RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781181|ref|YP_003065594.1| hypothetical protein
CLIBASIA_05440 [Candidatus Liberibacter asiaticus str. psy62]
         (85 letters)



>gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
          Length = 284

 Score = 28.6 bits (65), Expect = 0.36
 Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 8/36 (22%)

Query: 55 NSIMFLYPEQRQELAKRYKEKYND-------VLIHL 83
          N I  L  E+   LAKR +E   D       VL HL
Sbjct: 24 NKIPMLTAEEEYMLAKRLREH-GDLEAAKQLVLSHL 58


>gnl|CDD|162835 TIGR02392, rpoH_proteo, alternative sigma factor RpoH.  A sigma
          factor is a DNA-binding protein protein that binds to
          the DNA-directed RNA polymerase core to produce the
          holoenzyme capable of initiating transcription at
          specific sites. Different sigma factors act in
          vegetative growth, heat shock, extracytoplasmic
          functions (ECF), etc. This model represents the clade
          of sigma factors called RpoH and further restricted to
          the Proteobacteria. This protein may be called
          sigma-32, sigma factor H, heat shock sigma factor, and
          alternative sigma factor RpoH. Note that in some
          species the single locus rpoH may be replaced by two or
          more differentially regulated stress response sigma
          factors.
          Length = 270

 Score = 26.5 bits (59), Expect = 1.8
 Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 8/36 (22%)

Query: 55 NSIMFLYPEQRQELAKRYKEKYND-------VLIHL 83
          N I  L PE+  +LAKR +E   D       VL HL
Sbjct: 11 NRIPMLTPEEEYQLAKRLREH-GDLDAAKKLVLSHL 45


>gnl|CDD|183827 PRK12906, secA, preprotein translocase subunit SecA; Reviewed.
          Length = 796

 Score = 25.4 bits (56), Expect = 3.1
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 10/55 (18%)

Query: 28 LKRIVKVQKQAKSLANASQKLTVDQIDNSIMFLYPEQRQELAKRYK--EKYNDVL 80
          LKR+ K+  +  +L +  +KL+ +Q+             E   R K  E  +D+L
Sbjct: 16 LKRLEKIADKVNALEDEYEKLSDEQLQAKTP--------EFRDRIKDGESLDDLL 62


>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
           Members of this family show a distant relationship to
           alpha/beta (TIM) barrel enzymes such as dihydroorotate
           dehydrogenase and glycolate oxidase.
          Length = 319

 Score = 25.4 bits (56), Expect = 3.1
 Identities = 6/11 (54%), Positives = 8/11 (72%)

Query: 23  NFGCPLKRIVK 33
           N GCP+ +I K
Sbjct: 95  NMGCPVPKITK 105


>gnl|CDD|177416 PHA02587, 30, DNA ligase; Provisional.
          Length = 488

 Score = 24.3 bits (53), Expect = 7.3
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 60  LYPEQRQELAKRYKEK 75
           L PEQ Q LA  + EK
Sbjct: 129 LIPEQPQMLASSFSEK 144


>gnl|CDD|150842 pfam10231, DUF2315, Uncharacterized conserved protein (DUF2315). 
          This is a family of small conserved proteins found from
          worms to humans. The function is not known.
          Length = 127

 Score = 24.4 bits (53), Expect = 7.3
 Identities = 4/23 (17%), Positives = 9/23 (39%)

Query: 57 IMFLYPEQRQELAKRYKEKYNDV 79
          I+   PE    L ++ +    + 
Sbjct: 17 IVLHIPENETPLERKLRLLRQET 39


>gnl|CDD|183248 PRK11636, mrcA, penicillin-binding protein 1a; Provisional.
          Length = 850

 Score = 24.3 bits (53), Expect = 7.9
 Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 1/28 (3%)

Query: 52  QIDNSIMFLYPEQRQELAKRYKEK-YND 78
           +I  S  +L    RQE+  RY E  Y D
Sbjct: 256 EIAFSAPYLSEMVRQEMYNRYGENAYED 283


>gnl|CDD|183692 PRK12704, PRK12704, phosphodiesterase; Provisional.
          Length = 520

 Score = 24.0 bits (53), Expect = 9.5
 Identities = 9/16 (56%), Positives = 12/16 (75%), Gaps = 2/16 (12%)

Query: 67  ELAKRYKEKYNDVLIH 82
           ELAK+YKE    V+I+
Sbjct: 388 ELAKKYKES--PVVIN 401


>gnl|CDD|179016 PRK00419, PRK00419, DNA primase small subunit; Reviewed.
          Length = 376

 Score = 23.8 bits (52), Expect = 9.9
 Identities = 6/24 (25%), Positives = 11/24 (45%)

Query: 62 PEQRQELAKRYKEKYNDVLIHLPD 85
             R+ L  R+++ Y    + LP 
Sbjct: 3  ERTREYLKSRFRDYYRRAELPLPP 26


  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
   0.323    0.137    0.387 

Gapped
Lambda     K      H
   0.267   0.0769    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,324,303
Number of extensions: 65703
Number of successful extensions: 219
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 29
Length of query: 85
Length of database: 5,994,473
Length adjustment: 54
Effective length of query: 31
Effective length of database: 4,827,641
Effective search space: 149656871
Effective search space used: 149656871
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: 50 (23.0 bits)