RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254781090|ref|YP_003065503.1| hypothetical protein
CLIBASIA_04960 [Candidatus Liberibacter asiaticus str. psy62]
         (71 letters)



>1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR
          regulatory domain, oxidized form, transcription; 2.30A
          {Escherichia coli} SCOP: c.94.1.1 PDB: 1i69_A
          Length = 219

 Score = 28.8 bits (63), Expect = 0.35
 Identities = 4/24 (16%), Positives = 10/24 (41%)

Query: 48 LADFIKDYPDCDLELENLVTDDIL 71
          +    + +P  ++ L    T  +L
Sbjct: 24 IPMLHQTFPKLEMYLHEAQTHQLL 47


>3geb_A EYES absent homolog 2; hydrolase, activator, alternative
          splicing, cytoplasm, developmental protein, magnesium,
          nucleus, polymorphism; 2.40A {Homo sapiens}
          Length = 274

 Score = 28.6 bits (64), Expect = 0.36
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 13 VNFRFLLDGYRSGKTSKDKYQKIVKIGDHAES-IKTLAD---FIKDYPDCD-LELENLVT 67
          + F  LL G  + +  KD     V+IG   E  I  LAD   F  D  DCD + ++++ +
Sbjct: 16 IIFHSLLTGTFASRYGKD-TTTSVRIGLMMEEMIFNLADTHLFFNDLEDCDQIHVDDVSS 74

Query: 68 DD 69
          DD
Sbjct: 75 DD 76


>3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription,
          transcriptio regulation; 1.58A {Porphyromonas
          gingivalis}
          Length = 232

 Score = 27.4 bits (60), Expect = 0.91
 Identities = 3/24 (12%), Positives = 9/24 (37%)

Query: 48 LADFIKDYPDCDLELENLVTDDIL 71
             + K+    ++ +  + T   L
Sbjct: 30 FPIWKKELAGLEIHVSEMQTSRCL 53


>3hsq_A Acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine
           O-acyltransferase; L.interrogans LPXA, LPXA, LPXA
           acyltransferase; 2.10A {Leptospira interrogans} PDB:
           3i3a_A* 3i3x_A*
          Length = 259

 Score = 26.9 bits (58), Expect = 1.2
 Identities = 8/33 (24%), Positives = 17/33 (51%)

Query: 22  YRSGKTSKDKYQKIVKIGDHAESIKTLADFIKD 54
           Y SG +++    ++   G+  E +K +  F +D
Sbjct: 218 YHSGISTRKALDELEASGNLIEQVKYIIKFFRD 250


>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A
           {Xanthomonas campestris}
          Length = 129

 Score = 26.7 bits (59), Expect = 1.3
 Identities = 6/21 (28%), Positives = 9/21 (42%)

Query: 37  KIGDHAESIKTLADFIKDYPD 57
             G + E+ +TL      YP 
Sbjct: 88  GEGKNTEAQQTLQQVATQYPG 108



 Score = 24.4 bits (53), Expect = 6.5
 Identities = 6/32 (18%), Positives = 14/32 (43%), Gaps = 3/32 (9%)

Query: 29 KDKYQKIV---KIGDHAESIKTLADFIKDYPD 57
          +  Y       K G + ++ +    F++ YP+
Sbjct: 3  RTAYNVAFDALKNGKYDDASQLFLSFLELYPN 34


>3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type
          transcriptional regulator, LTTR, redox, structural
          genomics, OPPF; 2.39A {Neisseria meningitidis}
          Length = 219

 Score = 26.2 bits (57), Expect = 2.1
 Identities = 5/24 (20%), Positives = 8/24 (33%)

Query: 48 LADFIKDYPDCDLELENLVTDDIL 71
          +    +  P   L LE   T  + 
Sbjct: 23 IVSLRRTAPKMPLMLEENYTHTLT 46


>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich,
          DNA-binding, transcription regulation; HET: MES; 1.83A
          {Citrobacter freundii} PDB: 3kot_A
          Length = 219

 Score = 25.4 bits (55), Expect = 2.9
 Identities = 7/17 (41%), Positives = 10/17 (58%)

Query: 48 LADFIKDYPDCDLELEN 64
          L+DF + YP  DL +  
Sbjct: 31 LSDFKRSYPHIDLHIST 47


>3op5_A Serine/threonine-protein kinase VRK1; adenosine triphosphate, amino
           acid sequence, binding sites, domain, models, molecular;
           HET: REB; 2.40A {Homo sapiens}
          Length = 364

