Citrus Sinensis ID: 033970

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------
Protein Sequence
MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQLEA
Secondary Structure (PSIPRED)
ccEEEEEEEccccccEEEEEEEEEccccccccEEEEEEcEEEEccccccccccEEEEEEcccccccccEEEEEEEccccccccccccccccccccccccccHHHHHc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEcccccEEEEEEEEccccccccEEEEEcEEEEEcccccccccccEEEEEEcccccccccEEEEHHHHHHcccccccccccccccccccccccHHHHcc
Coil and Loop (DISEMBL)
mkkmqgrvvcassdktVAVEvvrldphpkykrrirkkkkyqahdpenqfqvgDLVQleksrpisktksfiavampprnaskkaagessnagnnelgipleseqqlea
Flexible Loop (DISEMBL)
mkkmqgrvvcassdktvavevvrldphpkykrrirkkkkyqahdpenqfqvgdlvqlEKSRPISKTksfiavampprNASKKaagessnagnnelgipleseqqlea
Low Complexity Region (SEG)
MKKMQGRVVCASSDKTVAVEVVRLDPHPkykrrirkkkkyQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQLEA
Disordered region (IsUnstruct)
***************TVAVEVVRL***********************************************************************************
Disordered Region (DISOPRED)
MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPP*******************************
Disordered Region (DISEMBL)
************SDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPP*************AGNNELGIPLESEQQLEA
Disordered Region (DISPRO)
MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA****************************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQLEA
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	107	2.2.26 [Sep-21-2011]
P16180	149	30S ribosomal protein S17	yes	no	0.915	0.657	0.718	1e-36
P17092	134	30S ribosomal protein S17	N/A	no	0.906	0.723	0.653	6e-32
Q9ZST1	145	30S ribosomal protein S17	yes	no	0.757	0.558	0.691	6e-28
Q9TJN6	132	30S ribosomal protein S17	N/A	no	0.766	0.621	0.658	2e-27
A9BH96	110	30S ribosomal protein S17	yes	no	0.719	0.7	0.441	5e-15
Q1RHN0	77	30S ribosomal protein S17	yes	no	0.644	0.896	0.521	2e-14
A8GVC3	77	30S ribosomal protein S17	yes	no	0.644	0.896	0.521	2e-14
C3PP98	82	30S ribosomal protein S17	yes	no	0.644	0.841	0.521	1e-13
A8GPE1	77	30S ribosomal protein S17	yes	no	0.644	0.896	0.521	1e-13
A8EZK7	77	30S ribosomal protein S17	yes	no	0.644	0.896	0.521	2e-13

>sp|P16180|RR17_ARATH 30S ribosomal protein S17, chloroplastic OS=Arabidopsis thaliana GN=RPS17 PE=2 SV=1

 Score =  151 bits (382), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 86/103 (83%), Gaps = 5/103 (4%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKS
Sbjct: 50  MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 109

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
           RPISKTKSF+A+ +  R A K  AG     G+  LG+PLES+Q
Sbjct: 110 RPISKTKSFVALPVIARAARKAEAG-----GDELLGLPLESQQ 147

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.
Arabidopsis thaliana (taxid: 3702)

>sp|P17092|RR17_PEA 30S ribosomal protein S17, chloroplastic (Fragment) OS=Pisum sativum GN=RPS17 PE=2 SV=1

 Score =  135 bits (341), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 68/104 (65%), Positives = 82/104 (78%), Gaps = 7/104 (6%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK M+G+VVCAS +KTVAVEV RL PHPKY++RIR KKKYQAHDPEN F+VGD+VQL K+
Sbjct: 38  MKTMEGKVVCASGNKTVAVEVTRLAPHPKYQKRIRLKKKYQAHDPENDFKVGDIVQLLKT 97

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQ 104
           RPISK K+F+AV  P R + K  AG S      ELGIPL+S+Q+
Sbjct: 98  RPISKKKTFLAVPAPSRKSKK--AGSS-----GELGIPLQSQQE 134

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Pisum sativum (taxid: 3888)

>sp|Q9ZST1|RR17_ORYSJ 30S ribosomal protein S17, chloroplastic OS=Oryza sativa subsp. japonica GN=RPS17 PE=2 SV=1

 Score =  122 bits (306), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 56/81 (69%), Positives = 68/81 (83%)

Query: 2   KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
           K++ GRVV   +DKTV VEVVRL PHPKYKRR R KKKYQAHDP+NQF+VGD+V+L +SR
Sbjct: 38  KQLTGRVVTTKADKTVGVEVVRLAPHPKYKRRERIKKKYQAHDPDNQFKVGDVVELRRSR 97

Query: 62  PISKTKSFIAVAMPPRNASKK 82
           PISKTK F+AV +PPR+  +K
Sbjct: 98  PISKTKHFLAVPLPPRDTRRK 118

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9TJN6|RR17_MAIZE 30S ribosomal protein S17, chloroplastic OS=Zea mays GN=RPS17 PE=2 SV=1

 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 54/82 (65%), Positives = 69/82 (84%)

Query: 2   KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
           +++ GRVV   +DKTV VEVVRL PHPKYKRR R KKKYQAHDP+NQF+VGD+V+L+ SR
Sbjct: 33  RQLTGRVVTTKADKTVGVEVVRLAPHPKYKRRERIKKKYQAHDPDNQFKVGDVVELQPSR 92

Query: 62  PISKTKSFIAVAMPPRNASKKA 83
           PISKTK F+A+ +PPR+  +K+
Sbjct: 93  PISKTKHFLAIPLPPRDTRRKS 114

In the hcf60 mutation the Activator tag is inserted 17 base pars upstream of the initiation codon. This mutation is seedling lethal, due to plastid ribosome insufficiency. However under non-light stressed conditions photosynthesis and oxygen evolution can occur.

Zea mays (taxid: 4577)

>sp|A9BH96|RS17_PETMO 30S ribosomal protein S17 OS=Petrotoga mobilis (strain DSM 10674 / SJ95) GN=rpsQ PE=3 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 54/77 (70%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K + G+VV  + DKT+ VE  RL  HPKY + +RK ++Y AHD  N+ ++GD+V++E+SR
Sbjct: 4  KIITGKVVSNAMDKTITVETDRLTKHPKYHKFVRKTRRYHAHDENNECEIGDIVEIEESR 63

Query: 62 PISKTKSFIAVAMPPRN 78
           +SKTK+F+   +  +N
Sbjct: 64 KLSKTKAFVLKRIVRKN 80

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Petrotoga mobilis (strain DSM 10674 / SJ95) (taxid: 403833)

>sp|Q1RHN0|RS17_RICBR 30S ribosomal protein S17 OS=Rickettsia bellii (strain RML369-C) GN=rpsQ PE=3 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 4  MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPI 63
          +QG V+ + +DKTV V+V R   HP YK+ I+  KKY AHDP N+FQ GD V + +SRPI
Sbjct: 6  LQGVVISSKTDKTVTVKVERRFKHPIYKKFIKVSKKYAAHDPNNKFQEGDKVNIIESRPI 65

Query: 64 SKTKSFIAV 72
          SKTK+++ +
Sbjct: 66 SKTKTWVVI 74

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Rickettsia bellii (strain RML369-C) (taxid: 336407)

>sp|A8GVC3|RS17_RICB8 30S ribosomal protein S17 OS=Rickettsia bellii (strain OSU 85-389) GN=rpsQ PE=3 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 4  MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPI 63
          +QG V+ + +DKTV V+V R   HP YK+ I+  KKY AHDP N+FQ GD V + +SRPI
Sbjct: 6  LQGVVISSKTDKTVTVKVERRFKHPIYKKFIKVSKKYAAHDPNNKFQEGDKVNIIESRPI 65

Query: 64 SKTKSFIAV 72
          SKTK+++ +
Sbjct: 66 SKTKTWVVI 74

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Rickettsia bellii (strain OSU 85-389) (taxid: 391896)

>sp|C3PP98|RS17_RICAE 30S ribosomal protein S17 OS=Rickettsia africae (strain ESF-5) GN=rpsQ PE=3 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 4  MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPI 63
          +QG V+ + +DKTV V+V R   HP YK+ ++  KKY AHD EN++Q GD V + +SRPI
Sbjct: 11 LQGVVISSKADKTVTVKVERKFKHPIYKKFVKVSKKYAAHDSENKYQEGDKVSIIESRPI 70

Query: 64 SKTKSFIAV 72
          SKTK++I V
Sbjct: 71 SKTKTWIVV 79

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Rickettsia africae (strain ESF-5) (taxid: 347255)

>sp|A8GPE1|RS17_RICAH 30S ribosomal protein S17 OS=Rickettsia akari (strain Hartford) GN=rpsQ PE=3 SV=1

 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 4  MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPI 63
          +QG V+ + +DKTV V+V R   HP YK+ ++  KKY AHD EN++Q GD V + +SRPI
Sbjct: 6  LQGVVISSKADKTVTVKVERKFKHPIYKKFVKVSKKYAAHDSENKYQEGDKVSIIESRPI 65

Query: 64 SKTKSFIAV 72
          SKTK++I V
Sbjct: 66 SKTKTWIVV 74

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Rickettsia akari (strain Hartford) (taxid: 293614)

>sp|A8EZK7|RS17_RICCK 30S ribosomal protein S17 OS=Rickettsia canadensis (strain McKiel) GN=rpsQ PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query: 4  MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPI 63
          +QG V+ + +DKTV V+V R   HP YK+ ++  KKY AHD EN++Q GD V + +SRPI
Sbjct: 6  LQGVVISSKADKTVTVKVERKFKHPIYKKFVKVSKKYAAHDSENRYQEGDKVSIIESRPI 65

Query: 64 SKTKSFIAV 72
          SKTK++I V
Sbjct: 66 SKTKTWIVV 74

One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.

