RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 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|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon.  lux regulon
           (activates the bioluminescence operon.
          Length = 58

 Score = 77.2 bits (191), Expect = 3e-15
 Identities = 25/55 (45%), Positives = 36/55 (65%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
           LT RE E L  ++EG T+ EIA  LGIS  TV  ++++IMRK   ++R+ A+  A
Sbjct: 4   LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58


>gnl|CDD|163106 TIGR03020, EpsA, transcriptional regulator EpsA.  Proteins in this
           family include a C-terminal LuxR transcriptional
           regulator domain (pfam00196). These proteins are
           positioned proximal to either EpsH-containing
           exopolysaccharide biosynthesis operons of the
           Methylobacillus type, or the associated
           PEP-CTERM-containing genes.
          Length = 247

 Score = 63.3 bits (154), Expect = 6e-11
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
           +T RE E L W+ +GKT++EIA ILGIS  TV N++  I +K   + R+ A+A A+ 
Sbjct: 191 ITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAIA 247


>gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory,
           chaperone HchA-associated.  Members of this protein
           family belong to the LuxR transcriptional regulator
           family, and contain both autoinducer binding (pfam03472)
           and transcriptional regulator (pfam00196) domains.
           Members, however, occur only in a few members of the
           Gammaproteobacteria that have the
           chaperone/aminopeptidase HchA, and are always encoded by
           the adjacent gene.
          Length = 232

 Score = 53.2 bits (128), Expect = 5e-08
 Identities = 26/57 (45%), Positives = 34/57 (59%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
           L+ RE E L W + G+   +IA ILGIS  TV N++ S  RK    T + AIA A+R
Sbjct: 172 LSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALR 228


>gnl|CDD|182292 PRK10188, PRK10188, DNA-binding transcriptional activator SdiA;
           Provisional.
          Length = 240

 Score = 52.1 bits (125), Expect = 1e-07
 Identities = 24/53 (45%), Positives = 32/53 (60%)

Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241
           RE E L W +EGKTS EIA+IL IS NTVN +  ++ +K     ++    YA 
Sbjct: 183 REKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAA 235


>gnl|CDD|182241 PRK10100, PRK10100, DNA-binding transcriptional regulator CsgD;
           Provisional.
          Length = 216

 Score = 43.3 bits (102), Expect = 6e-05
 Identities = 23/58 (39%), Positives = 36/58 (62%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRN 243
           LT RE E L  +  G +++EIA  L IS NTV  ++ ++ +K A K R+ A+++A  N
Sbjct: 156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213


>gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional.
          Length = 215

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 18/51 (35%), Positives = 33/51 (64%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGA 236
           LT RE++ L  +++G ++ +IA +L IS  TV  +I +++RK   ++R  A
Sbjct: 154 LTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204


>gnl|CDD|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional.
          Length = 216

 Score = 39.2 bits (92), Expect = 0.001
 Identities = 26/96 (27%), Positives = 48/96 (50%), Gaps = 7/96 (7%)

Query: 151 GRIILRDRLWEIGLLAAYQANMFKSYDVHWGKDFE-LTGREVECLTWISEGKTSDEIAVI 209
           G ++L + L  + L A+ +AN   +      +D   LT RE + L  I++G  +  IA  
Sbjct: 126 GEMVLSEALTPV-LAASLRANRATT-----ERDVNQLTPRERDILKLIAQGLPNKMIARR 179

Query: 210 LGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
           L I+ +TV  ++  +++K   K+R  A  +  +  I
Sbjct: 180 LDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215


>gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional.
          Length = 234

 Score = 36.5 bits (84), Expect = 0.006
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
           L  +E   L WI+ GKT +EIA + G+  N+V   +   M++   ++++   A A+R  +
Sbjct: 174 LDPKEATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKL 233

Query: 246 V 246
           +
Sbjct: 234 I 234


>gnl|CDD|116865 pfam08281, Sigma70_r4_2, 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.
          Length = 54

 Score = 35.1 bits (82), Expect = 0.015
 Identities = 12/29 (41%), Positives = 18/29 (62%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRK 227
           EG +  EIA +LGIS  TV + ++   +K
Sbjct: 25  EGLSYAEIAELLGISEGTVKSRLSRARKK 53


>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
           family.  Several PFAM models hit segments of these
           sequences including Sigma-70 region 2 (pfam04542) and
           Sigma-70, region 4 (pfam04545), but not always above
           their respective trusted cutoffs.
          Length = 158

 Score = 35.4 bits (82), Expect = 0.015
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 189 REVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
           REV  L ++ EG +  EIA ILGIS  TV   +    +K
Sbjct: 116 REVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKK 153


>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB;
           Provisional.
          Length = 211

