RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780946|ref|YP_003065359.1| hypothetical protein
CLIBASIA_04225 [Candidatus Liberibacter asiaticus str. psy62]
         (98 letters)



>gnl|CDD|32761 COG2938, COG2938, Uncharacterized conserved protein [Function
          unknown].
          Length = 94

 Score = 70.7 bits (173), Expect = 8e-14
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 1  MKKNMNLQCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFK 60
            ++ + +  ++ +R  R G RE+DLILG F +     LS  EL   E ++E +D++LF 
Sbjct: 7  STEDDDARKARLRWRSRR-GMRELDLILGPFAEKEFDSLSDEELDEFERLLECEDNDLFN 65

Query: 61 WFTGMEKPPEYLRTPIFKKIYDY 83
          W  G  +PP+   TP+ +KI   
Sbjct: 66 WIMGHGEPPDAELTPMVRKIQAR 88


>gnl|CDD|146523 pfam03937, Sdh5, Protein of unknown function (DUF339).  This
          family of uncharacterized proteins. Based on personal
          observation it was previously annotated in Pfam as
          being a divergent TPR repeat but structural evidence
          has indicated this is not true.
          Length = 51

 Score = 69.4 bits (171), Expect = 2e-13
 Identities = 23/51 (45%), Positives = 32/51 (62%)

Query: 14 YRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTG 64
          +R WRRG  E+DL+LG F D  +  LS  EL   E +++ +D +LF W TG
Sbjct: 1  WRSWRRGMLELDLLLGRFADAHLDTLSEEELDAFERLLDLEDPDLFDWLTG 51


>gnl|CDD|38536 KOG3326, KOG3326, KOG3326, Uncharacterized conserved protein
           [Function unknown].
          Length = 154

 Score = 43.9 bits (103), Expect = 1e-05
 Identities = 21/81 (25%), Positives = 45/81 (55%), Gaps = 3/81 (3%)

Query: 11  KIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEE--DDSNLFKWFTGMEKP 68
           +++Y+  +RG  E DL+L +F    + ++S  +L   + +I E  +D +++ W T  + P
Sbjct: 62  RLLYQSRKRGILENDLLLSNFAAKNLKKMSEEQLKEYDQLINEESNDWDIYYWATETKPP 121

Query: 69  PEYLRT-PIFKKIYDYYSNNL 88
           PE + +  +FK + ++  N  
Sbjct: 122 PEKVESSEVFKLLKEFVKNKE 142


>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
           Translocation is mediated by EF-G (also called
           translocase).  The structure of EF-G closely resembles
           that of the complex between EF-Tu and tRNA.  This is an
           example of molecular mimicry; a protein domain evolved
           so that it mimics the shape of a tRNA molecule.  EF-G in
           the GTP form binds to the ribosome, primarily through
           the interaction of its EF-Tu-like domain with the 50S
           subunit.  The binding of EF-G to the ribosome in this
           manner stimulates the GTPase activity of EF-G.  On GTP
           hydrolysis, EF-G undergoes a conformational change that
           forces its arm deeper into the A site on the 30S
           subunit.  To accommodate this domain, the peptidyl-tRNA
           in the A site moves to the P site, carrying the mRNA and
           the deacylated tRNA with it.  The ribosome may be
           prepared for these rearrangements by the initial binding
           of EF-G as well.  The dissociation of EF-G leaves the
           ribosome ready to accept the next aminoacyl-tRNA into
           the A site.  This group contains only bacterial members.
          Length = 268

 Score = 27.5 bits (62), Expect = 0.79
 Identities = 10/33 (30%), Positives = 16/33 (48%)

Query: 44  LTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPI 76
             +LE++ E DD  + K+  G E   E L   +
Sbjct: 199 EELLEAVAETDDELMEKYLEGGELTEEELHAGL 231


>gnl|CDD|34302 COG4685, COG4685, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 571

 Score = 25.8 bits (56), Expect = 2.4
 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 5/36 (13%)

Query: 68  PPEYLRTPIFKKIYD-----YYSNNLDRKNMLGSLQ 98
           P + LR P+ + +       YY NN DR  + G+L+
Sbjct: 80  PKDVLRVPLLRDVLTEDFVFYYENNEDRLGVAGALR 115


>gnl|CDD|147160 pfam04858, TH1, TH1 protein.  TH1 is a highly conserved but
           uncharacterized metazoan protein. No homologue has been
           identified in Caenorhabditis elegans. TH1 binds
           specifically to A-Raf kinase.
          Length = 582

