|+++ .|.+.   .|-|
T Consensus        47 ~kyR~ivr~~n~~iicqi~~~~i~gd~v~~~a~s~elpkyg~~-~GLtNyaAay-~TglLLarR~l~~~gmD~---~yeg  121 (264)
T KOG0875|consen   47 PKYRMIVRVINKDIICQIAYATIEGDVIVRAAYAHELPKYGVK-VGLTNYAAAY-CTGLLLACRLLKRFGMDK---IYEG  121 (264)
T ss_pred             CceEEEEEEechhhHHHHHhheecceEEEEeeccccccccccc-cccchhHHHH-hhHHHHHHHHHHHhCccc---cccc
Confidence            58899999999999999994  356677888888888766643 3346889999 999999999874 45554   3554


Q ss_pred             eeeh
Q 029135          148 MIVM  151 (198)
Q Consensus       148 ~i~~  151 (198)
                      -..+
T Consensus       122 ~~e~  125 (264)
T KOG0875|consen  122 QVEV  125 (264)
T ss_pred             ceee
Confidence            4433

>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed

Probab=94.14  E-value=0.16  Score=41.57  Aligned_cols=70  Identities=7%  Similarity=-0.082  Sum_probs=55.4

Q ss_pred             eEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135           74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL  147 (198)
Q Consensus        74 RLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg  147 (198)
                      -+-|+-|-++.++.|-|..+.+||+.+|.-...+++.   ..++--||. ..++.++++|++.||..+-=+.+|
T Consensus        11 i~hI~as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~---kK~TpyAAq-~aae~~~~~~~~~Gi~~v~v~vkG   80 (132)
T PRK09607         11 IAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADR---DESSPYAAM-QAAEKAAEDAKEKGITGVHIKVRA   80 (132)
T ss_pred             EEEEEcccCCeEEEEEcCCCCEEEEEecCcceeeCCC---ccCCHHHHH-HHHHHHHHHHHHcCCcEEEEEEEe
Confidence            6789999999999999866667998888876666552   235666888 999999999999999877655544

>TIGR03628 arch_S11P archaeal ribosomal protein S11P

Probab=93.76  E-value=0.22  Score=39.84  Aligned_cols=69  Identities=7%  Similarity=-0.077  Sum_probs=53.6

Q ss_pred             EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHHHhhhh
Q 029135           75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTLRKFHL  147 (198)
Q Consensus        75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v~kyHg  147 (198)
                      +-|+-|-++..+.|-|..+..+|+.+|+-...+++..   .++--||. ...+.++++|++.||..+-=+.+|
T Consensus         5 ~hI~as~NNTiitvTD~~G~~~~~~~S~G~~g~kg~k---k~TpyAAq-~aa~~~~~~~~~~Gi~~v~v~ikG   73 (114)
T TIGR03628         5 AHIYSSFNNTIITITDITGAETIARSSGGMVVKADRD---ESSPYAAM-QAAGRAAEKAKERGITGLHIKVRA   73 (114)
T ss_pred             EEEEccCCCeEEEEEcCCCCEEEEEecCcceEeCCCc---cCCHHHHH-HHHHHHHHHHHHcCCcEEEEEEEe
Confidence            4578888999999998777788999888777776532   35667788 999999999999999866544443

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

>PTZ00129 40S ribosomal protein S14; Provisional

Probab=90.31  E-value=1.3  Score=37.03  Aligned_cols=67  Identities=9%  Similarity=0.025  Sum_probs=51.2

Q ss_pred             CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      .--+-|+-|-++....|-| ..|.+++..|+-...+++..  ..++--||. ...+.++++|++.||..+-
T Consensus        28 ~Gi~hI~as~NNTiItiTD-~~G~~~~w~SsG~~gfKg~r--~KsTpyAAq-~aa~~~a~k~~~~Gi~~v~   94 (149)
T PTZ00129         28 FGVAHIFASFNDTFIHVTD-LSGRETLVRVTGGMKVKADR--DESSPYAAM-MAAQDVAARCKELGINALH   94 (149)
T ss_pred             EEEEEEEcccCCeEEEEEc-ccCCEEEEEecCcceecccc--cCCCHHHHH-HHHHHHHHHHHHcCCeEEE
Confidence            3478899999999999987 55677777787666676522  135556788 9999999999999987653

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

Probab=82.18  E-value=3.1  Score=34.19  Aligned_cols=63  Identities=11%  Similarity=0.066  Sum_probs=45.7

Q ss_pred             EEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           75 LSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        75 LsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      .-|+.|-++....|- |..|+.+..+||=-..+++.-   .++--||. ..++..++.+++.||..+=
T Consensus        21 ahI~asfNNTivtit-D~~Gn~i~wassG~~gfk~~r---k~tpyAA~-~aa~~aa~~a~e~Gi~~v~   83 (129)
T COG0100          21 AHIHASFNNTIVTIT-DLTGNVIIWASSGGMGFKGSR---KSTPYAAQ-LAAEDAAKKAKEHGIKSVE   83 (129)
T ss_pred             EEEEcccCCcEEEec-CCCCCEEEEEecCCceEcCCC---CCCHHHHH-HHHHHHHHHHHHhCccEEE
Confidence            445556555555554 588899999999877777622   35556666 9999999999999987653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	198
3bbo_Q	161	Homology Model For The Spinach Chloroplast 50s Subu		6e-11
1ovy_A	120	Solution Structure Of Ribosomal Protein L18 From Ba		1e-06

>pdb|3BBO|Q Chain Q, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 161

Iteration: 1
 Score = 63.5 bits (153), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 41/65 (63%)
Query: 43  VVEARANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGST 102
           ++EA+A  R E    R+ RI+KK  GTP +PRL VF S+K LY  ++DD     L   ST
Sbjct: 36  IIEAKAKTRREDRTARHVRIRKKVEGTPERPRLCVFRSNKHLYVQVIDDSKMHTLASAST 95
Query: 103 LQQSI 107
           +Q+SI
Sbjct: 96  MQKSI 100

>pdb|1OVY|A Chain A, Solution Structure Of Ribosomal Protein L18 From Bacillus Stearothermophilus Length = 120

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 56  KIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQS 106
           K R+ RI+KK  GT  +PRLSVF S+K +YA ++DD     +   STL + 
Sbjct: 12  KKRHARIRKKIFGTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKE 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	198
3bbo_Q	161	Ribosomal protein L18; large ribosomal subunit, sp	9e-15
1ovy_A	120	50S ribosomal protein L18; ribosome; NMR {Geobacil	1e-12
2zjr_L	114	50S ribosomal protein L18; ribosome, large ribosom	1e-12
3v2d_S	112	50S ribosomal protein L18; ribosome associated inh	8e-11
3r8s_O	116	50S ribosomal protein L18; protein biosynthesis, R	2e-09

