RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780187|ref|YP_003064600.1| 30S ribosomal protein S4
[Candidatus Liberibacter asiaticus str. psy62]
         (206 letters)



>gnl|CDD|30868 COG0522, RpsD, Ribosomal protein S4 and related proteins
           [Translation, ribosomal structure and biogenesis].
          Length = 205

 Score =  189 bits (480), Expect = 6e-49
 Identities = 88/209 (42%), Positives = 122/209 (58%), Gaps = 7/209 (3%)

Query: 1   MSKRESSKHKIDRRIGENLWGRPKSPVNTR-SYGPGLHGQRRKSKPSYFGLQLRAKQKMK 59
           M++    K K+ RR+G N W + +     +  Y PG HGQ R  K S +GLQLR KQK++
Sbjct: 1   MARYPGPKKKLSRRLGFNPWLKERLCKERKLPYKPGQHGQERWKKLSDYGLQLREKQKLR 60

Query: 60  KYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHR 119
            +YG + EK+FR   KEA R +G T  NL++ LE RLD +VYR  F  T   ARQ V+H 
Sbjct: 61  AFYG-VLEKQFRRYLKEAGRLKGVTGLNLLALLERRLDNVVYRLGFAKTRRQARQLVSHG 119

Query: 120 HVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE--RDVPEYISVNHDNMVA 177
           H+LVNG+ VNI SY    GD I V++KSK    + EA +LA      P ++ V+ + +  
Sbjct: 120 HILVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALELAAQRGIPPAWLEVDEEKLEG 179

Query: 178 TFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
           TF R+P   +    P  +   L+VEFYS+
Sbjct: 180 TFKRLP---ERSDLPAPINEQLIVEFYSK 205


>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed.
          Length = 201

 Score =  148 bits (376), Expect = 1e-36
 Identities = 81/213 (38%), Positives = 116/213 (54%), Gaps = 21/213 (9%)

Query: 1   MSKRESSKHKIDRRIGENLWG----RPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQ 56
           MS+    + KI RR+G  L G     P+        G  L  Q R  K S + ++L  KQ
Sbjct: 1   MSRYRGPRLKIIRRLGA-LPGLTSKTPR-------PGSDLRNQSRSGKKSQYRIRLEEKQ 52

Query: 57  KMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFV 116
           K++  YG ++E++     + A +++G T   L+  LE RLD I++R    PTI AARQ V
Sbjct: 53  KLRFNYG-LTERQLLKYVRIARKAKGSTGQVLLQLLEMRLDNILFRLGMAPTIPAARQLV 111

Query: 117 NHRHVLVNGRSVNIGSYRCKEGDVIEVK--QKSKQLA-SVLEASQLAERDVPEYISVNHD 173
           NH H+LVNGR V+I SYRCK  D+I VK  QKSK L  + LE+S   E  +P +++++  
Sbjct: 112 NHGHILVNGRIVDIPSYRCKPKDIITVKDKQKSKNLIQNNLESSPREE--LPNHLTLDKL 169

Query: 174 NMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
                  +I    K V   + +   LVVE+YSR
Sbjct: 170 QYKGLVNQIIDR-KWV--GLKINELLVVEYYSR 199


>gnl|CDD|144902 pfam01479, S4, S4 domain.  The S4 domain is a small domain
           consisting of 60-65 amino acid residues that was
           detected in the bacterial ribosomal protein S4,
           eukaryotic ribosomal S9, two families of pseudouridine
           synthases, a novel family of predicted RNA methylases, a
           yeast protein containing a pseudouridine synthetase and
           a deaminase domain, bacterial tyrosyl-tRNA synthetases,
           and a number of uncharacterized, small proteins that may
           be involved in translation regulation. The S4 domain
           probably mediates binding to RNA.
          Length = 48

 Score = 67.5 bits (166), Expect = 2e-12
 Identities = 22/47 (46%), Positives = 27/47 (57%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVI 141
           RLD ++ R     +   ARQ + H HV VNG+ V   SYR K GDVI
Sbjct: 2   RLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48


>gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain
           surface is populated by conserved, charged residues that
           define a likely RNA-binding site;  Found in stress
           proteins, ribosomal proteins and tRNA synthetases; This
           may imply a hitherto unrecognized functional similarity
           between these three protein classes..
          Length = 70

 Score = 66.8 bits (163), Expect = 4e-12
 Identities = 31/66 (46%), Positives = 38/66 (57%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVL 154
           RLD I+ R    P+   ARQ + H HVLVNG+ V   SY+ K GDVIEV  KS +   V 
Sbjct: 2   RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIVY 61

Query: 155 EASQLA 160
           E  +L 
Sbjct: 62  EDKKLL 67


>gnl|CDD|143931 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-terminal
          domain.  This family includes small ribosomal subunit
          S9 from prokaryotes and S16 from metazoans. This domain
          is predicted to bind to ribosomal RNA. This domain is
          composed of four helices in the known structure.
          However the domain is discontinuous in sequence and the
          alignment for this family contains only the first three
          helices.
          Length = 94

 Score = 52.3 bits (126), Expect = 9e-08
 Identities = 31/96 (32%), Positives = 47/96 (48%), Gaps = 6/96 (6%)

Query: 2  SKRESSKHKIDRRIGENLWGRPKSPVNTRSYG--PGLHGQRRKS--KPSYFGLQLRAKQK 57
          S+      K+ RR+GE      K+ +    YG  PG HG R K   + S + L+L  KQK
Sbjct: 1  SRYRGPTLKLPRRLGELPRLTAKTKLA-GEYGLRPGQHGWRVKKGRRLSRYLLRLDEKQK 59

Query: 58 MKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLE 93
          ++ +YG + E++ R     A +  G    NL+  LE
Sbjct: 60 LRFFYG-LLERQLRRYGVLAKKLDGSLGLNLLDLLE 94


>gnl|CDD|38511 KOG3301, KOG3301, KOG3301, Ribosomal protein S4 [Translation,
           ribosomal structure and biogenesis].
          Length = 183

 Score = 50.4 bits (120), Expect = 3e-07
 Identities = 18/46 (39%), Positives = 26/46 (56%)

Query: 91  FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCK 136
           FLE RL TIV++     +I  AR  +  RH+ V  + VNI S+  +
Sbjct: 94  FLERRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVR 139


>gnl|CDD|31381 COG1188, COG1188, Ribosome-associated heat shock protein implicated
           in the recycling of the 50S subunit (S4 paralog)
           [Translation, ribosomal structure and biogenesis].
          Length = 100

 Score = 31.0 bits (70), Expect = 0.24
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVL 154
           RLD  ++ A+F+     A++ +    V VNG+     S   K GD++ ++  +K+    +
Sbjct: 10  RLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRAK-PSKEVKVGDILTIRFGNKEF--TV 66

Query: 155 EASQLAERDVPE 166
           +   L E+  P 
Sbjct: 67  KVLALGEQRRPA 78


>gnl|CDD|31382 COG1189, COG1189, Predicted rRNA methylase [Translation, ribosomal
           structure and biogenesis].
          Length = 245

 Score = 31.0 bits (70), Expect = 0.26
 Identities = 17/58 (29%), Positives = 26/58 (44%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLAS 152
           RLD ++       +   A++ +   +VLVNG  V   S      D IEVK + +   S
Sbjct: 4   RLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDIDDEIEVKGEEQPYVS 61


>gnl|CDD|32457 COG2302, COG2302, Uncharacterized conserved protein, contains
           S4-like domain [Function unknown].
          Length = 257

 Score = 30.6 bits (69), Expect = 0.34
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 13/60 (21%)

Query: 95  RLDTIV------YRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148
           RLD ++       RAK         Q +    V VN + V+  SY  +EGD+I ++   +
Sbjct: 182 RLDVVISEGFGLSRAKAQ-------QLIEKGKVKVNWKVVDKASYEVQEGDLISIRGFGR 234


