RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498
methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
         (245 letters)



>gnl|CDD|183286 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
           Provisional.
          Length = 234

 Score =  197 bits (503), Expect = 2e-51
 Identities = 83/251 (33%), Positives = 129/251 (51%), Gaps = 31/251 (12%)

Query: 7   LKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK-SI 65
           + RLFV   L         G++ H+L  VLR+KEGD + LF+G  GE+L++I+ +GK  +
Sbjct: 1   MPRLFV--LLAAGETLILDGEEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEV 58

Query: 66  RFKV-EYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQ------ 118
             ++ E           +    +  K +RL+ ++QK+ E+G+ AI P+I+  +       
Sbjct: 59  ELEILEKLELEPEPPLRLTLAQALPKGDRLELILQKATELGVSAIIPLISERSVVKLDGE 118

Query: 119 NTHYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHN-----CQIVFADETCG 173
                ++R +   I AAEQ     +P + PP +L+  L+           ++V   E  G
Sbjct: 119 RADKKLERWQKIAIEAAEQSGRTRIPEVRPPISLKEFLEELLPADLKAGLKLVLHPEAGG 178

Query: 174 SENSLEKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAA 233
                           V +LIGPEGG+  EE E L    F TP+SLGPRILR++TAA+AA
Sbjct: 179 ---------------KVLLLIGPEGGFSPEEIELLREAGF-TPVSLGPRILRTETAALAA 222

Query: 234 MALVQAICGDW 244
           +A +QA+ GD 
Sbjct: 223 LAALQALLGDL 233


>gnl|CDD|129157 TIGR00046, TIGR00046, RNA methyltransferase, RsmE family.  Members
           of this protein family, previously called conserved
           hypothetical protein TIGR00046, include the YggJ protein
           of E. coli, which has now been shown to methylate U1498
           in 16S rRNA.
          Length = 240

 Score =  110 bits (277), Expect = 3e-25
 Identities = 63/245 (25%), Positives = 118/245 (48%), Gaps = 16/245 (6%)

Query: 8   KRLFVDFPLCIKTQG-KASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK-SI 65
            R+    P  ++      + ++ H+L  VLR+K+GD + L +G    +  +I  + K  +
Sbjct: 2   MRIVYH-PEQLEEATISLTEEEAHHLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFV 60

Query: 66  RFKVEYQSRSQTKQSDVQYIFSP-IKTNRLDYMIQKSVEMGMGAIRPVIT-----RYTQN 119
           + ++      + +     ++    IK  +++++I+K  E+G+  I P        +    
Sbjct: 61  KCELLEGESEKRELPLKIHLAIVLIKGKKMEFIIRKLTELGVSKIIPFNAERSVVKLDIE 120

Query: 120 THYNMDRVRTYTISAAEQCDILTLPFIYPPTTL-EFLLKNWDHNCQIVFADETCGSENSL 178
               ++R +   I AAEQ     +P I PP  L E   + ++   ++ F  E      +L
Sbjct: 121 AIKKLERWQKIAIEAAEQSGRNIVPEIKPPKNLKEKCAEAYEEALKLNFHPEASPLSANL 180

Query: 179 EKLHAIAHIPNVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238
                     N+ I+IGPEGG+  +E + L    F TP+ LGPRILR++TA + A++++Q
Sbjct: 181 PIP-----AGNIVIIIGPEGGFSEKEIQLLKEKGF-TPVLLGPRILRTETAPLYALSILQ 234

Query: 239 AICGD 243
           A+  D
Sbjct: 235 ALLED 239


>gnl|CDD|130944 TIGR01889, Staph_reg_Sar, staphylococcal accessory regulator
           family.  This model represents a family of
           transcriptional regulatory proteins in Staphylococcus
           aureus and Staphylococcus epidermidis. Some members
           contain two tandem copies of this region. This family is
           related to the MarR transcriptional regulator family
           described by pfam model pfam01047.
          Length = 109

 Score = 29.9 bits (68), Expect = 0.62
 Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 4/86 (4%)

Query: 18  IKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVE----YQS 73
           +K +   S ++   L ++ +++  +  L       E L K S + K I+   +     + 
Sbjct: 17  LKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE 76

Query: 74  RSQTKQSDVQYIFSPIKTNRLDYMIQ 99
           RS+  +  V    +  + ++++ +I 
Sbjct: 77  RSEDDERKVIISINKEQRSKIESLIS 102


>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
          Length = 1205

 Score = 29.2 bits (65), Expect = 0.94
 Identities = 13/44 (29%), Positives = 24/44 (54%)

Query: 53  EWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDY 96
           EW+  +  +G+ I FK +Y++  +T    V ++FS +  N   Y
Sbjct: 193 EWVKTVERIGRWIDFKNDYKTMDKTFMESVWWVFSELYKNNYVY 236