>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 161

 Score = 67.8 bits (166), Expect = 9e-15
 Identities = 37/106 (34%), Positives = 54/106 (50%), Gaps = 2/106 (1%)

Query: 7   AAALQFNACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEARANARTESAKIRNRRIQKKF 66
            A+L F    F  ++  P   LP     +  +    ++EA+A  R E    R+ RI+KK 
Sbjct: 2   CASLSFLQSAFASSQQLPL--LPKFAAAKPLLPSFPIIEAKAKTRREDRTARHVRIRKKV 59

Query: 67  NGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGN 112
            GTP +PRL VF S+K LY  ++DD     L   ST+Q+SI    +
Sbjct: 60  EGTPERPRLCVFRSNKHLYVQVIDDSKMHTLASASTMQKSISEELD 105

>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus stearothermophilus} SCOP: c.55.4.1 Length = 120

 Score = 61.1 bits (149), Expect = 1e-12
 Identities = 24/62 (38%), Positives = 34/62 (54%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           R    K R+ RI+KK  GT  +PRLSVF S+K +YA ++DD     +   STL +    +
Sbjct: 7   RNAVRKKRHARIRKKIFGTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFGLD 66

Query: 111 GN 112
             
Sbjct: 67  ST 68

>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 Length = 114

 Score = 60.7 bits (148), Expect = 1e-12
 Identities = 19/63 (30%), Positives = 28/63 (44%)

Query: 48  ANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSI 107
           A A T   K+R RR  +       + RLSV+ S K +YA ++DD   + L   S+     
Sbjct: 2   ATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKS 61

Query: 108 RGN 110
              
Sbjct: 62  GNK 64

>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 ... Length = 112

 Score = 55.6 bits (135), Expect = 8e-11
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 50  ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRG 109
           AR  + + R  R++ +   T  + RLSVF S K +YA ++DD+    L   S+L   ++G
Sbjct: 2   ARLTAYERRKFRVRNRIKRTG-RLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLKG 60

Query: 110 N 110
           N
Sbjct: 61  N 61

>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 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 2i2v_O ... Length = 116

 Score = 52.2 bits (126), Expect = 2e-09
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           +  +   R  R ++K        RL V  + + +YA ++     + L   ST++++I   
Sbjct: 2   KKSARIRRATRARRKLQELG-ATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQ 60

Query: 111 GN 112
             
Sbjct: 61  LK 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	198
3bbo_Q	161	Ribosomal protein L18; large ribosomal subunit, sp	100.0
3r8s_O	116	50S ribosomal protein L18; protein biosynthesis, R	100.0
3v2d_S	112	50S ribosomal protein L18; ribosome associated inh	100.0
1ovy_A	120	50S ribosomal protein L18; ribosome; NMR {Geobacil	100.0
2zjr_L	114	50S ribosomal protein L18; ribosome, large ribosom	99.97
1vq8_N	187	50S ribosomal protein L18P; ribosome 50S, protein-	99.93
3j21_O	203	50S ribosomal protein L18P; archaea, archaeal, KIN	99.92
2zkr_n	297	60S ribosomal protein L5; protein-RNA complex, 60S	99.82
4a17_M	301	RPL5, 60S ribosomal protein L5; eukaryotic ribosom	99.8
3u5e_D	297	60S ribosomal protein L5; translation, ribosome, r	99.8
3iz5_Q	304	60S ribosomal protein L5 (L18P); eukaryotic riboso	99.62
3bbn_K	140	Ribosomal protein S11; small ribosomal subunit, sp	95.86
2vqe_K	129	30S ribosomal protein S11, 30S ribosomal protein S	95.86
3j20_M	137	30S ribosomal protein S11P; archaea, archaeal, KIN	95.22
3r8n_K	117	30S ribosomal protein S11; protein biosynthesis, R	94.66
2xzm_K	151	RPS14E; ribosome, translation; 3.93A {Tetrahymena	91.83
3u5c_O	137	RP59A, 40S ribosomal protein S14-A; translation, r	89.5

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

Probab=100.00  E-value=1.2e-39  Score=268.19  Aligned_cols=142  Identities=27%  Similarity=0.328  Sum_probs=103.8

Q ss_pred             cccccCCCCCccccccCCccccccccchhhhhhh-hcchHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecC
Q 029135           14 ACDFFGTKAKPFNLLPSQTQRRSFILKPLVVEAR-ANARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQ   92 (198)
Q Consensus        14 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~a~-~~~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~   92 (198)
                      .+.+|++++.++...+.+. ...  ..++.+||+ .++|++.|.+||+|+|+||.||+++|||+|||||+|||||||||+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~k~~~R~rR~~RiR~ki~gt~~rPRL~V~rSnkhIyAQvIdd~   85 (161)
T 3bbo_Q            9 QSAFASSQQLPLLPKFAAA-KPL--LPSFPIIEAKAKTRREDRTARHVRIRKKVEGTPERPRLCVFRSNKHLYVQVIDDS   85 (161)
T ss_dssp             ----------------------------------CCCCCCCCGGGTSCCSCSGGGGSSSCCCCEEEECSSCEEEEEECCT
T ss_pred             HHhhccccccccccccCCC-CCC--CCceeeEeeccCchHHHHHHHHHHHHHhhccCCCCCEEEEEecCCeEEEEEEECC
Confidence            3345566655554444331 111  124555666 778989999999999999999999999999999999999999999


Q ss_pred             CCeEEEEEechhhhhcCCCC-CCCCCHHHHHHHHHHHHHHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135           93 NKKCLFFGSTLQQSIRGNGN-PPCSTIFPLSRKLLSVLVKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus        93 ~gkTLaSASTlek~lk~~l~-~~~~NieAA~~~VGklLAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      +|+||++|||+|+++++.++ ++++|+++|+ +||++|||+|+++||++++     ++|||+|..+++-.||-
T Consensus        86 ~g~tLasASTlek~lk~~l~~g~~~n~~AA~-~VG~liAeRA~e~GI~~VvFDRgg~~YhGRVkAladaaRe~  157 (161)
T 3bbo_Q           86 KMHTLASASTMQKSISEELDYSSSPTIEVAK-KVGEVIASACLEKGITKVAFDRGGYPYHGRVKALADAAREK  157 (161)
T ss_dssp             TSCEEEEEEHHHHHHHHCCTTCCSSSHHHHH-HHHHHSSSHHHHTSSCCCCCCCSSSCSSSTTHHHHHHHTTT
T ss_pred             CCEEEEEEeCCcHHHHhhccccCCCCHHHHH-HHHHHHHHHHHHCCCCEEEEeCCCCcchHHHHHHHHHHHHh
Confidence            99999999999999985431 2579999999 9999999999999999999     89999999999999874

>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=100.00  E-value=2.3e-36  Score=236.36  Aligned_cols=106  Identities=14%  Similarity=0.144  Sum_probs=100.8