 Score = 34.7 bits (80), Expect = 0.021
 Identities = 19/42 (45%), Positives = 26/42 (61%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
           LT RE + L  I+EG T+ +IA  L IS  TV  +  ++MRK
Sbjct: 150 LTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRK 191


>gnl|CDD|132030 TIGR02985, Sig70_bacteroi1, RNA polymerase sigma-70 factor,
           Bacteroides expansion family 1.  This group of sigma
           factors are members of the sigma-70 family (TIGR02937)
           and are found primarily in the genus Bacteroides. This
           family appears to have resulted from a lineage-specific
           expansion as B. thetaiotaomicron VPI-5482, Bacteroides
           forsythus ATCC 43037, Bacteroides fragilis YCH46 and
           Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23
           members, respectively. There are currentlyonly two known
           members of this family outside of the Bacteroides, in
           Rhodopseudomonas and Bradyrhizobium.
          Length = 161

 Score = 34.5 bits (80), Expect = 0.029
 Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 3/32 (9%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIA---SIMRK 227
           EGK+  EIA  LGIS  TV  +I+     +RK
Sbjct: 128 EGKSYKEIAEELGISVKTVEYHISKALKELRK 159


>gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional.
          Length = 200

 Score = 33.9 bits (78), Expect = 0.044
 Identities = 14/40 (35%), Positives = 25/40 (62%)

Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221
           K ++LTG+E +    + +G +  EIA  LG+SR T+  ++
Sbjct: 154 KKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFL 193


>gnl|CDD|163591 TIGR03879, near_KaiC_dom, probable regulatory domain.  This model
           describes a common domain shared by two different
           families of proteins, each of which occurs regularly
           next to its corresponding partner family, a probable
           regulatory with homology to KaiC. By implication, this
           protein family likely is also involved in sensory
           transduction and/or regulation.
          Length = 73

 Score = 33.6 bits (77), Expect = 0.051
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 20/61 (32%)

Query: 191 VECLTWIS-------------EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAI 237
            E LTW+               GKT+ EIA  LG +  TV N++         +T++G +
Sbjct: 10  AERLTWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG-------ETKAGGL 62

Query: 238 A 238
            
Sbjct: 63  V 63


>gnl|CDD|182168 PRK09958, PRK09958, DNA-binding transcriptional activator EvgA;
           Provisional.
          Length = 204

 Score = 32.9 bits (75), Expect = 0.069
 Identities = 19/60 (31%), Positives = 34/60 (56%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
           L+ +E+  + +I +GK +++IA  + IS  TV+ Y + +M K   K+      +A RN I
Sbjct: 144 LSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203


>gnl|CDD|116512 pfam07900, DUF1670, Protein of unknown function (DUF1670).  The
           hypothetical eukaryotic proteins found in this family
           are of unknown function.
          Length = 220

 Score = 31.3 bits (71), Expect = 0.25
 Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 6/40 (15%)

Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYI 221
           KDF      VE LT   +G + +EI  I GIS   V  Y+
Sbjct: 185 KDFT----RVEKLT--EKGMSEEEIRYITGISERLVEEYV 218


>gnl|CDD|182154 PRK09935, PRK09935, transcriptional regulator FimZ; Provisional.
          Length = 210

 Score = 31.0 bits (70), Expect = 0.30
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 183 DFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
           D  L+ REV  L ++  G ++ EIA  L +S  TV+ + ++I  K    +    I YA
Sbjct: 147 DTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204


>gnl|CDD|116863 pfam08279, HTH_11, HTH domain.  This family includes
           helix-turn-helix domains in a wide variety of proteins.
          Length = 55

 Score = 30.5 bits (70), Expect = 0.45
 Identities = 8/23 (34%), Positives = 14/23 (60%)

Query: 202 TSDEIAVILGISRNTVNNYIASI 224
           +  E+A  LG+SR T+   I ++
Sbjct: 17  SGQELAEKLGVSRRTIRRDIKAL 39


>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA;
           Provisional.
          Length = 196

 Score = 30.3 bits (68), Expect = 0.48
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 181 GKDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRK 227
           G+   LT RE +    +++G    EIA  LG+S  TV+ + A++M K
Sbjct: 133 GRQDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEK 179


>gnl|CDD|162580 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein.  Most
           but not all examples of this family are associated with
           CRISPR loci, a combination of DNA repeats and
           characteristic proteins encoded near the repeat cluster.
           The C-terminal region of this protein is homologous to
           DNA-binding helix-turn-helix domains with predicted
           transcriptional regulatory activity.
          Length = 203

 Score = 29.6 bits (67), Expect = 0.70
 Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 182 KDFELTGREVECL-TWISEGKTS-DEIAVILGISRNTVNNYIA 222
               L+  E++ L    +EG+ S   IA  LG S +T++ ++ 
Sbjct: 137 LLAGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR 179


>gnl|CDD|182165 PRK09954, PRK09954, putative kinase; Provisional.
          Length = 362

