RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7420
         (59 letters)



>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial. 
           Unlike all other known phenylalanyl-tRNA synthetases,
           the mitochondrial form demonstrated from yeast is
           monomeric. It is similar to but longer than the alpha
           subunit (PheS) of the alpha 2 beta 2 form found in
           Bacteria, Archaea, and eukaryotes, and shares the
           characteristic motifs of class II aminoacyl-tRNA
           ligases. This model models the experimental example from
           Saccharomyces cerevisiae (designated MSF1) and its
           orthologs from other eukaryotic species [Protein
           synthesis, tRNA aminoacylation].
          Length = 460

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M L+ IPDIR+F+S D GFL QF   D++    FK
Sbjct: 327 MLLFDIPDIRLFWSNDEGFLRQFSEGDLHLIPKFK 361


>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
          Length = 402

 Score = 38.2 bits (89), Expect = 4e-05
 Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 2/35 (5%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQFRTEDVNQKIVFK 35
           M L+ IPDIR+F+S+D  F +QF+   +  K  FK
Sbjct: 276 MVLFDIPDIRLFWSDDERFTSQFKEGQLGVK--FK 308


>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
           Validated.
          Length = 339

 Score = 33.5 bits (78), Expect = 0.002
 Identities = 12/23 (52%), Positives = 14/23 (60%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQF 23
           M  Y I DIR+F+  D  FL QF
Sbjct: 317 MLKYGIDDIRLFYENDLRFLKQF 339


>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
            Other tRNA synthetase sub-families are too dissimilar
           to be included. This family includes only
           phenylalanyl-tRNA synthetases. This is the core
           catalytic domain.
          Length = 245

 Score = 30.6 bits (70), Expect = 0.020
 Identities = 11/23 (47%), Positives = 12/23 (52%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQF 23
           M  Y I DIR  +  D  FL QF
Sbjct: 223 MLKYGIDDIRDLYENDLRFLRQF 245


>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
           [Translation, ribosomal structure and biogenesis].
          Length = 335

 Score = 30.3 bits (69), Expect = 0.029
 Identities = 11/22 (50%), Positives = 12/22 (54%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQ 22
           M  Y IPDIR  +  D  FL Q
Sbjct: 314 MLKYGIPDIRDLYENDLRFLRQ 335


>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
           alpha chain catalytic core domain. PheRS belongs to
           class II aminoacyl-tRNA synthetases (aaRS) based upon
           its structure and the presence of three characteristic
           sequence motifs. This domain is primarily responsible
           for ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. While class II aaRSs generally
           aminoacylate the 3'-OH ribose of the appropriate tRNA,
           PheRS is an exception in that it attaches the amino acid
           at the 2'-OH group, like class I aaRSs.  PheRS is an
           alpha-2/ beta-2 tetramer.
          Length = 218

 Score = 27.1 bits (61), Expect = 0.38
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 1   MQLYSIPDIRIFFSED 16
           M  Y IPDIR+F+S D
Sbjct: 201 MLKYGIPDIRLFYSND 216


>gnl|CDD|223372 COG0295, Cdd, Cytidine deaminase [Nucleotide transport and
           metabolism].
          Length = 134

 Score = 26.9 bits (60), Expect = 0.51
 Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 7/42 (16%)

Query: 19  FLNQFRTEDV------NQKIVFKFLLRELLLPRSYRPEIEER 54
            L +F  +D          IV    L ELL P ++ P+  E 
Sbjct: 94  VLAEFCGDDTLIILLPKDGIVKTMTLGELL-PDAFGPKDLEI 134


>gnl|CDD|185547 PTZ00304, PTZ00304, NADH dehydrogenase [ubiquinone] flavoprotein 1;
           Provisional.
          Length = 461

 Score = 26.7 bits (59), Expect = 0.54
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 43  LPRSYRPEIEERMK 56
           L R +RPEIEER++
Sbjct: 426 LIRHFRPEIEERIE 439


