RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254781180|ref|YP_003065593.1| hypothetical protein
CLIBASIA_05435 [Candidatus Liberibacter asiaticus str. psy62]
         (71 letters)



>gnl|CDD|133285 cd01885, EF2, EF2 (for archaea and eukarya).  Translocation
           requires hydrolysis of a molecule of GTP and is mediated
           by EF-G in bacteria and by eEF2 in eukaryotes.  The
           eukaryotic elongation factor eEF2 is a GTPase involved
           in the translocation of the peptidyl-tRNA from the A
           site to the P site on the ribosome.  The 95-kDa protein
           is highly conserved, with 60% amino acid sequence
           identity between the human and yeast proteins.  Two
           major mechanisms are known to regulate protein
           elongation and both involve eEF2.  First, eEF2 can be
           modulated by reversible phosphorylation.  Increased
           levels of phosphorylated eEF2 reduce elongation rates
           presumably because phosphorylated eEF2 fails to bind the
           ribosomes.  Treatment of mammalian cells with agents
           that raise the cytoplasmic Ca2+ and cAMP levels reduce
           elongation rates by activating the kinase responsible
           for phosphorylating eEF2.  In contrast, treatment of
           cells with insulin increases elongation rates by
           promoting eEF2 dephosphorylation.  Second, the protein
           can be post-translationally modified by
           ADP-ribosylation.  Various bacterial toxins perform this
           reaction after modification of a specific histidine
           residue to diphthamide, but there is evidence for
           endogenous ADP ribosylase activity.  Similar to the
           bacterial toxins, it is presumed that modification by
           the endogenous enzyme also inhibits eEF2 activity.
          Length = 222

 Score = 27.2 bits (61), Expect = 1.0
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 6/59 (10%)

Query: 13  LVNNEQLTEIEEPQKV--TVDQINNAIASLIPEERRDLQDRMAKYSTRKLKPRGRVIFA 69
           L+   +L+  E  Q++   ++Q+N  I +   EE ++  D    +S +K    G V F 
Sbjct: 138 LILELKLSPEEAYQRLARIIEQVNAIIGTYADEEFKEKDDEKWYFSPQK----GNVAFG 192


>gnl|CDD|100023 cd06059, Tubulin, The tubulin superfamily includes five distinct
           families, the alpha-, beta-, gamma-, delta-, and
           epsilon-tubulins and a sixth family (zeta-tubulin) which
           is present only in kinetoplastid protozoa. The alpha-
           and beta-tubulins are the major components of
           microtubules, while gamma-tubulin plays a major role in
           the nucleation of microtubule assembly.  The delta- and
           epsilon-tubulins are widespread but unlike the alpha,
           beta, and gamma-tubulins they are not ubiquitous among
           eukaryotes. The alpha/beta-tubulin heterodimer is the
           structural subunit of microtubules.  The alpha- and
           beta-tubulins share 40% amino-acid sequence identity,
           exist in several isotype forms, and undergo a variety of
           posttranslational modifications.  The structures of
           alpha- and beta-tubulin are basically identical: each
           monomer is formed by a core of two beta-sheets
           surrounded by alpha-helices. The monomer structure is
           very compact, but can be divided into three regions
           based on function: the amino-terminal nucleotide-binding
           region, an intermediate taxol-binding region and the
           carboxy-terminal region which probably constitutes the
           binding surface for motor proteins. Also included in
           this group is the mitochondrial Misato/DML1 protein
           family, involved in mitochondrial fusion and in
           mitochondrial distribution and morphology..
          Length = 382

 Score = 26.5 bits (59), Expect = 1.6
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 7/47 (14%)

Query: 3   SIHQSTNSCDLVN---NEQL----TEIEEPQKVTVDQINNAIASLIP 42
           S++    + D V    NE L    T   +  + + D +NN IA +I 
Sbjct: 147 SLNHLLENSDSVILFDNEALYNILTRQLDIDEPSFDDLNNIIAQIIS 193


>gnl|CDD|33927 COG4192, COG4192, Signal transduction histidine kinase regulating
           phosphoglycerate transport system [Signal transduction
           mechanisms].
          Length = 673

 Score = 26.2 bits (57), Expect = 2.3
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 3   SIHQSTNSCDLVNNEQLTEIEEPQKVTVDQINNAIASLIPEERRDLQDRMAKYSTR 58
           +IH    S        L +  +  +  + QIN+ +++ I     D+  R+A ++ +
Sbjct: 96  AIHALLASLPQNEQAALQQGLQELRQLLQQINDLVSARI-----DVDRRLALFAEQ 146


>gnl|CDD|36180 KOG0962, KOG0962, KOG0962, DNA repair protein RAD50, ABC-type
            ATPase/SMC superfamily [Replication, recombination and
            repair].
          Length = 1294

 Score = 26.0 bits (57), Expect = 2.5
 Identities = 14/51 (27%), Positives = 21/51 (41%)

Query: 16   NEQLTEIEEPQKVTVDQINNAIASLIPEERRDLQDRMAKYSTRKLKPRGRV 66
              +L E+E        QI  A    + EER  L++   K S+ K    G +
Sbjct: 1014 ERKLKELERELSELDKQILEADIKSVKEERVKLEEEREKLSSEKNLLLGEM 1064


>gnl|CDD|30399 COG0050, TufB, GTPases - translation elongation factors
           [Translation, ribosomal structure and biogenesis].
          Length = 394

 Score = 26.0 bits (57), Expect = 2.6
 Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 21  EIEEPQKVTVDQINNAIASLIPEERRDLQD--RMAKYSTRKLKPRGRVIF 68
           E +   +  ++++ +A+ S IP   RD+     M       +  RG V+ 
Sbjct: 180 EGDAKWEAKIEELMDAVDSYIPTPERDIDKPFLMPVEDVFSISGRGTVVT 229


>gnl|CDD|30569 COG0220, COG0220, Predicted S-adenosylmethionine-dependent
           methyltransferase [General function prediction only].
          Length = 227

 Score = 25.3 bits (55), Expect = 3.4
 Identities = 13/29 (44%), Positives = 15/29 (51%)

Query: 43  EERRDLQDRMAKYSTRKLKPRGRVIFADD 71
            +RR  Q    K   RKLKP G + FA D
Sbjct: 137 HKRRLTQPEFLKLYARKLKPGGVLHFATD 165


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.314    0.129    0.353 

Gapped
Lambda     K      H
   0.267   0.0735    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 781,439
Number of extensions: 30279
Number of successful extensions: 91
Number of sequences better than 10.0: 1
Number of HSP's gapped: 91
Number of HSP's successfully gapped: 12
Length of query: 71
Length of database: 6,263,737
Length adjustment: 42
Effective length of query: 29
Effective length of database: 5,356,159
Effective search space: 155328611
Effective search space used: 155328611
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.4 bits)