Rickettsia canadensis (strain McKiel) (taxid: 293613)

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	107
297839951	148	hypothetical protein ARALYDRAFT_477281 [	0.915	0.662	0.718	3e-35
15220003	149	30S ribosomal protein S17 [Arabidopsis t	0.915	0.657	0.718	4e-35
336392	159	ribosomal protein S17, partial (chloropl	0.915	0.616	0.718	4e-35
449448022	164	PREDICTED: 30S ribosomal protein S17, ch	0.943	0.615	0.663	1e-32
357454921	151	30S ribosomal protein S17 [Medicago trun	0.915	0.649	0.634	7e-31
388494368	151	unknown [Medicago truncatula]	0.915	0.649	0.634	1e-30
188036218	142	Chain Q, Homology Model For The Spinach	0.757	0.570	0.790	2e-30
133829	134	RecName: Full=30S ribosomal protein S17,	0.906	0.723	0.653	3e-30
224054362	160	predicted protein [Populus trichocarpa]	1.0	0.668	0.747	3e-30
225442609	145	PREDICTED: 30S ribosomal protein S17, ch	0.915	0.675	0.737	1e-28

>gi|297839951|ref|XP_002887857.1| hypothetical protein ARALYDRAFT_477281 [Arabidopsis lyrata subsp. lyrata] gi|297333698|gb|EFH64116.1| hypothetical protein ARALYDRAFT_477281 [Arabidopsis lyrata subsp. lyrata]

 Score =  152 bits (384), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 85/103 (82%), Gaps = 5/103 (4%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEV RL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKS
Sbjct: 49  MKTMQGRVVCATSDKTVAVEVTRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 108

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
           RPISKTKSF+A+ + PR A K  AG       + LGIPLES+Q
Sbjct: 109 RPISKTKSFVALPVVPRAARKAEAG-----AGDLLGIPLESQQ 146

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15220003|ref|NP_178103.1| 30S ribosomal protein S17 [Arabidopsis thaliana] gi|133815|sp|P16180.1|RR17_ARATH RecName: Full=30S ribosomal protein S17, chloroplastic; AltName: Full=CS17; Flags: Precursor gi|12324576|gb|AAG52237.1|AC011717_5 30S ribosomal protein S17, chloroplast precursor (CS17); 62258-62707 [Arabidopsis thaliana] gi|14423474|gb|AAK62419.1|AF386974_1 30S ribosomal protein S17, chloroplast precursor (CS17) [Arabidopsis thaliana] gi|16503|emb|CAA77502.1| Plastid ribosomal protein CS17 [Arabidopsis thaliana] gi|18377576|gb|AAL66954.1| 30S ribosomal protein S17, chloroplast precursor (CS17) [Arabidopsis thaliana] gi|332198192|gb|AEE36313.1| 30S ribosomal protein S17 [Arabidopsis thaliana]

 Score =  151 bits (382), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 86/103 (83%), Gaps = 5/103 (4%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKS
Sbjct: 50  MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 109

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
           RPISKTKSF+A+ +  R A K  AG     G+  LG+PLES+Q
Sbjct: 110 RPISKTKSFVALPVIARAARKAEAG-----GDELLGLPLESQQ 147

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|336392|gb|AAA84030.1| ribosomal protein S17, partial (chloroplast) [Arabidopsis thaliana]

 Score =  151 bits (382), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 74/103 (71%), Positives = 86/103 (83%), Gaps = 5/103 (4%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKS
Sbjct: 60  MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 119

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
           RPISKTKSF+A+ +  R A K  AG     G+  LG+PLES+Q
Sbjct: 120 RPISKTKSFVALPVIARAARKAEAG-----GDELLGLPLESQQ 157

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448022|ref|XP_004141765.1| PREDICTED: 30S ribosomal protein S17, chloroplastic-like [Cucumis sativus] gi|449519627|ref|XP_004166836.1| PREDICTED: 30S ribosomal protein S17, chloroplastic-like [Cucumis sativus]

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 69/104 (66%), Positives = 82/104 (78%), Gaps = 3/104 (2%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           M+ +QGRVVCA++DKTVAVEVVRL PHPKYKRRIR KKKYQAHDP+NQFQVGD V+LEK 
Sbjct: 62  MRSLQGRVVCATNDKTVAVEVVRLAPHPKYKRRIRIKKKYQAHDPDNQFQVGDFVELEKC 121

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQ 104
           RPISK K+F+A+ +P RN+ KKA             IPLES+Q+
Sbjct: 122 RPISKMKTFLAIPVPARNSKKKAVEGGEGGELG---IPLESQQE 162

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357454921|ref|XP_003597741.1| 30S ribosomal protein S17 [Medicago truncatula] gi|217075408|gb|ACJ86064.1| unknown [Medicago truncatula] gi|355486789|gb|AES67992.1| 30S ribosomal protein S17 [Medicago truncatula] gi|388491878|gb|AFK34005.1| unknown [Medicago truncatula]

 Score =  137 bits (346), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 66/104 (63%), Positives = 83/104 (79%), Gaps = 6/104 (5%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK M+G+VVCA++DKTV+VEV RL PHPKYK+RIR KKKYQAHDPEN F+VGD+VQL K 
Sbjct: 47  MKTMEGKVVCATNDKTVSVEVTRLAPHPKYKKRIRMKKKYQAHDPENVFKVGDVVQLCKI 106

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQ 104
           RPISK K+F+AV +P RN+ K      +N  + +L IPL+SEQ+
Sbjct: 107 RPISKNKTFLAVPVPARNSGK------ANNSSGDLDIPLQSEQE 144

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388494368|gb|AFK35250.1| unknown [Medicago truncatula]

 Score =  136 bits (343), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/104 (63%), Positives = 82/104 (78%), Gaps = 6/104 (5%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK M+G+VVCA++DKTV+VEV RL PHPKYK+RIR KKKYQAHDPEN F+VGD+VQL K 
Sbjct: 47  MKTMEGKVVCATNDKTVSVEVTRLAPHPKYKKRIRMKKKYQAHDPENVFKVGDVVQLCKI 106

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQ 104
           RPISK K+F+AV  P RN+ K      +N  + +L IPL+SEQ+
Sbjct: 107 RPISKNKTFLAVPAPARNSGK------ANNSSGDLDIPLQSEQE 144

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188036218|pdb|3BBN|Q Chain Q, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 73/81 (90%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKS
Sbjct: 60  MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 119

Query: 61  RPISKTKSFIAVAMPPRNASK 81
           RPISKTKSF+A+ +  R A K
Sbjct: 120 RPISKTKSFVALPVIARAARK 140

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|133829|sp|P17092.1|RR17_PEA RecName: Full=30S ribosomal protein S17, chloroplastic; AltName: Full=CS17; Flags: Precursor gi|169068|gb|AAA33658.1| ribosomal protein S17, partial [Pisum sativum]

 Score =  135 bits (341), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 68/104 (65%), Positives = 82/104 (78%), Gaps = 7/104 (6%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK M+G+VVCAS +KTVAVEV RL PHPKY++RIR KKKYQAHDPEN F+VGD+VQL K+
Sbjct: 38  MKTMEGKVVCASGNKTVAVEVTRLAPHPKYQKRIRLKKKYQAHDPENDFKVGDIVQLLKT 97

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQ 104
           RPISK K+F+AV  P R + K  AG S      ELGIPL+S+Q+
Sbjct: 98  RPISKKKTFLAVPAPSRKSKK--AGSS-----GELGIPLQSQQE 134

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054362|ref|XP_002298222.1| predicted protein [Populus trichocarpa] gi|222845480|gb|EEE83027.1| predicted protein [Populus trichocarpa]

 Score =  135 bits (341), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 80/107 (74%), Positives = 92/107 (85%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK +QG+VVCA+SDKTVAVEV RL PHPKYKRR+RKKKKYQAHDPENQF+VGDLVQLEKS
Sbjct: 54  MKSLQGKVVCATSDKTVAVEVTRLAPHPKYKRRVRKKKKYQAHDPENQFKVGDLVQLEKS 113

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQQLEA 107
           RPISKTKSF+AV +P R   +K  GE    G+ ELGIPLES+Q+L+A
Sbjct: 114 RPISKTKSFLAVPVPARKKKEKKEGEEGGVGSQELGIPLESQQELQA 160

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442609|ref|XP_002284468.1| PREDICTED: 30S ribosomal protein S17, chloroplastic-like [Vitis vinifera]