>gnl|CDD|36152 KOG0934, KOG0934, KOG0934, Clathrin adaptor complex, small subunit
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 145

 Score = 27.2 bits (60), Expect = 3.7
 Identities = 14/49 (28%), Positives = 28/49 (57%)

Query: 55  KQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRA 103
           K +++K+Y  +S K+ + I +E  +S       + SF+E + + +VYR 
Sbjct: 13  KTRLQKWYEALSIKERKKIERELIKSVLARKPKMCSFIEYKDEKVVYRR 61


>gnl|CDD|107256 cd01543, PBP1_XylR, Ligand-binding domain of DNA transcription
           repressor specific for xylose (XylR).  Ligand-binding
           domain of DNA transcription repressor specific for
           xylose (XylR), a member of the LacI-GalR family of
           bacterial transcription regulators. The ligand-binding
           domain of XylR is structurally homologous to the
           periplasmic sugar-binding domain of ABC-type
           transporters and both domains contain the type I
           periplasmic binding protein-like fold. The LacI-GalR
           family repressors are composed of two functional
           domains: an N-terminal HTH (helix-turn-helix) domain,
           which is responsible for the DNA-binding specificity,
           and a C-terminal ligand-binding domain, which is
           homologous to the type I periplasmic binding proteins.
           As also observed in the periplasmic binding proteins,
           the C-terminal domain of the bacterial transcription
           repressor undergoes a conformational change upon ligand
           binding which in turn changes the DNA binding affinity
           of the repressor.
          Length = 265

 Score = 26.4 bits (59), Expect = 6.5
 Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 4/37 (10%)

Query: 153 VLEASQLAERDVPEYISV---NHDNMVATFVRIP-SS 185
           +LEA + A   VPE ++V   ++D ++    R P SS
Sbjct: 186 LLEACRRAGIAVPEEVAVLGVDNDELICELSRPPLSS 222


>gnl|CDD|145636 pfam02597, ThiS, ThiS family.  ThiS (thiaminS) is a 66 aa protein
           involved in sulphur transfer. ThiS is coded in the
           thiCEFSGH operon in E. coli. This family of proteins
           have two conserved Glycines at the COOH terminus.
           Thiocarboxylate is formed at the last G in the
           activation process. Sulphur is transferred from ThiI to
           ThiS in a reaction catalysed by IscS. MoaD, a protein
           involved sulphur transfer in molybdopterin synthesis, is
           about the same length and shows limited sequence
           similarity to ThiS. Both have the conserved GG at the
           COOH end.
          Length = 70

 Score = 26.0 bits (58), Expect = 7.3
 Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 2/25 (8%)

Query: 121 VLVNGRSVN--IGSYRCKEGDVIEV 143
           V VNG  V         K+GD + +
Sbjct: 39  VAVNGEIVPRSQADTPLKDGDEVAI 63


>gnl|CDD|34758 COG5157, CDC73, RNA polymerase II assessory factor [Transcription].
          Length = 362

 Score = 25.9 bits (56), Expect = 9.3
 Identities = 18/114 (15%), Positives = 36/114 (31%), Gaps = 9/114 (7%)

Query: 41  RKSKPSYFGLQLRAKQKMKKYYGD-------ISEKKFRSIFKEADRSRGDTSHNLISFLE 93
           R    + +    R       Y+ D       +      S + +A   + +TS        
Sbjct: 76  RDKSYAVYMTLCRESGIGNIYFLDRTDLIEWLEGNTESSQYLKAPGQKKETSSTTSISA- 134

Query: 94  SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS 147
            R+D+ V     V T+   R  V H   L+  + ++       + D +   +  
Sbjct: 135 -RIDSEVSDPVVVETMKHERILVGHNSRLIGLKPISFLGLLKDKEDKLVQSEGG 187


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.319    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0591    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,402,077
Number of extensions: 117295
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 275
Number of HSP's successfully gapped: 16
Length of query: 206
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,340,536
Effective search space: 507842712
Effective search space used: 507842712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.3 bits)