Citrus Sinensis ID: 034908

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------8
Protein Sequence
MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Secondary Structure (PSIPRED)
ccccEEEEEEcccccHHHHHHHHHHHHHcHHccccEEEEEccccEEEEEEEEEEccccEEEEEEEcEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHEEEEEcccccHHHHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEEEEcccccEEEEEEEEEEccccEEEcccc
Coil and Loop (DISEMBL)
mplydcmlllkphvrKESLMELVARVGkhvygrngvltditsfgtvqlgygikkldgryyqliptwefnsgsifegfmw
Flexible Loop (DISEMBL)
MPLYDCMLLLKPHVRKESLMELVARVGKhvygrngvltditsfgtvQLGYGIKKLDGRYYQLIptwefnsgsifegfmw
Low Complexity Region (SEG)
MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Disordered region (IsUnstruct)
**LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGF**
Disordered Region (DISOPRED)
*PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Disordered Region (DISEMBL)
MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Disordered Region (DISPRO)
MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFEGFMW
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	79
313586453	163	30S ribosomal protein S6A [Hevea brasili	0.772	0.374	0.934	6e-27
313586455	163	30S ribosomal protein S6B [Hevea brasili	0.772	0.374	0.918	2e-26
224144016	136	predicted protein [Populus trichocarpa]	0.772	0.448	0.885	4e-25
225463002	162	PREDICTED: uncharacterized protein LOC10	0.772	0.376	0.885	4e-24
449529120	153	PREDICTED: 37S ribosomal protein MRP17,	0.772	0.398	0.786	3e-21
145332631	134	small subunit ribosomal protein S6 [Arab	0.784	0.462	0.758	4e-21
449463238	140	PREDICTED: LOW QUALITY PROTEIN: 37S ribo	0.772	0.435	0.786	4e-21
18401997	139	small subunit ribosomal protein S6 [Arab	0.772	0.438	0.770	5e-21
297834792	139	ribosomal protein S6 family protein [Ara	0.772	0.438	0.770	6e-21
255565089	162	structural constituent of ribosome, puta	0.772	0.376	0.754	7e-21

>gi|313586453|gb|ADR71237.1| 30S ribosomal protein S6A [Hevea brasiliensis]

 Score =  124 bits (312), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 57/61 (93%), Positives = 60/61 (98%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLLLKPHVRKE+LM+LVARVGKHVYGRNGVLTDI SFGT+QLGYGIKKLDGRYY
Sbjct: 1  MPLYDCMLLLKPHVRKEALMDLVARVGKHVYGRNGVLTDIKSFGTIQLGYGIKKLDGRYY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|313586455|gb|ADR71238.1| 30S ribosomal protein S6B [Hevea brasiliensis]

 Score =  123 bits (308), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 56/61 (91%), Positives = 59/61 (96%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLLLKPHVRKE+LM+LVARVGKHVY RNGVLTDI SFGT+QLGYGIKKLDGRYY
Sbjct: 1  MPLYDCMLLLKPHVRKEALMDLVARVGKHVYARNGVLTDIKSFGTIQLGYGIKKLDGRYY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Hevea brasiliensis

Species: Hevea brasiliensis

Genus: Hevea

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144016|ref|XP_002325157.1| predicted protein [Populus trichocarpa] gi|222866591|gb|EEF03722.1| predicted protein [Populus trichocarpa]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 54/61 (88%), Positives = 59/61 (96%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCML+LKPHVRKE+LM+LVARVGKHVY RNGV+TDI SFGTVQLGYGIKKLDGR+Y
Sbjct: 1  MPLYDCMLMLKPHVRKEALMDLVARVGKHVYSRNGVVTDIKSFGTVQLGYGIKKLDGRHY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463002|ref|XP_002264271.1| PREDICTED: uncharacterized protein LOC100256785 [Vitis vinifera]

 Score =  115 bits (287), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 54/61 (88%), Positives = 56/61 (91%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MP YDCMLLLKPHV KESLM+LVARVGKHVY RNGVLTDI SFG V+LGYGIKKLDGRYY
Sbjct: 1  MPFYDCMLLLKPHVNKESLMDLVARVGKHVYRRNGVLTDIKSFGIVRLGYGIKKLDGRYY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449529120|ref|XP_004171549.1| PREDICTED: 37S ribosomal protein MRP17, mitochondrial-like [Cucumis sativus]