 Score = 29.9 bits (67), Expect = 0.71
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 204 DEIAVILGISRNTVNNYIASIMRKTATK 231
           +EIA IL ISR+ V  +I  +MRK   K
Sbjct: 21  NEIADILQISRSRVAAHIMDLMRKGRIK 48


>gnl|CDD|180757 PRK06930, PRK06930, positive control sigma-like factor; Validated.
          Length = 170

 Score = 29.7 bits (67), Expect = 0.80
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 186 LTGREVEC-LTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKT 232
           LT RE E  L     G +  EIA  L I ++TV + I    +K A + 
Sbjct: 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162


>gnl|CDD|179885 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
          Length = 903

 Score = 29.1 bits (66), Expect = 1.0
 Identities = 16/55 (29%), Positives = 30/55 (54%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYA 240
           LT RE + L  I  G ++++IA  L ++  T+  +I ++ +K     R  A+ +A
Sbjct: 839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893


>gnl|CDD|171560 PRK12527, PRK12527, RNA polymerase sigma factor; Reviewed.
          Length = 159

 Score = 29.4 bits (66), Expect = 1.0
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIASIMRKTATKTR 233
           EG +  +IA  LGISR+ V  +I + M+    + R
Sbjct: 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154


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

 Score = 29.1 bits (66), Expect = 1.2
 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 9/51 (17%)

Query: 186 LTGREVECLT-----WISEGKTSDEIAVILGISRNTVNNYIASIMRKTATK 231
           L  RE E +         + KT  EIA  LGISR    +Y++ I ++   K
Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISR----SYVSRIEKRALKK 222


>gnl|CDD|185123 PRK15201, PRK15201, fimbriae regulatory protein FimW; Provisional.
          Length = 198

 Score = 28.5 bits (63), Expect = 1.7
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 182 KDFELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAV 241
           + F +T R +  L  I+ G    E A +L +S     +   SIMRK   KT    + Y +
Sbjct: 132 RHFSVTERHL--LKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLKY-I 188

Query: 242 RNNI 245
           R N+
Sbjct: 189 RVNL 192


>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 = 28.5 bits (64), Expect = 1.7
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 9/51 (17%)

Query: 186 LTGREVECLTW---ISEG--KTSDEIAVILGISRNTVNNYIASIMRKTATK 231
           L GRE E +     + +G  KT  EIA ILGISR    +Y++ I ++   K
Sbjct: 175 LDGREREVIEMRYGLGDGRRKTQREIAKILGISR----SYVSRIEKRALMK 221


>gnl|CDD|182069 PRK09775, PRK09775, putative DNA-binding transcriptional regulator;
           Provisional.
          Length = 442

 Score = 28.0 bits (63), Expect = 2.2
 Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 195 TWISEGK-TSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVRNNI 245
           T + +G  ++ E+A  LG+S+ T++  +A++  +     ++ A  YA+   +
Sbjct: 7   TLLLQGPLSAAELAARLGVSQATLSRLLAALGDQVVRFGKARATRYALLRPL 58


>gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional.
          Length = 202

 Score = 27.7 bits (62), Expect = 2.8
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 185 ELTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242
            L+ RE + +  +  G ++  IA  L IS  TV  Y A++M    TK ++G+++  VR
Sbjct: 141 SLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVM----TKMQAGSLSELVR 194


>gnl|CDD|181897 PRK09483, PRK09483, response regulator; Provisional.
          Length = 217

 Score = 27.8 bits (62), Expect = 2.9
 Identities = 13/35 (37%), Positives = 24/35 (68%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNY 220
           L+ RE++ +  I++G+  +EI+  L +S  TVN+Y
Sbjct: 149 LSERELQIMLMITKGQKVNEISEQLNLSPKTVNSY 183


>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
          Length = 179

 Score = 27.6 bits (62), Expect = 3.4
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 199 EGKTSDEIAVILGISRNTVNNYIA 222
           EG +  EIA ILG+   TV + + 
Sbjct: 140 EGLSYREIAEILGVPVGTVKSRLR 163


>gnl|CDD|152436 pfam12001, DUF3496, Domain of unknown function (DUF3496).  This
          presumed domain is functionally uncharacterized. This
          domain is found in eukaryotes. This domain is about 110
          amino acids in length.
          Length = 111

 Score = 27.5 bits (61), Expect = 3.5
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 2  NFEIQQVNIVLNREDEQRTSFVSHLPTRSDL 32
          N  + +V+  L  E EQ  S +S LPTR DL
Sbjct: 56 NERLAEVSTKLLMEKEQSRSLLSTLPTRPDL 86


>gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein
           (SU).  The bovine lentivirus also known as the bovine
           immunodeficiency-like virus (BIV) has conserved and
           hypervariable regions in the surface envelope gene. This
           family corresponds to the SU surface protein.
          Length = 548

