RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780694|ref|YP_003065107.1| probable transcriptional
regulator protein, LuxR family [Candidatus Liberibacter asiaticus str.
psy62]
         (246 letters)



>gnl|CDD|99777 cd06170, LuxR_C_like, C-terminal DNA-binding domain of LuxR-like
           proteins. This domain contains a helix-turn-helix motif
           and binds DNA. Proteins belonging to this group are
           response regulators; some act as transcriptional
           activators, others as transcriptional repressors. Many
           are active as homodimers. Many are two domain proteins
           in which the DNA binding property of the C-terminal DNA
           binding domain is modulated by modifications of the
           N-terminal domain.  For example in the case of Lux R
           which participates in the regulation of gene expression
           in response to fluctuations in cell-population density
           (quorum-sensing), a signaling molecule, the pheromone
           Acyl HSL (N-acyl derivatives of homoserine lactone),
           binds to the N-terminal domain and leads to LuxR
           dimerization.  For others phophorylation of the
           N-terminal domain leads to multimerization, for example
           Escherichia coli NarL and Sinorhizobium melilot FixJ.
           NarL controls gene expression of many
           respiratory-related operons when environmental nitrate
           or nitrite is present under anerobic conditions. FixJ is
           involved in the transcriptional activation of nitrogen
           fixation genes. The group also includes small proteins
           which lack an N-terminal signaling domain, such as
           Bacillus subtilis GerE.  GerE is dimeric and acts in
           conjunction with sigmaK as an activator or a repressor
           modulating the expression of various genes in particular
           those encoding the spore-coat. These LuxR family
           regulators may share a similar organization of their
           target binding sites. For example the LuxR dimer binds
           the lux box, a 20bp inverted repeat, GerE dimers bind
           two 12bp consensus sequences in inverted orientation
           having the central four bases overlap, and the NarL
           dimer binds two 7bp inverted repeats separated by 2 bp..
          Length = 57

 Score = 78.0 bits (193), Expect = 2e-15
 Identities = 30/57 (52%), Positives = 40/57 (70%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
           LT RE E L  ++EGKT+ EIA ILGIS  TV  ++ +IMRK   K+R+  +AYA+R
Sbjct: 1   LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57


>gnl|CDD|32632 COG2771, CsgD, DNA-binding HTH domain-containing proteins
           [Transcription].
          Length = 65

 Score = 69.6 bits (170), Expect = 7e-13
 Identities = 26/61 (42%), Positives = 37/61 (60%)

Query: 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
             +LT RE E L  +++GK++ EIA ILGIS  TV  ++ +I RK   K R   +A A+R
Sbjct: 2   TADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALR 61

Query: 243 N 243
            
Sbjct: 62  L 62


>gnl|CDD|109261 pfam00196, GerE, Bacterial regulatory proteins, luxR family. 
          Length = 58

 Score = 67.2 bits (165), Expect = 4e-12
 Identities = 24/55 (43%), Positives = 33/55 (60%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
           L+ RE E L  ++ GK++ EIA ILGIS  TV  + ++IMRK    +R   I  A
Sbjct: 4   LSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 58


>gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver
           domain and an HTH DNA-binding domain [Signal
           transduction mechanisms / Transcription].
          Length = 211

 Score = 63.0 bits (153), Expect = 7e-11
 Identities = 25/82 (30%), Positives = 43/82 (52%)

Query: 165 LAAYQANMFKSYDVHWGKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASI 224
           +A   A +  S          LT RE+E L  ++EG ++ EIA  L +S  TV  ++++I
Sbjct: 128 IARKLAGLLPSSSAEAPLAELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNI 187

Query: 225 MRKTATKTRSGAIAYAVRNNIV 246
           +RK   + R+ A   A+R  ++
Sbjct: 188 LRKLGVRNRTEAAIRALRLGLI 209


>gnl|CDD|34204 COG4566, TtrR, Response regulator [Signal transduction mechanisms].
          Length = 202

 Score = 41.8 bits (98), Expect = 2e-04
 Identities = 17/47 (36%), Positives = 26/47 (55%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232
           LT RE + L  +  G  + +IA  LGIS  TV  + A++M K   ++
Sbjct: 143 LTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189


>gnl|CDD|32733 COG2909, MalT, ATP-dependent transcriptional regulator
           [Transcription].
          Length = 894

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 21/55 (38%), Positives = 33/55 (60%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
           L+ RE+E L  I++G +++EIA  L IS  TV  +I +I +K     R+ A+  A
Sbjct: 832 LSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRA 886


>gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most
           C-terminal of four conserved domains found in
           Escherichia coli (Ec) sigma70, the main housekeeping
           sigma, and related sigma-factors (SFs). A SF is a
           dissociable subunit of RNA polymerase, it directs
           bacterial or plastid core RNA polymerase to specific
           promoter elements located upstream of transcription
           initiation points. The SR4 of Ec sigma70 and other
           essential primary SFs contact promoter sequences located
           35 base-pairs upstream of the initiation point,
           recognizing a 6-base-pair -35 consensus TTGACA.  Sigma70
           related SFs also include SFs which are dispensable for
           bacterial cell growth for example Ec sigmaS, SFs which
           activate regulons in response to a specific signal for
           example heat-shock Ec sigmaH, and a group of SFs which
           includes the extracytoplasmic function (ECF) SFs and is
           typified by Ec sigmaE which contains SR2 and -4 only.
           ECF SFs direct the transcription of genes that regulate
           various responses including periplasmic stress and
           pathogenesis.   Ec sigmaE SR4 also contacts the -35
           element, but recognizes a different consensus (a
           7-base-pair GGAACTT).  Plant SFs recognize sigma70 type
           promoters and direct transcription of the major plastid
           RNA polymerase, plastid-encoded RNA polymerase (PEP)..
          Length = 55

 Score = 34.4 bits (80), Expect = 0.031
 Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 185 ELTGREVECLTWIS-EGKTSDEIAVILGISRNTVNNYIASIMRK 227
           +L  RE E +     EG + +EIA ILGISR+TV   +   ++K
Sbjct: 10  KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKK 53


>gnl|CDD|110930 pfam01978, TrmB, Sugar-specific transcriptional regulator TrmB.
           One member of this family, TrmB, has been shown to be a
           sugar-specific transcriptional regulator of the
           trehalose/maltose ABC transporter in Thermococcus
           litoralis.
          Length = 68

 Score = 32.5 bits (75), Expect = 0.13
 Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 182 KDFELTGREVECLTWI--SEGKTSDEIAVILGISRNTVNNYIASIMRK 227
           +   L+  E +    +      T+DEIA   G+ R+ V   + S+ +K
Sbjct: 2   QKLGLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKK 49


>gnl|CDD|31509 COG1318, COG1318, Predicted transcriptional regulators
           [Transcription].
          Length = 182

 Score = 31.6 bits (71), Expect = 0.21
 Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 6/42 (14%)

Query: 200 GKTSDEIAVILGISRNTVNNYIAS------IMRKTATKTRSG 235
           G T  EIA  LG +  TV N++        ++R+T  K + G
Sbjct: 61  GMTISEIAEELGRTEQTVRNHLKGETKAGQLVRETYEKLKEG 102


>gnl|CDD|32535 COG2390, DeoR, Transcriptional regulator, contains sigma
           factor-related N-terminal domain [Transcription].
          Length = 321

 Score = 31.3 bits (71), Expect = 0.25
 Identities = 14/24 (58%), Positives = 16/24 (66%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222
           EG T  EIA  LGISR TV+  +A
Sbjct: 25  EGLTQSEIAERLGISRATVSRLLA 48


>gnl|CDD|119388 cd00569, HTH_Hin_like, Helix-turn-helix domain of Hin and related
           proteins, a family of DNA-binding domains unique to
           bacteria and represented by the Hin protein of
           Salmonella. The basic HTH domain is a simple fold
           comprised of three core helices that form a right-handed
           helical bundle. The principal DNA-protein interface is
           formed by the third helix, the recognition helix,
           inserting itself into the major groove of the DNA. A
           diverse array of HTH domains participate in a variety of
           functions that depend on their DNA-binding properties.
           HTH_Hin represents one of the simplest versions of the
           HTH domains; the characterization of homologous
           relationships between various sequence-diverse HTH
           domain families remains difficult. The Hin recombinase
           induces the site-specific inversion of a chromosomal DNA
           segment containing a promoter, which controls the
           alternate expression of two genes by reversibly
           switching orientation. The Hin recombinase consists of a
           single polypeptide chain containing a DNA-binding domain
           (HTH_Hin) and a catalytic domain..
          Length = 42

 Score = 29.7 bits (68), Expect = 0.71
 Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 1/37 (2%)

Query: 186 LTGREVE-CLTWISEGKTSDEIAVILGISRNTVNNYI 221
           LT  ++E     ++ G++  EIA  LG+SR+T+  Y+
Sbjct: 6   LTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42


>gnl|CDD|31783 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma
           subunit, sigma24 homolog [Transcription].
          Length = 182

 Score = 29.3 bits (65), Expect = 0.90
 Identities = 13/29 (44%), Positives = 18/29 (62%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227
           EG + +EIA ILGIS  TV + +    +K
Sbjct: 142 EGLSYEEIAEILGISVGTVKSRLHRARKK 170