 Score =  105 bits (263), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYD M L+KPHV+KE+L++LVARVGKHV+ RNGV+ DI SFG VQLGYGIKKLDGRYY
Sbjct: 1  MPLYDVMFLMKPHVKKEALLDLVARVGKHVFRRNGVVCDIKSFGVVQLGYGIKKLDGRYY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145332631|ref|NP_001078181.1| small subunit ribosomal protein S6 [Arabidopsis thaliana] gi|332642622|gb|AEE76143.1| small subunit ribosomal protein S6 [Arabidopsis thaliana]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 56/62 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLL KP +RKE L++LVAR+GKHVY RNGVLT+I SFG V+LGYGI+KLDGR+Y
Sbjct: 1  MPLYDCMLLFKPIIRKEGLIDLVARIGKHVYSRNGVLTEIKSFGKVELGYGIRKLDGRHY 60

Query: 61 QL 62
          Q+
Sbjct: 61 QI 62

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463238|ref|XP_004149341.1| PREDICTED: LOW QUALITY PROTEIN: 37S ribosomal protein MRP17, mitochondrial-like [Cucumis sativus]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 48/61 (78%), Positives = 55/61 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYD M L+KPHV+KE+L++LVARVGKHV+ RNGV+ DI SFG VQLGYGIKKLDGRYY
Sbjct: 1  MPLYDVMFLMKPHVKKEALLDLVARVGKHVFRRNGVVCDIKSFGVVQLGYGIKKLDGRYY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18401997|ref|NP_566618.1| small subunit ribosomal protein S6 [Arabidopsis thaliana] gi|9293899|dbj|BAB01802.1| unnamed protein product [Arabidopsis thaliana] gi|21617981|gb|AAM67031.1| unknown [Arabidopsis thaliana] gi|26451219|dbj|BAC42712.1| unknown protein [Arabidopsis thaliana] gi|28827770|gb|AAO50729.1| unknown protein [Arabidopsis thaliana] gi|332642621|gb|AEE76142.1| small subunit ribosomal protein S6 [Arabidopsis thaliana]

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 55/61 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLL KP +RKE L++LVAR+GKHVY RNGVLT+I SFG V+LGYGI+KLDGR+Y
Sbjct: 1  MPLYDCMLLFKPIIRKEGLIDLVARIGKHVYSRNGVLTEIKSFGKVELGYGIRKLDGRHY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297834792|ref|XP_002885278.1| ribosomal protein S6 family protein [Arabidopsis lyrata subsp. lyrata] gi|297331118|gb|EFH61537.1| ribosomal protein S6 family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  104 bits (260), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 47/61 (77%), Positives = 55/61 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLL KP +RKE L++LVAR+GKHVY RNGVLT+I SFG V+LGYGI+KLDGR+Y
Sbjct: 1  MPLYDCMLLFKPIIRKEGLIDLVARIGKHVYSRNGVLTEIKSFGKVELGYGIRKLDGRHY 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565089|ref|XP_002523537.1| structural constituent of ribosome, putative [Ricinus communis] gi|223537244|gb|EEF38876.1| structural constituent of ribosome, putative [Ricinus communis]

 Score =  104 bits (259), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 46/61 (75%), Positives = 55/61 (90%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          MPLYDCMLLLKPH+ KE++++LVARVGKHV  RNGVLTD+ SFGT+QLGYGIKK + RY+
Sbjct: 1  MPLYDCMLLLKPHIHKEAVIDLVARVGKHVQSRNGVLTDMKSFGTIQLGYGIKKRENRYF 60

Query: 61 Q 61
          Q
Sbjct: 61 Q 61

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	79
TAIR|locus:2094009	139	AT3G18760 [Arabidopsis thalian	0.772	0.438	0.770	2.1e-22

TAIR|locus:2094009 AT3G18760 [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 47/61 (77%), Positives = 55/61 (90%)

Query:     1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
             MPLYDCMLL KP +RKE L++LVAR+GKHVY RNGVLT+I SFG V+LGYGI+KLDGR+Y
Sbjct:     1 MPLYDCMLLFKPIIRKEGLIDLVARIGKHVYSRNGVLTEIKSFGKVELGYGIRKLDGRHY 60

Query:    61 Q 61
             Q
Sbjct:    61 Q 61


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        0.325   0.144   0.462    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       79        79   0.00091  102 3  11 22  0.38    29
                                                     29  0.39    30


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:  1
  No. of states in DFA:  533 (57 KB)
  Total size of DFA:  104 KB (2072 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:  7.93u 0.15s 8.08t   Elapsed:  00:00:01
  Total cpu time:  7.93u 0.15s 8.08t   Elapsed:  00:00:01
  Start:  Fri May 10 03:30:33 2013   End:  Fri May 10 03:30:34 2013

