RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12790
         (98 letters)



>gnl|CDD|197727 smart00443, G_patch, glycine rich nucleic binding domain.  A
          predicted glycine rich nucleic binding domain found in
          the splicing factor 45, SON DNA binding protein and
          D-type Retrovirus- polyproteins.
          Length = 47

 Score = 41.0 bits (97), Expect = 2e-06
 Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)

Query: 18 LDESNKGHQMLKRMGW-GGAGLGAKEQGIEAPISGGEVRERE 58
          +  SN G ++L++MGW  G GLG  EQGI  PIS    ++R+
Sbjct: 1  ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRK 42


>gnl|CDD|144978 pfam01585, G-patch, G-patch domain.  This domain is found in a
          number of RNA binding proteins, and is also found in
          proteins that contain RNA binding domains. This
          suggests that this domain may have an RNA binding
          function. This domain has seven highly conserved
          glycines.
          Length = 45

 Score = 39.4 bits (93), Expect = 6e-06
 Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 20 ESNKGHQMLKRMGW-GGAGLGAKEQGIEAPISGGEVRERE 58
           SN G ++L++MGW  G GLG  EQGI  PI      +R+
Sbjct: 1  TSNIGFKLLQKMGWKPGQGLGKNEQGITEPIEAKIRPDRK 40


>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
          Length = 963

 Score = 27.5 bits (61), Expect = 1.2
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 4   GHPGGAYGKSGVEKLDESNKGHQMLKRMGWGGAGLGAKEQGIE 46
           GHP G Y  + +    +  +G+ +L  MGW   GL A++  IE
Sbjct: 129 GHPEG-YTATDILARYKRMQGYNVLHPMGWDAFGLPAEQYAIE 170


>gnl|CDD|214345 CHL00043, cemA, envelope membrane protein.
          Length = 261

 Score = 25.9 bits (58), Expect = 3.8
 Identities = 6/13 (46%), Positives = 9/13 (69%)

Query: 73 ENFRKSKKQAFIS 85
          + FR +KK+A  S
Sbjct: 29 QEFRMAKKKALTS 41


>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
           protein DltB.  Members of this protein family are DltB,
           part of a four-gene operon for D-alanyl-lipoteichoic
           acid biosynthesis that is present in the vast majority
           of low-GC Gram-positive organisms. This protein may be
           involved in transport of D-alanine across the plasma
           membrane [Cell envelope, Biosynthesis and degradation of
           murein sacculus and peptidoglycan].
          Length = 380

 Score = 25.2 bits (56), Expect = 6.6
 Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 2/21 (9%)

Query: 60  LYKGVGVSLNDPYENFRKSKK 80
           LY G+ ++L D ++  RKSKK
Sbjct: 329 LYHGLLLALTDAWQ--RKSKK 347


>gnl|CDD|220200 pfam09357, RteC, RteC protein.  Human colonic Bacteroides species
           harbor a family of large conjugative transposons, called
           tetracycline resistance (Tcr) elements. Activities of
           these elements are enhanced by pregrowth of bacteria in
           medium containing tetracycline, indicating that at least
           some Tcr element genes are regulated by tetracycline. An
           insertional disruption in the rteC gene abolished
           self-transfer of the Tcr element to Bacteroides
           recipients, indicating that the gene was essential for
           self-transfer.
          Length = 218

 Score = 25.0 bits (55), Expect = 7.5
 Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 5/36 (13%)

Query: 60  LYKGVGVSLNDPYENF-----RKSKKQAFISRMKER 90
             K   + L D Y  +     RK  +  F+ ++K++
Sbjct: 174 FEKVFNIDLGDIYRTYVEIKERKKSRTKFLDKLKDK 209


>gnl|CDD|240267 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
          Length = 390

 Score = 25.0 bits (55), Expect = 7.7
 Identities = 9/24 (37%), Positives = 12/24 (50%)

Query: 72  YENFRKSKKQAFISRMKERQEHTR 95
           Y+N+ KSKK+AF    K       
Sbjct: 119 YKNWYKSKKKAFTKYKKFAATKKA 142


  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
   0.310    0.133    0.384 

Gapped
Lambda     K      H
   0.267   0.0809    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,054,974
Number of extensions: 427281
Number of successful extensions: 254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 16
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.0 bits)