 Score =  130 bits (326), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 76/103 (73%), Positives = 87/103 (84%), Gaps = 5/103 (4%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+RKKKKYQAHDP+NQF+VGD+VQLEKS
Sbjct: 47  MKSMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRKKKKYQAHDPDNQFKVGDVVQLEKS 106

Query: 61  RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
           RPISKTK+F+A+ +P RN +K     S  A   EL IPLES+Q
Sbjct: 107 RPISKTKTFVAIPVPNRNRAK-----SQEAAAGELEIPLESQQ 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	107
TAIR|locus:2017849	149	RPS17 "ribosomal protein S17"	0.915	0.657	0.621	1.9e-26
TIGR_CMR|SO_0240	82	SO_0240 "ribosomal protein S17	0.672	0.878	0.375	2e-08
TIGR_CMR|CHY_2300	98	CHY_2300 "ribosomal protein S1	0.794	0.867	0.369	2.6e-08
UNIPROTKB|P0AG63	84	rpsQ [Escherichia coli K-12 (t	0.672	0.857	0.333	3.3e-08
UNIPROTKB|Q9KNZ3	84	rpsQ "30S ribosomal protein S1	0.626	0.797	0.373	4.2e-08
TIGR_CMR|VC_2587	84	VC_2587 "ribosomal protein S17	0.626	0.797	0.373	4.2e-08
TIGR_CMR|CBU_0247	89	CBU_0247 "ribosomal protein S1	0.719	0.865	0.363	5.3e-08
TIGR_CMR|BA_0119	87	BA_0119 "ribosomal protein S17	0.635	0.781	0.367	6.1e-07
TIGR_CMR|ECH_0418	83	ECH_0418 "ribosomal protein S1	0.663	0.855	0.352	1.6e-06
TAIR|locus:2010227	116	emb1129 "embryo defective 1129	0.841	0.775	0.336	4.3e-06

TAIR|locus:2017849 RPS17 "ribosomal protein S17" [Arabidopsis thaliana (taxid:3702)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 64/103 (62%), Positives = 75/103 (72%)

Query:     1 MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
             MK MQGRVVCA+SDKTVAVEVVRL PHP            QAHDP+NQF+VGD+V+LEKS
Sbjct:    50 MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 109

Query:    61 RPISKTKSFIAVAMPPRNASKKAAGESSNAGNNELGIPLESEQ 103
             RPISKTKSF+A+ +  R A K  AG     G+  LG+PLES+Q
Sbjct:   110 RPISKTKSFVALPVIARAARKAEAG-----GDELLGLPLESQQ 147

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

GO:0006412 "translation" evidence=ISS;TAS

GO:0009507 "chloroplast" evidence=ISM;IDA

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

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0032544 "plastid translation" evidence=IMP

GO:0000312 "plastid small ribosomal subunit" evidence=ISS

TIGR_CMR|SO_0240 SO_0240 "ribosomal protein S17" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 128 (50.1 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 27/72 (37%), Positives = 37/72 (51%)

Query:     1 MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
             ++ +QGRV     DKT+ V + R   HP             AHD  NQ   GD+V + + 
Sbjct:     5 IRTLQGRVTSNKMDKTITVAIERQVKHPIYGKYIKRTTKIHAHDEANQCNEGDVVAIREC 64

Query:    61 RPISKTKSFIAV 72
             RP+SKTKS+  V
Sbjct:    65 RPLSKTKSWTLV 76

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CHY_2300 CHY_2300 "ribosomal protein S17" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 34/92 (36%), Positives = 45/92 (48%)

Query:     2 KKMQ----GRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQL 57
             KK+Q    GRVV    DKTV V V  L  HP            +AHD  N  + GD+V++
Sbjct:     4 KKVQKIKIGRVVSDKMDKTVVVAVEELVSHPLYKKTIRRTKKFKAHDEHNACRTGDIVKI 63

Query:    58 EKSRPISKTKSFIAVAMPPRNASKKAAGESSN 89
              ++RP+SK K +  V +  R    K  GE  N
Sbjct:    64 AETRPLSKEKRWRVVEIIERG---KVLGEEEN 92

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

GO:0006412 "translation" evidence=ISS

UNIPROTKB|P0AG63 rpsQ [Escherichia coli K-12 (taxid:83333)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query:     1 MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
             ++ +QGRVV    +K++ V + R   HP              HD  N+  +GD+V++ + 
Sbjct:     5 IRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC 64

Query:    61 RPISKTKSFIAV 72
             RP+SKTKS+  V
Sbjct:    65 RPLSKTKSWTLV 76

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

GO:0019843 "rRNA binding" evidence=IDA

GO:0070181 "SSU rRNA binding" evidence=IDA

GO:0046677 "response to antibiotic" evidence=IEA;IMP

GO:0006412 "translation" evidence=IEA

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

UNIPROTKB|Q9KNZ3 rpsQ "30S ribosomal protein S17" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query:     6 GRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSRPISK 65
             GRVV    DK++ V + R+  HP             AHD  N+  +GD V++ + RP+SK
Sbjct:    10 GRVVSDKMDKSIVVAIERMVKHPIYGKFVKRTTKVHAHDENNECGIGDTVEIRECRPLSK 69

Query:    66 TKSFIAV 72
             TKS+  V
Sbjct:    70 TKSWTLV 76

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|VC_2587 VC_2587 "ribosomal protein S17" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query:     6 GRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSRPISK 65
             GRVV    DK++ V + R+  HP             AHD  N+  +GD V++ + RP+SK
Sbjct:    10 GRVVSDKMDKSIVVAIERMVKHPIYGKFVKRTTKVHAHDENNECGIGDTVEIRECRPLSK 69

Query:    66 TKSFIAV 72
             TKS+  V
Sbjct:    70 TKSWTLV 76

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|CBU_0247 CBU_0247 "ribosomal protein S17" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 124 (48.7 bits), Expect = 5.3e-08, P = 5.3e-08
 Identities = 28/77 (36%), Positives = 39/77 (50%)

Query:     1 MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
             ++ + G VV    + TV V V R   HP             AHD  N+ Q+GD+V + + 
Sbjct:     8 VRSLMGTVVSNKMNDTVVVRVERRVKHPKYGKFIKRSTKIHAHDKGNEGQIGDIVTIREC 67

Query:    61 RPISKTKSFIAVAMPPR 77
             RPISKTKS+  V +  R
Sbjct:    68 RPISKTKSWTLVKINER 84

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

TIGR_CMR|BA_0119 BA_0119 "ribosomal protein S17" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 114 (45.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 25/68 (36%), Positives = 36/68 (52%)

Query:     2 KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
             K   GRVV    DKT+ V V     H             +AHD +NQ ++GD+V++ ++R
Sbjct:     8 KVYTGRVVSDKMDKTITVLVETYKTHSLYGKRVKYSKKYKAHDEQNQAKLGDIVKIMETR 67

Query:    62 PISKTKSF 69
             P+S TK F
Sbjct:    68 PLSATKRF 75

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

GO:0006412 "translation" evidence=ISS

TIGR_CMR|ECH_0418 ECH_0418 "ribosomal protein S17" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 110 (43.8 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 25/71 (35%), Positives = 37/71 (52%)

Query:     2 KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
             K + G VV A  DKT+ V V R+  H               HD  NQ++ GD+V++++  
Sbjct:    13 KVLTGIVVDAKCDKTIKVMVSRMIMHKTYKKIVKKRKNYVVHDEHNQYKCGDVVKIQEHI 72

Query:    62 PISKTKSFIAV 72
             PIS TK +I +
Sbjct:    73 PISATKRWIVI 83

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

GO:0006412 "translation" evidence=ISS

GO:0015935 "small ribosomal subunit" evidence=ISS

GO:0042255 "ribosome assembly" evidence=ISS

TAIR|locus:2010227 emb1129 "embryo defective 1129" [Arabidopsis thaliana (taxid:3702)]

 Score = 106 (42.4 bits), Expect = 4.3e-06, P = 4.3e-06
 Identities = 31/92 (33%), Positives = 44/92 (47%)

Query:     1 MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
             MK + G VV     K+V V V RL  +              AHD ++   +GD V+L+ S
Sbjct:     1 MKPVIGTVVSNKMQKSVVVAVDRLFHNKIYNRYVKRTSKFMAHDDKDACNIGDRVKLDPS 60

Query:    61 RPISKTKSFIA--VAMPPRNASKKAAGESSNA 90
             RP+SK K +I   +    R  S KAA  + +A
Sbjct:    61 RPLSKNKHWIVAEIIKKARIYSPKAAAAAVSA 92

