RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780238|ref|YP_003064651.1| 30S ribosomal protein S11
[Candidatus Liberibacter asiaticus str. psy62]
         (129 letters)



>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
          Length = 128

 Score =  192 bits (490), Expect = 3e-50
 Identities = 70/127 (55%), Positives = 94/127 (74%)

Query: 3   KSPSRIRNRERKNIVSGRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFA 62
           K    ++ + +KNI SG AH+ +TFNNT +TITD  GN I+W+S   +GF GSRK++P+A
Sbjct: 2   KKKKTVKKKVKKNIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYA 61

Query: 63  AQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCR 122
           AQVA +D + KA+ HGM ++EV V G G+GR+SA+RAL+A G  + SI DVT I HNGCR
Sbjct: 62  AQVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCR 121

Query: 123 PRKRRRI 129
           P KRRR+
Sbjct: 122 PPKRRRV 128


>gnl|CDD|163365 TIGR03632, bact_S11, 30S ribosomal protein S11.  This model
           describes the bacterial 30S ribosomal protein S11.
           Cutoffs are set such that the model excludes archaeal
           and eukaryotic ribosomal proteins, but many chloroplast
           and mitochondrial equivalents of S11 are detected.
          Length = 108

 Score =  163 bits (414), Expect = 2e-41
 Identities = 61/108 (56%), Positives = 82/108 (75%)

Query: 19  GRAHVVSTFNNTRITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHG 78
           G AH+ +TFNNT +TITDP GN ++W+S   VGF GS+K++P+AAQ+A +D + KA+  G
Sbjct: 1   GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFG 60

Query: 79  MSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
           M +++V V G GAGR+SA+RAL+A G  + SI DVT I HNGCRP KR
Sbjct: 61  MKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108


>gnl|CDD|181987 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
          Length = 132

 Score = 72.7 bits (179), Expect = 2e-14
 Identities = 47/126 (37%), Positives = 66/126 (52%), Gaps = 9/126 (7%)

Query: 12  ERKNIVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDC 70
             +    G AH+ ++FNNT ITITD  G  TIA SS  +V  +   ++SP+AA  A +  
Sbjct: 3   SMRKEKWGIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKA 62

Query: 71  SAKAQNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCR 122
           +  A+  G++ + +KV   G         G  +A+RAL   G  I  I DVT I H+G R
Sbjct: 63  AEDAKEKGITGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTR 122

Query: 123 PRKRRR 128
           P   RR
Sbjct: 123 PPGGRR 128


>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P.  This model
           describes exclusively the archaeal ribosomal protein
           S11P. It excludes homologous ribosomal proteins S14 from
           eukaryotes and S11 from bacteria.
          Length = 114

 Score = 67.5 bits (165), Expect = 8e-13
 Identities = 46/112 (41%), Positives = 61/112 (54%), Gaps = 9/112 (8%)

Query: 19  GRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77
           G AH+ S+FNNT ITITD  G  TIA SS  +V  +   ++SP+AA  A    + KA+  
Sbjct: 3   GIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKER 62

Query: 78  GMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGC 121
           G++ L +KV   G         G  +A+RAL   G  I  I DVT I H+G 
Sbjct: 63  GITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114


>gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional.
          Length = 149

 Score = 52.6 bits (126), Expect = 3e-08
 Identities = 39/122 (31%), Positives = 64/122 (52%), Gaps = 9/122 (7%)

Query: 16  IVSGRAHVVSTFNNTRITITDPHG-NTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKA 74
           +V G AH+ ++FN+T I +TD  G  T+   +  +   +   ++SP+AA +A  D +A+ 
Sbjct: 26  LVFGVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARC 85

Query: 75  QNHGMSSLEVKVSGLGA--------GRDSALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
           +  G+++L +K+   G         G  +ALRAL   G  I  I DVT I  +  R +  
Sbjct: 86  KELGINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGG 145

Query: 127 RR 128
           RR
Sbjct: 146 RR 147


>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
          Length = 409

 Score = 28.2 bits (63), Expect = 0.59
 Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 4/42 (9%)

Query: 88  GLGAGRDS---ALRALRAIGFTIVSICDVTMIAHNGCRPRKR 126
           GL AG D    A+  L  +GF  V I  VT +   G  P+ R
Sbjct: 88  GLAAGFDKNAEAVEGLLGLGFGFVEIGSVTPLPQPG-NPKPR 128


