RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781147|ref|YP_003065560.1| transcriptional regulator
[Candidatus Liberibacter asiaticus str. psy62]
         (83 letters)



>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
          Prokaryotic DNA binding proteins belonging to the
          xenobiotic response element family of transcriptional
          regulators..
          Length = 58

 Score = 46.7 bits (111), Expect = 1e-06
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
             + +RKE  LTQ+E+  + G ++S IS +E GK   +++ +  LA  L   L +L
Sbjct: 2  ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58


>gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix.  This large family of DNA
          binding helix-turn helix proteins includes Cro and CI.
          Length = 55

 Score = 42.9 bits (102), Expect = 2e-05
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77
          + +R+E  L+Q+E+  + G ++S IS++E GK   +++ +  LA  L   L
Sbjct: 2  KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52


>gnl|CDD|33419 COG3620, COG3620, Predicted transcriptional regulator with
          C-terminal CBS domains [Transcription].
          Length = 187

 Score = 34.9 bits (80), Expect = 0.005
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58
          R  RKE  +TQK++  R G +Q +I+ LE GK
Sbjct: 11 RKRRKELGITQKDLARRAGVSQPYIARLEAGK 42


>gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators
          [Transcription].
          Length = 120

 Score = 32.3 bits (71), Expect = 0.030
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTPLWK 79
                + +RK+  L+Q+E+  R G ++S IS +E G+S + +++ +  LA  L   L +
Sbjct: 1  SIGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDE 60

Query: 80 LLKP 83
          LL+ 
Sbjct: 61 LLEE 64


>gnl|CDD|31665 COG1476, COG1476, Predicted transcriptional regulators
          [Transcription].
          Length = 68

 Score = 28.6 bits (64), Expect = 0.33
 Identities = 13/54 (24%), Positives = 26/54 (48%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77
          N  + +R E  LTQ+E+    G ++  I  +E GK   +++  + +A      +
Sbjct: 4  NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTI 57


>gnl|CDD|31895 COG1709, COG1709, Predicted transcriptional regulator
          [Transcription].
          Length = 241

 Score = 27.9 bits (62), Expect = 0.69
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58
          R  R+   ++Q E+    G + S IS+ E+G+
Sbjct: 33 RKWREIFNVSQTELARELGVSPSVISDYESGR 64


>gnl|CDD|31615 COG1426, COG1426, Uncharacterized protein conserved in bacteria
          [Function unknown].
          Length = 284

 Score = 25.8 bits (56), Expect = 2.9
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58
           R  R+E  L+ +++  RT   +S++  LE G 
Sbjct: 8  LRQAREEKGLSLEDVAARTKIRKSYLRALEEGN 40


>gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma
           subunit [Transcription].
          Length = 247

 Score = 24.9 bits (54), Expect = 4.5
 Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 5/40 (12%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56
           RE+++ V      R + +LTQKEI    G ++S +S L  
Sbjct: 200 REKLVLVL-----RYKEELTQKEIAEVLGISESRVSRLHK 234


  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
   0.321    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0762    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,018,805
Number of extensions: 42462
Number of successful extensions: 116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 17
Length of query: 83
Length of database: 6,263,737
Length adjustment: 53
Effective length of query: 30
Effective length of database: 5,118,460
Effective search space: 153553800
Effective search space used: 153553800
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: 51 (23.4 bits)