RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780986|ref|YP_003065399.1| hypothetical protein
CLIBASIA_04435 [Candidatus Liberibacter asiaticus str. psy62]
         (94 letters)



>gnl|CDD|34047 COG4325, COG4325, Predicted membrane protein [Function unknown].
          Length = 464

 Score = 29.2 bits (65), Expect = 0.24
 Identities = 7/43 (16%), Positives = 14/43 (32%)

Query: 43 AFKKKGSMKKDPTLLLLQGIHDALWDIAKATSALVFLYGASLL 85
          A+    +        +L  +  A+W I      +   +G  L 
Sbjct: 15 AYSVTATSMLVRRKAILDYLQGAVWVIPAFGVVIALGFGFVLS 57


>gnl|CDD|112292 pfam03467, Smg4_UPF3, Smg-4/UPF3 family.  This family contains
           proteins that are involved in nonsense mediated mRNA
           decay. A process that is triggered by premature stop
           codons in mRNA. The family includes Smg-4 and UPF3.
          Length = 176

 Score = 26.0 bits (57), Expect = 2.3
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 4/40 (10%)

Query: 18  ISIALVYLYIHQHFKKRTKQKKVDIAFKKKGSMKKDPTLL 57
              A+V L  +Q   K +K  K D    ++GS+++DP  +
Sbjct: 87  TYPAIVELAPYQKIPKPSK-VKKD---AREGSIEQDPEFM 122


>gnl|CDD|38762 KOG3554, KOG3554, KOG3554, Histone deacetylase complex, MTA1
           component [Chromatin structure and dynamics].
          Length = 693

 Score = 25.8 bits (56), Expect = 2.5
 Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)

Query: 62  IHDALWDIAKATSALVFLYGASLLCK 87
           +H   +D++KA S LV L G  +LC+
Sbjct: 258 LHRNNYDLSKAISYLVPL-GGPVLCR 282


>gnl|CDD|36844 KOG1631, KOG1631, KOG1631, Translocon-associated complex TRAP,
           alpha subunit [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 261

 Score = 25.7 bits (56), Expect = 3.2
 Identities = 7/39 (17%), Positives = 16/39 (41%), Gaps = 6/39 (15%)

Query: 1   MNSLPLFGWMAGIGCLGISIALVYLYIHQHFKKRTKQKK 39
             ++ L+  + G+  L +      +   Q   K +K+ K
Sbjct: 182 GETVFLYILLIGLSLLLL------VLSQQFLSKLSKKTK 214


>gnl|CDD|35172 COG5613, COG5613, Uncharacterized conserved protein [Function
           unknown].
          Length = 400

 Score = 25.4 bits (55), Expect = 3.9
 Identities = 6/18 (33%), Positives = 13/18 (72%)

Query: 6   LFGWMAGIGCLGISIALV 23
           +FGW++  G L +++ +V
Sbjct: 175 IFGWVSAFGSLIVALIMV 192


>gnl|CDD|48387 cd02140, Nitroreductase_4, Nitroreductase-like family 4.  A
          subfamily of the nitroreductase family containing
          uncharacterized proteins that are similar to
          nitroreductase. Nitroreductase catalyzes the reduction
          of nitroaromatic compounds such as nitrotoluenes,
          nitrofurans and nitroimidazoles. This process requires
          NAD(P)H as electron donor in an obligatory two-electron
          transfer and uses FMN as cofactor.  The enzyme is
          typically a homodimer. Members of this family are also
          called NADH dehydrogenase, oxygen-insensitive NAD(P)H
          nitrogenase or dihydropteridine reductase..
          Length = 192

 Score = 24.0 bits (52), Expect = 8.1
 Identities = 8/18 (44%), Positives = 11/18 (61%)

Query: 56 LLLLQGIHDALWDIAKAT 73
          ++L    H+ LWDI K T
Sbjct: 48 VILFGEEHEKLWDIVKDT 65


  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
   0.328    0.142    0.451 

Gapped
Lambda     K      H
   0.267   0.0689    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,162,094
Number of extensions: 50324
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 20
Length of query: 94
Length of database: 6,263,737
Length adjustment: 62
Effective length of query: 32
Effective length of database: 4,923,979
Effective search space: 157567328
Effective search space used: 157567328
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (23.5 bits)