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

GO:0005622 "intracellular" evidence=IEA

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;ISS

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

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q92GX5	RS17_RICCN	No assigned EC number	0.5072	0.6448	0.8961	yes	no
A8F4S0	RS17_THELT	No assigned EC number	0.4193	0.8411	0.9473	yes	no
B0BUQ1	RS17_RICRO	No assigned EC number	0.5072	0.6448	0.8414	yes	no
A8GVC3	RS17_RICB8	No assigned EC number	0.5217	0.6448	0.8961	yes	no
C3PP98	RS17_RICAE	No assigned EC number	0.5217	0.6448	0.8414	yes	no
C4K2H0	RS17_RICPU	No assigned EC number	0.5072	0.6448	0.8961	yes	no
A8EZK7	RS17_RICCK	No assigned EC number	0.5217	0.6448	0.8961	yes	no
Q1RHN0	RS17_RICBR	No assigned EC number	0.5217	0.6448	0.8961	yes	no
B5YG38	RS17_THEYD	No assigned EC number	0.5147	0.6355	0.8192	yes	no
A8GT60	RS17_RICRS	No assigned EC number	0.5072	0.6448	0.8961	yes	no
A8GPE1	RS17_RICAH	No assigned EC number	0.5217	0.6448	0.8961	yes	no
B6IRR5	RS17_RHOCS	No assigned EC number	0.5142	0.6542	0.8235	yes	no
P16180	RR17_ARATH	No assigned EC number	0.7184	0.9158	0.6577	yes	no
Q6FZD1	RS17_BARQU	No assigned EC number	0.5072	0.6448	0.8734	yes	no
Q4UMS0	RS17_RICFE	No assigned EC number	0.5072	0.6448	0.8414	yes	no
A9IW16	RS17_BART1	No assigned EC number	0.5072	0.6448	0.8734	yes	no
P38519	RS17_THEMA	No assigned EC number	0.3977	0.8224	0.8224	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	fgenesh2_kg.2__2411__AT1G79850.1	annotation not avaliable (148 aa)
		(Arabidopsis lyrata)
Predicted Functional Partners:
	fgenesh2_kg.1__3924__AT1G48350.1	annotation not avaliable (170 aa)	•			•			•		0.956
	fgenesh2_kg.1__466__AT1G05190.1	annotation not avaliable (223 aa)	•			•			•		0.948
	fgenesh2_kg.6__3575__AT4G01310.1	annotation not avaliable (264 aa)	•			•			•		0.948
	fgenesh2_kg.4__2465__AT2G43030.1	annotation not avaliable (271 aa)	•			•			•		0.917
	fgenesh1_pg.C_scaffold_1061000001	annotation not avaliable (103 aa)	•			•	•		•		0.907
	fgenesh2_kg.5__350__AT3G25920.1	annotation not avaliable (275 aa)	•			•			•		0.898
	fgenesh1_pg.C_scaffold_4000116	annotation not avaliable (224 aa)	•			•	•		•		0.883
	scaffold_303456.1	annotation not avaliable (125 aa)	•			•	•		•		0.878
	fgenesh2_kg.1__705__AT1G07320.2	annotation not avaliable (280 aa)	•			•			•		0.872
	fgenesh2_kg.3__3475__AT2G18710.1	annotation not avaliable (549 aa)	•			•			•		0.868

---

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	107
pfam00366	69	pfam00366, Ribosomal_S17, Ribosomal protein S17	4e-29
TIGR03635	71	TIGR03635, S17_bact, 30S ribosomal protein S17	1e-26
PRK05610	84	PRK05610, rpsQ, 30S ribosomal protein S17; Reviewe	3e-26
COG0186	87	COG0186, RpsQ, Ribosomal protein S17 [Translation,	1e-23
CHL00142	84	CHL00142, rps17, ribosomal protein S17; Validated	3e-18
TIGR03630	102	TIGR03630, arch_S17P, archaeal ribosomal protein S	4e-13
PRK08572	108	PRK08572, rps17p, 30S ribosomal protein S17P; Revi	4e-12

>gnl|CDD|109426 pfam00366, Ribosomal_S17, Ribosomal protein S17

 Score = 99.3 bits (248), Expect = 4e-29
 Identities = 33/67 (49%), Positives = 44/67 (65%)

Query: 6  GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISK 65
          G VV    +KT+ V V RL PHPKY +  ++ KKY AHDP    +VGD+V++ + RP+SK
Sbjct: 1  GVVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFRKVGDVVKIGECRPLSK 60

Query: 66 TKSFIAV 72
          TK F  V
Sbjct: 61 TKRFRVV 67

Length = 69

>gnl|CDD|213841 TIGR03635, S17_bact, 30S ribosomal protein S17

 Score = 93.0 bits (232), Expect = 1e-26
 Identities = 31/68 (45%), Positives = 46/68 (67%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K +QG VV    DKT+ V V R   HP Y + +++ KKY AHD  N+ +VGD+V++ ++R
Sbjct: 2  KTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIETR 61

Query: 62 PISKTKSF 69
          P+SKTK +
Sbjct: 62 PLSKTKRW 69

This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 71

>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed

 Score = 92.5 bits (231), Expect = 3e-26
 Identities = 32/71 (45%), Positives = 48/71 (67%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K +QGRVV    DKT+ V V R   HP Y + +++ KKY AHD  N+ ++GD+V++ ++R
Sbjct: 7  KTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMETR 66

Query: 62 PISKTKSFIAV 72
          P+SKTK +  V
Sbjct: 67 PLSKTKRWRLV 77

Length = 84

>gnl|CDD|223264 COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]

 Score = 86.1 bits (214), Expect = 1e-23
 Identities = 35/68 (51%), Positives = 48/68 (70%)

Query: 5  QGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPIS 64
          +G VV    DKTV VEV R   HPKY + +R+ KKY AHD  N+ +VGD+V++ ++RP+S
Sbjct: 12 EGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPLS 71

Query: 65 KTKSFIAV 72
          KTK F+ V
Sbjct: 72 KTKRFVVV 79

Length = 87

>gnl|CDD|177064 CHL00142, rps17, ribosomal protein S17; Validated

 Score = 72.4 bits (178), Expect = 3e-18
 Identities = 31/70 (44%), Positives = 43/70 (61%)

Query: 1  MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS 60
          +K+  G VV    +KT+ V V     HP Y + I K KKY  HD EN+  +GD V +E++
Sbjct: 3  VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEET 62

Query: 61 RPISKTKSFI 70
          RP+SKTK +I
Sbjct: 63 RPLSKTKRWI 72

Length = 84

>gnl|CDD|132669 TIGR03630, arch_S17P, archaeal ribosomal protein S17P

 Score = 59.6 bits (145), Expect = 4e-13
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 6  GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-QFQVGDLVQLEKSRPIS 64
          G VV    +KTV VE   L    KY+R  R++ K  AH+P     + GD+V + ++RP+S
Sbjct: 32 GVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLS 91

Query: 65 KTKSFIAV 72
          KTKSF+ +
Sbjct: 92 KTKSFVVL 99

This model describes exclusively the archaeal ribosomal protein S17P. It excludes the homologous ribosomal protein S17 from bacteria, and is not intended for use on eukaryotic sequences, where some instances of ribosomal proteins S11 score above the trusted cutoff [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 102

>gnl|CDD|236296 PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed

 Score = 57.2 bits (139), Expect = 4e-12
 Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 6   GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-QFQVGDLVQLEKSRPIS 64
           G VV     KTV VE   L   PKY+R  +++ +  AH+P     +VGD V++ + RP+S
Sbjct: 34  GTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAECRPLS 93

Query: 65  KTKSFIAVA 73
           KTKSF+ V 
Sbjct: 94  KTKSFVVVE 102

Length = 108

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	107
CHL00142	84	rps17 ribosomal protein S17; Validated	100.0
PRK05610	84	rpsQ 30S ribosomal protein S17; Reviewed	100.0
COG0186	87	RpsQ Ribosomal protein S17 [Translation, ribosomal	100.0
PRK08572	108	rps17p 30S ribosomal protein S17P; Reviewed	100.0
TIGR03635	71	S17_bact 30S ribosomal protein S17. This model des	100.0
TIGR03630	102	arch_S17P archaeal ribosomal protein S17P. This mo	100.0
KOG1740	107	consensus Predicted mitochondrial/chloroplast ribo	100.0
PF00366	69	Ribosomal_S17: Ribosomal protein S17; InterPro: IP	100.0
PTZ00241	158	40S ribosomal protein S11; Provisional	99.98
KOG1728	156	consensus 40S ribosomal protein S11 [Translation,	99.85
KOG3447	150	consensus Mitochondrial/chloroplast ribosomal S17-	99.81

>CHL00142 rps17 ribosomal protein S17; Validated

Probab=100.00  E-value=9.2e-37  Score=206.24  Aligned_cols=80  Identities=39%  Similarity=0.576  Sum_probs=77.0

Q ss_pred             CceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            1 MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         1 ~k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ++.|.|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||.|+|++||+|+|.|||||||+|+|.|.+|++++..
T Consensus         3 ~~~~~G~Vvs~km~KTivV~v~r~~~h~kY~K~~~r~kk~~aHDe~n~~~~GD~V~I~e~RPlSKtK~~~v~~i~~~~~~   82 (84)
T CHL00142          3 VKEKIGIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKYLVHDEENECNIGDQVLIEETRPLSKTKRWILKEILSKSSL   82 (84)
T ss_pred             ceEEEEEEEeCCCCceEEEEEEEEEEcCcccEEEEeeEEEEEeCCCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEEeeec
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999987753

>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed

Probab=100.00  E-value=3e-36  Score=203.53  Aligned_cols=77  Identities=42%  Similarity=0.682  Sum_probs=75.2