Q ss_pred             hHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLV  130 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLA  130 (198)
                      |++.|.+|++|+|+||.| +++|||+||+||+|||||||||++|+||+||||+|+++++++ .+++|++||+ .||++||
T Consensus         2 ~~~~r~~r~~r~R~ki~~-~~rpRL~V~rSnkhIyAQiidd~~g~tlasAST~e~~~~~~~-~~~~n~~AA~-~vG~llA   78 (116)
T 3r8s_O            2 KKSARIRRATRARRKLQE-LGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQL-KYTGNKDAAA-AVGKAVA   78 (116)
T ss_dssp             HHHHHHHHHHHHHHHHHT-TTCCEEEEEECSSCEEEEEECTTSSCEEEECCSSSHHHHTTC-SCSSSHHHHH-HHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhcc-CCCCEEEEEEeCCEEEEEEEEcCCCeEEEEEeeCchhhcccc-CCCCCHHHHH-HHHHHHH
Confidence            677899999999999999 799999999999999999999999999999999999999987 6789999999 9999999


Q ss_pred             HHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          131 KSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       131 erAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ++|+++||++++     ++|||+|.-+++-.||.
T Consensus        79 ~Ral~~GI~~vvfDrgg~~yhGrV~Ala~~are~  112 (116)
T 3r8s_O           79 ERALEKGIKDVSFDRSGFQYHGRVQALADAAREA  112 (116)
T ss_dssp             HHHHTTTCCCCEEECTTSCSSSHHHHHHHHHHHT
T ss_pred             HHHHHCCCCEEEEecCCCcccHHHHHHHHHHHHh
Confidence            999999999999     89999999999998874

>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=100.00  E-value=1.8e-35  Score=230.92  Aligned_cols=102  Identities=25%  Similarity=0.271  Sum_probs=95.9

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL  129 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL  129 (198)
                      +|++.|.+|++|+|+||+||+ +|||+||+||+|||||||||++|+||+||||+|++++      ++|++||+ +||++|
T Consensus         2 ~~~~~r~~r~~r~r~ki~gt~-rpRL~V~rSnkhiyAQiidd~~~~tlasAsT~e~~~k------~~n~~AA~-~vG~ll   73 (112)
T 3v2d_S            2 ARLTAYERRKFRVRNRIKRTG-RLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLK------GNKTEVAR-QVGRAL   73 (112)
T ss_dssp             -CCCHHHHHHHHHHHHHHHTC-CCEEEEEECSSCEEEEEEETTTTEEEEEEETTTTTCC------CCHHHHHH-HHHHHH
T ss_pred             ChHHHHHHHHHHHHHHhcCCC-CCEEEEEEeCCeEEEEEEecCCCeEEEEEEecchhcc------CCCHHHHH-HHHHHH
Confidence            567789999999999999998 9999999999999999999999999999999999974      37999999 999999


Q ss_pred             HHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      |++|+++||++++     ++|||+|.-+++-.||.
T Consensus        74 A~ra~~~GI~~vvfDrgg~~yhGrV~Ala~~are~  108 (112)
T 3v2d_S           74 AEKALALGIKQVAFDRGPYKYHGRVKALAEGAREG  108 (112)
T ss_dssp             HHHHHTTTCCBCEEECTTSCSCSSTTHHHHHHHHT
T ss_pred             HHHHHHCCCCEEEEecCCCcccHHHHHHHHHHHHc
Confidence            9999999999999     89999999999998874

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

Probab=100.00  E-value=1.8e-35  Score=233.02  Aligned_cols=106  Identities=28%  Similarity=0.366  Sum_probs=83.2

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVL  129 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklL  129 (198)
                      +|++.|.+||+|+|+||+||+++|||+||+||+|||||||||++|+||+||||+|++++  + .+++|++||+ .||++|
T Consensus         6 ~~~~~r~~r~~R~r~ki~gt~~rpRL~V~rSnkhIyAQiidd~~~~tl~sAsT~e~~~~--~-~~~~n~~AA~-~vG~ll   81 (120)
T 1ovy_A            6 DRNAVRKKRHARIRKKIFGTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFG--L-DSTNNIEAAK-KVGELV   81 (120)
T ss_dssp             ------------------CCSSCCSEEEEEETTEEEEEEECCSSCCCEEEESTTSTTTC--S-SCTTSHHHHH-HHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcCCCCCCEEEEEEeCCeEEEEEEEcCCCEEEEEEecCchhhC--c-CCCCcHHHHH-HHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999986  3 4578999999 999999


Q ss_pred             HHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          130 VKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       130 AerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      |++|+++||++++     ++|||+|.-+++-.||.
T Consensus        82 A~Ral~~GI~~vvfDrgg~~yhgrV~ala~~are~  116 (120)
T 1ovy_A           82 AKRALEKGIKQVVFDRGGYLYHGRVKALADAAREA  116 (120)
T ss_dssp             HHHHHHHSSSCCCCCSTTCSSCSSTHHHHHHHHHH
T ss_pred             HHHHHHCCCCEEEEecCCccccHHHHHHHHHHHHh
Confidence            9999999999998     89999999999988874

>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=99.97  E-value=2.2e-33  Score=219.67  Aligned_cols=100  Identities=22%  Similarity=0.258  Sum_probs=89.4

Q ss_pred             HHHHHHHHHHHHhhhcCC---CCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHH
Q 029135           52 TESAKIRNRRIQKKFNGT---PTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSV  128 (198)
Q Consensus        52 ~e~R~rR~rRiRkKI~GT---a~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGkl  128 (198)
                      +++|.+|++|+|+||+||   +++|||+||+||+|||||||||++|+||+||||+|  + +    +++|++||+ .||++
T Consensus         3 ~~~r~~r~~r~r~ki~gt~~~~~rpRL~V~rSnkhIyAQiidd~~~~tl~sAST~e--l-~----~~~n~~AA~-~vG~l   74 (114)
T 2zjr_L            3 TATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAA--L-K----SGNKTDTAA-AVGKA   74 (114)
T ss_dssp             -----CHHHHHHHHHHSCSTTTCSEEECCCTTSSCCCCCEEETTTTEECCCCCSCS--C-C----TTCSSSSHH-HHHHH
T ss_pred             hHHHHHHHHHHHhhhccccCCCCCCEEEEEEeCCeEEEEEEEcCCCEEEEEEEchH--h-c----CCCCHHHHH-HHHHH
Confidence            457789999999999999   99999999999999999999999999999999999  3 2    358999999 99999


Q ss_pred             HHHHHHhcChhHHH-----Hhhhheeehhhhhhhcc
Q 029135          129 LVKSLSRLVLHLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       129 LAerAkeaGI~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      |||+|+++||++++     ++|||+|.-+++-.||.
T Consensus        75 lA~Ral~~GI~~vvfDrgg~~yhgrV~Ala~~are~  110 (114)
T 2zjr_L           75 LAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREG  110 (114)
T ss_dssp             HHHHHHTTCCCCCEECCCSSCSCSHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCEEEEecCCccccHHHHHHHHHHHHh
Confidence            99999999999998     89999999999988863