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

GO:0005840 "ribosome" evidence=IEA;ISS

GO:0006412 "translation" evidence=IEA;ISS

GO:0019843 "rRNA binding" evidence=IEA

---

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

Your Input: gw1.XVIII.3383.1 hypothetical protein (136 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	79
PRK00453	108	PRK00453, rpsF, 30S ribosomal protein S6; Reviewed	2e-05
pfam01250	92	pfam01250, Ribosomal_S6, Ribosomal protein S6	3e-04
TIGR00166	93	TIGR00166, S6, ribosomal protein S6	0.001

>gnl|CDD|179034 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed

 Score = 38.6 bits (91), Expect = 2e-05
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKL-DGRY 59
          M  Y+ + +L+P + +E +  LV R    +    G +  +  +G  +L Y I KL  G Y
Sbjct: 1  MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHY 60

Query: 60 YQL 62
            L
Sbjct: 61 VLL 63

Length = 108

>gnl|CDD|216388 pfam01250, Ribosomal_S6, Ribosomal protein S6

 Score = 35.5 bits (83), Expect = 3e-04
 Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 3  LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKL-DGRYYQ 61
           Y+ M +L+P + +E +  L+ +  K +    G +  +  +G  +L Y IKK  +G Y  
Sbjct: 2  KYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVL 61

Query: 62 LI 63
          + 
Sbjct: 62 IN 63

Length = 92

>gnl|CDD|129270 TIGR00166, S6, ribosomal protein S6

 Score = 33.9 bits (78), Expect = 0.001
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 4/68 (5%)

Query: 3  LYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQL 62
           Y+ + L++P +  E +   + R  K +      +     +G  +L Y IKK    +Y L
Sbjct: 2  HYEIIFLVRPTL-SEEVKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYVL 60

Query: 63 IPTWEFNS 70
               F+ 
Sbjct: 61 ---MNFSG 65

The ribosomal protein S6 ortholog family, including yeast MRP17, shows more than two-fold length variation from 95 residues in Bacillus subtilis to 215 in Mycoplasma pneumoniae. This length variation comes primarily from poorly conserved C-terminal extensions that are particularly long in the Mycoplasmas. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 93

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	79
CHL00123	97	rps6 ribosomal protein S6; Validated	99.96
PRK00453	108	rpsF 30S ribosomal protein S6; Reviewed	99.94
COG0360	112	RpsF Ribosomal protein S6 [Translation, ribosomal	99.94
TIGR00166	93	S6 ribosomal protein S6. MRP17 protein is a compon	99.93
PF01250	92	Ribosomal_S6: Ribosomal protein S6; InterPro: IPR0	99.93
KOG4708	141	consensus Mitochondrial ribosomal protein MRP17 [T	99.66
PRK14074	257	rpsF 30S ribosomal protein S6; Provisional	99.61
PRK14074	257	rpsF 30S ribosomal protein S6; Provisional	98.87
COG4911	123	Uncharacterized conserved protein [Function unknow	83.75

>CHL00123 rps6 ribosomal protein S6; Validated

Probab=99.96  E-value=3.3e-29  Score=157.93  Aligned_cols=74  Identities=23%  Similarity=0.359  Sum_probs=71.6

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      |+.||+|+|++|++++++++++++++.++|.++||+|.++++||+|+|||||+|+++|||+ ++.|+++|+.+.|
T Consensus         5 mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~k~~~G~Yv-~~~f~~~~~~i~e   78 (97)
T CHL00123          5 LNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYI-QMNYSGNGKLVNS   78 (97)
T ss_pred             ccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCeeeeEEcCCCCEEEEE-EEEEEECHHHHHH
Confidence            7899999999999999999999999999999999999999999999999999999999999 9999999988766

>PRK00453 rpsF 30S ribosomal protein S6; Reviewed

Probab=99.94  E-value=4.2e-27  Score=149.86  Aligned_cols=74  Identities=26%  Similarity=0.484  Sum_probs=71.4

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+|+|++|++++++++++++++.++|.++||+|.++++||.|+|||+|+|+++|||. ++.|.++|+.+.|
T Consensus         1 M~~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LAY~I~k~~~G~Y~-~~~f~~~~~~i~e   74 (108)
T PRK00453          1 MRKYEIVFILRPDLSEEQVKALVERFKGVITENGGTIHKVEDWGRRRLAYPINKLRKGHYV-LLNFEAPPAAIAE   74 (108)
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEecccccccceEcCCCcEEEEE-EEEEEeCHHHHHH
Confidence            8999999999999999999999999999999999999999999999999999999999999 8999998887765

>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]

Probab=99.94  E-value=2.8e-27  Score=153.07  Aligned_cols=73  Identities=23%  Similarity=0.462  Sum_probs=70.5

