RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780424|ref|YP_003064837.1| transcriptional regulator
protein [Candidatus Liberibacter asiaticus str. psy62]
         (144 letters)



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

 Score = 50.6 bits (122), Expect = 1e-07
 Identities = 13/56 (23%), Positives = 28/56 (50%)

Query: 18 RIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFF 73
          R++  R   G++QE+L E LG++   + + E G  +     L+ +++ L   +   
Sbjct: 1  RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56


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

 Score = 39.1 bits (91), Expect = 4e-04
 Identities = 30/134 (22%), Positives = 55/134 (41%), Gaps = 28/134 (20%)

Query: 15  VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLE-SPISFF 73
           +G+RIR RR  L +SQ  L + + ++   + ++E+         L  +++ L+ SP    
Sbjct: 6   LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65

Query: 74  F---DVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQK-IIELVRSIVSS 129
           F   D  PT                  P  L      +++ +    QK ++EL  ++  S
Sbjct: 66  FGDEDKQPT-----------------PPVPLNQP---VELSE---DQKELLELFDALPES 102

Query: 130 EKKYRTIEEECMVE 143
           E+  +  E    VE
Sbjct: 103 EQDAQLSEMRARVE 116


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

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 18/66 (27%), Positives = 29/66 (43%)

Query: 9  NPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68
          +   +  GKR+   R   G+SQ +  E  G+T   +   E+       S LQ + +V   
Sbjct: 2  SDEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGL 61

Query: 69 PISFFF 74
           +S FF
Sbjct: 62 SLSEFF 67


>gnl|CDD|179747 PRK04140, PRK04140, hypothetical protein; Provisional.
          Length = 317

 Score = 33.3 bits (77), Expect = 0.022
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 11  VDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70
           V I+ G  +R  R  LG+S  +L   LG++ + + KYE G           + E+L+ P+
Sbjct: 124 VKID-GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182


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

 Score = 33.0 bits (76), Expect = 0.028
 Identities = 14/56 (25%), Positives = 29/56 (51%)

Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPI 70
          +G+R+R  R   GMS++ L +  G++ + + + E G   V    L+ ++  L   +
Sbjct: 29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSL 84


>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 = 29.1 bits (66), Expect = 0.43
 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)

Query: 17  KRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
           +RIR +   LG+SQ +  E LG       +YE+G
Sbjct: 71  RRIRKK---LGLSQREAAELLGGGVNAFSRYERG 101


>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 = 28.8 bits (65), Expect = 0.51
 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 15 VGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLES 68
          +G  +R RR  LG++Q  L +  G+  + ++  E G   V   RL  +  VL++
Sbjct: 3  IGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTV---RLDKVLRVLDA 53


>gnl|CDD|131661 TIGR02612, mob_myst_A, mobile mystery protein A.  Members of this
          protein family are found in mobization-related contexts
          more often than not, including within a
          CRISPR-associated gene region in Geobacter
          sulfurreducens PCA, and on plasmids in Agrobacterium
          tumefaciens and Coxiella burnetii, always together with
          mobile mystery protein B, a member of the Fic protein
          family (pfam02661). This protein is encoded by the
          upstream member of the gene pair and belongs to a
          family of helix-turn-helix DNA binding proteins
          (pfam01381).
          Length = 150

 Score = 27.9 bits (62), Expect = 1.1
 Identities = 14/31 (45%), Positives = 19/31 (61%)

Query: 19 IRLRRMILGMSQEKLGECLGITFQQVQKYEK 49
          +R  R  LGMS  +L   LG+T Q+V+  EK
Sbjct: 30 VRAIRKALGMSGAQLAGRLGVTPQRVEALEK 60


>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 = 27.4 bits (61), Expect = 1.5
 Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 9/46 (19%)

Query: 28 MSQEKLGECLGITFQQVQKY--EKGVNRV-------GASRLQHISE 64
          M+ E+L E  G + Q + ++  ++G           G +RL HI E
Sbjct: 1  MTPEELAELTGYSRQTINRWVRKEGWKTSPKPGVKGGKARLIHIDE 46


>gnl|CDD|183883 PRK13188, PRK13188, bifunctional UDP-3-O-[3-hydroxymyristoyl]
           N-acetylglucosamine
           deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein]
           dehydratase; Reviewed.
          Length = 464

 Score = 26.0 bits (58), Expect = 3.6
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 106 YFIQIDDVKVRQKII 120
           YF++ID VK RQK++
Sbjct: 403 YFMKIDKVKFRQKVV 417


>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 = 26.2 bits (58), Expect = 3.8
 Identities = 9/33 (27%), Positives = 20/33 (60%)

Query: 17  KRIRLRRMILGMSQEKLGECLGITFQQVQKYEK 49
           + + + R + G+S +++ E LGI+   V++  K
Sbjct: 116 REVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148