>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=99.93  E-value=9.1e-27  Score=195.34  Aligned_cols=105  Identities=14%  Similarity=0.036  Sum_probs=93.9

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLS  127 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGk  127 (198)
                      .|+|.++.+++|.|..+.   ++|||+||+||+|||||||  ||++|+||+||||+|++-.++. .+++|++||+ .||+
T Consensus        13 rrregkTdy~~R~rl~~~---~rpRL~V~rSnkhIyAQII~~dd~~~~tlasAsT~e~~k~~~k-~~~~N~~AA~-~vG~   87 (187)
T 1vq8_N           13 RRREARTDYHQRLRLLKS---GKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYGWE-APTGNMPSAY-LTGL   87 (187)
T ss_dssp             HHHTTCCCHHHHHHHHTT---CSCEEEEEECSSCEEEEEEECCTTSCEEEEEEESGGGGGGTCC-SCSSSHHHHH-HHHH
T ss_pred             chhccchhHHHHHHHHhc---CCCEEEEEEeCCcEEEEEEEecCCCCEEEEEEEccchhccccc-cCCCcHHHHH-HHHH
Confidence            356677788999987774   7999999999999999999  9999999999999999932443 3578999999 9999


Q ss_pred             HHHHHHHhcChhHHH-----Hhhh--heeehhhhhhhcc
Q 029135          128 VLVKSLSRLVLHLTL-----RKFH--LMIVMAPVVVREC  159 (198)
Q Consensus       128 lLAerAkeaGI~~~v-----~kyH--g~i~~~~~~~~~~  159 (198)
                      +||+||+++||++++     ++||  |+|.-+++-.|+.
T Consensus        88 llA~Ral~kGI~~vvfDrgg~~yh~GgRV~Ala~gAre~  126 (187)
T 1vq8_N           88 LAGLRAQEAGVEEAVLDIGLNSPTPGSKVFAIQEGAIDA  126 (187)
T ss_dssp             HHHHHHHHTTCCBCEEECTTSCCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCCEEEEcCCCceeccchHHHHHHHHhhcC
Confidence            999999999999998     9999  9999999999986

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

Probab=99.92  E-value=1e-26  Score=197.09  Aligned_cols=105  Identities=14%  Similarity=0.036  Sum_probs=94.4

Q ss_pred             chHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEe--cCCCeEEEEEechhhhh-cCCCCCCCCCHHHHHHHHH
Q 029135           50 ARTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVD--DQNKKCLFFGSTLQQSI-RGNGNPPCSTIFPLSRKLL  126 (198)
Q Consensus        50 ~K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIID--D~~gkTLaSASTlek~l-k~~l~~~~~NieAA~~~VG  126 (198)
                      .|++.+++|++|.|.++.   ++|||+||+||+||||||||  |++|+||+||||+|+++ .+|. .+++|++||+ .||
T Consensus        13 rRregkt~y~~R~rl~~~---~kpRL~V~rSnkhIyAQIId~d~~g~~tLasAST~El~lk~g~~-~~~~N~~AA~-~vG   87 (203)
T 3j21_O           13 RRREGKTNYRKRLKLLKS---GKPRLVVRKSLNHHIAQIIVYDPKGDRTLVSAHTRELIRDFGWK-GHCGNTPSAY-LLG   87 (203)
T ss_dssp             HHHHTCCCHHHHHHHHTT---CCCEEEEEECSSCEEEEEEECCTTSCEEEEEECSTTTSSSSSCC-SCTTSHHHHH-HHH
T ss_pred             hHHHHhHHHHHHHHHHhc---CCCEEEEEEeCCeEEEEEEEecCCCCeEEEEEEccchhhhhccc-CCCCcHHHHH-HHH
Confidence            466777889999998877   59999999999999999997  88899999999999985 4665 5678999999 999


Q ss_pred             HHHHHHHHhcChhHHH-----Hhh--hheeehhhhhhhcc
Q 029135          127 SVLVKSLSRLVLHLTL-----RKF--HLMIVMAPVVVREC  159 (198)
Q Consensus       127 klLAerAkeaGI~~~v-----~ky--Hg~i~~~~~~~~~~  159 (198)
                      ++||+||+++||+.++     ++|  ||+|.-+++-.|+.
T Consensus        88 ~llA~Ral~kGI~~vvfDrgg~~y~~hgRV~Ala~gAre~  127 (203)
T 3j21_O           88 LLIGYKAKQAGIEEAILDIGLHPPVRGSSVFAVLKGAVDA  127 (203)
T ss_dssp             HHSSSSTTSSCCCCCEEECCSSCCCTTSHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCEEEEecCcceeccCcchhhhhhhcccC
Confidence            9999999999999998     788  89999999988875

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

Probab=99.82  E-value=4.2e-21  Score=170.33  Aligned_cols=107  Identities=9%  Similarity=-0.052  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHHHhhhcCC----CCCCeEEEEeccceEEEEEEecC--CCeEEEEEechhhhhcCCCCCCCCCHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNGT----PTKPRLSVFCSDKQLYAMLVDDQ--NKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRK  124 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~GT----a~RPRLsVfRSNKHIYAQIIDD~--~gkTLaSASTlek~lk~~l~~~~~NieAA~~~  124 (198)
                      |.|.++.++.|.|.-+.+.    ..+|||+||+||+|||||||||.  +|+||+||||+|++-.++. ..++|.+||+ .
T Consensus        23 RReGKTdY~~R~rLi~qdknkynt~kpRLvVrrSNk~I~aQII~~~~~gd~tLasAsS~El~kyg~k-~g~tN~aAAy-~  100 (297)
T 2zkr_n           23 RREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGDMIVCARYAHELPKYGVK-VGLTNYAAAY-C  100 (297)
T ss_dssp             HHTTCSCHHHHHHHHCCCSTTCSCCSEEEEEEEETTEEEEEEEECCSSSCEEEEEEEGGGGGGTCCC-SCSSSHHHHH-H
T ss_pred             hccccchHHHHHHHHhcCCcccCCCCceEEEEEecCcEEEEEEeccCCCCEEEEEeecCcccccccc-cCCCcHHHHH-H
Confidence            3445566777877766653    25799999999999999999987  9999999999999844554 3568999999 9


