RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780133|ref|YP_003064546.1| hypothetical protein
CLIBASIA_00060 [Candidatus Liberibacter asiaticus str. psy62]
         (63 letters)



>gnl|CDD|88595 cd05795, Ribosomal_P0_L10e, Ribosomal protein L10 family, P0 and
          L10e subfamily; composed of eukaryotic 60S ribosomal
          protein P0 and the archaeal P0 homolog, L10e. P0 or
          L10e forms a tight complex with multiple copies of the
          small acidic protein L12(e). This complex forms a stalk
          structure on the large subunit of the ribosome. The
          stalk is known to contain the binding site for
          elongation factors G and Tu (EF-G and EF-Tu,
          respectively); however, there is disagreement as to
          whether or not L10 is involved in forming the binding
          site. The stalk is believed to be associated with
          GTPase activities in protein synthesis. In a
          neuroblastoma cell line, L10 has been shown to interact
          with the SH3 domain of Src and to activate the binding
          of the Nck1 adaptor protein with skeletal proteins such
          as the Wiskott-Aldrich Syndrome Protein (WASP) and the
          WASP-interacting protein (WIP). These eukaryotic and
          archaeal P0 sequences have an additional C-terminal
          domain homologous with acidic proteins P1 and P2..
          Length = 175

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 7/56 (12%)

Query: 14 RVDIRDIAVIASETNTRIEIELEGA------IYRFEPMIRGDNPCLIVDNDNPLDL 63
          R  +R  A I    NT I   L         + +  P ++G N   I  N +P ++
Sbjct: 37 RRSLRGKAEILMGKNTLIRRALRNLGDENPELEKLLPYLKG-NVGFIFTNGDPFEI 91


>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members.  This
           group contains a structure identified as an arginate
           lyase. Other members are identified quinone reductases,
           alginate lyases, and other proteins related to the
           zinc-dependent dehydrogenases/reductases. QOR catalyzes
           the conversion of a quinone and NAD(P)H to a
           hydroquinone and NAD(P+. Quinones are cyclic diones
           derived from aromatic compounds. Membrane bound QOR acts
           in the respiratory chains of bacteria and mitochondria,
           while soluble QOR acts to protect from toxic quinones
           (e.g. DT-diaphorase) or as a soluble eye-lens protein in
           some vertebrates (e.g. zeta-crystalin). QOR reduces
           quinones through a semi-quinone intermediate via a
           NAD(P)H-dependent single electron transfer. QOR is a
           member of the medium chain dehydrogenase/reductase
           family, but lacks the zinc-binding sites of the
           prototypical alcohol dehydrogenases of this group.
           Alcohol dehydrogenase in the liver converts ethanol and
           NAD+ to acetaldehyde and NADH, while in yeast and some
           other microorganisms ADH catalyzes the conversion
           acetaldehyde to ethanol in alcoholic fermentation. ADH
           is a member of the medium chain alcohol dehydrogenase
           family (MDR), which has a NAD(P)(H)-binding domain in a
           Rossmann fold of a beta-alpha form.  The NAD(H)-binding
           region is comprised of 2 structurally similar halves,
           each of which contacts a mononucleotide.  The N-terminal
           catalytic domain has a distant homology to GroES. These
           proteins typically form dimers (typically higher plants,
           mammals) or tetramers (yeast, bacteria), and have 2
           tightly bound zinc atoms per subunit, a catalytic zinc
           at the active site and a structural zinc in a lobe of
           the catalytic domain. NAD(H) binding occurs in the cleft
           between the catalytic and coenzyme-binding domains at
           the active site, and coenzyme binding induces a
           conformational closing of this cleft. Coenzyme binding
           typically precedes and contributes to substrate binding.
            In human ADH catalysis, the zinc ion helps coordinate
           the alcohol, followed by deprotonation of  a histidine,
           the ribose of NAD, a serine, then the alcohol, which
           allows the transfer of a hydride to NAD+, creating NADH
           and a zinc-bound aldehyde or ketone. In yeast and some
           bacteria, the active site zinc binds an aldehyde,
           polarizing it, and leading to the reverse reaction.
          Length = 336

 Score = 24.4 bits (54), Expect = 6.7
 Identities = 9/12 (75%), Positives = 9/12 (75%)

Query: 52  CLIVDNDNPLDL 63
           CLIVD   PLDL
Sbjct: 245 CLIVDPQEPLDL 256


  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
   0.321    0.140    0.395 

Gapped
Lambda     K      H
   0.267   0.0759    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 729,468
Number of extensions: 28109
Number of successful extensions: 72
Number of sequences better than 10.0: 1
Number of HSP's gapped: 72
Number of HSP's successfully gapped: 4
Length of query: 63
Length of database: 6,263,737
Length adjustment: 35
Effective length of query: 28
Effective length of database: 5,507,422
Effective search space: 154207816
Effective search space used: 154207816
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: 51 (23.4 bits)