>gnl|CDD|173384 PTZ00090, PTZ00090, 40S ribosomal protein S11; Provisional.
          Length = 233

 Score = 28.0 bits (62), Expect = 0.66
 Identities = 28/121 (23%), Positives = 50/121 (41%), Gaps = 18/121 (14%)

Query: 20  RAHVVSTFNNTRITITDPHGN--TIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNH 77
              + ++ NN    + +   N  T+  S    VGF    + S   A    ++ + K +  
Sbjct: 120 MLVITTSKNNVHAQVVNKSKNYKTVFGSFAGNVGFRKKLQQSERCAYRIGENIAKKCRRL 179

Query: 78  GMSSLEVKVSGLGAGRDSALRALRAIGFTIVSICDVTMIAH---------NGCRPRKRRR 128
           G+ ++++K   +    ++ L+A  A G        VT I H         N  +PRKRRR
Sbjct: 180 GIFAVDIKFRRI-MRVETVLQAFYANGL------QVTQIIHEPRLPKCGLNAVKPRKRRR 232

Query: 129 I 129
           +
Sbjct: 233 V 233


>gnl|CDD|180064 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
          Length = 288

 Score = 27.8 bits (63), Expect = 0.84
 Identities = 13/24 (54%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 86  VSGL-GAGRDSALRALRAIGFTIV 108
           V+GL GAG+  ALRAL  +G+  V
Sbjct: 11  VTGLSGAGKSVALRALEDLGYYCV 34


>gnl|CDD|162334 TIGR01391, dnaG, DNA primase, catalytic core.  This protein
           contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim
           domain (Pfam:PF01751).
          Length = 415

 Score = 26.0 bits (58), Expect = 2.6
 Identities = 17/49 (34%), Positives = 17/49 (34%), Gaps = 21/49 (42%)

Query: 23  VVSTFNNTRIT--ITDPHGNTIAWSSPKVVGFSGSRK---------NSP 60
               F N RI   I DP G         VVGF G R          NSP
Sbjct: 195 YYDRFRN-RIMFPIHDPKGR--------VVGFGG-RALGDEKPKYLNSP 233


>gnl|CDD|164924 PHA02523, 43B, DNA polymerase subunit B; Provisional.
          Length = 391

 Score = 25.8 bits (56), Expect = 3.0
 Identities = 13/52 (25%), Positives = 23/52 (44%)

Query: 32  ITITDPHGNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLE 83
           + + D  G   A    K++G    R ++P A Q +  +   +    G SSL+
Sbjct: 197 LNVYDMEGTRYAEPHLKIMGLETQRSSTPLACQKSLKESIRRLLQEGESSLQ 248


>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX.  The family
           of proteins found in this equivalog include the
           characterized LysX from Thermus thermophilus which is
           part of a well-organized lysine biosynthesis gene
           cluster. LysX is believed to carry out an ATP-dependent
           acylation of the amino group of alpha-aminoadipate in
           the prokaryotic version of the fungal AAA lysine
           biosynthesis pathway. No species having a sequence in
           this equivalog contains the elements of the more common
           diaminopimelate lysine biosythesis pathway, and none has
           been shown to be a lysine auxotroph. These sequences
           have mainly recieved the name of the related enzyme,
           "ribosomal protein S6 modification protein RimK". RimK
           has been characterized in E. coli, and acts by
           ATP-dependent condensation of S6 with glutamate
           residues.
          Length = 280

 Score = 25.8 bits (57), Expect = 3.3
 Identities = 7/23 (30%), Positives = 14/23 (60%)

Query: 87  SGLGAGRDSALRALRAIGFTIVS 109
           + L   R++AL+   A+G+ +V 
Sbjct: 105 TYLAFDREAALKLAEALGYPVVL 127


>gnl|CDD|182962 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
          Length = 475

 Score = 25.6 bits (57), Expect = 3.5
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 28  NNTRITITDPHGNTIAWSSPKVVGFSGSRKN 58
            + R+ +TD  G  +  S  + VG   SR N
Sbjct: 91  VDYRVYVTDAQGIVLFDSEGRAVGQDYSRWN 121


>gnl|CDD|140255 PTZ00228, PTZ00228, variable surface protein Vir21; Provisional.
          Length = 350

 Score = 25.5 bits (56), Expect = 3.9
 Identities = 8/19 (42%), Positives = 11/19 (57%), Gaps = 2/19 (10%)

