RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780632|ref|YP_003065045.1| hypothetical protein
CLIBASIA_02595 [Candidatus Liberibacter asiaticus str. psy62]
         (71 letters)



>gnl|CDD|88599 cd04823, ALAD_PBGS_aspartate_rich, Porphobilinogen synthase (PBGS),
           which is also called delta-aminolevulinic acid
           dehydratase (ALAD), catalyzes the condensation of two
           5-aminolevulinic acid (ALA) molecules to form the
           pyrrole porphobilinogen (PBG), which is the second step
           in the biosynthesis of tetrapyrroles, such as heme,
           vitamin B12 and chlorophyll. This reaction involves the
           formation of a Schiff base link between the substrate
           and the enzyme. PBGSs are metalloenzymes, some of which
           have a second, allosteric metal binding site, beside the
           metal ion binding site in their active site. Although
           PBGS is a family of homologous enzymes, its metal ion
           utilization at catalytic site varies between zinc and
           magnesium and/or potassium. PBGS can be classified into
           two groups based on differences in their active site
           metal binding site. All of PBGS_aspartate_rich contain
           an aspartate rich metal binding site with the general
           sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an
           allosteric magnesium binding sequence RX~164DX~65EXXXD
           and are activated by magnesium and/or potassium, but not
           by zinc. PBGSs_aspartate_rich are found in some
           bacterial species and photosynthetic organisms such as
           vascular plants, mosses and algae, but not in archaea..
          Length = 320

 Score = 24.7 bits (54), Expect = 4.9
 Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 14/51 (27%)

Query: 19  MSPA--------VQLQCGLGSSIVAVKPVVPYITDVARGQINVRLGDNYGV 61
           M PA        V L    G+ +V VKP +PY+ D+ R     R+ D +GV
Sbjct: 219 MDPANSREALREVALDIAEGADMVMVKPGMPYL-DIIR-----RVKDEFGV 263


>gnl|CDD|147130 pfam04816, DUF633, Family of unknown function (DUF633).  This
          family of proteins are uncharacterized have no known
          function.
          Length = 204

 Score = 24.2 bits (53), Expect = 7.8
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 50 QINVRLGDNYGVLHSVDLV 68
          +I+VRLGD   V+  +DL+
Sbjct: 49 RIDVRLGDGLAVIEELDLI 67


  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    0.137    0.389 

Gapped
Lambda     K      H
   0.267   0.0740    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 769,166
Number of extensions: 29960
Number of successful extensions: 53
Number of sequences better than 10.0: 1
Number of HSP's gapped: 53
Number of HSP's successfully gapped: 2
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)