RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780305|ref|YP_003064718.1| hypothetical protein
CLIBASIA_00950 [Candidatus Liberibacter asiaticus str. psy62]
         (95 letters)



>gnl|CDD|184876 PRK14876, PRK14876, conjugal transfer mating pair stabilization
           protein TraN; Provisional.
          Length = 928

 Score = 33.7 bits (77), Expect = 0.010
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 6   IEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIH---IDDIIHHTG 58
           I   F    ++T   +N    H PEY +C+RV + QS +   +H      + H++G
Sbjct: 184 IAGGFGDCSAETTINQNTINAHIPEYERCQRV-VDQSGDCEVVHDYDAGVVKHYSG 238


>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
          Length = 815

 Score = 27.1 bits (60), Expect = 1.1
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 9   NFFSSQSDTNHTKNINITHYP-EYTQCER-VRIKQSLNNVPIHIDDIIH 55
           ++F++  D NH++N++   YP + T   R +R++Q    V   + DI+ 
Sbjct: 251 DYFAAVEDKNHSENVSRVLYPDDSTYSGRELRLRQEYFLVSATVQDILS 299


>gnl|CDD|149509 pfam08482, HrpB_C, ATP-dependent helicase C-terminal.  This
          domain is found near the C-terminus of bacterial
          ATP-dependent helicases such as HrpB.
          Length = 133

 Score = 26.7 bits (60), Expect = 1.3
 Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 6/44 (13%)

Query: 54 IHHTGIEAPVVYLVLLELDLAGRLCHHP---EGKVSLTMHLPSP 94
          I ++G   PV+ + L EL   G L   P    G+V LT+HL SP
Sbjct: 54 IDYSGDGGPVLAVRLQEL--FG-LTETPTIAGGRVPLTLHLLSP 94


>gnl|CDD|162630 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB.  This model
           represents HrpB, one of two related but uncharacterized
           DEAH-box ATP-dependent helicases in many Proteobacteria,
           but also in a few species of other lineages. The member
           from Rhizobium meliloti has been designated HelO. HrpB
           is typically about 800 residues in length, while its
           paralog HrpA (TIGR01967), also uncharacterized, is about
           1300 amino acids long. Related characterized eukarotic
           proteins are RNA helicases associated with pre-mRNA
           processing.
          Length = 819

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 9/47 (19%)

Query: 57  TGIEAPVVYLVLLELDLAGRL------CHHP---EGKVSLTMHLPSP 94
           TG    + Y +     LA RL         P   +G+V LT+ L SP
Sbjct: 721 TGNFIAIRYSLDGPPLLAVRLQELFGLAESPRVAQGRVPLTLELLSP 767


>gnl|CDD|161893 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit.  Most
           phenylalanyl-tRNA synthetases are heterodimeric, with 2
           alpha (pheS) and 2 beta (pheT) subunits. This model
           describes the alpha subunit, which shows some similarity
           to class II aminoacyl-tRNA ligases. Mitochondrial
           phenylalanyl-tRNA synthetase is a single polypeptide
           chain, active as a monomer, and similar to this chain
           rather than to the beta chain, but excluded from this
           model. An interesting feature of the alignment of all
           sequences captured by this model is a deep split between
           non-spirochete bacterial examples and all other
           examples; supporting this split is a relative deletion
           of about 50 residues in the former set between two
           motifs well conserved throughout the alignment.
          Length = 294

 Score = 25.7 bits (57), Expect = 2.7
 Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 2/44 (4%)

Query: 22  NINITHYPEYTQCERVRIKQ--SLNNVPIHIDDIIHHTGIEAPV 63
            ++ TH PE+ Q E + I +  S  N+   +++ +     E  +
Sbjct: 164 TVDATHLPEFHQVEGLVIDKNVSFTNLKGFLEEFLKKMFGETEI 207


>gnl|CDD|178382 PLN02785, PLN02785, Protein HOTHEAD.
          Length = 587

 Score = 25.5 bits (56), Expect = 2.8
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 16/65 (24%)