 Score = 25.6 bits (56), Expect = 2.8
 Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 1/25 (4%)

Query: 54  DDSNLFKWFTGMEKPP-EYLRTPIF 77
           D + L + +T  + PP + +R P F
Sbjct: 303 DITVLLRMYTSSDPPPVDLIRHPDF 327


>gnl|CDD|33320 COG3517, COG3517, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 495

 Score = 25.6 bits (56), Expect = 3.4
 Identities = 8/17 (47%), Positives = 13/17 (76%)

Query: 65  MEKPPEYLRTPIFKKIY 81
            EK PE+ ++ +FKK+Y
Sbjct: 131 FEKAPEFDQSGLFKKVY 147


>gnl|CDD|144189 pfam00500, Late_protein_L1, L1 (late) protein. 
          Length = 503

 Score = 25.0 bits (55), Expect = 4.9
 Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 16/45 (35%)

Query: 35  FILELSSVELT---------MLESIIEEDDSNLFKWFTGMEKPPE 70
           FI +L  V LT         M  SI+E+       W  G+  PP 
Sbjct: 376 FIFQLCKVTLTPEVMAYIHTMNPSILED-------WNLGVSPPPS 413


>gnl|CDD|145572 pfam02503, PP_kinase, Polyphosphate kinase.  Polyphosphate kinase
           (Ppk) catalyses the formation of polyphosphate from ATP,
           with chain lengths of up to a thousand or more
           orthophosphate molecules.
          Length = 678

 Score = 24.7 bits (55), Expect = 6.4
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 51  IEEDDSNLFKWFTGMEKPPEY 71
           I ED + LF + TG  +PP+Y
Sbjct: 475 IGEDVAKLFNFLTGYSRPPKY 495


>gnl|CDD|73041 cd03282, ABC_MSH4_euk, MutS4 homolog in eukaryotes.  The MutS
          protein initiates DNA mismatch repair by recognizing
          mispaired and unpaired bases embedded in duplex DNA and
          activating endo- and exonucleases to remove the
          mismatch.  Members of the MutS family possess
          C-terminal domain with a conserved ATPase activity that
          belongs to the ATP binding cassette (ABC) superfamily. 
          MutS homologs (MSH) have been identified in most
          prokaryotic and all eukaryotic organisms examined.
          Prokaryotes have two homologs (MutS1 and MutS2),
          whereas seven MSH proteins (MSH1 to MSH7) have been
          identified in eukaryotes.  The homodimer MutS1 and
          heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily
          involved in mitotic mismatch repair, whereas MSH4-MSH5
          is involved in resolution of Holliday junctions during
          meiosis.  All members of the MutS family contain the
          highly conserved Walker A/B ATPase domain, and many
          share a common mechanism of action.  MutS1, MSH2-MSH3,
          MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding
          clamps, and recognition of specific DNA structures or
          lesions results in ADP/ATP exchange..
          Length = 204

 Score = 24.1 bits (52), Expect = 8.3
 Identities = 8/22 (36%), Positives = 11/22 (50%)

Query: 68 PPEYLRTPIFKKIYDYYSNNLD 89
          P EY   PIF ++    SN+  
Sbjct: 63 PAEYATLPIFNRLLSRLSNDDS 84


>gnl|CDD|34842 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
          Length = 3164

 Score = 23.9 bits (51), Expect = 8.9
 Identities = 6/40 (15%), Positives = 16/40 (40%), Gaps = 2/40 (5%)

Query: 23   EMDLILGSFVD--HFILELSSVELTMLESIIEEDDSNLFK 60
            +M  I    +    F+ ++   E  + +++ +     LF 
Sbjct: 2583 DMGSIEWKQLIQVMFVSKVLGCETEIPDALEKLVSGPLFV 2622


  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
   0.323    0.139    0.425 

Gapped
Lambda     K      H
   0.267   0.0658    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,255,627
Number of extensions: 57950
Number of successful extensions: 156
Number of sequences better than 10.0: 1
Number of HSP's gapped: 155
Number of HSP's successfully gapped: 17
Length of query: 98
Length of database: 6,263,737
Length adjustment: 66
Effective length of query: 32
Effective length of database: 4,837,543
Effective search space: 154801376
Effective search space used: 154801376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.6 bits)