RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14162
         (90 letters)



>gnl|CDD|217575 pfam03464, eRF1_2, eRF1 domain 2.  The release factor eRF1
          terminates protein biosynthesis by recognising stop
          codons at the A site of the ribosome and stimulating
          peptidyl-tRNA bond hydrolysis at the peptidyl
          transferase centre. The crystal structure of human eRF1
          is known. The overall shape and dimensions of eRF1
          resemble a tRNA molecule with domains 1, 2, and 3 of
          eRF1 corresponding to the anticodon loop, aminoacyl
          acceptor stem, and T stem of a tRNA molecule,
          respectively. The position of the essential GGQ motif
          at an exposed tip of domain 2 suggests that the Gln
          residue coordinates a water molecule to mediate the
          hydrolytic activity at the peptidyl transferase centre.
          A conserved groove on domain 1, 80 A from the GGQ
          motif, is proposed to form the codon recognition site.
          This family also includes other proteins for which the
          precise molecular function is unknown. Many of them are
          from Archaebacteria. These proteins may also be
          involved in translation termination but this awaits
          experimental verification.
          Length = 129

 Score = 51.5 bits (124), Expect = 6e-10
 Identities = 14/45 (31%), Positives = 26/45 (57%)

Query: 21 EKALVRFYDNVMQGILRHVNFDIVKCVLLASPGFVKDKFFEYMFQ 65
          E+    FY  V +   ++ + D VK ++LA PGF K++F++  + 
Sbjct: 47 EEKRHEFYRKVAEAANQYFDKDNVKGIILAGPGFTKNEFYDSDYL 91


>gnl|CDD|129217 TIGR00111, pelota, mRNA surveillance protein pelota.  This model
           describes the Drosophila protein Pelota, the budding
           yeast protein DOM34 which it can replace, and a set of
           closely related archaeal proteins. Members contain a
           proposed RNA binding motif. The meiotic defect in pelota
           mutants may be a complex result of a protein translation
           defect, as suggested in yeast by ribosomal protein
           RPS30A being a multicopy suppressor and by an altered
           polyribosome profile in DOM34 mutants rescued by RPS30A.
           This family is homologous to a family of peptide chain
           release factors. Pelota is proposed to act in protein
           translation [Protein synthesis, Translation factors].
          Length = 351

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 14/64 (21%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 2   IDRGAEDGKLMWEGDVKQHEKALVRFYDNVMQGILRHVNFDIVKCVLLASPGFVKDKFFE 61
            +    +  +  +    +  +    FY  + + +L   NFD +K +++A PGF K+ F++
Sbjct: 157 EEIQKIEYHMPGKKRTLKFGELRKEFYKEIAKKLL---NFDDLKTIIVAGPGFYKNDFYD 213

Query: 62  YMFQ 65
           ++F+
Sbjct: 214 FIFE 217


>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
           prediction only].
          Length = 352

 Score = 33.4 bits (77), Expect = 0.008
 Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 7/52 (13%)

Query: 14  EGDVKQHEKALVRFYDNVMQGILRHVNFDIVKCVLLASPGFVKDKFFEYMFQ 65
           EGD++   K    F+D + + +  + N DI+   ++A PGF K+ F++++ +
Sbjct: 169 EGDIRAERK----FFDEIAKALKEYANLDII---IVAGPGFAKEDFYDFLRE 213


>gnl|CDD|129509 TIGR00415, serS_MJ, seryl-tRNA synthetase, Methanococcus jannaschii
           family.  The seryl-tRNA synthetases from a few of the
           Archaea, represented by this model, are very different
           from the set of mutually more closely related seryl-tRNA
           synthetases from Eubacteria, Eukaryotes, and other
           Archaea. Although distantly homologous, the present set
           differs enough not to be recognized by the pfam model
           tRNA-synt_2b that recognizes the remainder of seryl-tRNA
           synthetases among oither class II amino-acyl tRNA
           synthetases [Protein synthesis, tRNA aminoacylation].
          Length = 520

 Score = 27.2 bits (60), Expect = 1.2
 Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 13/62 (20%)