>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit.  Most
           phenylalanyl-tRNA synthetases are heterodimeric, with 2
           alpha (pheS) and 2 beta (pheT) subunits. This model
           describes the alpha subunit, which shows some similarity
           to class II aminoacyl-tRNA ligases. Mitochondrial
           phenylalanyl-tRNA synthetase is a single polypeptide
           chain, active as a monomer, and similar to this chain
           rather than to the beta chain, but excluded from this
           model. An interesting feature of the alignment of all
           sequences captured by this model is a deep split between
           non-spirochete bacterial examples and all other
           examples; supporting this split is a relative deletion
           of about 50 residues in the former set between two
           motifs well conserved throughout the alignment [Protein
           synthesis, tRNA aminoacylation].
          Length = 293

 Score = 26.5 bits (59), Expect = 0.64
 Identities = 11/23 (47%), Positives = 12/23 (52%)

Query: 1   MQLYSIPDIRIFFSEDSGFLNQF 23
           M  Y I DIR  +  D  FL QF
Sbjct: 270 MLKYGITDIRDLYENDLRFLRQF 292


>gnl|CDD|237441 PRK13596, PRK13596, NADH dehydrogenase I subunit F; Provisional.
          Length = 433

 Score = 25.7 bits (57), Expect = 1.4
 Identities = 9/14 (64%), Positives = 11/14 (78%)

Query: 43  LPRSYRPEIEERMK 56
           L R +RPEIEER+ 
Sbjct: 405 LIRHFRPEIEERID 418


>gnl|CDD|214840 smart00829, PKS_ER, Enoylreductase.  Enoylreductase in Polyketide
           synthases.
          Length = 287

 Score = 24.7 bits (55), Expect = 3.0
 Identities = 8/23 (34%), Positives = 10/23 (43%)

Query: 4   YSIPDIRIFFSEDSGFLNQFRTE 26
             IPD  IF S D  F ++    
Sbjct: 147 LGIPDDHIFSSRDLSFADEILRA 169


>gnl|CDD|236247 PRK08345, PRK08345, cytochrome-c3 hydrogenase subunit gamma;
           Provisional.
          Length = 289

 Score = 24.4 bits (53), Expect = 3.5
 Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 6/32 (18%)

Query: 32  IVFKFLLRELLLPRSYRPE-----IEERMKTG 58
           +++KF+ +EL+  R YRPE     +E RM+ G
Sbjct: 222 VMYKFVFKELI-NRGYRPERIYVTLERRMRCG 252


>gnl|CDD|214545 smart00182, CULLIN, Cullin. 
          Length = 143

 Score = 23.8 bits (52), Expect = 5.3
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 27 DVNQKIVFKFLLRELLLPRSYRPEIEERM 55
          DV +K   K L + L+L RS   + EE M
Sbjct: 6  DVFEKYYKKHLAKRLILNRSASDDAEENM 34


>gnl|CDD|216109 pfam00770, Peptidase_C5, Adenovirus endoprotease.  This family of
           adenovirus thiol endoproteases specifically cleave
           Gly-Ala peptides in viral precursor peptides.
          Length = 183

 Score = 23.5 bits (51), Expect = 7.2
 Identities = 9/31 (29%), Positives = 14/31 (45%)

Query: 29  NQKIVFKFLLRELLLPRSYRPEIEERMKTGY 59
           NQ+ ++KFL R     RS+   I+       
Sbjct: 151 NQEFLYKFLNRHSPYFRSHERTIKRNTAFDK 181


  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
   0.327    0.145    0.414 

Gapped
Lambda     K      H
   0.267   0.0902    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,215,157
Number of extensions: 236725
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 281
Number of HSP's successfully gapped: 17
Length of query: 59
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 28
Effective length of database: 9,562,628
Effective search space: 267753584
Effective search space used: 267753584
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 (21.7 bits)
S2: 53 (23.9 bits)