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN   78 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~   78 (107)
                      +.|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||.|.|++||+|+|.|||||||+|+|.|.+|++++
T Consensus         7 ~~l~G~Vvs~km~KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~rPlSK~K~~~v~~i~~~~   83 (84)
T PRK05610          7 KTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMETRPLSKTKRWRLVEIVEKA   83 (84)
T ss_pred             CEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEcccCCCCEEEEEEEEEecc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999875

>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3e-36  Score=204.96  Aligned_cols=78  Identities=45%  Similarity=0.724  Sum_probs=75.8

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      +.|+|+|+|++|+|||+|++++.++||+|+|+++++++|+||||.|+|++||+|+|.|||||||+|+|.|++|++++.
T Consensus         9 k~l~G~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~EtRPLSKtK~~~vv~i~~~a~   86 (87)
T COG0186           9 RVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPLSKTKRFVVVEIVEKAV   86 (87)
T ss_pred             eEEEEEEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEccccCCcceEEEEEEeeecc
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999998864

>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed

Probab=100.00  E-value=8.1e-35  Score=204.64  Aligned_cols=77  Identities=39%  Similarity=0.598  Sum_probs=74.9

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-NQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN   78 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~   78 (107)
                      +.|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|.|.+|++++
T Consensus        30 k~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~RPiSKtK~w~v~~i~~~~  107 (108)
T PRK08572         30 QVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPCIDAKVGDKVKIAECRPLSKTKSFVVVEKKERA  107 (108)
T ss_pred             EEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEEEEcC
Confidence            579999999999999999999999999999999999999999999 79999999999999999999999999999876

>TIGR03635 S17_bact 30S ribosomal protein S17

Probab=100.00  E-value=7.7e-35  Score=191.30  Aligned_cols=70  Identities=44%  Similarity=0.694  Sum_probs=68.6

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEE
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIA   71 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V   71 (107)
                      ++|.|+|+|++|+||++|+|+++++||+|+|+++++++|+||||.|+|++||+|.|.|||||||+|+|.|
T Consensus         2 ~~l~G~Vvs~km~KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ecrPlSK~K~~~~   71 (71)
T TIGR03635         2 KTLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIETRPLSKTKRWRL   71 (71)
T ss_pred             eEEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEcCCcCCceEeEC
Confidence            5799999999999999999999999999999999999999999999999999999999999999999975

This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.

>TIGR03630 arch_S17P archaeal ribosomal protein S17P

Probab=100.00  E-value=1.7e-34  Score=201.30  Aligned_cols=74  Identities=38%  Similarity=0.559  Sum_probs=72.1

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCCceeEEEEEee
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-NQFQVGDLVQLEKSRPISKTKSFIAVAMP   75 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv   75 (107)
                      +.|+|+|+|++|+|||+|+|+|+++||+|+|+++++++|+||||+ |+|++||.|+|+|||||||+|+|.|.+|+
T Consensus        28 k~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky~aHDe~cn~~kvGD~V~I~E~RPlSKtK~w~vv~i~  102 (102)
T TIGR03630        28 QILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLSKTKSFVVLGKV  102 (102)
T ss_pred             EEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeEEEECCCCCCCCCCCEEEEEEcCCCCCceEEEEEEeC
Confidence            689999999999999999999999999999999999999999999 79999999999999999999999999985

This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.

>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-35  Score=207.14  Aligned_cols=99  Identities=45%  Similarity=0.619  Sum_probs=92.7

Q ss_pred             CceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            1 MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         1 ~k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      |+-++|+|+|.+|+||++|+|+++.+||+|+||++++++|+|||+.|.|++||.|+|++||||||+|+|++.+||.++.+
T Consensus         2 m~~~vg~VvS~kmqKTv~V~V~rl~~n~~ynryv~~~~kymahD~~n~cnvGD~VrlepsRPlSk~K~f~i~eII~~a~r   81 (107)
T KOG1740|consen    2 MKNVVGTVVSNKMQKTVKVRVDRLFFNPKYNRYVKRTSKYMAHDDKNQCNVGDRVRLEPSRPLSKTKHFIIAEIIKKARR   81 (107)
T ss_pred             CccceeeeeecccCceeEEEeeeccccHHHHHHHHHhhheeecCccccccccceEEeccCCcccccceeehHHHHHHHhh
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCccccccccchhh
Q 033970           81 KKAAGESSNAGNNELGIPLESEQQ  104 (107)
Q Consensus        81 ~~~a~~~~~~~~~~~~~~~~~~~~  104 (107)
                      ..+|.|.+.     ||+|..+|||
T Consensus        82 ~spa~~~ea-----~~s~~~~~~~  100 (107)
T KOG1740|consen   82 YSPAAEAEA-----LGSSASSQQQ  100 (107)
T ss_pred             hCcchhhhh-----hcCchhhhcc
Confidence            877766654     6778888887

>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=100.00  E-value=6.7e-34  Score=185.57  Aligned_cols=69  Identities=54%  Similarity=0.791  Sum_probs=67.0

Q ss_pred             EEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEe
Q 033970            6 GRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAM   74 (107)
Q Consensus         6 G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~I   74 (107)
                      |+|+|++|+||++|+|+++++||+|+|+++++++|+||||+|.|++||+|+|+|||||||+|+|.|.+|
T Consensus         1 G~Vvs~km~KTv~V~v~~~~~~~ky~K~~~~~kk~~aHD~~~~~~vGD~V~I~e~rPiSk~K~~~v~~v   69 (69)
T PF00366_consen    1 GVVVSDKMDKTVVVRVERLVYHPKYKKYIKRTKKYMAHDENNICKVGDKVRIRECRPISKTKRFVVVEV   69 (69)
T ss_dssp             EEEEEEESTTEEEEEEEEEEEETTTEEEEEEEEEEEEE-TTSSSTTTSEEEEEEEEEEETTEEEEEEEE
T ss_pred             CEEEEcCCCCeEEEEEEEEEEcceEeeccCccccEEEeCCccCCCCCCEEEEEeeeccCCcEeEEEEEC
Confidence            999999999999999999999999999999999999999999999999999999999999999999986

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 [, ]. The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....

>PTZ00241 40S ribosomal protein S11; Provisional

Probab=99.98  E-value=6.7e-32  Score=200.16  Aligned_cols=77  Identities=23%  Similarity=0.369  Sum_probs=74.1

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECC-CCCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDP-ENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN   78 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe-~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~   78 (107)
                      ++|.|+|+|++|+|||+|+++++++||+|+||++++++|+|||| .+.|++||+|+|.|||||||+|+|+|++|+.++
T Consensus        69 ril~G~VvS~KM~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~~kvGD~V~I~EcRPLSKTKrf~Vv~V~~~~  146 (158)
T PTZ00241         69 RILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVEKNE  146 (158)
T ss_pred             eEEEEEEEEccCCccEEEEEEEEEecCccceEEEeeecEEEeCCccCCCCCCCEEEEEEcCCCCCceeEEEEEEEecc
Confidence            68999999999999999999999999999999999999999995 669999999999999999999999999999865

>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]

Probab=99.85  E-value=5e-22  Score=145.68  Aligned_cols=81  Identities=30%  Similarity=0.396  Sum_probs=76.3

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCC--CCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN--QFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~--~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      ++|.|+|++.+|++||+|+.+|++|.++|++|.+|++++-||-..+  ..++||+|.|.|||||||+++|.|++++..++
T Consensus        69 ril~G~V~k~Km~rTIvvrrdYlHy~~KY~ryekrHkN~svh~SPcFrdi~~gDiVtvGecrPLSKtvrfnVLkv~k~~g  148 (156)
T KOG1728|consen   69 RILTGTVVKMKMQRTIVVRRDYLHYIKKYNRYEKRHKNMSVHVSPCFRDIQEGDIVTVGECRPLSKTVRFNVLKVIKAAG  148 (156)
T ss_pred             EEEeeEEeeeceeEEEEEEhhhhhHhHHhhHHHHhccCCccccchhhhccccCCEEEEeecccccceEEEEEEEEeecCC
Confidence            5899999999999999999999999999999999999999999887  69999999999999999999999999998875


Q ss_pred             ccc
Q 033970           80 SKK   82 (107)
Q Consensus        80 ~~~   82 (107)
                      ..+
T Consensus       149 ~~k  151 (156)
T KOG1728|consen  149 SKK  151 (156)
T ss_pred             Ccc
Confidence            443

>KOG3447 consensus Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis]

Probab=99.81  E-value=6.3e-21  Score=139.15  Aligned_cols=105  Identities=26%  Similarity=0.299  Sum_probs=99.3

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeec-ccCCCceeEEEEEeecCCcc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKS-RPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~-RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ..|.|.|+..+|++|++|++.++.++|+..|||.|++.|||||+-..|++||+|+|++. -|..+..+|.|.+|+++-+-
T Consensus        11 ~~lmGk~ig~~~q~~akVR~~r~eld~yL~kYf~k~~~yfAhD~~~~c~vGDtVLir~lp~r~t~~V~H~v~~VVfk~G~   90 (150)
T KOG3447|consen   11 QWLMGKVIGTKMQKTAKVRVTRLELDPYLLKYFNKRKTYFAHDALQQCTVGDTVLIRALPVRRTKHVKHEVAEVVFKVGK   90 (150)
T ss_pred             EEEEeeeeeccccccceeeeehhhcCHHHHHHhccccceeecchhhccccCCEEEEecCCcchhhhhhhhhHhheeeccc
Confidence            47899999999999999999999999999999999999999999999999999999998 78889999999999999888


