RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780154|ref|YP_003064567.1| hypothetical protein
CLIBASIA_00185 [Candidatus Liberibacter asiaticus str. psy62]
         (68 letters)



>gnl|CDD|131342 TIGR02289, M3_not_pepF, oligoendopeptidase, M3 family.  This family
           consists of probable oligoendopeptidases in the M3
           family, related to lactococcal PepF and group B
           streptococcal PepB (TIGR00181) but in a distinct clade
           with considerable sequence differences. The likely
           substrate is small peptides and not whole proteins, as
           with PepF, but members are not characterized and the
           activity profile may differ. Several bacteria have both
           a member of this family and a member of the PepF family.
          Length = 549

 Score = 30.1 bits (68), Expect = 0.13
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 14  LSTLAGCDSESKKIEKNINDTRRENAKLSTKYREIVESYTPAMEG 58
           L  L     +    EKNI   ++EN  LSTKYREI+ + +   EG
Sbjct: 99  LFKLIKNKLKLFN-EKNIPLLQKEN-ILSTKYREIISNISIIFEG 141


>gnl|CDD|163209 TIGR03302, OM_YfiO, outer membrane assembly lipoprotein YfiO.
          Members of this protein family include YfiO, a
          near-essential protein of the outer membrane, part of a
          complex involved in protein insertion into the
          bacterial outer membrane. Many proteins in this family
          are annotated as ComL, based on the involvement of this
          protein in natural transformation with exogenous DNA in
          Neisseria gonorrhoeae. This protein family shows
          sequence similarity to, but is distinct from, the
          tol-pal system protein YbgF (TIGR02795).
          Length = 235

 Score = 26.0 bits (58), Expect = 2.3
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 4  RKKTIVLITILSTLAGCDSESKKIE 28
              I+L+ +L  LAGC S+ KK  
Sbjct: 1  LLLLILLLALLLLLAGCSSKKKKEA 25


>gnl|CDD|150456 pfam09789, DUF2353, Uncharacterized coiled-coil protein (DUF2353). 
           Members of this family of uncharacterized proteins have
           no known function.
          Length = 319

 Score = 25.6 bits (56), Expect = 3.2
 Identities = 9/45 (20%), Positives = 22/45 (48%)

Query: 22  SESKKIEKNINDTRRENAKLSTKYREIVESYTPAMEGISIIDVTL 66
           ++ + + + +   R EN +LST  +E+ +        I ++  T+
Sbjct: 65  TKRQDLSQLLEKYREENQQLSTDVQELRQRKAELQGDIKLLRQTI 109


>gnl|CDD|180770 PRK06946, PRK06946, lipid A biosynthesis lauroyl acyltransferase;
           Provisional.
          Length = 293

 Score = 25.0 bits (55), Expect = 4.4
 Identities = 9/20 (45%), Positives = 11/20 (55%)

Query: 33  DTRRENAKLSTKYREIVESY 52
           D RR NA L  + R + E Y
Sbjct: 256 DARRMNAFLEEQIRLMPEQY 275


>gnl|CDD|169557 PRK08706, PRK08706, lipid A biosynthesis lauroyl acyltransferase;
           Provisional.
          Length = 289

 Score = 24.8 bits (54), Expect = 4.6
 Identities = 7/20 (35%), Positives = 10/20 (50%)

Query: 33  DTRRENAKLSTKYREIVESY 52
           D +R N  +  + RE  E Y
Sbjct: 252 DAQRMNRFIEERVREHPEQY 271


>gnl|CDD|183507 PRK12407, flgH, flagellar basal body L-ring protein; Reviewed.
          Length = 221

 Score = 24.8 bits (54), Expect = 5.0
 Identities = 8/26 (30%), Positives = 17/26 (65%)

Query: 5  KKTIVLITILSTLAGCDSESKKIEKN 30
          K+ ++L  +L  L GC+S +  ++K+
Sbjct: 2  KRFLILTALLLALCGCESPALLVQKD 27


>gnl|CDD|179539 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
          Length = 409

 Score = 24.6 bits (54), Expect = 6.2
 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 4/28 (14%)

Query: 42  STKYREIVESYTPAMEGISI----IDVT 65
           S +   I+E +T  +E  SI    +DVT
Sbjct: 85  SLQITRILEDFTDLVEPFSIDEQFLDVT 112


>gnl|CDD|129718 TIGR00632, vsr, DNA mismatch endonuclease Vsr.  All proteins in
           this family for which functions are known are G:T
           mismatch endonucleases that function in a specialized
           mismatch repair process used usually to repair G:T
           mismatches in specific sections of the genome. This
           family was based on the phylogenomic analysis of JA
           Eisen (1999, Ph.D. Thesis, Stanford University). Members
           of this family typically are found near to a DNA
           cytosine methyltransferase.
          Length = 117

 Score = 23.7 bits (51), Expect = 10.0
 Identities = 10/18 (55%), Positives = 13/18 (72%)

Query: 24  SKKIEKNINDTRRENAKL 41
           S KIEKN+   RR N++L
Sbjct: 86  SPKIEKNVERDRRVNSRL 103


  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
   0.314    0.130    0.341 

Gapped
Lambda     K      H
   0.267   0.0804    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 982,943
Number of extensions: 44116
Number of successful extensions: 131
Number of sequences better than 10.0: 1
Number of HSP's gapped: 131
Number of HSP's successfully gapped: 23
Length of query: 68
Length of database: 5,994,473
Length adjustment: 39
Effective length of query: 29
Effective length of database: 5,151,761
Effective search space: 149401069
Effective search space used: 149401069
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (22.9 bits)