Q ss_pred             CceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         2 ~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ++||+|||++|+++++++++.++++.++|+++||+|.++++||+|+|||||+|+++|||+ ++.|+++|+.+.|
T Consensus         1 ~~YEi~~iv~p~~see~~~~~ve~~~~~l~~~gg~i~~~e~wG~R~LAY~IkK~~~g~Y~-l~~f~~~~~~i~E   73 (112)
T COG0360           1 RKYEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYV-LMNFEAEPAAIAE   73 (112)
T ss_pred             CceEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEehhhhhhhhcceecccceEEEE-EEEEEcCHHHHHH
Confidence            579999999999999999999999999999999999999999999999999999999999 9999999888876

>TIGR00166 S6 ribosomal protein S6

Probab=99.93  E-value=1.8e-26  Score=143.69  Aligned_cols=72  Identities=21%  Similarity=0.311  Sum_probs=68.2

Q ss_pred             CceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         2 ~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      +.||+|+|++|+++++ +++++++++++|.++||+|.++++||+|+|||||+|+++|||+ ++.|+++|+.+.|
T Consensus         1 ~~YE~~~Il~p~~~~~-~~~~~~~~~~~i~~~gg~i~~~~~~G~r~LaY~I~k~~~G~Y~-~~~f~~~~~~i~e   72 (93)
T TIGR00166         1 RHYEIIFLVRPTLSEE-VKGQIERYKKVITLNGAEIVRSEDWGKRRLAYPIKKQLRAHYV-LMNFSGEAQVIKE   72 (93)
T ss_pred             CceeEEEEECCCCcHH-HHHHHHHHHHHHHhCCCEEEEEEeecceecceEcCCCceEEEE-EEEEEeCHHHHHH
Confidence            5799999999999988 9999999999999999999999999999999999999999999 8888888887765

MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.

>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=99.93  E-value=5e-26  Score=140.69  Aligned_cols=73  Identities=27%  Similarity=0.511  Sum_probs=68.8

Q ss_pred             CceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            2 PLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         2 ~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      |.||+++|++|++++++++++++++.++|.++||+|+++++||.|+|||||+|+.+|||. ++.|.++|+.+.|
T Consensus         1 r~YE~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~~G~Y~-~~~f~~~~~~i~e   73 (92)
T PF01250_consen    1 RKYELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQKEGHYF-LFNFDASPSAIKE   73 (92)
T ss_dssp             EEEEEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTECEEEEE-EEEEEESTTHHHH
T ss_pred             CceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCCEEEEE-EEEEEeCHHHHHH
Confidence            579999999999999999999999999999999999999999999999999999999999 8889988887765

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 S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....

>KOG4708 consensus Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]

Probab=99.66  E-value=2.4e-17  Score=109.88  Aligned_cols=71  Identities=44%  Similarity=0.662  Sum_probs=64.6

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEE-EEEEEeecCc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQL-IPTWEFNSGS   72 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~-~~~~~~~~~~   72 (79)
                      ||.||++.|+++...++ +...+.|..+.+.+.||+|++++++|.|.|||+|+|+++.||.+ +|.+.|.+++
T Consensus         3 mp~yelali~~~~~rpe-la~~l~rt~~~lid~ngVvrdveslG~r~Lpy~i~K~~~~h~~g~~f~m~f~ss~   74 (141)
T KOG4708|consen    3 MPLYELALITRSLSRPE-LAKLLARTGGHLIDRNGVVRDVESLGKRELPYKIKKLDQRHYRGQHFLMTFYSSP   74 (141)
T ss_pred             chHHHHHHHhcccCCHH-HHHHHHHHhhHHhhcCCeEeechhcchhhhcchHHHhcCccccceEEEEeecCCH
Confidence            89999999999775555 88889999999999999999999999999999999999999999 8899887654

>PRK14074 rpsF 30S ribosomal protein S6; Provisional

Probab=99.61  E-value=3.9e-16  Score=112.01  Aligned_cols=59  Identities=17%  Similarity=0.176  Sum_probs=53.9

Q ss_pred             CCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908           14 VRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus        14 l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      +++++++++++++.++|+++|  +.++++||+|+|||||+|+++|||+ ++.|+++|+.+.|
T Consensus       160 v~PDQveevvEkik~iIe~~G--iikvE~WGkRkLAYpIkK~~eGyYv-L~nFeAep~aIaE  218 (257)
T PRK14074        160 NGPNQSNKTLEMLLKNIEASG--LIKYEYWGLLDFAYPINKMKSGHYC-IMCISSTSSIMDE  218 (257)
T ss_pred             CCHHHHHHHHHHHHHHHHhcC--eeehHhhcchhhccccCCCCeEEEE-EEEEEcCHHHHHH
Confidence            456889999999999999995  5699999999999999999999999 9999999988776