Q ss_pred             HHHHHHHHHHhc---------------------------ChhHHH-----Hhh--hheeehhhhhhhcc
Q 029135          125 LLSVLVKSLSRL---------------------------VLHLTL-----RKF--HLMIVMAPVVVREC  159 (198)
Q Consensus       125 VGklLAerAkea---------------------------GI~~~v-----~ky--Hg~i~~~~~~~~~~  159 (198)
                      +|.+||+||+++                           ||..++     +.|  ||||.-+++-.|+-
T Consensus       101 tGlLlArRal~k~~ld~~y~G~~e~~g~~~~ve~~~~~~gi~~vvfDrGl~ryttggRVfa~akGArDg  169 (297)
T 2zkr_n          101 TGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDG  169 (297)
T ss_dssp             HHHHHHHHHHCCCSCCCCCSSCCSSSSCCCCCSSSCSSSCCCBEEEECTTSCCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhccchhhcCccccccccccccccccCCCceEEEEecCCcccCCCchHHHHHHHHHhc
Confidence            999999999999                           888777     899  99999998888874

>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=99.80  E-value=3.8e-20  Score=164.51  Aligned_cols=84  Identities=14%  Similarity=0.088  Sum_probs=71.7

Q ss_pred             hHHHHHHHHHHHHhhhcCC----CCCCeEEEEeccceEEEEEEec--CCCeEEEEEechhhhhcCCCCCCCCCHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNGT----PTKPRLSVFCSDKQLYAMLVDD--QNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRK  124 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~GT----a~RPRLsVfRSNKHIYAQIIDD--~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~  124 (198)
                      |.|.++.+..|.|.-+.+.    +.+|||+|||||+|||||||||  ++|+||+||||+|++.++|. ..++|++||+ +
T Consensus        23 RReGKTdY~~R~rlv~qdknKynspkpRLvV~rSNrhIyAQIIdd~~~Gd~tLaSASS~El~~~g~k-~~~~N~~AAy-~  100 (301)
T 4a17_M           23 RREGLTDYYARKRLIIQDKDKYNTPKYRLVARATNTRIIAQIVYATLKCDRVLCAADSYELKRFGVS-TGLASYAAAY-A  100 (301)
T ss_dssp             HHTTCCCHHHHHHHHCCCTTSCSCCCEEEEEEECSSCEEEEEEEECSSCEEEEEEEETTHHHHTTCC-SCTTSHHHHH-H
T ss_pred             cccccccHHHHHHHHHccccccCCCCceEEEEEcCCeEEEEEeecCCCCCEEEEEEeeccchhcccc-CCCCcHHHHH-H
Confidence            3445566778877777652    3699999999999999999998  68899999999999987765 4678999999 9


Q ss_pred             HHHHHHHHHHhc
Q 029135          125 LLSVLVKSLSRL  136 (198)
Q Consensus       125 VGklLAerAkea  136 (198)
                      ||.+||+||+++
T Consensus       101 vG~LiAeRAl~k  112 (301)
T 4a17_M          101 TGLLLARRLLKQ  112 (301)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999999999

>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=99.80  E-value=5e-20  Score=163.49  Aligned_cols=88  Identities=11%  Similarity=0.010  Sum_probs=75.0

Q ss_pred             hHHHHHHHHHHHHhhhcC----CCCCCeEEEEeccceEEEEEEec--CCCeEEEEEechhhhhcCCCCCCCCCHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNG----TPTKPRLSVFCSDKQLYAMLVDD--QNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRK  124 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~G----Ta~RPRLsVfRSNKHIYAQIIDD--~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~  124 (198)
                      |.|.++.+..|.|.-+..    -..+|||+|||||+|||||||||  ++|+||+||||+|++.++|. ..++|++||+ +
T Consensus        23 RReGKTdY~~R~rLi~qdknKynt~kpRLvV~rSNrhIyAQIIdd~~~Gd~tLaSASS~El~k~g~k-~~~~N~~AAy-~  100 (297)
T 3u5e_D           23 RREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGIT-HGLTNWAAAY-A  100 (297)
T ss_dssp             TTTTCCCHHHHHHHHCCCGGGTTCCCCEEEEEEETTEEEEEEEECCTTCCEEEEEEEGGGGGGGTCC-SCTTSHHHHH-H
T ss_pred             hccccccHHHHHHHHHccccccCCCCceEEEEEcCCeEEEEEeecCCCCCEEEEEEeecchhhcccC-CCCCcHHHHH-H
Confidence            456667777787766653    13699999999999999999998  79999999999999877765 4578999999 9


Q ss_pred             HHHHHHHHHHhc--------ChhH
Q 029135          125 LLSVLVKSLSRL--------VLHL  140 (198)
Q Consensus       125 VGklLAerAkea--------GI~~  140 (198)
                      ||.+||+||+++        |+++
T Consensus       101 vG~LiAeRAl~k~~ld~~y~G~~e  124 (297)
T 3u5e_D          101 TGLLIARRTLQKLGLDETYKGVEE  124 (297)
T ss_dssp             HHHHHHHHHHHHTSTTSSCCCCSS
T ss_pred             HHHHHHHHHHHhhCCcccccCccc
Confidence            999999999999        7776

>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=95.86  E-value=0.01  Score=47.65  Aligned_cols=65  Identities=14%  Similarity=0.122  Sum_probs=55.2

Q ss_pred             CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhH
Q 029135           71 TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHL  140 (198)
Q Consensus        71 ~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~  140 (198)
                      ..+.+-|+-|-+++.+.|-| .+|+++..+|+-...+++.   ..++-.||. .+++.++++|++.||..
T Consensus        28 ~~gi~hI~as~NNTivtiTD-~~G~~i~~~SaG~~GfKg~---rksTp~AA~-~aa~~~~~~a~e~Gi~~   92 (140)
T 3bbn_K           28 PKGVIHVQASFNNTIVTVTD-VRGRVVSWASAGTCGFRGT---KRGTPFAAQ-TAAGNAIRTVVEQGMQR   92 (140)
T ss_dssp             CCCEEEEEECSSCEEEEEEC-SSSCEEEEEETTTSSCCTT---SCSSHHHHH-HHHTSGGGTSTTTCCCE
T ss_pred             eeeEEEEEecCCCEEEEEEc-CCCCEEEEEeccceeEccc---ccCCHHHHH-HHHHHHHHHHHHhCCeE
Confidence            57899999999999999987 6678899989877777763   357888999 99999999999999754

>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=95.86  E-value=0.017  Score=45.62  Aligned_cols=65  Identities=11%  Similarity=0.031  Sum_probs=54.9

Q ss_pred             CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhH
Q 029135           71 TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHL  140 (198)
Q Consensus        71 ~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~  140 (198)
                      ..+.+-|+-|-++..+.|-| ..|+++..+|+-...+++.   ..++-.||. .+++.++++|++.||..
T Consensus        15 ~~gi~hI~as~NNTivtiTd-~~G~~~~~~SaG~~gfKg~---rk~tp~AA~-~aa~~~~~~~~~~Gi~~   79 (129)
T 2vqe_K           15 ASGRAYIHASYNNTIVTITD-PDGNPITWSSGGVIGYKGS---RKGTPYAAQ-LAALDAAKKAMAYGMQS   79 (129)
T ss_dssp             SEEEEEEEECSSCEEEEEEC-TTSCEEEECCTTTTTCCSG---GGGSHHHHH-HHHHHHHHHHHTTTCCE
T ss_pred             cceEEEEEecCCCEEEEEEc-CCCCEEEEEeccceeEcCC---CcCCHHHHH-HHHHHHHHHHHHhCCeE
Confidence            46899999999999999987 6678888889887777763   246788999 99999999999998754