Q ss_pred             c-cccccCCCCCCccccccccchhhhc
Q 033970           81 K-KAAGESSNAGNNELGIPLESEQQLE  106 (107)
Q Consensus        81 ~-~~a~~~~~~~~~~~~~~~~~~~~~~  106 (107)
                      - ++.|+.+|++-||+++|..-+-|++
T Consensus        91 IidPvTGkk~~~~ty~e~~~~~~~~~~  117 (150)
T KOG3447|consen   91 IIDPVTGKKCAGDTYLESPLSKETTQL  117 (150)
T ss_pred             ccCCCcCccccCcchhcchHHHHHHHh
Confidence            7 9999999999999999988776653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	107
3bbn_Q	142	Homology Model For The Spinach Chloroplast 30s Subu		7e-26
2j00_Q	105	Structure Of The Thermus Thermophilus 70s Ribosome		8e-09
1i94_Q	104	Crystal Structures Of The Small Ribosomal Subunit W		8e-09
1fjg_Q	105	Structure Of The Thermus Thermophilus 30s Ribosomal		8e-09
1j5e_Q	104	Structure Of The Thermus Thermophilus 30s Ribosomal		9e-09
3mr8_Q	99	Recognition Of The Amber Stop Codon By Release Fact		9e-09
3fic_Q	100	T. Thermophilus 70s Ribosome In Complex With Mrna,		9e-09
1vs5_Q	84	Crystal Structure Of The Bacterial Ribosome From Es		3e-08
3fih_Q	80	Ternary Complex-Bound E.Coli 70s Ribosome. This Ent		3e-08
1p6g_Q	83	Real Space Refined Coordinates Of The 30s Subunit F		3e-08
2gy9_Q	79	Structure Of The 30s Subunit Of A Pre-Translocation		4e-08
1eg0_G	93	Fitting Of Components With Known Structure Into An		6e-08
1rip_A	81	Ribosomal Protein S17: Characterization Of The Thre		7e-08
1qd7_I	89	Partial Model For 30s Ribosomal Subunit Length = 89		7e-08

>pdb|3BBN|Q Chain Q, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 142

Iteration: 1
 Score =  112 bits (279), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 54/81 (66%), Positives = 62/81 (76%)
Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
           MK MQGRVVCA+SDKTVAVEVVRL PHP            QAHDP+NQF+VGD+V+LEKS
Sbjct: 60  MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKS 119
Query: 61  RPISKTKSFIAVAMPPRNASK 81
           RPISKTKSF+A+ +  R A K
Sbjct: 120 RPISKTKSFVALPVIARAARK 140

>pdb|2J00|Q Chain Q, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 1 Of 4). This File Contains The 30s Subunit, Mrna, A-, P- And E-Site Trnas And Paromomycin For Molecule I. Length = 105

Iteration: 1
 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE ++++GD+V++ +SR
Sbjct: 4  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 63
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 64 PISKRKRF 71

>pdb|1I94|Q Chain Q, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 104

Iteration: 1
 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE +++VGD+V++ ++R
Sbjct: 3  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEERYKVGDVVEIIEAR 62
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 63 PISKRKRF 70

>pdb|1FJG|Q Chain Q, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 105

Iteration: 1
 Score = 55.5 bits (132), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE ++++GD+V++ +SR
Sbjct: 4  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 63
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 64 PISKRKRF 71

>pdb|1J5E|Q Chain Q, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit Length = 104

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE ++++GD+V++ +SR
Sbjct: 3  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 62
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 63 PISKRKRF 70

>pdb|3MR8|Q Chain Q, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s Ribosomal Subunit Can Be Found In Pdb Entry 3ms1. Molecule B In The Same Asymmetric Unit Is Deposited As 3mrz (50s) And 3ms0 (30s). Length = 99

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE ++++GD+V++ +SR
Sbjct: 3  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 62
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 63 PISKRKRF 70

>pdb|3FIC|Q Chain Q, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 30s Subunit And The Ligands Length = 100

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP             AHDPE ++++GD+V++ +SR
Sbjct: 3  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 62
Query: 62 PISKTKSF 69
          PISK K F
Sbjct: 63 PISKRKRF 70

>pdb|1VS5|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 84

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 1  MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
          ++ +QGRVV    +K++ V + R   HP              HD  N+  +GD+V++ + 
Sbjct: 5  IRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC 64
Query: 61 RPISKTKSFIAV 72
          RP+SKTKS+  V
Sbjct: 65 RPLSKTKSWTLV 76

>pdb|3FIH|Q Chain Q, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 80

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 1  MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
          ++ +QGRVV    +K++ V + R   HP              HD  N+  +GD+V++ + 
Sbjct: 2  IRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC 61
Query: 61 RPISKTKSFIAV 72
          RP+SKTKS+  V
Sbjct: 62 RPLSKTKSWTLV 73

>pdb|1P6G|Q Chain Q, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 83

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 1  MKKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKS 60
          ++ +QGRVV    +K++ V + R   HP              HD  N+  +GD+V++ + 
Sbjct: 4  IRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIREC 63
Query: 61 RPISKTKSFIAV 72
          RP+SKTKS+  V
Sbjct: 64 RPLSKTKSWTLV 75

>pdb|2GY9|Q Chain Q, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 79

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 38/71 (53%)
Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSR 61
          + +QGRVV    +K++ V + R   HP              HD  N+  +GD+V++ + R
Sbjct: 1  RTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECR 60
Query: 62 PISKTKSFIAV 72
          P+SKTKS+  V
Sbjct: 61 PLSKTKSWTLV 71

>pdb|1RIP|A Chain A, Ribosomal Protein S17: Characterization Of The Three- Dimensional Structure By 1h-And 15n-Nmr Length = 81

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 35/64 (54%)
Query: 6  GRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSRPISK 65
          GRVV    DKT+ V V     HP            +AHD  N+ +VGD+V++ ++RP+S 
Sbjct: 7  GRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSA 66
Query: 66 TKSF 69
          TK F
Sbjct: 67 TKRF 70

>pdb|1QD7|I Chain I, Partial Model For 30s Ribosomal Subunit Length = 89

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 35/64 (54%)
Query: 6  GRVVCASSDKTVAVEVVRLDPHPXXXXXXXXXXXXQAHDPENQFQVGDLVQLEKSRPISK 65
          GRVV    DKT+ V V     HP            +AHD  N+ +VGD+V++ ++RP+S 
Sbjct: 7  GRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSA 66
Query: 66 TKSF 69
          TK F
Sbjct: 67 TKRF 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	107
3bbn_Q	142	Ribosomal protein S17; small ribosomal subunit, sp	2e-26
3r8n_Q	80	30S ribosomal protein S17; protein biosynthesis, R	4e-25
1qd7_I	89	S17 ribosomal protein; 30S ribosomal subunit, low	1e-24
2vqe_Q	105	30S ribosomal protein S17; tRNA-binding, rRNA-bind	2e-24
2zkq_q	158	40S ribosomal protein S11E; protein-RNA complex, 4	2e-20
3iz6_P	161	40S ribosomal protein S11 (S17P); eukaryotic ribos	2e-20
2xzm_Q	157	Ribosomal protein S17 containing protein; ribosome	4e-19
3u5c_L	156	RP41, S18, YS12, 40S ribosomal protein S11-A; tran	5e-18

>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 142

 Score = 94.5 bits (235), Expect = 2e-26
 Identities = 60/71 (84%), Positives = 68/71 (95%)

Query: 2   KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
           K MQGRVVCA+SDKTVAVEVVRL PHPKYKRR+R KKKYQAHDP+NQF+VGD+V+LEKSR
Sbjct: 61  KTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKSR 120

Query: 62  PISKTKSFIAV 72
           PISKTKSF+A+
Sbjct: 121 PISKTKSFVAL 131

>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model, ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1eg0_G 1rip_A Length = 89

 Score = 88.1 bits (219), Expect = 1e-24
 Identities = 32/71 (45%), Positives = 45/71 (63%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K   GRVV    DKT+ V V     HP Y +R++  KKY+AHD  N+ +VGD+V++ ++R
Sbjct: 3  KVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETR 62

Query: 62 PISKTKSFIAV 72
          P+S TK F  V
Sbjct: 63 PLSATKRFRLV 73

>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T* 1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q 1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q* 1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ... Length = 105

 Score = 87.8 bits (218), Expect = 2e-24
 Identities = 34/71 (47%), Positives = 47/71 (66%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP Y + I++ KKY AHDPE ++++GD+V++ +SR
Sbjct: 4  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 63

Query: 62 PISKTKSFIAV 72
          PISK K F  +
Sbjct: 64 PISKRKRFRVL 74

>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_Q* 1s1h_Q Length = 158

 Score = 79.1 bits (195), Expect = 2e-20
 Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 4   MQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE--NQFQVGDLVQLEKSR 61
           + G V      +T+ +    L    KY R  ++ K    H        Q+GD+V + + R
Sbjct: 73  LSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECR 132