>gnl|CDD|162728 TIGR02146, LysS_fung_arch, homocitrate synthase.  This model
           includes the yeast LYS21 gene which carries out the
           first step of the alpha-aminoadipate (AAA) lysine
           biosynthesis pathway. A related pathway is found in
           Thermus thermophilus. This enzyme is closely related to
           2-isopropylmalate synthase (LeuA) and citramalate
           synthase (CimA), both of which are present in the
           euryarchaeota. Some archaea have a separate homocitrate
           synthase (AksA) which also synthesizes longer
           homocitrate analogs.
          Length = 344

 Score = 29.0 bits (65), Expect = 1.2
 Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 5/40 (12%)

Query: 56  SKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLD 95
           S    + +S R  +EY        + ++  FS   T R +
Sbjct: 103 SDAKSILESARETIEYAKS-----AGLEVRFSAEDTFRSE 137


>gnl|CDD|131898 TIGR02851, spore_V_T, stage V sporulation protein T.  Members of
          this protein family are the stage V sporulation protein
          T (SpoVT), a protein of the sporulation/germination
          program in Bacillus subtilis and related species. The
          amino-terminal 50 amino acids are nearly perfectly
          conserved across all endospore-forming bacteria. SpoVT
          is a DNA-binding transcriptional regulator related to
          AbrB (See PFAM model pfam04014).
          Length = 180

 Score = 28.6 bits (64), Expect = 1.7
 Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 36 LRMKEGDNILLFNGKDGE-WLSKISYVGKSIRFKVEY 71
          LR++EGD + +F  ++GE  L K S +G+   F  EY
Sbjct: 25 LRIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEY 61


>gnl|CDD|165154 PHA02791, PHA02791, ankyrin-like protein; Provisional.
          Length = 284

 Score = 28.1 bits (62), Expect = 2.3
 Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 6/40 (15%)

Query: 65  IRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEM 104
           I   VEY+S S TK  D+      +K N+LD +I K+ E+
Sbjct: 240 IEKHVEYKSDSYTKDLDI------VKNNKLDEIISKNKEL 273


>gnl|CDD|182204 PRK10037, PRK10037, cell division protein; Provisional.
          Length = 250

 Score = 27.9 bits (62), Expect = 2.5
 Identities = 29/101 (28%), Positives = 43/101 (42%), Gaps = 7/101 (6%)

Query: 140 ILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEGG 199
           +L LP    P T + LL   DH+  IV  D  C      + L A AHI    + IG    
Sbjct: 122 LLDLPRGASPLTRQ-LLSLCDHSLAIVNVDANCHIRLHQQALPAGAHILINDLRIG---- 176

Query: 200 YHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQAI 240
             S+ ++ L+ L   +   L P ++  D A    +A  Q +
Sbjct: 177 --SQLQDDLYQLWLQSQRRLLPMLIHRDEAMAECLAAKQPL 215


>gnl|CDD|182706 PRK10760, PRK10760, murein hydrolase B; Provisional.
          Length = 359

 Score = 27.0 bits (60), Expect = 4.7
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 112 VITRYTQNTHYNM 124
            ITRY  +THY M
Sbjct: 332 TITRYNHSTHYAM 344


>gnl|CDD|185015 PRK15055, PRK15055, anaerobic sulfite reductase subunit A;
           Provisional.
          Length = 344

 Score = 26.1 bits (58), Expect = 7.8
 Identities = 8/45 (17%), Positives = 20/45 (44%)

Query: 34  HVLRMKEGDNILLFNGKDGEWLSKISYVGKSIRFKVEYQSRSQTK 78
           +   ++  ++ +L + KD E+       G+   F  E+   ++ K
Sbjct: 155 YSAAVRFDEDGVLVDIKDEEFEKYFQGGGEEEEFTPEFVEENKVK 199


>gnl|CDD|178278 PLN02673, PLN02673, quinolinate synthetase A.
          Length = 724

 Score = 25.8 bits (56), Expect = 9.6
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 6/57 (10%)

Query: 142 TLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEK-LHAIAHIPNVAILIGPE 197
           +L  +Y  T+LE   K + H    +    TC S N ++  L A A +P + I  GP+
Sbjct: 380 SLHVVYINTSLE--TKAYAHE---LVPTITCTSSNVVQTILQAFAQMPELNIWYGPD 431


  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
   0.321    0.136    0.414 

Gapped
Lambda     K      H
   0.267   0.0658    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,934,995
Number of extensions: 239072
Number of successful extensions: 408
Number of sequences better than 10.0: 1
Number of HSP's gapped: 399
Number of HSP's successfully gapped: 16
Length of query: 245
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,028,145
Effective search space: 620334330
Effective search space used: 620334330
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 (21.9 bits)
S2: 56 (25.5 bits)