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

Probab=95.22  E-value=0.077  Score=42.38  Aligned_cols=66  Identities=5%  Similarity=-0.185  Sum_probs=54.3

Q ss_pred             CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135           72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT  141 (198)
Q Consensus        72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~  141 (198)
                      ...+-|+-|-++..+.|-|..+.++|+.+|.-...+++.   ..++-.||. ..++.++++|++.||..+
T Consensus        14 ~gi~hI~asfNNTivtiTD~~G~~~i~~~S~G~~gfkg~---~ksTp~AA~-~aa~~~~~~a~e~Gi~~v   79 (137)
T 3j20_M           14 WGIAHIYSSFNNTIIHITDITGAETISRWSGGMVVKADR---DEPSPYAAM-LAARRAAEEALEKGIVGV   79 (137)
T ss_dssp             EEEEEEEECSSCEEEEEEESSSCSEEEEEEGGGTCSCTT---TSSSHHHHH-HHHHHHHHHHHHHTEEEE
T ss_pred             ceEEEEEcCCCCEEEEEEcCCCCEEEEEEccceeeecCC---ccCCHHHHH-HHHHHHHHHHHHcCCeEE
Confidence            567889999999999999877667999988877766652   246778888 999999999999987654

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

Probab=91.83  E-value=0.2  Score=40.63  Aligned_cols=65  Identities=8%  Similarity=0.042  Sum_probs=48.9

Q ss_pred             CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhH
Q 029135           72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHL  140 (198)
Q Consensus        72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~  140 (198)
                      ...+-|+-|-++..+.|-|..+..++..+|.- ..+++  +...++-.||. ..++.++++|++.||..
T Consensus        28 ~gi~hI~asfNNTiVtiTD~~G~~~~~~ssgg-~~~k~--~r~ksTpyAAq-~aa~~~a~~a~e~Gi~~   92 (151)
T 2xzm_K           28 FGVCHIMATWNDTFIHVTDLSGRETLVRVTGG-MKVKA--DREESSPYAAM-QAAIDVVNRCKELKINA   92 (151)
T ss_dssp             EEEEEEEBCSSCBCCEEECTTCCSEEEECCHH-HHCSS--GGGGSCHHHHH-HHHHHHHHHHHHHTCCE
T ss_pred             eeEEEEEccCCCEEEEEECCCCCEEEEEecCc-ceEeC--CCCcCCHHHHH-HHHHHHHHHHHHcCCeE
Confidence            57899999999999999987766677665443 33332  11246778888 99999999999999854

>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=89.50  E-value=0.27  Score=39.21  Aligned_cols=66  Identities=8%  Similarity=-0.007  Sum_probs=48.4

Q ss_pred             CCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhH
Q 029135           71 TKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHL  140 (198)
Q Consensus        71 ~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~  140 (198)
                      ....+-||-|-++.++.|-|..+ +++...|+-...+++.-  ..++--||. ..++.++++|++.||..
T Consensus        13 ~~gi~hI~asfNNTivtvTD~~G-~~~~~~ssG~~gfKg~r--~ksTpyAAq-~aa~~~a~~a~e~Gi~~   78 (137)
T 3u5c_O           13 VFGVARIYASFNDTFVHVTDLSG-KETIARVTGGMKVKADR--DESSPYAAM-LAAQDVAAKCKEVGITA   78 (137)
T ss_dssp             CEEECCEEEETTEEEECCEETTS-SSCCCCCBTTTTSCCST--TTTCHHHHH-HHHHHHHHHHHHHTCCE
T ss_pred             eeEEEEEEccCCCEEEEEEcCCC-CEEEEEeCCCcEEeCCc--ccCCHHHHH-HHHHHHHHHHHHcCCeE
Confidence            35577799999999999998554 44444455544666521  136777888 99999999999999765

---

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	198
d1ovya_	97	c.55.4.1 (A:) Ribosomal protein L18 (L18p) {Bacill	3e-08
d2zjrl1	104	c.55.4.1 (L:8-111) Ribosomal protein L18 (L18p) {D	6e-08
d2gycm1	113	c.55.4.1 (M:3-115) Ribosomal protein L18 (L18p) {E	3e-07
d2j01s1	86	c.55.4.1 (S:23-108) Ribosomal protein L18 (L18p) {	1e-06
d1vqon1	186	c.55.4.1 (N:1-186) Ribosomal protein L18 (L18p) {A	3e-05

>d1ovya_ c.55.4.1 (A:) Ribosomal protein L18 (L18p) {Bacillus stearothermophilus [TaxId: 1422]} Length = 97

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]

 Score = 47.5 bits (113), Expect = 3e-08
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 68  GTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLS 127
           GT  +PRLSVF S+K +YA ++DD     +   STL +    +          +   +  
Sbjct: 1   GTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFGLDSTNNIEAAKKVGELVAK 60

Query: 128 VLV-KSLSRLVLHLTLRKFH 146
             + K + ++V       +H
Sbjct: 61  RALEKGIKQVVFDRGGYLYH 80

>d2zjrl1 c.55.4.1 (L:8-111) Ribosomal protein L18 (L18p) {Deinococcus radiodurans [TaxId: 1299]} Length = 104

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]

 Score = 46.8 bits (111), Expect = 6e-08
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 56 KIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLF 98
          K+R RR  +       + RLSV+ S K +YA ++DD   + L 
Sbjct: 3  KLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLA 45

>d2gycm1 c.55.4.1 (M:3-115) Ribosomal protein L18 (L18p) {Escherichia coli [TaxId: 562]} Length = 113

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]

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 51  RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           +  +   R  R ++K        RL V  + + +YA ++     + L   ST++++I   
Sbjct: 1   KKSARIRRATRARRKLQELG-ATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQ 59

Query: 111 GN 112
             
Sbjct: 60  LK 61

>d2j01s1 c.55.4.1 (S:23-108) Ribosomal protein L18 (L18p) {Thermus thermophilus [TaxId: 274]} Length = 86

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]

 Score = 42.8 bits (101), Expect = 1e-06
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 72  KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGN 110
           + RLSVF S K +YA ++DD+    L   S+L   ++GN
Sbjct: 1   RLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLKGN 39

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

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]