Query: 62  PISKTKSFIAVAMPPRNASKKA 83
           P+SKT  F  + +     +KK 
Sbjct: 133 PLSKTVRFNVLKVTKAAGTKKQ 154

>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 161

 Score = 79.2 bits (195), Expect = 2e-20
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-QFQVGDLVQLEK 59
            + + G    A  ++T+ V    L    KY+R  ++     AH     + + GD V + +
Sbjct: 69  GRIIAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQ 128

Query: 60  SRPISKTKSFIAVAMPPRNASKKAAGE 86
            RP+SKT  F  + + P  ++  + G+
Sbjct: 129 CRPLSKTVRFNVLKVIPAGSTGGSGGK 155

>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Q Length = 157

 Score = 76.1 bits (187), Expect = 4e-19
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 1   MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPEN-QFQVGDLVQLEK 59
            K ++G V+    ++TV +    L    KY R  ++ +    H       + GD++   +
Sbjct: 67  GKIIKGLVISTKMNRTVIIRRDYLHYVRKYNRYEKRHRNIPVHISPCFSVKEGDILVAGQ 126

Query: 60  SRPISKTKSFIAVAMPPRNASKKA 83
            RPISKT  F A+ + P       
Sbjct: 127 CRPISKTVRFNALQVVPNEIIGSV 150

>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q* 1s1h_Q Length = 156

 Score = 73.3 bits (180), Expect = 5e-18
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 2   KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAH-DPENQFQVGDLVQLEKS 60
           K + G VV     +T+ +    L   PKY R  ++ K    H  P  + QVGD+V + + 
Sbjct: 69  KILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQC 128

Query: 61  RPISKTKSFIAV 72
           RPISKT  F  V
Sbjct: 129 RPISKTVRFNVV 140

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	107
1qd7_I	89	S17 ribosomal protein; 30S ribosomal subunit, low	100.0
3r8n_Q	80	30S ribosomal protein S17; protein biosynthesis, R	100.0
2vqe_Q	105	30S ribosomal protein S17; tRNA-binding, rRNA-bind	100.0
3j20_R	113	30S ribosomal protein S17P; archaea, archaeal, KIN	100.0
3bbn_Q	142	Ribosomal protein S17; small ribosomal subunit, sp	100.0
2xzm_Q	157	Ribosomal protein S17 containing protein; ribosome	100.0
3u5c_L	156	RP41, S18, YS12, 40S ribosomal protein S11-A; tran	100.0
2zkq_q	158	40S ribosomal protein S11E; protein-RNA complex, 4	100.0
3iz6_P	161	40S ribosomal protein S11 (S17P); eukaryotic ribos	99.96

>1qd7_I S17 ribosomal protein; 30S ribosomal subunit, low resolution model, ribosome; 5.50A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1eg0_G 1rip_A

Probab=100.00  E-value=5.8e-38  Score=213.11  Aligned_cols=80  Identities=40%  Similarity=0.635  Sum_probs=77.4

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCccc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNASK   81 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~~   81 (107)
                      ++|+|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|.+|++++...
T Consensus         3 k~l~G~VvS~Km~KTivV~ve~~~~hp~Y~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~RPlSKtK~~~vv~iv~~a~~~   82 (89)
T 1qd7_I            3 KVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAVRA   82 (89)
T ss_pred             EEEEEEEEecCCCceEEEEEEEEEEcCccceEEeccEEEEEeCCccCCCCCCEEEEEEcccCCCCEEEEEEEEEeeceee
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999988644

>2vqe_Q 30S ribosomal protein S17; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: b.40.4.5 PDB: 1gix_T* 1hnw_Q* 1hnx_Q* 1hnz_Q* 1hr0_Q 1ibk_Q* 1ibl_Q* 1ibm_Q 1jgo_T* 1jgp_T* 1jgq_T* 1ml5_T* 1xmo_Q* 1xmq_Q* 1xnq_Q* 1xnr_Q* 1yl4_T 2b64_Q* 2b9m_Q* 2b9o_Q* ...

Probab=100.00  E-value=1.7e-36  Score=211.15  Aligned_cols=79  Identities=43%  Similarity=0.675  Sum_probs=77.1

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ++|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+|+|++||+|+|.|||||||+|+|.|.+|++++..
T Consensus         4 k~l~G~VvS~Km~KTivV~ver~~~hpkY~K~~kr~kk~~aHDe~n~~k~GD~V~I~E~RPlSKtKr~~vv~iv~~a~~   82 (105)
T 2vqe_Q            4 KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRM   82 (105)
T ss_dssp             CEEEEEEEEEEETTEEEEEEEEEEECTTTCCEEEEEEEEEEECTTCCCCTTCEEEEEEEEEEETTEEEEEEEEEECCCH
T ss_pred             eEEEEEEEecCCCcEEEEEEEEEEEcCccceEEecceEEEEECCCCCCCCCCEEEEEEcccCCCCEEEEEEEEeecccc
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999999874

>3j20_R 30S ribosomal protein S17P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=100.00  E-value=3.4e-35  Score=206.89  Aligned_cols=79  Identities=37%  Similarity=0.479  Sum_probs=76.5

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECC-CCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDP-ENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe-~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ++|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+|||| .|+|++||+|+|+|||||||+|+|.|.+|+++|..
T Consensus        32 r~l~G~VvS~KM~KTivV~ve~~~~hpkY~K~~kr~kk~~aHDe~~n~~~vGD~V~I~E~RPlSKtKr~~vv~i~~~a~~  111 (113)
T 3j20_R           32 RVFEGIVVSDKPRKTVTVERQYYFYLNKYERYELRRSKIHAHNPPCINAKVGDKVLIAETRPLSKTKHFVVVAVLERAEE  111 (113)
T ss_dssp             CEEEEEEEECCSTTEEEEEEEEEEEETTTTEEEEEEEEEEEECCTTSCCCTTSEEEEEECSCSSSSEEEEEEEECCCCCC
T ss_pred             EEEEEEEEeccCCceEEEEEEEEEEcCcccEEEECceEEEEECCCCCCCCCCCEEEEEecccCCCcEeEEEEEEEecccc
Confidence            68999999999999999999999999999999999999999999 78999999999999999999999999999998864

>3bbn_Q Ribosomal protein S17; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=100.00  E-value=8.8e-36  Score=216.72  Aligned_cols=80  Identities=79%  Similarity=1.177  Sum_probs=77.4

Q ss_pred             CceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            1 MKKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         1 ~k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      +++|.|+|+|++|+|||+|+|+++++||+|+|+++++++|+||||+|+|++||+|+|+|||||||+|+|.|++|++++..
T Consensus        60 ~k~l~G~VVS~KMdKTIvV~Ver~~~hpkY~K~vkr~kKy~AHDe~n~~kvGD~V~I~E~RPLSKtKrw~VveIveka~~  139 (142)
T 3bbn_Q           60 MKTMQGRVVCATSDKTVAVEVVRLAPHPKYKRRVRMKKKYQAHDPDNQFKVGDVVRLEKSRPISKTKSFVALPVIARAAR  139 (142)
T ss_dssp             CCEEEEEEEECCSTTEEEEEEEEEEECSSSCSEEEEEEEEEEECTTCCCCTTEEEEEEECCCSSSSCCEEECCCSEEECS
T ss_pred             eEEEEEEEEEccCCceEEEEEEEEEEcCccccEEecceEEEEECCCCCCCCCCEEEEEEccCCCCcEEEEEEEEEecccc
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999988763

>2xzm_Q Ribosomal protein S17 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_Q

Probab=100.00  E-value=6.4e-34  Score=209.81  Aligned_cols=78  Identities=28%  Similarity=0.416  Sum_probs=75.0

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEEC-CCCCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHD-PENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHD-e~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      ++|+|+|+|++|+|||+|+|+++++||+|+|+++++++|+||| |.|+|++||+|+|+|||||||+|+|.|++|++++.
T Consensus        68 r~l~G~VVS~KMdKTIvV~ve~~~~hpkY~K~vkr~kKy~AHDee~n~~kvGD~V~I~EcRPLSKtKrw~Vv~I~~ka~  146 (157)
T 2xzm_Q           68 KIIKGLVISTKMNRTVIIRRDYLHYVRKYNRYEKRHRNIPVHISPCFSVKEGDILVAGQCRPISKTVRFNALQVVPNEI  146 (157)
T ss_dssp             CEEEEEEEECCSTTEEEEEEEEEEEETTTTEEEEEEEEEEEECCTTSCCCTTCEEEEEECCCCSSSCCEEEEEECCCCC
T ss_pred             EEEEEEEEEecCCccEEEEEEEEEecCccceEeecceeEEEECCCCCCCCCCCEEEEEEcCCCCCcEEEEEEEEEeccc
Confidence            6899999999999999999999999999999999999999999 56799999999999999999999999999998864

>3u5c_L RP41, S18, YS12, 40S ribosomal protein S11-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_P 3o30_F 3o2z_F 3u5g_L 3jyv_Q* 1s1h_Q

