RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy13469
         (74 letters)



>gnl|CDD|219447 pfam07520, SrfB, Virulence factor SrfB.  This family includes
           homologues of SsrAB is a two-component regulatory system
           encoded within the Salmonella pathogenicity island
           SPI-2. Among the products of genes activated by SsrAB
           within epithelial and macrophage cells is Salmonella
           typhimurium srfB. Homologues are found in several other
           proteobacteria.
          Length = 999

 Score = 26.2 bits (58), Expect = 1.7
 Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 3/34 (8%)

Query: 44  VLLTIIANCVVLALEEHLPKG---DKTALAKKLI 74
           +LL +I   V+ AL+  L K    D  +L  KL 
Sbjct: 615 ILLDVIQRLVLPALQAALRKAGVTDPRSLLSKLF 648


>gnl|CDD|233857 TIGR02412, pepN_strep_liv, aminopeptidase N, Streptomyces lividans
           type.  This family is a subset of the members of the
           zinc metallopeptidase family M1 (pfam01433), with a
           single member characterized in Streptomyces lividans 66
           and designated aminopeptidase N. The spectrum of
           activity may differ somewhat from the aminopeptidase N
           clade of E. coli and most other Proteobacteria, well
           separated phylogenetically within the M1 family. The M1
           family also includes leukotriene A-4
           hydrolase/aminopeptidase (with a bifunctional active
           site).
          Length = 831

 Score = 25.5 bits (56), Expect = 2.6
 Identities = 7/30 (23%), Positives = 16/30 (53%)

Query: 41  EYAVLLTIIANCVVLALEEHLPKGDKTALA 70
           +YAV+  +++  +     ++ P  D+ AL 
Sbjct: 584 DYAVVQQVLSQLLRAVAAQYAPIADRPALL 613


>gnl|CDD|132230 TIGR03186, AKGDH_not_PDH, alpha-ketoglutarate dehydrogenase.
           Several bacterial species have a paralog to homodimeric
           form of the pyruvate dehydrogenase E1 component (see
           model TIGR00759), often encoded next to L-methionine
           gamma-lyase gene (mdeA). The member from a strain of
           Pseudomonas putida was shown to act on
           alpha-ketobutyrate, which is produced by MdeA.This model
           serves as an exception model to TIGR00759, as other
           proteins hitting TIGR00759 should be identified as the
           pyruvate dehydrogenase E1 component.
          Length = 889

 Score = 25.2 bits (55), Expect = 3.2
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 2   GPHSHHATASHRGPSSLFLLSETNTVRQYTRFIIEWPPFEYAVLLT 47
            PH   A  + +GP    +++ T+ VR     I  + P  Y  L T
Sbjct: 786 SPHVAQALGATQGP----VIAATDYVRAVPELIRAYVPRRYVTLGT 827


>gnl|CDD|233077 TIGR00661, MJ1255, conserved hypothetical protein.  This model
           represents nearly the full length of MJ1255 from
           Methanococcus jannaschii and of an unpublished protein
           from Vibrio cholerae, as well as the C-terminal half of
           a protein from Methanobacterium thermoautotrophicum. A
           small region (~50 amino acids) within the domain appears
           related to a family of sugar transferases [Hypothetical
           proteins, Conserved].
          Length = 321

 Score = 24.8 bits (54), Expect = 4.3
 Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%)

Query: 27  VRQYTRFIIEWPPFEYAVLLTIIAN 51
            R   RFI+   PF Y +   II N
Sbjct: 147 ERCE-RFIVPDYPFPYTICPKIIKN 170


>gnl|CDD|217890 pfam04097, Nic96, Nup93/Nic96.  Nup93/Nic96 is a component of the
           nuclear pore complex. It is required for the correct
           assembly of the nuclear pore complex. In Saccharomyces
           cerevisiae, Nic96 has been shown to be involved in the
           distribution and cellular concentration of the GTPase
           Gsp1. The structure of Nic96 has revealed a mostly alpha
           helical structure.
          Length = 607

 Score = 24.6 bits (54), Expect = 5.6
 Identities = 12/48 (25%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 5   SHHATASHRGPSSLFLLSETNTVRQYTRFIIEWPPFEYAVLLTIIANC 52
             +AT+  R               Q  R   E  P++ AV   II  C
Sbjct: 147 KAYATSPDRRLPPELEDKLHLEYNQRIRNSPEGDPYKLAV-YKIIGRC 193


>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
           structure and biogenesis].
          Length = 218

 Score = 24.5 bits (54), Expect = 6.2
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 1   MGPHSHHATASHRGPSSL 18
            GP SH ++ SHR P S+
Sbjct: 132 GGPASHGSSLSHRRPGSI 149


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.322    0.135    0.412 

Gapped
Lambda     K      H
   0.267   0.0708    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,662,308
Number of extensions: 274231
Number of successful extensions: 192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 9
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
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 (21.9 bits)
S2: 53 (24.2 bits)