>PRK14074 rpsF 30S ribosomal protein S6; Provisional

Probab=98.87  E-value=1.8e-09  Score=77.82  Aligned_cols=47  Identities=13%  Similarity=0.192  Sum_probs=46.0

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQ   47 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~   47 (79)
                      ||+||.+||++|+|+..+++.+++.++.++.++||.|.+.+.||.+.
T Consensus         1 m~lYE~~fIa~q~ls~~q~e~l~e~~~~~l~~~~~~v~~~e~wG~~~   47 (257)
T PRK14074          1 MNLYEFTFIAQQGLLQQEVEEMVQELAVLLKNIKADVMFQQIKGILE   47 (257)
T ss_pred             CCccceeeeecccccHHHHHHHHHHHHHHHHhcCCeeehhhhhhhhh
Confidence            99999999999999999999999999999999999999999999875

>COG4911 Uncharacterized conserved protein [Function unknown]

Probab=83.75  E-value=3.1  Score=27.22  Aligned_cols=51  Identities=14%  Similarity=0.240  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcc
Q 034908           17 ESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSI   73 (79)
Q Consensus        17 e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~   73 (79)
                      ++.++-.++.-.-|.+.|++|+++++ |.-.++=.+    .|.|. ++-++.|-+.+
T Consensus        47 ~e~e~q~k~~l~~i~e~G~iird~d~-glVDFpa~~----Ng~~~-~lCWK~DE~~i   97 (123)
T COG4911          47 QEYESQTKKILDEIIEKGIIIRDIDI-GLVDFPAII----NGKPA-FLCWKIDENDI   97 (123)
T ss_pred             HHHHHHHHHHHHHHHHcCceeecccc-ccccchhhh----CCceE-EEEEecCCcce
Confidence            45666677777778889999999987 777777666    36677 66777776654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	79
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	8e-04

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis} Length = 99

 Score = 34.1 bits (79), Expect = 8e-04
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKL-DGRY 59
          M  Y+ M +++P V +E+   LV R    +      + +   +G  +L Y I  L +G Y
Sbjct: 4  MRKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFY 63

Query: 60 YQL 62
            L
Sbjct: 64 MIL 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	79
1cqm_A	101	Ribosomal protein S6; alzheimer disease, oligomeri	99.96
2j5a_A	110	30S ribosomal protein S6; ribonucleoprotein, RIBO	99.96
3r8n_F	100	30S ribosomal protein S6; protein biosynthesis, RN	99.96
3r3t_A	99	30S ribosomal protein S6; structural genomics, cen	99.95
1vmb_A	140	30S ribosomal protein S6; TM0603, structural genom	99.95
3i1m_F	135	30S ribosomal protein S6; ribosome structure, prot	99.95
3bbn_F	168	Ribosomal protein S6; small ribosomal subunit, spi	99.94
2kjw_A	96	TS9, 30S ribosomal protein S6; S6 permutant, solut	99.88
3zzp_A	77	TS9, ribosomal protein S6; protein folding, RNA-bi	99.03

>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...

Probab=99.96  E-value=9.8e-31  Score=164.58  Aligned_cols=74  Identities=16%  Similarity=0.262  Sum_probs=71.5

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+++|++|++++++++++++++.++|.++||+|+++++||+|+|||+|+|+++|||+ ++.|.++|+.+.|
T Consensus         1 M~~YE~~~Il~p~l~~e~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~-l~~f~a~~~~i~e   74 (101)
T 1cqm_A            1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYFL-WYQVEMPEDRVND   74 (101)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEE-EEEEEECHHHHHH
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCcccccCcCCCCEEEEE-EEEEEeChHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999 9999998887765

>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1

Probab=99.96  E-value=4.3e-30  Score=163.93  Aligned_cols=74  Identities=20%  Similarity=0.373  Sum_probs=71.1

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEe-ecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEF-NSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~-~~~~~~e   75 (79)
                      ||.||+++|++|++++++++++++++.++|.++||+|+++++||+|+|||+|+|+++|||+ ++.|.+ +|+.+.|
T Consensus         7 M~~YE~~~Il~p~l~~e~~~~~v~~~~~~i~~~Gg~i~~~e~wG~R~LAY~I~K~~~G~Y~-l~~f~a~~~~~i~e   81 (110)
T 2j5a_A            7 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF-LVQFKTENPQLPNE   81 (110)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEECSSCSSSCSEEEEE-EEEEEESCTTHHHH
T ss_pred             CCcceEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecCcccccCcCCCCEEEEE-EEEEEeCCHHHHHH
Confidence            7899999999999999999999999999999999999999999999999999999999999 999999 8887765

>3r3t_A 30S ribosomal protein S6; structural genomics, center for structural genomics of infec diseases, csgid, beta-barrel, cytosol; 2.30A {Bacillus anthracis}