 Score = 25.3 bits (55), Expect = 3.7
 Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 3/58 (5%)

Query: 11  WGVNFRFLLDGYR--SGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLELENLV 66
            G      L G+          KY +  KI  + E+I +L D      +   E+   +
Sbjct: 247 LGYCMIQWLTGHLPWEDNLKDPKYVRDSKIR-YRENIASLMDKCFPAANAPGEIAKYM 303


>2qia_A UDP-N-acetylglucosamine acyltransferase; LEFT-handed parallel beta
           helix; HET: U20; 1.74A {Escherichia coli K12} SCOP:
           b.81.1.1 PDB: 1lxa_A 2jf3_A* 2aq9_A* 2qiv_X* 2jf2_A
          Length = 262

 Score = 24.4 bits (52), Expect = 6.1
 Identities = 10/33 (30%), Positives = 16/33 (48%)

Query: 22  YRSGKTSKDKYQKIVKIGDHAESIKTLADFIKD 54
           YRSGKT  +   +I ++ +    +K   DF   
Sbjct: 223 YRSGKTLDEVKPEIAELAETYPEVKAFTDFFAR 255


>2ckc_A Chromodomain-helicase-DNA-binding protein 7; protein-protein
          interaction, phosphorylation, disease mutation,
          nucleotide-binding; NMR {Homo sapiens} SCOP: d.76.2.1
          PDB: 2v0e_A
          Length = 80

 Score = 24.4 bits (53), Expect = 6.6
 Identities = 6/19 (31%), Positives = 11/19 (57%)

Query: 39 GDHAESIKTLADFIKDYPD 57
          G+ A   K L +++K +P 
Sbjct: 40 GEDAPKNKDLVEWLKLHPT 58


>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
          transcription factor, DNA-binding, DNA-directed RNA
          polymerase; 4.30A {Saccharomyces cerevisiae}
          Length = 197

 Score = 24.1 bits (52), Expect = 7.0
 Identities = 3/14 (21%), Positives = 6/14 (42%)

Query: 56 PDCDLELENLVTDD 69
          P+C +    +V   
Sbjct: 25 PECKVYPPKIVERF 38


>3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM
           radical, activase, glycyl radical, 4Fe- 4S, carbohydrate
           metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia
           coli} PDB: 3cb8_A*
          Length = 245

 Score = 24.2 bits (51), Expect = 7.2
 Identities = 6/34 (17%), Positives = 13/34 (38%)

Query: 26  KTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCD 59
                +Y  +    D  +S   L +F +D  + +
Sbjct: 161 VKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVE 194


>2dl6_A Chromodomain-helicase-DNA-binding protein 8; BRK, CHD8,
          structural genomics, NPPSFA, national project on
          protein structural and functional analyses; NMR {Homo
          sapiens} SCOP: d.76.2.1
          Length = 83

 Score = 24.1 bits (52), Expect = 8.5
 Identities = 4/19 (21%), Positives = 10/19 (52%)

Query: 39 GDHAESIKTLADFIKDYPD 57
          G+ A     L  +++ +P+
Sbjct: 33 GEDAPRRAELEMWLQGHPE 51


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 23.8 bits (50), Expect = 9.3
 Identities = 6/17 (35%), Positives = 10/17 (58%), Gaps = 1/17 (5%)

Query: 43 ESIKTLADFIKDYPDCD 59
          +++K L   +K Y D D
Sbjct: 20 QALKKLQASLKLYAD-D 35


>2cka_A Chromodomain-helicase-DNA-binding protein 8; BRK domain,
          transcription elongation, chromatin remodeling,
          protein-protein interaction, transcription; NMR {Homo
          sapiens} SCOP: d.76.2.1
          Length = 95

 Score = 23.7 bits (51), Expect = 9.8
 Identities = 4/19 (21%), Positives = 10/19 (52%)

Query: 39 GDHAESIKTLADFIKDYPD 57
          G+ A     L  +++ +P+
Sbjct: 59 GEDAPRRAELEMWLQGHPE 77


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.321    0.144    0.434 

Gapped
Lambda     K      H
   0.267   0.0573    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 653,255
Number of extensions: 23888
Number of successful extensions: 148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 25
Length of query: 71
Length of database: 5,693,230
Length adjustment: 41
Effective length of query: 30
Effective length of database: 4,699,226
Effective search space: 140976780
Effective search space used: 140976780
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: 50 (23.4 bits)