RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

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



>gnl|CDD|180018 PRK05327, rpsD, 30S ribosomal protein S4; Validated.
          Length = 203

 Score =  291 bits (747), Expect = 1e-79
 Identities = 101/208 (48%), Positives = 139/208 (66%), Gaps = 7/208 (3%)

Query: 1   MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQ-RRKSKPSYFGLQLRAKQKMK 59
           M++    K K+ RR+G +L+   K  +  + Y PG HGQ RRK K S +GLQLR KQK++
Sbjct: 1   MARYTGPKCKLSRRLGVDLFKSGKRCLKRK-YPPGQHGQRRRKPKLSDYGLQLREKQKLR 59

Query: 60  KYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHR 119
           + YG + EK+FR  FKEA R +G+T  NL+  LESRLD +VYR  F PT   ARQ V+H 
Sbjct: 60  RIYG-VLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHG 118

Query: 120 HVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVAT 178
           H+LVNG+ VNI SYR K GDVIEV++KSK+L  + EA +LAE R VP+++ V+ + +  T
Sbjct: 119 HILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGT 178

Query: 179 FVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
           F R+P   ++   PV +   L+VE YS+
Sbjct: 179 FKRLP-EREE--IPVPINEQLIVELYSK 203


>gnl|CDD|130089 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
           type.  This model finds organelle (chloroplast and
           mitochondrial) ribosomal protein S4 as well as bacterial
           ribosomal protein S4.
          Length = 200

 Score =  218 bits (557), Expect = 1e-57
 Identities = 93/201 (46%), Positives = 134/201 (66%), Gaps = 6/201 (2%)

Query: 7   SKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDIS 66
            K K+ RR+G NL+G+ +  +  R Y PG HGQRRK K S +GLQL+ KQK+K  YG I+
Sbjct: 5   PKFKLSRRLGVNLFGKSRKLLLKRKYPPGQHGQRRK-KLSDYGLQLQEKQKLKFMYG-IT 62

Query: 67  EKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGR 126
           EK+FR  FKEA + +G+T  NL+  LESRLD +VYR  F PT FAARQ V+H H+LVNG+
Sbjct: 63  EKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK 122

Query: 127 SVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA-ERDVPEYISVNHDNMVATFVRIPSS 185
            V+I SY+ + GD+I +K+KSK++  V E  +   +R++P ++ V+   +    +R+P  
Sbjct: 123 KVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPE- 181

Query: 186 LKDVPYPVIMQPNLVVEFYSR 206
                 P+ +  +LVVE+YSR
Sbjct: 182 --RSQLPLPINESLVVEYYSR 200


>gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain. 
          Length = 60

 Score = 66.1 bits (162), Expect = 6e-12
 Identities = 21/55 (38%), Positives = 27/55 (49%)

Query: 94  SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148
            RLD  + R    P+   AR+ +    V VNG+ V   SY  K GDVI V+ K  
Sbjct: 1   RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55


>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
          Length = 177

 Score = 54.9 bits (133), Expect = 1e-08
 Identities = 23/44 (52%), Positives = 25/44 (56%)

Query: 90  SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
             LE RL TIVYR     T   ARQF+ H H+ VNGR V   SY
Sbjct: 99  DILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142


>gnl|CDD|130090 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
           type)/S9(eukaryote cytosolic type).  This model finds
           eukaryotic ribosomal protein S9 as well as archaeal
           ribosomal protein S4.
          Length = 162

 Score = 50.1 bits (120), Expect = 4e-07
 Identities = 20/43 (46%), Positives = 25/43 (58%)

Query: 91  FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
           FLE RL T V++     TI  ARQ + H H+ V+GR V   SY
Sbjct: 101 FLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSY 143


>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
          Length = 194

 Score = 42.4 bits (100), Expect = 9e-05
 Identities = 16/44 (36%), Positives = 27/44 (61%)

Query: 90  SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
           +FLE RL T+V+++    +I  AR  +  RH+ V  + VN+ S+
Sbjct: 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSF 148


>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
          Length = 181

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 91  FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133
            LE RL T V++     +I  AR  +  RH+ V  + V+I S+
Sbjct: 104 LLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146


>gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional.
          Length = 3095

 Score = 29.9 bits (67), Expect = 0.44
 Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 12/85 (14%)

Query: 2   SKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKY 61
           S+  +S+HK  RR     W  P S  N  S GP     R+ S+ S   L L         
Sbjct: 456 SRGSNSRHK--RR--RPSWTPPSSSENVSSDGPTFSQSRKPSRKSKRALDLD-------- 503

Query: 62  YGDISEKKFRSIFKEADRSRGDTSH 86
           YG +S +      + +D   G  S+
Sbjct: 504 YGHLSNEPSDVDGENSDSPAGAISN 528


>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily.  This
           subfamily of the AAA family ATPases includes two members
           each from three archaeal species. It also includes yeast
           CDC48 (cell division control protein 48) and the human
           ortholog, transitional endoplasmic reticulum ATPase
           (valosin-containing protein). These proteins in
           eukaryotes are involved in the budding and transfer of
           membrane from the transitional endoplasmic reticulum to
           the Golgi apparatus.
          Length = 733