Probab=99.95  E-value=7.9e-31  Score=164.63  Aligned_cols=74  Identities=26%  Similarity=0.442  Sum_probs=70.7

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+|+|++|++++++++++++++.++|.++||+|+++++||+|+|||||+|+++|||+ ++.|.++|+.+.|
T Consensus         4 M~~YE~~~Il~p~~~~e~~~~~~~~~~~~i~~~gg~i~~~e~wG~R~LAY~I~k~~~G~Y~-l~~f~a~~~~i~e   77 (99)
T 3r3t_A            4 MRKYEIMYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFYM-ILNVNANAEAINE   77 (99)
T ss_dssp             CCCCCCCCCCCTTSCHHHHHHHHHHHHHHHHTTTCCCCCCCCCCSCCCCCCCCCCCCSCCC-CCCCCCCHHHHHH
T ss_pred             CcceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEeeccccCcCcCCCCEEEEE-EEEEEeCHHHHHH
Confidence            8999999999999999999999999999999999999999999999999999999999999 8888888877665

>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, structure initiative, PSI, joint center for structural GENO translation; 1.70A {Thermotoga maritima} SCOP: d.58.14.1

Probab=99.95  E-value=8.6e-29  Score=164.18  Aligned_cols=74  Identities=26%  Similarity=0.492  Sum_probs=71.9

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccC-CcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGR-NGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~-GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+|+|++|++++++++++++++.++|.++ ||+|+++++||+|+|||||+|+++|||+ ++.|.++|+.+.|
T Consensus        18 Mr~YE~~~Il~P~l~ee~v~~~ve~~~~~I~~~~GG~I~~ve~wG~R~LAY~I~K~~~G~Yv-l~~f~a~~~~i~E   92 (140)
T 1vmb_A           18 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYT-VIYFRCDGQNLQE   92 (140)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEEEEEEEEEEEEEEETTEEEEEEE-EEEEEECSSSTHH
T ss_pred             cccceEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEEEEEeecCcccccccCCCCEEEEE-EEEEEECHHHHHH
Confidence            899999999999999999999999999999999 9999999999999999999999999999 9999999988876

>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ...

Probab=99.95  E-value=1.3e-28  Score=162.43  Aligned_cols=73  Identities=25%  Similarity=0.414  Sum_probs=70.0

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||+||+|+|++|+++ ++++++++++.++|.++||+|+++++||+|+|||+|+|+++|||+ ++.|.++|+.+.|
T Consensus         1 Mr~YE~~~Il~P~~~-e~v~~~ve~~~~~I~~~GG~I~~ve~wG~R~LAY~I~K~~~G~Y~-l~~f~a~~~~i~E   73 (135)
T 3i1m_F            1 MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV-LMNVEAPQEVIDE   73 (135)
T ss_dssp             CCEECBEEEECSTTT-TSHHHHHHHHHHHHHHTTCEECCCEEEEEECCSSCTTSSSCEEEE-ECCEECCTTHHHH
T ss_pred             CCceEEEEEECCCch-HHHHHHHHHHHHHHHHCCCEEEEEEeeccccCceEcCCCCeEEEE-EEEEEeCHHHHHH
Confidence            999999999999998 799999999999999999999999999999999999999999999 8999998887765

>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=99.94  E-value=1.2e-27  Score=162.72  Aligned_cols=74  Identities=19%  Similarity=0.377  Sum_probs=71.5

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCC---------eeeEEEEEEEEeecC
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLD---------GRYYQLIPTWEFNSG   71 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~---------~g~Y~~~~~~~~~~~   71 (79)
                      ||.||+|+|++|++++++++++++++.++|.++||+|+++++||+|+|||+|+|++         +|||+ ++.|.++|+
T Consensus        62 Mr~YE~m~IlrPdl~eeev~alver~~~iI~~~GG~I~~ve~WG~RrLAY~IkK~~kgg~~~~h~eG~Yv-lm~F~a~p~  140 (168)
T 3bbn_F           62 LRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGETNNYLDGIYL-LFTYFTKPE  140 (168)
T ss_dssp             CEEEEEEEEECTTSCHHHHHSTTHHHHHHHTTTSCEEEEEEEEEECCCSSCTTSCSSSCSSCCCCCCEEE-EEEEEECTT
T ss_pred             CCceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEecccccccceeccCcccccccccceEEEE-EEEEEeCHH
Confidence            89999999999999999999999999999999999999999999999999999999         79999 999999998


Q ss_pred             cccc
Q 034908           72 SIFE   75 (79)
Q Consensus        72 ~~~e   75 (79)
                      .+.|
T Consensus       141 ~I~E  144 (168)
T 3bbn_F          141 SISP  144 (168)
T ss_dssp             SSHH
T ss_pred             HHHH
Confidence            8876

