RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins. 
          Length = 56

 Score = 46.0 bits (110), Expect = 2e-06
 Identities = 17/56 (30%), Positives = 32/56 (57%)

Query: 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
            + +R+E  LTQ+E+  + G ++S +S +E GK   +++ +  LA  L   L +L
Sbjct: 1  RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56


>gnl|CDD|163124 TIGR03070, couple_hipB, transcriptional regulator, y4mF family.
          Members of this family belong to a clade of
          helix-turn-helix DNA-binding proteins, among the larger
          family pfam01381 (HTH_3; Helix-turn-helix). Members are
          similar in sequence to the HipB protein of E. coli.
          Genes for members of the seed alignment for this
          protein family were found to be closely linked to genes
          encoding proteins related to HipA. The HibBA operon
          appears to have some features in common with
          toxin-antitoxin post-segregational killing systems.
          Length = 58

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73
          R  RK   LTQ ++ +  G    +I ++E GK T+ +D ++ +   L
Sbjct: 8  RARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDAL 54


>gnl|CDD|184374 PRK13890, PRK13890, conjugal transfer protein TrbA; Provisional.
          Length = 120

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 23/61 (37%), Positives = 37/61 (60%)

Query: 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80
          IF  N   +  E  +T+KE+  R+G + S++S+L TGK+  ++  M  +A  L+TPL  L
Sbjct: 5  IFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLL 64

Query: 81 L 81
          L
Sbjct: 65 L 65


>gnl|CDD|181367 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed.
          Length = 234

 Score = 29.1 bits (66), Expect = 0.26
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55
           RE+ I    F     E K TQKE+ +  G +QS+IS LE
Sbjct: 182 REKQIMELRFGLNGGEEK-TQKEVADMLGISQSYISRLE 219


>gnl|CDD|182039 PRK09706, PRK09706, transcriptional repressor DicA; Reviewed.
          Length = 135

 Score = 27.5 bits (61), Expect = 0.76
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD-TPLWKL 80
          R  RK+ KL+Q+ +      +   IS+ E  ++     N+  LA  L  +P W L
Sbjct: 11 RYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65


>gnl|CDD|180113 PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional.
          Length = 330

 Score = 26.6 bits (60), Expect = 1.4
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)

Query: 30  RKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62
           +KE K   K+I++   FA+ WI E + G+ T  
Sbjct: 272 KKEMKEVLKDIQSGE-FAKEWILENKAGRPTFK 303


>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor.  Members of
           this family comprise the Firmicutes lineage endospore
           formation-specific sigma factor SigE, also called
           SpoIIGB and sigma-29. As characterized in Bacillus
           subtilis, this protein is synthesized as a precursor,
           specifically in the mother cell compartment, and must
           cleaved by the SpoIIGA protein to be made active.
          Length = 234

 Score = 26.7 bits (59), Expect = 1.5
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55
           RE+ I    F  +    K TQKE+ +  G +QS+IS LE
Sbjct: 182 REKKIMELRFGLVGGTEK-TQKEVADMLGISQSYISRLE 219


>gnl|CDD|182049 PRK09726, PRK09726, antitoxin HipB; Provisional.
          Length = 88

 Score = 26.5 bits (58), Expect = 1.6
 Identities = 11/51 (21%), Positives = 22/51 (43%)

Query: 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74
          N  + +R++   TQ E+  + G  Q+ IS  E       +     +  +L+
Sbjct: 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLE 65


>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
           protein, YgiT family.  This model describes a family of
           predicted regulatory proteins with a conserved zinc
           finger/HTH architecture. The amino-terminal region
           contains a novel domain, featuring two CXXC motifs and
           occuring in a number of small bacterial proteins as well
           as in the present family. The carboxyl-terminal region
           consists of a helix-turn-helix domain, modeled by
           pfam01381. The predicted function is DNA binding and
           transcriptional regulation.
          Length = 127

 Score = 26.4 bits (59), Expect = 1.7
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 27  RNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58
           R IRK+  L+Q+E     G   +  S  E G+
Sbjct: 71  RRIRKKLGLSQREAAELLGGGVNAFSRYERGE 102


>gnl|CDD|182158 PRK09943, PRK09943, DNA-binding transcriptional repressor PuuR;
          Provisional.
          Length = 185

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 10/30 (33%), Positives = 16/30 (53%)

Query: 29 IRKEAKLTQKEIRNRTGFAQSWISELETGK 58
          IR++  L+Q+     +G   S IS +E  K
Sbjct: 15 IRQQQGLSQRRAAELSGLTHSAISTIEQDK 44


>gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
          regulator; Reviewed.
          Length = 309

 Score = 26.1 bits (58), Expect = 2.4
 Identities = 13/55 (23%), Positives = 31/55 (56%)