 Score = 29.9 bits (67), Expect = 0.49
 Identities = 13/21 (61%), Positives = 17/21 (80%), Gaps = 1/21 (4%)

Query: 58  MKKYYGDISEKKFRSIFKEAD 78
           M KYYG+ SE++ R IFKEA+
Sbjct: 249 MSKYYGE-SEERLREIFKEAE 268


>gnl|CDD|162487 TIGR01687, moaD_arch, MoaD family protein, archaeal.  Members of
           this family appear to be archaeal versions of MoaD,
           subunit 1 of molybdopterin converting factor. This model
           has been split from the bacterial/eukaryotic equivalog
           model TIGR01682 because the presence of two members of
           this family in a substantial number of archaeal species
           suggests that roles might not be interchangeable.
          Length = 88

 Score = 29.7 bits (67), Expect = 0.52
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 60  KYYGDISEKKFRSIFK-EADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNH 118
           KY+  + +   +   + E +   G T  +L++ L +R     Y  +F          V +
Sbjct: 4   KYFATLRDITGKKSEEIEIE---GKTVGDLLNELMAR-----YPKEFSELFKEGLGLVPN 55

Query: 119 RHVLVNGRSVNIG-SYRCKEGDVIEV 143
             +LVNGR+V+ G     K+GDV+ +
Sbjct: 56  VIILVNGRNVDWGLGTELKDGDVVAI 81


>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
           Provisional.
          Length = 267

 Score = 27.4 bits (61), Expect = 2.8
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 13/60 (21%)

Query: 95  RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148
           RLD +      + R+K V  I +         V VN R V       K GDV+ V  K +
Sbjct: 193 RLDALASAGFRMSRSKLVDLISSG-------DVRVNWREVTKNGTTLKTGDVVSVSGKGR 245


>gnl|CDD|184784 PRK14667, uvrC, excinuclease ABC subunit C; Provisional.
          Length = 567

 Score = 27.4 bits (61), Expect = 2.9
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 34 PGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDI-SEKKFRSIFKEAD 78
          PG++  ++K +  Y G     K ++ ++Y    ++ K R+IF E+ 
Sbjct: 17 PGVYLFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESS 62


>gnl|CDD|165244 PHA02933, PHA02933, unchracterized protein; Provisional.
          Length = 149

 Score = 26.5 bits (58), Expect = 4.5
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 62  YGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLD 97
           Y  ISE +F+S+    D    D  + LI FLE +L+
Sbjct: 114 YKKISESRFQSLGNITDLMTDDNINILILFLEKKLN 149


>gnl|CDD|180858 PRK07139, PRK07139, amidase; Provisional.
          Length = 439

 Score = 26.6 bits (59), Expect = 4.8
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%)

Query: 28  NTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKE 76
           NTRS G G   Q+R    SYF      ++  +KY+  +  KK R + K 
Sbjct: 304 NTRSEGFGKMVQKRLILGSYF----LEEENQEKYF--LKAKKVRRVIKN 346


>gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein.  Members of
           this protein family are about 265 residues long and each
           contains an S4 RNA-binding domain of about 48 residues.
           The member from the Cyanobacterium, Synechocystis sp.
           PCC 6803, was detected as a novel polypeptide in a
           highly purified preparation of active photosystem II
           (Kashino, et al., 2002). The phylogenetic distribution,
           including Cyanobacteria and Arabidopsis, supports a role
           in photosystem II, although the high bit score cutoffs
           for this model reflect similar sequences in
           non-photosynthetic organisms such as Carboxydothermus
           hydrogenoformans, a Gram-positive bacterium.
          Length = 257

 Score = 26.1 bits (58), Expect = 6.5
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 13/58 (22%)

Query: 95  RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146
           R+D I      + R+K V  I A R       + +N ++V   S   K GD ++++ K
Sbjct: 185 RIDAIASAGFGLSRSKIVDQIKAGR-------LRLNWKTVTQPSRELKVGDRLQLRGK 235


>gnl|CDD|179455 PRK02645, ppnK, inorganic polyphosphate/ATP-NAD kinase;
           Provisional.
          Length = 305

 Score = 25.6 bits (57), Expect = 9.6
 Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 5/27 (18%)

Query: 180 VRIPSSLKDVPYPVIM-----QPNLVV 201
           +  PS  KD PYPV +       +L +
Sbjct: 36  LMGPSGPKDNPYPVFLASASELIDLAI 62


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.319    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0733    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,269,490
Number of extensions: 193724
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 407
Number of HSP's successfully gapped: 21
Length of query: 206
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,071,361
Effective search space: 476349237
Effective search space used: 476349237
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 (25.0 bits)