Query: 4   PQIEQNFFSSQSDTNH--------TKNINITHYPEYTQCER--------VRIKQSLNNVP 47
           P +  N+F    D            K +   H+  +TQC++        + +K ++N +P
Sbjct: 441 PSVTFNYFKHPQDLQRCVYGIRTIEKIVKTNHFTNFTQCDKQTMEKVLNMSVKANINLIP 500

Query: 48  IHIDD 52
            H +D
Sbjct: 501 KHTND 505


>gnl|CDD|178973 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase;
          Reviewed.
          Length = 264

 Score = 25.8 bits (58), Expect = 2.8
 Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 8/24 (33%)

Query: 42 SLNNV--------PIHIDDIIHHT 57
          SL  V        P+ +DD+I+HT
Sbjct: 44 SLGMVVLGYDSTLPVTLDDMIYHT 67


>gnl|CDD|116156 pfam07537, CamS, CamS sex pheromone cAM373 precursor.  This family
           includes CamS, from which Staphylococcus aureus sex
           pheromone staph-cAM373 is processed.
          Length = 318

 Score = 25.5 bits (56), Expect = 2.8
 Identities = 7/16 (43%), Positives = 9/16 (56%)

Query: 35  ERVRIKQSLNNVPIHI 50
            R+R   +L NVPI  
Sbjct: 154 NRIRQNDNLKNVPITF 169


>gnl|CDD|183810 PRK12881, acnA, aconitate hydratase; Provisional.
          Length = 889

 Score = 24.9 bits (55), Expect = 4.8
 Identities = 6/12 (50%), Positives = 9/12 (75%)

Query: 2   VHPQIEQNFFSS 13
           +HP I+ NF +S
Sbjct: 536 IHPNIKANFLAS 547


>gnl|CDD|178118 PLN02502, PLN02502, lysyl-tRNA synthetase.
          Length = 553

 Score = 25.0 bits (55), Expect = 4.9
 Identities = 7/13 (53%), Positives = 9/13 (69%)

Query: 23  INITHYPEYTQCE 35
           I+  H PE+T CE
Sbjct: 312 ISTRHNPEFTTCE 324


>gnl|CDD|181987 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
          Length = 132

 Score = 24.6 bits (54), Expect = 5.9
 Identities = 10/24 (41%), Positives = 11/24 (45%), Gaps = 3/24 (12%)

Query: 37 VRIKQSLNNVPIHIDDIIHHTGIE 60
            I  S NN  I I D+   TG E
Sbjct: 12 AHIYASFNNTIITITDL---TGAE 32


>gnl|CDD|163018 TIGR02784, addA_alphas, double-strand break repair helicase AddA,
           alphaproteobacterial type.  AddAB, also called RexAB,
           substitutes for RecBCD in several bacterial lineages.
           These DNA recombination proteins act before synapse and
           are particularly important for DNA repair of
           double-stranded breaks by homologous recombination. The
           term AddAB is used broadly, with AddA homologous between
           the alphaproteobacteria (as modeled here) and the
           Firmicutes, while the partner AddB proteins show no
           strong homology across the two groups of species.
          Length = 1141

 Score = 24.3 bits (53), Expect = 6.5
 Identities = 8/10 (80%), Positives = 10/10 (100%)

Query: 58  GIEAPVVYLV 67
           G+EAPVV+LV
Sbjct: 786 GLEAPVVFLV 795


>gnl|CDD|178385 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
          Length = 402

 Score = 24.0 bits (52), Expect = 9.5
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 23  INITHYPEYTQCERVRI 39
           I+ THYP + Q E VR+
Sbjct: 162 IDATHYPVFHQMEGVRV 178


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.320    0.136    0.415 

Gapped
Lambda     K      H
   0.267   0.0690    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,551,551
Number of extensions: 83127
Number of successful extensions: 137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 137
Number of HSP's successfully gapped: 19
Length of query: 95
Length of database: 5,994,473
Length adjustment: 63
Effective length of query: 32
Effective length of database: 4,633,169
Effective search space: 148261408
Effective search space used: 148261408
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: 50 (23.1 bits)