RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781015|ref|YP_003065428.1| hypothetical protein
CLIBASIA_04585 [Candidatus Liberibacter asiaticus str. psy62]
         (78 letters)



>gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM)
           that belongs to the alpha-D-phosphohexomutase
           superfamily. It is required for the interconversion of
           glucosamine-6-phosphate and glucosamine-1-phosphate in
           the biosynthetic pathway of UDP-N-acetylglucosamine, an
           essential precursor to components of the cell envelope. 
           In order to be active, GlmM must be phosphorylated,
           which can occur via autophosphorylation or by the
           Ser/Thr kinase StkP. GlmM functions in a classical
           ping-pong bi-bi mechanism with
           glucosamine-1,6-diphosphate as an intermediate.  Other
           members of the alpha-D-phosphohexomutase superfamily
           include phosphoglucosamine mutase (PNGM),
           phosphoacetylglucosamine mutase (PAGM), the bacterial
           phosphomannomutase ManB, and the bifunctional
           phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
           these enzymes has four domains with a centrally located
           active site formed by four loops, one from each domain.
           All four domains are included in this alignment model..
          Length = 434

 Score = 25.1 bits (56), Expect = 4.0
 Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 2/27 (7%)

Query: 45  KDKGITFKVEKVGDQH--NKILLKEYS 69
           K+ GI     KVGD++   ++L    +
Sbjct: 291 KELGIKLVRTKVGDRYVLEEMLKHGAN 317


>gnl|CDD|88445 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal
          protein S1 (RPS1) domain. RPS1 is a component of the
          small ribosomal subunit thought to be involved in the
          recognition and binding of mRNA's during translation
          initiation. The bacterial RPS1 domain architecture
          consists of 4-6 tandem S1 domains. In some bacteria,
          the tandem S1 array is located C-terminal to a
          4-hydroxy-3-methylbut-2-enyl diphosphate reductase
          (HMBPP reductase) domain. While RPS1 is found primarily
          in bacteria, proteins with tandem RPS1-like domains
          have been identified in plants and humans, however
          these lack the N-terminal HMBPP reductase domain. This
          CD includes S1 repeat 5 (ec5) of the Escherichia coli
          RPS1. Autoantibodies to double-stranded DNA from
          patients with systemic lupus erythematosus cross-react
          with the human RPS1 homolog..
          Length = 69

 Score = 24.1 bits (52), Expect = 9.0
 Identities = 7/17 (41%), Positives = 11/17 (64%)

Query: 9  LSNALWNQTGKHPSPIF 25
          +S+  W Q  +HPS I+
Sbjct: 30 ISDISWTQRVRHPSEIY 46


>gnl|CDD|146115 pfam03315, SDH_beta, Serine dehydratase beta chain.  L-serine
           dehydratase (EC:4.2.1.13) is a found as a heterodimer of
           alpha and beta chain or as a fusion of the two chains in
           a single protein. This enzyme catalyses the deamination
           of serine to form pyruvate. This enzyme is part of the
           gluconeogenesis pathway.
          Length = 148

 Score = 24.0 bits (53), Expect = 9.5
 Identities = 4/32 (12%), Positives = 14/32 (43%), Gaps = 2/32 (6%)

Query: 31  QSYRIFLGSGSEV--SKDKGITFKVEKVGDQH 60
           +  ++ L     +  + ++ I F  +++   H
Sbjct: 81  EEGKLNLAGEHSIPFAPERDIVFHFKEILPFH 112


  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
   0.318    0.135    0.419 

Gapped
Lambda     K      H
   0.267   0.0812    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 949,732
Number of extensions: 38682
Number of successful extensions: 81
Number of sequences better than 10.0: 1
Number of HSP's gapped: 81
Number of HSP's successfully gapped: 4
Length of query: 78
Length of database: 6,263,737
Length adjustment: 48
Effective length of query: 30
Effective length of database: 5,226,505
Effective search space: 156795150
Effective search space used: 156795150
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 (21.7 bits)
S2: 51 (23.3 bits)