RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy6519
         (208 letters)



>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator.  This is a
          family of transcriptional regulators. In mammals, it
          activates the transcription of mitochondrially-encoded
          COX1. In bacteria, it negatively regulates the
          quorum-sensing response regulator by binding to its
          promoter region.
          Length = 234

 Score =  100 bits (253), Expect = 2e-26
 Identities = 32/68 (47%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 31 SKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPM 90
          SKW NI+H KAA+D ++  +FT L K++ +A K GG  DP  N RL   I+  K ++MP 
Sbjct: 1  SKWANIKHRKAAQDAKRGKIFTKLGKEITVAAKMGGP-DPEGNPRLRLAIEKAKAANMPK 59

Query: 91 TTIENAIK 98
            IE AIK
Sbjct: 60 DNIERAIK 67


>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
          Length = 245

 Score = 96.7 bits (242), Expect = 1e-24
 Identities = 35/71 (49%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 28 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSS 87
          AGHSKW NI+H K A+D ++  +FT L +++ +A K GGG DP  N RL   ID  K ++
Sbjct: 2  AGHSKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGG-DPEGNPRLRLAIDKAKAAN 60

Query: 88 MPMTTIENAIK 98
          MP   IE AIK
Sbjct: 61 MPKDNIERAIK 71


>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
          unknown].
          Length = 241

 Score = 96.1 bits (240), Expect = 2e-24
 Identities = 35/71 (49%), Positives = 50/71 (70%), Gaps = 1/71 (1%)

Query: 28 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSS 87
          AGHSKW NI+H KAA+D +++ +FT L K++ +A K+GG  DP +N RL + I+  K ++
Sbjct: 2  AGHSKWANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGP-DPESNPRLRTAIEKAKAAN 60

Query: 88 MPMTTIENAIK 98
          MP   IE AIK
Sbjct: 61 MPKDNIERAIK 71


>gnl|CDD|233240 TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR
          family.  This model describes a minimally characterized
          protein family, restricted to bacteria excepting for
          some eukaryotic sequences that have possible transit
          peptides. YebC from E. coli is crystallized, and PA0964
          from Pseudomonas aeruginosa has been shown to be a
          sequence-specific DNA-binding regulatory protein
          [Regulatory functions, DNA interactions].
          Length = 238

 Score = 90.4 bits (225), Expect = 2e-22
 Identities = 36/72 (50%), Positives = 49/72 (68%), Gaps = 1/72 (1%)

Query: 28 AGHSKWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSS 87
          AGHSKW NI+H KAA+D ++  +FT L K++ +A K GGG DP +N RL + I+  K ++
Sbjct: 2  AGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGG-DPESNPRLRTAIEKAKAAN 60

Query: 88 MPMTTIENAIKS 99
          MP   IE AIK 
Sbjct: 61 MPKDNIERAIKK 72


>gnl|CDD|237084 PRK12378, PRK12378, hypothetical protein; Provisional.
          Length = 235

 Score = 77.1 bits (191), Expect = 2e-17
 Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 32 KWQNIRHIKAAKDQEKATLFTNLSKKLKLAVKEGGGTDPNTNYRLASTIDYCKKSSMPMT 91
           W+NI+  KA KD  K+ +F  L K++ +A K+GG  DP +N  L   I+  KK+++P  
Sbjct: 4  AWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGG-PDPESNPALRFVIERAKKANVPKD 62

Query: 92 TIENAIK 98
           IE AIK
Sbjct: 63 VIERAIK 69


>gnl|CDD|222943 PHA02927, PHA02927, secreted complement-binding protein;
          Provisional.
          Length = 263

 Score = 26.9 bits (59), Expect = 6.8
 Identities = 10/28 (35%), Positives = 15/28 (53%)

Query: 55 SKKLKLAVKEGGGTDPNTNYRLASTIDY 82
          S+ + +  K    TD N NY +  TI+Y
Sbjct: 25 SRPINMKFKNSVETDANANYNIGDTIEY 52


>gnl|CDD|236049 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
           alpha; Validated.
          Length = 1220

 Score = 27.2 bits (61), Expect = 6.9
 Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 11/69 (15%)

Query: 40  KAAKDQEKATLFTN---LSKKLKLAVKE--------GGGTDPNTNYRLASTIDYCKKSSM 88
           K  ++Q+ A L T    +SK LK  +K             DP  N  L   I   KK+ +
Sbjct: 297 KVKEEQKVAALVTGSKIVSKHLKAIMKACVNCEGDGDDCFDPAKNPALKREIKAAKKALV 356

Query: 89  PMTTIENAI 97
           P   I+  I
Sbjct: 357 PENYIKRVI 365


>gnl|CDD|215156 PLN02276, PLN02276, gibberellin 20-oxidase.
          Length = 361

 Score = 26.9 bits (60), Expect = 9.9
 Identities = 11/26 (42%), Positives = 11/26 (42%), Gaps = 6/26 (23%)

Query: 103 PENIYGYLE------LSCLPWKPTLS 122
           P    GY         S LPWK TLS
Sbjct: 111 PGESCGYASSHTGRFSSKLPWKETLS 136


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.319    0.135    0.408 

Gapped
Lambda     K      H
   0.267   0.0868    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,405,239
Number of extensions: 917522
Number of successful extensions: 643
Number of sequences better than 10.0: 1
Number of HSP's gapped: 638
Number of HSP's successfully gapped: 11
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
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: 57 (25.5 bits)