RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780890|ref|YP_003065303.1| hypothetical protein
CLIBASIA_03935 [Candidatus Liberibacter asiaticus str. psy62]
         (104 letters)



>gnl|CDD|147763 pfam05788, Orbi_VP1, Orbivirus RNA-dependent RNA polymerase (VP1). 
           This family consists of the RNA-dependent RNA polymerase
           protein VP1 from the Orbiviruses. VP1 may have both
           enzymatic and structural roles in the virus life cycle.
          Length = 1301

 Score = 27.0 bits (60), Expect = 1.3
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 39  PNQEIRTKIYIITARIIALIVFREGEK 65
           PN E R +   I +RI AL++F EG K
Sbjct: 460 PNAEKRKEFIRIVSRIKALVIFTEGHK 486


>gnl|CDD|111930 pfam03089, RAG2, Recombination activating protein 2.  V-D-J
           recombination is the combinatorial process by which the
           huge range of immunoglobulin and T cell binding
           specificity is generated from a limited amount of
           genetic material. This process is synergistically
           activated by RAG1 and RAG2 in developing lymphocytes.
           Defects in RAG2 in humans are a cause of severe combined
           immunodeficiency B cell negative and Omenn syndrome.
          Length = 528

 Score = 26.7 bits (59), Expect = 1.5
 Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 2/35 (5%)

Query: 38  TPNQEIRTKIYIIT--ARIIALIVFREGEKSLIFD 70
           TPN E+ +K+YI+T  +R    +  R  EK L+ D
Sbjct: 98  TPNNELSSKLYIMTVDSRCNKKVTLRCSEKDLVGD 132


>gnl|CDD|176969 CHL00028, clpP, ATP-dependent Clp protease proteolytic subunit.
          Length = 200

 Score = 26.7 bits (60), Expect = 1.5
 Identities = 10/35 (28%), Positives = 17/35 (48%)

Query: 2   FYDSREKEVFLESEVVHNIRLQIEEISAILSKKSR 36
           FY+ +  E  LE+E +  +R  I  + A  + K  
Sbjct: 132 FYEGQASEFVLEAEELLKLRETITRVYAQRTGKPL 166


>gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General
           function prediction only].
          Length = 641

 Score = 25.0 bits (54), Expect = 5.1
 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 43  IRTKIYIITARIIALIVFREGEKSLIFDLLRTNQKTNSSLTQAIIQEIDTLQHQCKSI 100
           I+   YI   R    +VFREG    +  +     + + S  +A  ++     +   S+
Sbjct: 518 IKQPEYI---RPGQRLVFREGRTKAVGTISSVLPQESLSPQRAKPKDGRQKSYGKGSM 572


>gnl|CDD|33103 COG3294, COG3294, Uncharacterized conserved protein [Function
           unknown].
          Length = 269

 Score = 24.9 bits (54), Expect = 5.1
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 2   FYDSREKEVFLESEVVHNIRLQIEEISAI 30
            Y   EK V + SEV+H I    E  + +
Sbjct: 137 IYPDPEKAVRVRSEVLHAIYCHDENETPL 165


>gnl|CDD|33432 COG3634, AhpF, Alkyl hydroperoxide reductase, large subunit
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 520

 Score = 24.9 bits (54), Expect = 5.5
 Identities = 11/37 (29%), Positives = 16/37 (43%)

Query: 10  VFLESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTK 46
           VFL  E     R+ +EEI A +   +     +E   K
Sbjct: 173 VFLNGEEFGQGRMTLEEILAKIDTGAAKRDAEEFNAK 209


>gnl|CDD|30439 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
           structure and biogenesis].
          Length = 275

 Score = 24.8 bits (54), Expect = 5.5
 Identities = 8/14 (57%), Positives = 11/14 (78%)

Query: 55  IALIVFREGEKSLI 68
           IAL+V+ +GEK  I
Sbjct: 91  IALVVYEDGEKRYI 104


>gnl|CDD|147664 pfam05622, HOOK, HOOK protein.  This family consists of several
           HOOK1, 2 and 3 proteins from different eukaryotic
           organisms. The different members of the human gene
           family are HOOK1, HOOK2 and HOOK3. Different domains
           have been identified in the three human HOOK proteins,
           and it was demonstrated that the highly conserved
           NH2-domain mediates attachment to microtubules, whereas
           the central coiled-coil motif mediates homodimerization
           and the more divergent C-terminal domains are involved
           in binding to specific organelles (organelle-binding
           domains). It has been demonstrated that endogenous HOOK3
           binds to Golgi membranes, whereas both HOOK1 and HOOK2
           are localized to discrete but unidentified cellular
           structures. In mice the Hook1 gene is predominantly
           expressed in the testis. Hook1 function is necessary for
           the correct positioning of microtubular structures
           within the haploid germ cell. Disruption of Hook1
           function in mice causes abnormal sperm head shape and
           fragile attachment of the flagellum to the sperm head.
          Length = 713

 Score = 24.0 bits (52), Expect = 8.5
 Identities = 16/42 (38%), Positives = 21/42 (50%)

Query: 12  LESEVVHNIRLQIEEISAILSKKSRDTPNQEIRTKIYIITAR 53
           LE +   N+  +I E+ A L KK  D    E R K Y+  AR
Sbjct: 566 LEPDQDQNLSRKIAELEAALQKKDEDMRAMEERYKKYVEKAR 607


  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
   0.319    0.133    0.345 

Gapped
Lambda     K      H
   0.267   0.0657    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,093,508
Number of extensions: 47617
Number of successful extensions: 105
Number of sequences better than 10.0: 1
Number of HSP's gapped: 105
Number of HSP's successfully gapped: 20
Length of query: 104
Length of database: 6,263,737
Length adjustment: 71
Effective length of query: 33
Effective length of database: 4,729,498
Effective search space: 156073434
Effective search space used: 156073434
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 (23.6 bits)