 Score = 27.3 bits (60), Expect = 3.6
 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 115 TLPENITPPAGMDNRYCSLTFDVARIRIGLMLLFPKGRIILRDRLWEIGLLAAYQA 170
           ++PENIT     D    +L        +GL+     G II   R    G+LAA  A
Sbjct: 130 SVPENITKIPIKDTDPWTLILLGLVCILGLL-----GVIIAMRRSNPEGILAARDA 180


>gnl|CDD|179690 PRK03975, tfx, putative transcriptional regulator; Provisional.
          Length = 141

 Score = 26.8 bits (60), Expect = 4.9
 Identities = 19/44 (43%), Positives = 22/44 (50%), Gaps = 5/44 (11%)

Query: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTA 229
           LT R++E L     G T  EIA ILG SR  V     S + K A
Sbjct: 7   LTERQIEVLRLRERGLTQQEIADILGTSRANV-----SSIEKRA 45


>gnl|CDD|183569 PRK12517, PRK12517, RNA polymerase sigma factor; Provisional.
          Length = 188

 Score = 26.6 bits (59), Expect = 6.4
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 200 GKTSDEIAVILGISRNTVN 218
           G + +EIA IL +++NTV 
Sbjct: 144 GFSGEEIAEILDLNKNTVM 162


>gnl|CDD|181871 PRK09455, rseB, anti-sigma E factor; Provisional.
          Length = 319

 Score = 26.0 bits (58), Expect = 8.7
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 6/26 (23%)

Query: 16  DEQRTSFV------SHLPTRSDLLAR 35
           D  R S++      S LP R DLL R
Sbjct: 151 DGTRYSYIVWIDEESKLPLRVDLLDR 176


>gnl|CDD|163020 TIGR02786, addB_alphas, double-strand break repair protein AddB,
          alphaproteobacterial type.  AddAB is a system well
          described in the Firmicutes as a replacement for RecBCD
          in many prokaryotes for the repair of double stranded
          break DNA damage. More recently, a distantly related
          gene pair conserved in many alphaproteobacteria was
          shown also to function in double-stranded break repair
          in Rhizobium etli. This family consists of AddB
          proteins of the alphaproteobacteial type.
          Length = 1021

 Score = 26.2 bits (58), Expect = 8.7
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 19 RTSFVSHLPTRSDLLARMIPL 39
          R +FV  L  R+ LL R+ PL
Sbjct: 55 REAFVDVLDGRAALLPRIRPL 75


>gnl|CDD|163347 TIGR03599, YloV, DAK2 domain fusion protein YloV.  This model
           describes a protein family that contains an N-terminal
           DAK2 domain (pfam02734), so named because of similarity
           to the dihydroxyacetone kinase family family. The
           GTP-binding protein CgtA (a member of the obg family) is
           a bacterial GTPase associated with ribosome biogenesis,
           and it has a characteristic extension (TIGR03595) in
           certain lineages. This protein family described here was
           found, by the method of partial phylognetic profiling,
           to have a phylogenetic distribution strongly correlated
           to that of TIGR03595. This correlation implies some form
           of functional coupling.
          Length = 530

 Score = 26.0 bits (58), Expect = 8.9
 Identities = 8/22 (36%), Positives = 11/22 (50%)

Query: 222 ASIMRKTATKTRSGAIAYAVRN 243
              M +     RSG + YAVR+
Sbjct: 416 KEAMEEAIKAVRSGEVTYAVRD 437


>gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
          Length = 509

 Score = 26.1 bits (58), Expect = 9.6
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 201 KTSDEIAVILGISRNTVNNYIASIMRK 227
           KT DEI  + G++R  +    +  +RK
Sbjct: 468 KTLDEIGQVYGVTRERIRQIESKTLRK 494


>gnl|CDD|148573 pfam07037, DUF1323, Putative transcription regulator (DUF1323).
           This family consists of several hypothetical
           Enterobacterial proteins of around 120 residues in
           length. This family appears to have an HTH domain and is
           therefore likely to act as a transcriptional regulator.
          Length = 122

 Score = 25.9 bits (57), Expect = 10.0
 Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 4/31 (12%)

Query: 202 TSDEIAVILGISRNTVNNYIASIMRKTATKT 232
           T +E+A + G SR T+N ++    RK   KT
Sbjct: 2   TPEELAELTGYSRQTINRWV----RKEGWKT 28


  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
   0.324    0.137    0.423 

Gapped
Lambda     K      H
   0.267   0.0675    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,061,959
Number of extensions: 255195
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 618
Number of HSP's successfully gapped: 43
Length of query: 246
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 155
Effective length of database: 4,028,145
Effective search space: 624362475
Effective search space used: 624362475
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 (25.5 bits)