Query: 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81
          R +R    +++K +   +G ++ ++++LE+G+  ++I  +  +A  L   L  LL
Sbjct: 34 RTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLL 88


>gnl|CDD|163094 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G
           subfamily.  This group of similar sigma-70 factors
           includes clades found in Bacilli (including the
           sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as
           well as SigB:TIGR02941), and the high GC gram positive
           bacteria (Actinobacteria) where a variable number of
           them are found depending on the lineage.
          Length = 227

 Score = 25.6 bits (57), Expect = 2.6
 Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 5/39 (12%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55
           RER I +  F         TQ EI  R G +Q  +S L 
Sbjct: 182 RERRILLLRF-----FEDKTQSEIAERLGISQMHVSRLL 215


>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor.  The
           sporulation-specific transcription factor sigma-K (also
           called sigma-27) is expressed in the mother cell
           compartment of endospore-forming bacteria such as
           Bacillus subtilis. Like its close homolog sigma-E
           (sigma-29) (see TIGR02835), also specific to the mother
           cell compartment, it must be activated by a proteolytic
           cleavage. Note that in Bacillus subtilis (and apparently
           also Clostridium tetani), but not in other endospore
           forming species such as Bacillus anthracis, the sigK
           gene is generated by a non-germline (mother cell only)
           chromosomal rearrangement that recombines coding regions
           for the N-terminal and C-terminal regions of sigma-K.
          Length = 227

 Score = 25.4 bits (56), Expect = 3.2
 Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55
           RER +    +       K TQ+EI    G ++S++S +E
Sbjct: 178 REREVIEMRYGLGDGRRK-TQREIAKILGISRSYVSRIE 215


>gnl|CDD|106361 PRK13403, PRK13403, ketol-acid reductoisomerase; Provisional.
          Length = 335

 Score = 25.1 bits (54), Expect = 4.5
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)

Query: 30  RKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62
           +KE K    EI+ +  FA+ WI E + G+ T N
Sbjct: 270 KKEMKRVLTEIQ-QGEFAKKWILENQAGRPTYN 301


>gnl|CDD|181097 PRK07737, fliD, flagellar capping protein; Validated.
          Length = 501

 Score = 24.4 bits (53), Expect = 6.1
 Identities = 11/41 (26%), Positives = 15/41 (36%)

Query: 27  RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMI 67
           R +R   K T K I  + G       +   GK    I+  I
Sbjct: 417 RRLRDTLKETIKSIEQKAGNTTMTNQQFAIGKDLNQIETQI 457


>gnl|CDD|178434 PLN02841, PLN02841, GPI mannosyltransferase.
          Length = 440

 Score = 24.4 bits (53), Expect = 6.4
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 39  EIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82
           E + R  F Q WI+ L    +   +  MII  H   +PL++ L+
Sbjct: 386 EFKGRNVFLQLWIASLLFLAANTFVLLMIIQHHRF-SPLFQRLE 428


>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
          Length = 233

 Score = 24.5 bits (54), Expect = 6.7
 Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 3/46 (6%)

Query: 17  RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62
           RE+ +    +  +    + TQ+EI    G ++S++S +E  K  + 
Sbjct: 179 REKEVIEMRY-GLGNGKEKTQREIAKALGISRSYVSRIE--KRALK 221


>gnl|CDD|128413 smart00102, ADF, Actin depolymerisation factor/cofilin -like
           domains.  Severs actin filaments and binds to actin
           monomers.
          Length = 127

 Score = 24.6 bits (54), Expect = 6.7
 Identities = 6/29 (20%), Positives = 16/29 (55%)

Query: 12  SDAILRERMIFVNNFRNIRKEAKLTQKEI 40
             A ++ +M++ ++   ++KE    Q E+
Sbjct: 81  DGAPVKSKMLYASSKDTLKKELGGIQVEV 109


>gnl|CDD|106954 PHA00542, PHA00542, putative Cro-like protein.
          Length = 82

 Score = 24.0 bits (51), Expect = 8.5
 Identities = 6/25 (24%), Positives = 14/25 (56%)

Query: 35 LTQKEIRNRTGFAQSWISELETGKS 59
           +Q++I + T  +Q  I  + +G+ 
Sbjct: 32 WSQEQIADATDVSQPTICRIYSGRH 56


  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    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,382,635
Number of extensions: 71430
Number of successful extensions: 155
Number of sequences better than 10.0: 1
Number of HSP's gapped: 155
Number of HSP's successfully gapped: 28
Length of query: 83
Length of database: 5,994,473
Length adjustment: 52
Effective length of query: 31
Effective length of database: 4,870,857
Effective search space: 150996567
Effective search space used: 150996567
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: 50 (23.0 bits)