RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10415
         (130 letters)



>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
           [DNA replication, recombination, and repair].
          Length = 363

 Score = 28.7 bits (65), Expect = 0.69
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 83  PNRRARLFASLIFAVHPIHTEAVSDYHK 110
           P+ R R    L+F + P++ EA+S+Y K
Sbjct: 129 PSDRRRFLDWLLFQIEPVYLEALSNYEK 156


>gnl|CDD|232888 TIGR00233, trpS, tryptophanyl-tRNA synthetase.  This model
           represents tryptophanyl-tRNA synthetase. Some members of
           the family have a pfam00458 domain amino-terminal to the
           region described by this model [Protein synthesis, tRNA
           aminoacylation].
          Length = 327

 Score = 27.7 bits (62), Expect = 1.8
 Identities = 17/85 (20%), Positives = 26/85 (30%), Gaps = 7/85 (8%)

Query: 7   PDVQLKTPVGDLFNNDYWGTPITSPNSHGSYRPLTVLTFRLNYLACGLKPRSFHLINNLL 66
             V+L   + DL         IT   +              +YLA GL P    +     
Sbjct: 32  FGVELFICIADL-------HAITVKQTDPDALRKAREELAADYLAVGLDPEKTFIFLQSD 84

Query: 67  HSAITYLVYILSSYVLPNRRARLFA 91
           +     L ++LS  V      R+  
Sbjct: 85  YPEHYELAWLLSCQVTFGELKRMTQ 109


>gnl|CDD|220285 pfam09539, DUF2385, Protein of unknown function (DUF2385).  Members
           of this uncharacterized protein family are found in a
           number of alphaproteobacteria, including root nodule
           bacteria, Brucella suis, Caulobacter crescentus, and
           Rhodopseudomonas palustris. Conserved residues include
           two well-separated cysteines, suggesting a disulfide
           bond. The function is unknown.
          Length = 96

 Score = 26.1 bits (58), Expect = 2.7
 Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 6/42 (14%)

Query: 83  PNRRARLFASL-----IFA-VHPIHTEAVSDYHKTYLIQGER 118
           P RRARL A+       FA  +   T A     + Y  +GE 
Sbjct: 46  PARRARLIAAFNRGYRAFASTYRRCTPAARVAIERYAKEGET 87


>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
           domain fusion protein; Provisional.
          Length = 1460

 Score = 26.8 bits (59), Expect = 3.9
 Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 13/57 (22%)

Query: 3   ILTNPDVQLKTPVGDLFNNDYWGTPITSPNSHGSYRPLTVLT---------FRLNYL 50
           I+ N    L+  V  LF+N   G P+T P +    RPL  L          FR N L
Sbjct: 369 IVNNEKRMLQEAVDSLFDNGRRGRPVTGPGN----RPLKSLADMLKGKQGRFRQNLL 421


>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
          Length = 361

 Score = 26.3 bits (59), Expect = 6.1
 Identities = 6/18 (33%), Positives = 12/18 (66%)

Query: 93  LIFAVHPIHTEAVSDYHK 110
           L+F + P++  A+S Y +
Sbjct: 139 LLFQIEPVYASALSQYER 156


>gnl|CDD|198290 cd03181, GST_C_EF1Bgamma_like, Glutathione S-transferase
           C-terminal-like, alpha helical domain of the Gamma
           subunit of Elongation Factor 1B and similar proteins.
           Glutathione S-transferase (GST) C-terminal domain
           family, Gamma subunit of Elongation Factor 1B
           (EF1Bgamma) subfamily; EF1Bgamma is part of the
           eukaryotic translation elongation factor-1 (EF1) complex
           which plays a central role in the elongation cycle
           during protein biosynthesis. EF1 consists of two
           functionally distinct units, EF1A and EF1B. EF1A
           catalyzes the GTP-dependent binding of aminoacyl-tRNA to
           the ribosomal A site concomitant with the hydrolysis of
           GTP. The resulting inactive EF1A:GDP complex is recycled
           to the active GTP form by the guanine-nucleotide
           exchange factor EF1B, a complex composed of at least two
           subunits, alpha and gamma. Metazoan EFB1 contain a third
           subunit, beta. The EF1B gamma subunit contains a GST
           fold consisting of an N-terminal thioredoxin-fold domain
           and a C-terminal alpha helical domain. The GST-like
           domain of EF1Bgamma is believed to mediate the
           dimerization of the EF1 complex, which in yeast is a
           dimer of the heterotrimer EF1A:EF1Balpha:EF1Bgamma. In
           addition to its role in protein biosynthesis, EF1Bgamma
           may also display other functions. The recombinant rice
           protein has been shown to possess GSH conjugating
           activity. The yeast EF1Bgamma binds to membranes in a
           calcium dependent manner and is also part of a complex
           that binds to the msrA (methionine sulfoxide reductase)
           promoter suggesting a function in the regulation of its
           gene expression. Also included in this subfamily is the
           GST_C-like domain at the N-terminus of human valyl-tRNA
           synthetase (ValRS) and its homologs. Metazoan ValRS
           forms a stable complex with Elongation Factor-1H
           (EF-1H), and together, they catalyze consecutive steps
           in protein biosynthesis, tRNA aminoacylation and its
           transfer to EF.
          Length = 123

 Score = 25.2 bits (56), Expect = 7.1
 Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 2/23 (8%)

Query: 109 HKTYLIQGERCTLEDLYV-CLFV 130
            +TYL+ GER TL D++V    +
Sbjct: 58  TRTYLV-GERITLADIFVASALL 79


  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
   0.326    0.141    0.442 

Gapped
Lambda     K      H
   0.267   0.0807    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,625,871
Number of extensions: 568513
Number of successful extensions: 600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 600
Number of HSP's successfully gapped: 26
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)