Probab=100.00  E-value=1e-33  Score=208.52  Aligned_cols=78  Identities=32%  Similarity=0.479  Sum_probs=75.4

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-CCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-NQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      ++|.|+|+|++|+|||+|+++++++||+|+|+++++++|+||||+ |.|++||+|+|+|||||||+|+|.|.+|+++++
T Consensus        69 r~l~G~VVS~KMdKTIvV~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~EcRPLSKtKrw~Vv~Iv~ka~  147 (156)
T 3u5c_L           69 KILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKVSAAAG  147 (156)
T ss_dssp             EEEEEEEEECCSTTEEEEEEEEEEEEGGGTEEEEEEEEEEEECCTTSCCCTTCEEEEEEEEEEETTEEEEEEEECCCCS
T ss_pred             EEEEEEEEeecCCCeEEEEEEEEeecCccceEEECceEEEEECCCcCcCCCCCEEEEEecccCCCcEeEEEEEEEecCC
Confidence            589999999999999999999999999999999999999999984 699999999999999999999999999999985

>2zkq_q 40S ribosomal protein S11E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_Q* 1s1h_Q

Probab=100.00  E-value=1.6e-33  Score=207.86  Aligned_cols=78  Identities=24%  Similarity=0.363  Sum_probs=71.4

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCC-C-CCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPE-N-QFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~-~-~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      ++|+|+|+|++|+|||+|+++++++||+|+|+++++++|+||||+ | +|++||+|+|+|||||||+|+|.|++|+..++
T Consensus        71 r~l~G~VVS~KMdKTIvV~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~~kvGD~V~I~E~RPLSKtKrw~Vv~I~~~~~  150 (158)
T 2zkq_q           71 RILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTKAAG  150 (158)
T ss_dssp             CEEEEEEEECSSSCEEEEEEEEECSSTTCCCEEEEEEEECCBCCSSCCCC-CCCEEEEECCSCSSSCC-CEEEEEEEC--
T ss_pred             EEEEEEEEEccCCccEEEEEEEEEecCccceeeecceeEEEECCcccCcCCCCCEEEEEEccccCCcEEEEEEEEecCCC
Confidence            689999999999999999999999999999999999999999986 4 79999999999999999999999999997654

>3iz6_P 40S ribosomal protein S11 (S17P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=99.96  E-value=2.4e-33  Score=207.43  Aligned_cols=79  Identities=25%  Similarity=0.356  Sum_probs=52.0

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECC-CCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDP-ENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe-~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ++|+|+|+|++|+|||+|+++++++||+|+|+++++++|+|||| .|+|++||+|+|+|||||||+|+|.|.+|++++..
T Consensus        70 ril~G~VVS~KMdKTIvV~ve~~~~hpkY~K~vkr~kKy~AHDe~~n~~kvGD~V~I~EcRPLSKtKrw~Vv~Iv~~~~~  149 (161)
T 3iz6_P           70 RIIAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGST  149 (161)
T ss_dssp             EECTTTCCEEEEEEEEEEECTTCCCCSSCEEEEEECCCSSSSCCEEEEECCCCCC-------------------------
T ss_pred             EEEEEEEEeccCCCeEEEEEEEEEecCccceEEECceeEEEECCCCCcCCCCCEEEEEeccCCCCcEeEEEEEEEecCcc
Confidence            57899999999999999999999999999999999999999998 57999999999999999999999999999998654

---

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	107
d2gy9q1	78	b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherich	3e-24
d2uubq1	100	b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus	4e-24
d1ripa_	81	b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stea	2e-22

>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]} Length = 78

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Escherichia coli [TaxId: 562]

 Score = 85.5 bits (212), Expect = 3e-24
 Identities = 27/71 (38%), Positives = 44/71 (61%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          + +QGRVV    +K++ V + R   HP Y + I++  K   HD  N+  +GD+V++ + R
Sbjct: 1  RTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECR 60

Query: 62 PISKTKSFIAV 72
          P+SKTKS+  V
Sbjct: 61 PLSKTKSWTLV 71

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]} Length = 100

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

 Score = 85.9 bits (213), Expect = 4e-24
 Identities = 34/71 (47%), Positives = 47/71 (66%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K + G VV     KTV V V R  PHP Y + I++ KKY AHDPE ++++GD+V++ +SR
Sbjct: 3  KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESR 62

Query: 62 PISKTKSFIAV 72
          PISK K F  +
Sbjct: 63 PISKRKRFRVL 73

>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]} Length = 81

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 81.3 bits (201), Expect = 2e-22
 Identities = 32/71 (45%), Positives = 45/71 (63%)

Query: 2  KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSR 61
          K   GRVV    DKT+ V V     HP Y +R++  KKY+AHD  N+ +VGD+V++ ++R
Sbjct: 3  KVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETR 62

Query: 62 PISKTKSFIAV 72
          P+S TK F  V
Sbjct: 63 PLSATKRFRLV 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	107
d2gy9q1	78	Ribosomal protein S17 {Escherichia coli [TaxId: 56	100.0
d2uubq1	100	Ribosomal protein S17 {Thermus thermophilus [TaxId	100.0
d1ripa_	81	Ribosomal protein S17 {Bacillus stearothermophilus	100.0

>d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4.1e-37  Score=202.68  Aligned_cols=77  Identities=35%  Similarity=0.651  Sum_probs=75.6

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCC
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRN   78 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~   78 (107)
                      |+|.|+|+|++|+||++|+|+|+++||+|+|+++++++|+||||+|.|++||+|+|.|||||||+|+|.|.+|+++|
T Consensus         1 r~l~G~Vvs~km~KTv~V~v~r~~~h~ky~K~~~~~kky~aHDe~~~~~~GD~V~I~e~rPlSK~K~~~v~~iv~ka   77 (78)
T d2gy9q1           1 RTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKA   77 (78)
T ss_dssp             CEEEEEEEECCSSSEEEEEEEEEEECSSSCCEEEEEEEEEEECTTCCCCTTCEEEEEECSCSSSSCCEEEEEEEESC
T ss_pred             CEEEEEEEecCCCCcEEEEEEEEEEcCccCEEEEeeEEEEEECCCCCCccccEEEEEEcCcCCCcEEEEEEEEEecc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999986

>d2uubq1 b.40.4.5 (Q:2-101) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=7.4e-36  Score=204.67  Aligned_cols=79  Identities=43%  Similarity=0.675  Sum_probs=76.9

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCcc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNAS   80 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~~   80 (107)
                      ++|.|+|+|++|+|||+|.|+++++||+|+|+++++++|+||||.|.|++||+|+|.|||||||+|+|.|.+|++++..
T Consensus         3 r~l~G~Vvs~km~KTv~V~v~r~~~h~ky~K~~~r~kk~~vHD~~n~~k~GD~V~I~e~rPlSK~K~~~v~~Iv~ka~~   81 (100)
T d2uubq1           3 KVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRM   81 (100)
T ss_dssp             CEEEEEECCCCBTTEEEEEEEEEEEETTTEEEEEEEEEEEEECTTCCCCTTCEEEEEEEEEEETTEEEEEEEEEECCCH
T ss_pred             eEEEEEEEEcCCCCcEEEEEEEEEeccccCEEEEeeEEEEEECCCCCCCCCCEEEEEECcCCCCceEEEEEEEEeccCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999999999998774

>d1ripa_ b.40.4.5 (A:) Ribosomal protein S17 {Bacillus stearothermophilus [TaxId: 1422]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S17
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=6.6e-37  Score=203.01  Aligned_cols=78  Identities=41%  Similarity=0.654  Sum_probs=76.1

Q ss_pred             ceEEEEEEeCCCCCeEEEEEeEEEeccccceEEEeeeeEEEECCCCCCCCCCEEEEeecccCCCceeEEEEEeecCCc
Q 033970            2 KKMQGRVVCASSDKTVAVEVVRLDPHPKYKRRIRKKKKYQAHDPENQFQVGDLVQLEKSRPISKTKSFIAVAMPPRNA   79 (107)
Q Consensus         2 k~l~G~VVs~km~KTvvV~V~r~~~hpky~K~~~r~kk~~vHDe~~~~~vGD~V~I~e~RPiSK~K~~~V~~Iv~~~~   79 (107)
                      ++|.|+|+|++|+||++|+|+|+++||+|+|+++++++|+||||+|.|++||+|+|.|||||||+|+|.|.+|+++|.
T Consensus         3 k~~~G~Vvs~km~KTv~V~v~r~~~~~ky~K~~kr~kk~~aHd~~~~~~~GD~V~I~e~rPlSK~K~~~v~~Ii~ka~   80 (81)
T d1ripa_           3 KVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAV   80 (81)
T ss_dssp             SCBCCEESCCCSSSCSCCCBCCSCCCSCSSSCCCCSBCCCCCCCSTTCSSCEECCBCCCCCSSSCCCCCCCCCBSSSC
T ss_pred             cEEEEEEEecCCCCcEEEEEEEEEEcCccCEEEEeeEEEEEECCCCCCccCCEEEEEEccCCCCCeeEEEEEEehHhC
Confidence            579999999999999999999999999999999999999999999999999999999999999999999999999875