>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus}

Probab=99.88  E-value=1.1e-23  Score=132.15  Aligned_cols=54  Identities=17%  Similarity=0.295  Sum_probs=53.2

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeeccccccccccccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKK   54 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k   54 (79)
                      ||+||+++|++|++++++++++++++.++|.++||+|.++++||+|+|||||+|
T Consensus        43 Mr~YE~m~Il~P~l~ee~~~~~ve~~~~iI~~~gG~i~~ve~WG~R~LAY~I~K   96 (96)
T 2kjw_A           43 PGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK   96 (96)
T ss_dssp             SSCEEEEEECCSSCCHHHHHHHHHHHHHHHHHHTCCCSCCEECCCCCCCCSCCC
T ss_pred             hhhhheeeeeCCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeccccccccccCCC
Confidence            899999999999999999999999999999999999999999999999999986

>3zzp_A TS9, ribosomal protein S6; protein folding, RNA-binding; 0.96A {Thermus thermophilus}

Probab=99.03  E-value=1.6e-10  Score=69.39  Aligned_cols=35  Identities=11%  Similarity=0.224  Sum_probs=33.6

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNG   35 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG   35 (79)
                      .|.||+|+|++|+++++++++++++++++|+++||
T Consensus        43 ~r~YE~m~Il~P~l~ee~~~~~vek~~~~i~~~Gg   77 (77)
T 3zzp_A           43 PGRYEVNIVLNPNLDQSQLQNEKEIIQRALENYGA   77 (77)
T ss_dssp             TTEEEEEEEECTTCCHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCceEEEEEECCCCCHHHHHHHHHHHHHHHHhcCC
Confidence            47899999999999999999999999999999997

---

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	79
d2qalf1	100	d.58.14.1 (F:1-100) Ribosomal protein S6 {Escheric	9e-07
d2j5aa1	106	d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex	3e-06
d1loua_	97	d.58.14.1 (A:) Ribosomal protein S6 {Thermus therm	4e-06
d1vmba_	107	d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga ma	5e-05

>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]} Length = 100

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]

 Score = 40.5 bits (95), Expect = 9e-07
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          M  Y+ + ++ P    E +  ++ R    + G  G +  +  +G  QL Y I KL   +Y
Sbjct: 1  MRHYEIVFMVHPDQ-SEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59

Query: 61 QLI 63
           L+
Sbjct: 60 VLM 62

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} Length = 106

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

 Score = 39.4 bits (92), Expect = 3e-06
 Identities = 14/63 (22%), Positives = 31/63 (49%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          +  Y+ +  +KP + +E + +   +V + +  + G +     +G  QL Y I+K +   Y
Sbjct: 5  LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARY 64

Query: 61 QLI 63
           L+
Sbjct: 65 FLV 67

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

 Score = 38.6 bits (90), Expect = 4e-06
 Identities = 11/63 (17%), Positives = 23/63 (36%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYY 60
          M  Y+  ++L P++ +  L      + +        +  +   G  +L Y I K    Y+
Sbjct: 1  MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYF 60

Query: 61 QLI 63
             
Sbjct: 61 LWY 63

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} Length = 107

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

 Score = 36.3 bits (84), Expect = 5e-05
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 1  MPLYDCMLLLKPHVRKESLMELVARVGKHVYGR-NGVLTDITSFGTVQLGYGIKKL-DGR 58
            +Y+ M ++ P+V +E    LV RV K +  R  G +  +   G  +  Y IKK  +G 
Sbjct: 2  ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGD 61

Query: 59 YYQLIPTWEFNSGSIFE 75
          Y  +   +  +  ++ E
Sbjct: 62 YTVI--YFRCDGQNLQE 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	79
d1loua_	97	Ribosomal protein S6 {Thermus thermophilus [TaxId:	99.95
d1vmba_	107	Ribosomal protein S6 {Thermotoga maritima [TaxId:	99.94
d2j5aa1	106	Ribosomal protein S6 {Aquifex aeolicus [TaxId: 633	99.94
d2qalf1	100	Ribosomal protein S6 {Escherichia coli [TaxId: 562	99.93
d1jjcb4	104	Phenylalanyl-tRNA synthetase {Thermus thermophilus	88.35

>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]

Probab=99.95  E-value=9.2e-29  Score=152.59  Aligned_cols=74  Identities=16%  Similarity=0.261  Sum_probs=71.8