>gnl|CDD|146939 pfam04545, Sigma70_r4, Sigma-70, region 4.  Region 4 of sigma-70
           like sigma-factors are involved in binding to the -35
           promoter element via a helix-turn-helix motif. Due to
           the way Pfam works, the threshold has been set
           artificially high to prevent overlaps with other
           helix-turn-helix families. Therefore there are many
           false negatives.
          Length = 50

 Score = 29.3 bits (67), Expect = 1.1
 Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 185 ELTGREVECLTWI-SEGKTSDEIAVILGISRNTVNNYIASIMRK 227
            L  RE E L     EG T +EI   LGISR  V       +RK
Sbjct: 4   SLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALRK 47


>gnl|CDD|33163 COG3355, COG3355, Predicted transcriptional regulator
           [Transcription].
          Length = 126

 Score = 29.0 bits (65), Expect = 1.2
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 184 FELTGREVEC---LTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
           + L+  +VE    L   +   T DE+A IL  SR+TV   + +++  
Sbjct: 23  YGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69


>gnl|CDD|33219 COG3413, COG3413, Predicted DNA binding protein [General function
           prediction only].
          Length = 215

 Score = 28.1 bits (62), Expect = 2.5
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 8/57 (14%)

Query: 183 DFELTGREVECLTW--------ISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231
             +LT R++E L               +  ++A  LGIS++T++ ++    RK    
Sbjct: 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEA 209


>gnl|CDD|113729 pfam04967, HTH_10, HTH DNA binding domain. 
          Length = 53

 Score = 27.9 bits (63), Expect = 2.7
 Identities = 8/29 (27%), Positives = 16/29 (55%)

Query: 202 TSDEIAVILGISRNTVNNYIASIMRKTAT 230
           T  ++A  LGIS++T++ ++     K   
Sbjct: 25  TLKDLAKELGISKSTLSEHLRRAESKLIE 53


>gnl|CDD|31547 COG1356, COG1356, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 143

 Score = 27.6 bits (61), Expect = 3.1
 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 5/44 (11%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229
           LT ++++ L    +G T  EIA IL  +R  V     S + K A
Sbjct: 9   LTEQQIKVLVLREKGLTQSEIARILKTTRANV-----SAIEKRA 47


>gnl|CDD|32592 COG2522, COG2522, Predicted transcriptional regulator [General
           function prediction only].
          Length = 119

 Score = 27.6 bits (61), Expect = 3.5
 Identities = 9/27 (33%), Positives = 17/27 (62%)

Query: 197 ISEGKTSDEIAVILGISRNTVNNYIAS 223
           I EG +   IA +LG+++  V+ Y++ 
Sbjct: 19  IEEGLSQYRIAKLLGLTQAAVSQYLSG 45


>gnl|CDD|32990 COG3177, COG3177, Uncharacterized conserved protein [Function
           unknown].
          Length = 348

 Score = 27.4 bits (60), Expect = 4.3
 Identities = 8/30 (26%), Positives = 14/30 (46%)

Query: 198 SEGKTSDEIAVILGISRNTVNNYIASIMRK 227
               T+ EI  ILG+S+ T    +  ++  
Sbjct: 302 EGYLTAAEIEAILGVSKATATRDLKELLEL 331


>gnl|CDD|144487 pfam00908, dTDP_sugar_isom, dTDP-4-dehydrorhamnose 3,5-epimerase.
           This family catalyse the isomerisation of
           dTDP-4-dehydro-6-deoxy -D-glucose with
           dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this
           enzyme is 5.1.3.13.
          Length = 177

 Score = 27.3 bits (61), Expect = 4.8
 Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 7/48 (14%)

Query: 49  MYALTEYVGASHFLLVRWDLFQEQKLDSIVSSDWPFDLVRCMALSEKD 96
           +Y ++ Y        +RW+       D  +  DWP       +LSEKD
Sbjct: 128 LYKVSAYYSPEAERGIRWN-------DPAIGIDWPLADGPEPSLSEKD 168


>gnl|CDD|34203 COG4565, CitB, Response regulator of citrate/malate metabolism
           [Transcription / Signal transduction mechanisms].
          Length = 224

 Score = 27.1 bits (60), Expect = 4.9
 Identities = 10/24 (41%), Positives = 15/24 (62%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222
           +  T++E+A  LGISR T   Y+ 
Sbjct: 172 QELTAEELAQALGISRVTARRYLE 195


  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
   0.324    0.137    0.423 

Gapped
Lambda     K      H
   0.267   0.0783    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,065,044
Number of extensions: 160792
Number of successful extensions: 442
Number of sequences better than 10.0: 1
Number of HSP's gapped: 442
Number of HSP's successfully gapped: 27
Length of query: 246
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,297,318
Effective search space: 666084290
Effective search space used: 666084290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.2 bits)