RPS-BLAST 2.2.22 [Sep-27-2009]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

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



>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli
           [TaxId: 562]}
          Length = 204

 Score =  187 bits (475), Expect = 7e-49
 Identities = 79/204 (38%), Positives = 122/204 (59%), Gaps = 10/204 (4%)

Query: 8   KHKIDRRIGENLWGRPK----SPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYG 63
           K K+ RR G +L+ +               PG HG R+  + S +G+QLR KQK+++ YG
Sbjct: 6   KLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKP-RLSDYGVQLREKQKVRRIYG 64

Query: 64  DISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLV 123
            + E++FR+ +KEA R +G+T  NL++ LE RLD +VYR  F  T   ARQ V+H+ ++V
Sbjct: 65  -VLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMV 123

Query: 124 NGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVATFVRI 182
           NGR VNI SY+    DV+ +++K+K+ + V  A +LAE R+ P ++ V+   M  TF R 
Sbjct: 124 NGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRK 183

Query: 183 PSSLKDVPYPVIMQPNLVVEFYSR 206
           P    D+   +    +L+VE YS+
Sbjct: 184 PER-SDLSADI--NEHLIVELYSK 204


>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus
           thermophilus [TaxId: 274]}
          Length = 208

 Score =  177 bits (450), Expect = 6e-46
 Identities = 81/206 (39%), Positives = 124/206 (60%), Gaps = 11/206 (5%)

Query: 8   KHKIDRRIGENLWGR------PKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKY 61
             ++ RR G  L+ +      PK  +  R Y PG HGQ+R  +PS + ++LR KQK+++ 
Sbjct: 7   VCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRI 66

Query: 62  YGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHV 121
           YG ISE++FR++F+EA + +G T    +  LESRLD +VYR  F  +   ARQ V H H+
Sbjct: 67  YG-ISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHI 125

Query: 122 LVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVATFV 180
            VNGR V++ SYR + GD I V +KS+ L  + +  +  + R V  ++S++ + M   F+
Sbjct: 126 TVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFL 185

Query: 181 RIPSSLKDVPYPVIMQPNLVVEFYSR 206
           R+P   +D+  PV     LV+EFYSR
Sbjct: 186 RLPDR-EDLALPV--NEQLVIEFYSR 208


>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus
           stearothermophilus [TaxId: 1422]}
          Length = 159

 Score =  158 bits (401), Expect = 3e-40
 Identities = 69/163 (42%), Positives = 99/163 (60%), Gaps = 5/163 (3%)

Query: 44  KPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRA 103
           K S +GLQL+ KQK++  YG ++E++FR  F+EA +  G    N +  LESRLD +VYR 
Sbjct: 2   KLSEYGLQLQEKQKLRHMYG-VNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRL 60

Query: 104 KFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERD 163
               T   ARQ V H H+LV+G  VNI SYR K G  I V++KS+ L  + EA + A   
Sbjct: 61  GLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALE-ANNY 119

Query: 164 VPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
           +P+Y+S + + M  T+ R+P    ++P  +     L+VEFYSR
Sbjct: 120 IPDYLSFDPEKMEGTYTRLP-ERSELPAEI--NEALIVEFYSR 159


>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli
           [TaxId: 562]}
          Length = 104

 Score = 56.9 bits (137), Expect = 1e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 92  LESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLA 151
           +E RLD  ++ A+F  T   AR+ +    V  NG+  +  S   +    + ++Q + +  
Sbjct: 3   VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQ-RSKPSKIVELNATLTLRQGNDERT 61

Query: 152 SVLEASQLAERDVPE 166
            +++A     R   E
Sbjct: 62  VIVKAITEQRRPASE 76


>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal
           domain {Haemophilus influenzae [TaxId: 727]}
          Length = 58

 Score = 47.4 bits (113), Expect = 1e-06
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146
           RLD  +     + T   A + +    V +NG  V  GS +  + D I  + +
Sbjct: 3   RLDKFIAENVGL-TRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDE 53


>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli
           [TaxId: 562]}
          Length = 79

 Score = 40.6 bits (95), Expect = 1e-04
 Identities = 8/58 (13%), Positives = 19/58 (32%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLAS 152
            L  ++    +  +   A+  +    V V+G        +   G  +     S Q+ +
Sbjct: 22  ELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA 79


>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal
           domain {Escherichia coli [TaxId: 562]}
          Length = 59

 Score = 40.5 bits (95), Expect = 1e-04
 Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 95  RLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146
           RLD  + +   V +   A + +    V V+G  V   +++      +     
Sbjct: 2   RLDKFIAQQLGV-SRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGN 52


>d1kbla2 c.8.1.1 (A:377-509) Pyruvate phosphate dikinase, central
           domain {Clostridium symbiosum [TaxId: 1512]}
          Length = 133

 Score = 27.3 bits (60), Expect = 0.90
 Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 4/45 (8%)

Query: 99  IVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEV 143
           +V R      +    +   +       ++  +G +   EGD I +
Sbjct: 82  VVARGMGTCCVSGCGEIKINEE----AKTFELGGHTFAEGDYISL 122


>d1ux5a_ a.207.1.1 (A:) Bni1 {Baker's yeast (Saccharomyces
           cerevisiae) [TaxId: 4932]}
          Length = 411

 Score = 25.8 bits (56), Expect = 2.6
 Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 6/67 (8%)

Query: 51  QLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIF 110
            +R  +  K    D ++       + AD+       NL S+  SR+  +     +     
Sbjct: 141 GVRNLEDAKPPEKDPND------LQRADQIYLQLMVNLESYWGSRMRALTVVTSYEREYN 194

Query: 111 AARQFVN 117
                + 
Sbjct: 195 ELLAKLR 201


>d1n82a_ c.1.8.3 (A:) Xylanase {Bacillus stearothermophilus, Ixt6
           [TaxId: 1422]}
          Length = 330

 Score = 25.2 bits (54), Expect = 3.9
 Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 7/42 (16%)

Query: 16  GENLWG-------RPKSPVNTRSYGPGLHGQRRKSKPSYFGL 50
               WG           PV+ R   P L  ++ K KP+++  
Sbjct: 286 SVTFWGIADDHTWLDNFPVHGRKNWPLLFDEQHKPKPAFWRA 327


>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH
           {Escherichia coli [TaxId: 562]}
          Length = 256

 Score = 24.4 bits (53), Expect = 6.6
 Identities = 4/24 (16%), Positives = 13/24 (54%), Gaps = 1/24 (4%)

Query: 58  MKKYYGDISEKKFRSIFKEADRSR 81
           ++ + G     + R +F++A ++ 
Sbjct: 82  VEMFVGV-GASRVRDMFEQAKKAA 104


>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH
           {Thermus thermophilus [TaxId: 274]}
          Length = 247

 Score = 24.4 bits (53), Expect = 7.0
 Identities = 5/31 (16%), Positives = 12/31 (38%), Gaps = 1/31 (3%)

Query: 50  LQLRAKQKMKKYYGDISEKKFRSIFKEADRS 80
           +       ++ + G     + R +F+ A R 
Sbjct: 71  ITASGSDFVEMFVGV-GAARVRDLFETAKRH 100


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.319    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0575    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 726,165
Number of extensions: 31425
Number of successful extensions: 81
Number of sequences better than 10.0: 1
Number of HSP's gapped: 68
Number of HSP's successfully gapped: 14
Length of query: 206
Length of database: 2,407,596
Length adjustment: 81
Effective length of query: 125
Effective length of database: 1,295,466
Effective search space: 161933250
Effective search space used: 161933250
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: 51 (23.8 bits)