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+++|++|++++++++++++++.++|.++||+|.++++||+|+|||+|+|+++|||. ++.|+++|+.+.|
T Consensus         1 M~~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~-~~~f~~~~~~i~e   74 (97)
T d1loua_           1 MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYFL-WYQVEMPEDRVND   74 (97)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEE-EEEEEECGGGHHH
T ss_pred             CCcceEEEEECCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeeeEEEeccccccccceeEEE-EEEEEeCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999 9999999988765

>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermotoga maritima [TaxId: 2336]

Probab=99.94  E-value=1.5e-27  Score=149.68  Aligned_cols=74  Identities=26%  Similarity=0.492  Sum_probs=71.2

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccC-CcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGR-NGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~-GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+++|++|++++++++++++++.++|+++ ||+|.++++||+|+|||||+|+++|||+ ++.|+++|+.+.|
T Consensus         2 ~R~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~-~~~f~~~~~~i~e   76 (107)
T d1vmba_           2 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGDYT-VIYFRCDGQNLQE   76 (107)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTCCEEEEEEEEEEEEEEEEETTEEEEEEE-EEEEEECSSSTHH
T ss_pred             CceeEEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCEEEEEEeeeeeccceEcCCCcEEEEE-EEEEEECHHHHHH
Confidence            799999999999999999999999999999886 9999999999999999999999999999 9999999988876

>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.94  E-value=2.6e-27  Score=148.23  Aligned_cols=70  Identities=19%  Similarity=0.400  Sum_probs=67.4

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecC
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSG   71 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~   71 (79)
                      ||.||+++|++|++++++++++++++.++|.++||+|.++++||+|+|||||+|+++|||+ ++.|+++++
T Consensus         5 Mr~YE~~~Il~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~Ikk~~~G~Y~-~~~f~~~~~   74 (106)
T d2j5aa1           5 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF-LVQFKTENP   74 (106)
T ss_dssp             CEEEEEEEEECTTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEECSSCSSSCSEEEEE-EEEEEESCT
T ss_pred             cccccEEEEECCCCCHHHHHHHHHHHHHHHHHCCCeEEEEecceeechhhhhhhccceEEE-EEEEEECcH
Confidence            9999999999999999999999999999999999999999999999999999999999999 888888644

>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=4.6e-28  Score=150.26  Aligned_cols=73  Identities=23%  Similarity=0.403  Sum_probs=69.2

Q ss_pred             CCceeEEEEEcCCCCHHHHHHHHHHHhhhhccCCcEEEeeecccccccccccccCCeeeEEEEEEEEeecCcccc
Q 034908            1 MPLYDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQLIPTWEFNSGSIFE   75 (79)
Q Consensus         1 M~~YE~~~I~~p~l~~e~~~~~~~~~~~~I~~~GG~I~~~e~wG~R~LAY~I~k~~~g~Y~~~~~~~~~~~~~~e   75 (79)
                      ||.||+++|++|++++ +++++++++.++|.++||+|.++++||+|+|||||+|+++|||+ ++.|+.+|+.+.|
T Consensus         1 M~~YE~~~Il~p~~~e-~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~-~~~f~~~~~~i~e   73 (100)
T d2qalf1           1 MRHYEIVFMVHPDQSE-QVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV-LMNVEAPQEVIDE   73 (100)
T ss_dssp             CCEECEEEEECGGGTT-HHHHHHHHHHHHHHHTTCCCCCCCCCBSCBCSSCTTSCSBCBBC-CCCEECCHHHHHH
T ss_pred             CCcceEEEEECCCcHH-HHHHHHHHHHHHHHhCCCEEEEEeeeeeeecccccccCCeeEEE-EEEEecCHHHHHH
Confidence            9999999999999985 79999999999999999999999999999999999999999999 8899988887665

>d1jjcb4 d.58.13.1 (B:682-785) Phenylalanyl-tRNA synthetase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Anticodon-binding domain of PheRS
family: Anticodon-binding domain of PheRS
domain: Phenylalanyl-tRNA synthetase
species: Thermus thermophilus [TaxId: 274]

Probab=88.35  E-value=0.13  Score=29.95  Aligned_cols=29  Identities=28%  Similarity=0.346  Sum_probs=27.0

Q ss_pred             CCCHHHHHHHHHHHhhhhccCCcEEEeee
Q 034908           13 HVRKESLMELVARVGKHVYGRNGVLTDIT   41 (79)
Q Consensus        13 ~l~~e~~~~~~~~~~~~I~~~GG~I~~~e   41 (79)
                      .|++++++++.+++.+.+.+.|+++|..|
T Consensus        74 TLtd~eV~~~~~~i~~~l~~~~a~lRG~~  102 (104)
T d1jjcb4          74 TLRDEEVEEAVSRVAEALRARGFGLRGLD  102 (104)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTTCBCSCCS
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCEeCCCC
Confidence            78999999999999999999999998876