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 59  NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGN 110
           +   + +   +  KPRL    S+K + A LV         L    +   +  G 
Sbjct: 19  DYHQRLRLLKSG-KPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYGW 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	198
d2gycm1	113	Ribosomal protein L18 (L18p) {Escherichia coli [Ta	100.0
d1ovya_	97	Ribosomal protein L18 (L18p) {Bacillus stearotherm	99.97
d2zjrl1	104	Ribosomal protein L18 (L18p) {Deinococcus radiodur	99.96
d2j01s1	86	Ribosomal protein L18 (L18p) {Thermus thermophilus	99.96
d1vqon1	186	Ribosomal protein L18 (L18p) {Archaeon Haloarcula	99.91
d2uubk1	119	Ribosomal protein S11 {Thermus thermophilus [TaxId	95.78
d2qalk1	117	Ribosomal protein S11 {Escherichia coli [TaxId: 56	94.88

>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=100.00  E-value=3.2e-36  Score=233.02  Aligned_cols=105  Identities=14%  Similarity=0.146  Sum_probs=98.9

Q ss_pred             hHHHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHH
Q 029135           51 RTESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLV  130 (198)
Q Consensus        51 K~e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLA  130 (198)
                      |++.|.+|+.|+|++|.|++ +|||+|||||+|||||||||.+++||+++||+|+++++++ +.++|+++|+ +||++||
T Consensus         1 k~~~r~rR~~R~R~ki~~~~-~pRL~V~rSnkhiyaQiIdd~~~~tl~saST~~k~~~~~~-~~~~n~~aA~-~vG~~la   77 (113)
T d2gycm1           1 KKSARIRRATRARRKLQELG-ATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQL-KYTGNKDAAA-AVGKAVA   77 (113)
T ss_dssp             CCCCHHHHTTCSCSTTTTTT-CCCCBEEECSSCEEEEEEETTTTEEEEEEETTGGGGTSCC-SCSSSHHHHH-HHHHHHH
T ss_pred             ChHHHHHHHHHHHHHhccCC-CCeEEEEEeCCcEEEEEEEccCCcEEEEeeehhhhhhhhc-CCCcchHHHH-HHHHHHH
Confidence            34568899999999999985 6999999999999999999999999999999999999877 6789999999 9999999


Q ss_pred             HHHHhcChhHHH-----Hhhhheeehhhhhhhc
Q 029135          131 KSLSRLVLHLTL-----RKFHLMIVMAPVVVRE  158 (198)
Q Consensus       131 erAkeaGI~~~v-----~kyHg~i~~~~~~~~~  158 (198)
                      |+|+++||++++     ++|||+|..++|-.||
T Consensus        78 ~ra~~~gI~~vvfDR~g~~YhGrVka~ad~aRe  110 (113)
T d2gycm1          78 ERALEKGIKDVSFDRSGFQYHGRVQALADAARE  110 (113)
T ss_dssp             HHHHHHTCCCCCCBCCSCCSSSHHHHHHHHHHH
T ss_pred             HHHHHCCCCEEEECCCCCccchHHHHHHHHHHH
Confidence            999999999999     9999999999999987

>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=99.97  E-value=8e-32  Score=202.92  Aligned_cols=87  Identities=26%  Similarity=0.351  Sum_probs=82.1

Q ss_pred             CCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH-----
Q 029135           68 GTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL-----  142 (198)
Q Consensus        68 GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v-----  142 (198)
                      ||++||||+|||||+|||||||||.+|+||+++||++++++.   ...+|+++|+ +||++||++|+++||++++     
T Consensus         1 gt~~rpRL~V~kSnkhiyaQlIdd~~~~tl~s~St~~k~~~~---~~~~n~~aA~-~vG~~~a~kak~~gi~~vvfDr~g   76 (97)
T d1ovya_           1 GTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFGL---DSTNNIEAAK-KVGELVAKRALEKGIKQVVFDRGG   76 (97)
T ss_dssp             CCSSCCSEEEEEETTEEEEEEECCSSCCCEEEESTTSTTTCS---SCTTSHHHHH-HHHHHHHHHHHHHSSSCCCCCSTT
T ss_pred             CCCCCCEEEEEEeCCeEEEEEEEcCCCeEEEEecchhhhhcc---cccCcHHHHH-HHHHHHHHHHHHcCCCEEEEcCCC
Confidence            789999999999999999999999999999999999999864   2347999999 9999999999999999998     


Q ss_pred             Hhhhheeehhhhhhhc
Q 029135          143 RKFHLMIVMAPVVVRE  158 (198)
Q Consensus       143 ~kyHg~i~~~~~~~~~  158 (198)
                      ++|||||..+++-.|+
T Consensus        77 ~~yhGrvka~a~~~R~   92 (97)
T d1ovya_          77 YLYHGRVKALADAARE   92 (97)
T ss_dssp             CSSCSSTHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHH
Confidence            9999999999999987

>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=99.96  E-value=6.5e-32  Score=205.95  Aligned_cols=92  Identities=20%  Similarity=0.242  Sum_probs=80.7

Q ss_pred             HHHHHhhhcCCCCCCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcCh
Q 029135           59 NRRIQKKFNGTPTKPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVL  138 (198)
Q Consensus        59 ~rRiRkKI~GTa~RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI  138 (198)
                      ++++|.++ ++.++|||+|||||+|||||||||++|+||+++||++++.       ++|+++|+ .||++|||+|+++||
T Consensus         7 r~k~r~~~-~~~~rpRL~V~rSnkhiyaQiIDd~~~~tl~s~St~~~~~-------~~~~~~a~-~vG~~ia~~a~~kgi   77 (104)
T d2zjrl1           7 RRKVRTTT-AASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKS-------GNKTDTAA-AVGKALAAAAAEKGI   77 (104)
T ss_dssp             HHHHHSCS-TTTCSEEECCCTTSSCCCCCEEETTTTEECCCCCSCSCCT-------TCSSSSHH-HHHHHHHHHHHTTCC
T ss_pred             HHHHhccc-ccCCCcEEEEEEccCeeEEEEEecCCCeEEEeeccccccc-------cchhhHHH-HHHHHHHHHHHHCCC
Confidence            33444433 3568999999999999999999999999999999987643       36899999 999999999999999


Q ss_pred             hHHH-----Hhhhheeehhhhhhhcc
Q 029135          139 HLTL-----RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       139 ~~~v-----~kyHg~i~~~~~~~~~~  159 (198)
                      ++++     ++|||+|-.|+|-+||.
T Consensus        78 ~~v~FDR~g~~YHGrvka~ad~~R~~  103 (104)
T d2zjrl1          78 KQVVFDRGSYKYHGRVKALADAAREG  103 (104)
T ss_dssp             CCCEECCCSSCSCSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCcchhHHHHHHHHHHhC
Confidence            9999     99999999999999973

>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=99.96  E-value=6.4e-31  Score=195.11  Aligned_cols=80  Identities=26%  Similarity=0.305  Sum_probs=76.6