>gnl|CDD|163142 TIGR03117, cas_csf4, CRISPR-associated DEAD/DEAH-box helicase Csf4.
            Members of this family show up near CRISPR repeats in
           Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
           EbN1, and Rhodoferax ferrireducens DSM 15236. In the
           latter two species, the CRISPR/cas locus is found on a
           plasmid. This family is one of several characteristic of
           a type of CRISPR-associated (cas) gene cluster we
           designate Aferr after A. ferrooxidans, where it is both
           chromosomal and the only type of cas gene cluster found.
           The gene is designated csf4 (CRISPR/cas Subtype as in A.
           ferrooxidans protein 1), as it lies farthest (fourth
           closest) from the repeats in the A. ferrooxidans genome.
          Length = 636

 Score = 25.7 bits (56), Expect = 4.2
 Identities = 19/103 (18%), Positives = 36/103 (34%), Gaps = 8/103 (7%)

Query: 19  IRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSP 78
           + LRR+ L + +   G   GI    V      + R+ A  +    + L        D   
Sbjct: 230 LSLRRLHLYVEKRHTGAGKGIVSAAVAAVSHCIQRLRALDVFGDGQTLC------LDAGN 283

Query: 79  TVCSDISSEENNVMDFISTPDGLQLNRY-FIQIDDVKVRQKII 120
                + ++ +  +D  S       N+     + DVK + + I
Sbjct: 284 KELETLFADLDAALDACSVGRNRDENKKALSVVKDVK-KARFI 325


>gnl|CDD|183574 PRK12529, PRK12529, RNA polymerase sigma factor; Provisional.
          Length = 178

 Score = 25.7 bits (56), Expect = 4.9
 Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 5/35 (14%)

Query: 18  RIRLRRMIL-----GMSQEKLGECLGITFQQVQKY 47
           R R+++  L     GM Q+ + + L I    V+KY
Sbjct: 129 RPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKY 163


>gnl|CDD|185111 PRK15189, PRK15189, fimbrial protein BcfD; Provisional.
          Length = 335

 Score = 25.5 bits (55), Expect = 5.7
 Identities = 10/22 (45%), Positives = 13/22 (59%)

Query: 78  PTVCSDISSEENNVMDFISTPD 99
           P  CS + S+ N  M  I+TPD
Sbjct: 237 PVKCSGLDSQVNLTMRLIATPD 258


>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
           factor; Provisional.
          Length = 614

 Score = 25.0 bits (55), Expect = 6.9
 Identities = 11/20 (55%), Positives = 11/20 (55%)

Query: 18  RIRLRRMILGMSQEKLGECL 37
           R RLRRM L M  E L   L
Sbjct: 442 RERLRRMALPMEDEALVLLL 461


>gnl|CDD|180858 PRK07139, PRK07139, amidase; Provisional.
          Length = 439

 Score = 25.0 bits (55), Expect = 7.2
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 23/85 (27%)

Query: 22  RRMILGM------SQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFD 75
           +R+ILG       +QEK        F + +K    V RV      +   +        + 
Sbjct: 316 KRLILGSYFLEEENQEKY-------FLKAKK----VRRVIK---NYYESIHNKFDIVIYP 361

Query: 76  VSPTVCSDI---SSEENNVMDFIST 97
               +  DI    ++ +N MD+I T
Sbjct: 362 AYADIAPDIDENENKSDNYMDYILT 386


>gnl|CDD|185607 PTZ00422, PTZ00422, glideosome-associated protein 50; Provisional.
          Length = 394

 Score = 24.8 bits (54), Expect = 7.8
 Identities = 13/68 (19%), Positives = 25/68 (36%)

Query: 55  GASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVK 114
           G+        ++++  S F+      C    + E  V  F+S   G  L  +   +   K
Sbjct: 274 GSGGNSGRKSIMKNSKSLFYSEDIGFCIHELNAEGMVTKFVSGNTGEVLYTHKQPLKKRK 333

Query: 115 VRQKIIEL 122
           +R +   L
Sbjct: 334 LRFQGNAL 341


>gnl|CDD|180894 PRK07226, PRK07226, fructose-bisphosphate aldolase; Provisional.
          Length = 267

 Score = 24.8 bits (55), Expect = 9.7
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 14 NVGKRIRLRRMI 25
          N+GKRIRL R+ 
Sbjct: 3  NIGKRIRLERIF 14


  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
   0.319    0.137    0.378 

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: 2,331,868
Number of extensions: 136488
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 287
Number of HSP's successfully gapped: 31
Length of query: 144
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 60
Effective length of database: 4,179,401
Effective search space: 250764060
Effective search space used: 250764060
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 (21.8 bits)
S2: 52 (23.7 bits)