Query: 14  EGDVKQHEKALVRFYDNV----------MQGILRHVNFDIVKCVLLASPGFV---KDKFF 60
           EG+V   E   ++F+D             +G+ R   F  V+CV +A P      +DK  
Sbjct: 325 EGEVIDAEDKPIKFFDRSGWTYRWEAGGAKGLDRVHEFLRVECVWIAEPEETEEIRDKTL 384

Query: 61  EY 62
           E 
Sbjct: 385 EL 386


>gnl|CDD|223580 COG0506, PutA, Proline dehydrogenase [Amino acid transport and
           metabolism].
          Length = 391

 Score = 27.0 bits (60), Expect = 1.2
 Identities = 10/40 (25%), Positives = 11/40 (27%)

Query: 34  GILRHVNFDIVKCVLLASPGFVKDKFFEYMFQVFTSQQAK 73
            I  H  F I     LA    V  +F   M         K
Sbjct: 349 QIASHNAFTIAAIYALAPELEVPGRFEFQMLHGMGEPLYK 388


>gnl|CDD|216936 pfam02223, Thymidylate_kin, Thymidylate kinase. 
          Length = 186

 Score = 25.3 bits (56), Expect = 3.9
 Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 2/37 (5%)

Query: 26  RFYDNVM--QGILRHVNFDIVKCVLLASPGFVKDKFF 60
           R+  + +  QG    +  D+V  +    PG   D  F
Sbjct: 87  RYLFSSIAYQGAAGGLGLDLVLSLNPDVPGPKPDLTF 123


>gnl|CDD|222254 pfam13598, DUF4139, Domain of unknown function (DUF4139).  This
           family is usually found at the C-terminus of proteins.
          Length = 264

 Score = 25.6 bits (57), Expect = 3.9
 Identities = 5/21 (23%), Positives = 8/21 (38%)

Query: 7   EDGKLMWEGDVKQHEKALVRF 27
           E G L W+  +   E   +  
Sbjct: 236 ERGILEWKLTLAPGETREIEL 256


>gnl|CDD|236613 PRK09693, PRK09693, Cascade antiviral complex protein; Validated.
          Length = 489

 Score = 25.1 bits (55), Expect = 5.5
 Identities = 15/69 (21%), Positives = 22/69 (31%), Gaps = 7/69 (10%)

Query: 8   DGKLMWEGDVKQHEKALVRFYDN---VMQGILRHVNFDIVKCVLLASPGFVKDKFFEYMF 64
             K      V  HE A+ RFY     ++   L  V+F     +         DK  +   
Sbjct: 404 KKKDFKGAGVSVHETAMRRFYRQSEQIILDTLADVDFKQADELRAG----AVDKLHQLCE 459

Query: 65  QVFTSQQAK 73
            +F    A 
Sbjct: 460 MLFNQSVAP 468


>gnl|CDD|183183 PRK11537, PRK11537, putative GTP-binding protein YjiA; Provisional.
          Length = 318

 Score = 24.7 bits (54), Expect = 7.8
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 5/42 (11%)

Query: 21  EKALVRFYDNVMQGILRHVNFD--IVKCVLLASPGFVKDKFF 60
           E AL+   DN+ +G +    FD  +++C  +A PG +   FF
Sbjct: 74  EDALLDLLDNLDKGNI---QFDRLVIECTGMADPGPIIQTFF 112


>gnl|CDD|236818 PRK11009, aphA, acid phosphatase/phosphotransferase; Provisional.
          Length = 237

 Score = 24.6 bits (54), Expect = 8.2
 Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 2/23 (8%)

Query: 39 VNFDIVKCVLLASPGFV--KDKF 59
          V FDI   VL +SPGF   K  F
Sbjct: 66 VGFDIDDTVLFSSPGFWRGKKTF 88


>gnl|CDD|105809 PRK12641, flgF, flagellar basal body rod protein FlgF; Reviewed.
          Length = 252

 Score = 24.5 bits (53), Expect = 8.8
 Identities = 6/25 (24%), Positives = 13/25 (52%)

Query: 16 DVKQHEKALVRFYDNVMQGILRHVN 40
          ++   +K + + Y N+  G LR+  
Sbjct: 49 NLYNSDKKITKEYYNLSPGTLRYTG 73


  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
   0.329    0.141    0.434 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,444,020
Number of extensions: 352355
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 15
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
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 (21.8 bits)
S2: 53 (24.1 bits)