Query: 6   SRIRNRERKNIVS--GRAH 22
           S +R  + KNIV+    AH
Sbjct: 313 SSLRKGKGKNIVNIDEEAH 331


>gnl|CDD|181813 PRK09382, ispDF, bifunctional 2-C-methyl-D-erythritol 4-phosphate
           cytidylyltransferase/2-C-methyl-D-erythritol
           2,4-cyclodiphosphate synthase protein; Provisional.
          Length = 378

 Score = 25.6 bits (57), Expect = 4.2
 Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)

Query: 96  ALRALRAIGFTIVSICDVTMIA 117
           A   +R  G  I++  DVT+IA
Sbjct: 297 AADFVREAGGEIIN-ADVTIIA 317


>gnl|CDD|178328 PLN02727, PLN02727, NAD kinase.
          Length = 986

 Score = 25.2 bits (55), Expect = 4.7
 Identities = 7/19 (36%), Positives = 15/19 (78%)

Query: 10  NRERKNIVSGRAHVVSTFN 28
           N+ R+ ++SGR+ ++S+F 
Sbjct: 147 NKGREEVLSGRSSIMSSFR 165


>gnl|CDD|182226 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
          Length = 186

 Score = 24.7 bits (54), Expect = 6.6
 Identities = 8/13 (61%), Positives = 10/13 (76%)

Query: 90  GAGRDSALRALRA 102
           G+G+DS L ALR 
Sbjct: 12  GSGKDSLLAALRQ 24


>gnl|CDD|180189 PRK05667, dnaG, DNA primase; Validated.
          Length = 580

 Score = 24.8 bits (55), Expect = 7.4
 Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)

Query: 88  GLG---AGRDSALRALRAIGFTIVSICDVTMIAHNGCRPRK----RRRI 129
           G+G    G D+ L+ L   GF+   + +  ++  N          R RI
Sbjct: 151 GIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRI 199


>gnl|CDD|183478 PRK12372, PRK12372, ribonuclease III; Reviewed.
          Length = 413

 Score = 24.5 bits (53), Expect = 7.5
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 12/61 (19%)

Query: 39  GNTIAWSSPKVVGFSGSRKNSPFAAQVATDDCSAKAQNHGMSSLEVKVSGLGAGRDSALR 98
           G+ IA  +  VV   G+  N  F  +     C+       +  L+VKVSG GA R +A +
Sbjct: 163 GHKIALPTYTVVATHGAAHNQQFEVE-----CT-------VPKLDVKVSGSGASRRAAEQ 210

Query: 99  A 99
           A
Sbjct: 211 A 211


>gnl|CDD|178970 PRK00302, lnt, apolipoprotein N-acyltransferase; Reviewed.
          Length = 505

 Score = 24.5 bits (54), Expect = 7.6
 Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 1/16 (6%)

Query: 29  NTRIT-ITDPHGNTIA 43
           NT IT + DP G  IA
Sbjct: 438 NTGITAVIDPLGRIIA 453


>gnl|CDD|185007 PRK15047, PRK15047, N-hydroxyarylamine O-acetyltransferase;
           Provisional.
          Length = 281

 Score = 24.4 bits (53), Expect = 8.8
 Identities = 8/32 (25%), Positives = 17/32 (53%)

Query: 98  RALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
           R LR +GF + S+    ++++    P +  R+
Sbjct: 78  RVLRELGFNVRSLLGRVVLSNPPALPPRTHRL 109


>gnl|CDD|179576 PRK03381, PRK03381, PII uridylyl-transferase; Provisional.
          Length = 774

 Score = 24.2 bits (53), Expect = 9.3
 Identities = 13/42 (30%), Positives = 14/42 (33%), Gaps = 1/42 (2%)

Query: 89  LGAG-RDSALRALRAIGFTIVSICDVTMIAHNGCRPRKRRRI 129
           LG G R    RAL     TI    DV         PR+    
Sbjct: 256 LGLGDRFDLARALSDAARTISYAVDVGWRTAANALPRRGLSA 297


  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    0.130    0.385 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,065,544
Number of extensions: 113915
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 257
Number of HSP's successfully gapped: 34
Length of query: 129
Length of database: 5,994,473
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,201,009
Effective search space: 193246414
Effective search space used: 193246414
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 (21.8 bits)
S2: 51 (23.3 bits)