Q ss_pred             CCeEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH-----Hhhh
Q 029135           72 KPRLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL-----RKFH  146 (198)
Q Consensus        72 RPRLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v-----~kyH  146 (198)
                      ||||+|||||+|||||||||++++||+++||+++++++      +|+++|+ .||++||++|+++||++++     ++||
T Consensus         1 R~RL~V~rSnk~iyaQiIDd~~~~tl~s~St~~k~~k~------~~~~~A~-~vG~~la~~ak~~gI~~v~FDR~g~~YH   73 (86)
T d2j01s1           1 RLRLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKLKG------NKTEVAR-QVGRALAEKALALGIKQVAFDRGPYKYH   73 (86)
T ss_dssp             SCEEECCBCSSCBCEEEEETTTTEEEEEECSTTTCCCS------CHHHHHH-HHHHHHHHHHHHTSCCCCBCCCSTTCSS
T ss_pred             CcEEEEEEcCCeEEEEEEEcCCCeEEEEEeccchhhcC------CCHHHHH-HHHHHHHHHHHHCCCCEEEEeCCCCccc
Confidence            79999999999999999999999999999999998764      6899999 9999999999999999999     9999


Q ss_pred             heeehhhhhhhc
Q 029135          147 LMIVMAPVVVRE  158 (198)
Q Consensus       147 g~i~~~~~~~~~  158 (198)
                      |+|..++|-.||
T Consensus        74 Grvka~Ad~~Re   85 (86)
T d2j01s1          74 GRVKALAEGARE   85 (86)
T ss_dssp             SSCCCCSSCTTC
T ss_pred             cHHHHHHHHHhC
Confidence            999999999987

>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=99.91  E-value=7.4e-26  Score=187.56  Aligned_cols=102  Identities=14%  Similarity=0.017  Sum_probs=90.0

Q ss_pred             HHHHHHHHHHHhhhcCCCCCCeEEEEeccceEEEEEE--ecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHH
Q 029135           53 ESAKIRNRRIQKKFNGTPTKPRLSVFCSDKQLYAMLV--DDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLV  130 (198)
Q Consensus        53 e~R~rR~rRiRkKI~GTa~RPRLsVfRSNKHIYAQII--DD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLA  130 (198)
                      +.++++++|.|...+   ++|||+||+||+|||||||  ||.+++||+|+||.|+..++|. .+++|++||+ ++|.++|
T Consensus        15 e~kT~y~~R~rl~~s---~kpRLvVrrSNk~IyaQII~~d~~gd~vlaSAsS~el~k~g~k-~~~~N~~AAy-~~G~liA   89 (186)
T d1vqon1          15 EARTDYHQRLRLLKS---GKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYGWE-APTGNMPSAY-LTGLLAG   89 (186)
T ss_dssp             TTCCCHHHHHHHHTT---CSCEEEEEECSSCEEEEEEECCTTSCEEEEEEESGGGGGGSCC-SCSSSHHHHH-HHHHHHH
T ss_pred             hhhhhHHHHHHHhcC---CCCeEEEEEeCCceEEEEEEecCCCCEEEEEEecchhhhhccc-cCccHHHHHH-HhHHHHH
Confidence            344455666665544   5999999999999999999  7889999999999999999887 6788999999 9999999


Q ss_pred             HHHHhcChhHHH-------Hhhhheeehhhhhhhcc
Q 029135          131 KSLSRLVLHLTL-------RKFHLMIVMAPVVVREC  159 (198)
Q Consensus       131 erAkeaGI~~~v-------~kyHg~i~~~~~~~~~~  159 (198)
                      ++|+++||++++       +.|||||-.+++-+|+.
T Consensus        90 ~ra~~~gi~~vvfD~G~~~~~yhgRV~A~akgard~  125 (186)
T d1vqon1          90 LRAQEAGVEEAVLDIGLNSPTPGSKVFAIQEGAIDA  125 (186)
T ss_dssp             HHHHHTTCCBCEEECTTSCCCTTCHHHHHHHHHHHT
T ss_pred             HHHHhhcccceEEeeCCCCCCccchHHHHHHHHHhc
Confidence            999999999998       79999999999999885

>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=95.78  E-value=0.011  Score=43.77  Aligned_cols=63  Identities=11%  Similarity=0.034  Sum_probs=52.4

Q ss_pred             eEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHH
Q 029135           74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLT  141 (198)
Q Consensus        74 RLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~  141 (198)
                      .+-|+-|.+++.+.+.|. +|++|..+|+-...+++.   ..++-.||+ .+++.+++++++.|+..+
T Consensus         8 ivhI~~t~NNT~itlTD~-~Gn~i~~~S~G~~gfkg~---rk~t~~Aa~-~~a~~~~~k~~~~g~~~v   70 (119)
T d2uubk1           8 RAYIHASYNNTIVTITDP-DGNPITWSSGGVIGYKGS---RKGTPYAAQ-LAALDAAKKAMAYGMQSV   70 (119)
T ss_dssp             EEEEEECSSCEEEEEECT-TSCEEEEEETTTSSCCSG---GGGSHHHHH-HHHHHHHHHHHTTTCCEE
T ss_pred             EEEEEeccCCEEEEEECC-CCCEEEEEecccceeccc---cccchhHHH-HHHHHHHHHHHHcCCcEE
Confidence            788999999999999874 557899988877777653   236778999 999999999999998764

>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=94.88  E-value=0.018  Score=42.63  Aligned_cols=64  Identities=13%  Similarity=0.077  Sum_probs=52.1

Q ss_pred             eEEEEeccceEEEEEEecCCCeEEEEEechhhhhcCCCCCCCCCHHHHHHHHHHHHHHHHHhcChhHHH
Q 029135           74 RLSVFCSDKQLYAMLVDDQNKKCLFFGSTLQQSIRGNGNPPCSTIFPLSRKLLSVLVKSLSRLVLHLTL  142 (198)
Q Consensus        74 RLsVfRSNKHIYAQIIDD~~gkTLaSASTlek~lk~~l~~~~~NieAA~~~VGklLAerAkeaGI~~~v  142 (198)
                      .+-|+.|.+++...+-| .+|+++...|+-...+++..   .++-.||. .+++.+++++++.|+..+.
T Consensus         8 i~hI~~t~NNTiitlTD-~~G~~~~~~S~G~~gfkg~~---K~t~~Aa~-~~a~~~~~~~~~~gi~~v~   71 (117)
T d2qalk1           8 VAHIHASFNNTIVTITD-RQGNALGWATAGGSGFRGSR---KSTPFAAQ-VAAERCADAVKEYGIKNLE   71 (117)
T ss_dssp             EEEEECCSSCCEEEEEE-TTSCEEEEEETTTSSCCHHH---HTSHHHHH-HHHHHHHHHHGGGTCCEEE
T ss_pred             EEEEEecCCCEEEEEEC-CCCCEEEEEecccccccccc---ccchHHHH-HHHHHHHHHHHHcCCcEEE
Confidence            67899999999999886 67788888888776666522   35778999 9999999999999987543