RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4238
         (67 letters)



>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional.
          Length = 194

 Score = 90.2 bits (224), Expect = 1e-24
 Identities = 42/59 (71%), Positives = 46/59 (77%), Gaps = 1/59 (1%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           RV KQ+VN+PSF+VR+DSQKHIDFSL SP GGG  GRVKRKN  KAAS      EEDEE
Sbjct: 137 RVGKQIVNVPSFMVRVDSQKHIDFSLTSPLGGGRPGRVKRKNQ-KAASGGGDGDEEDEE 194


>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional.
          Length = 181

 Score = 80.9 bits (200), Expect = 3e-21
 Identities = 30/47 (63%), Positives = 37/47 (78%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAA 55
           RV KQ+V+IPSF+VR+DS+KHIDF+  SPFG G  GRVKRK  + A 
Sbjct: 135 RVGKQIVDIPSFLVRVDSEKHIDFADTSPFGNGRPGRVKRKAAKAAK 181


>gnl|CDD|213577 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal
           type)/S9(eukaryote cytosolic type).  This model finds
           eukaryotic ribosomal protein S9 as well as archaeal
           ribosomal protein S4 [Protein synthesis, Ribosomal
           proteins: synthesis and modification].
          Length = 162

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFG 39
            V  + V  PS++VR + +K IDF+ +SPF 
Sbjct: 132 AVDGRRVTSPSYIVRREEEKKIDFAPSSPFK 162


>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
           [Translation, ribosomal structure and biogenesis].
          Length = 205

 Score = 33.4 bits (77), Expect = 0.003
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 9   RVRKQVVNIPSFVVRLDSQKHIDFSLNSPFGGGGAGRVKRKN 50
            V  + VNIPS++V    +  +     SP     A  +  + 
Sbjct: 122 LVNGKRVNIPSYLVSPGDEISVREKSKSPIKIKEALELAAQR 163


>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated.
          Length = 177

 Score = 28.7 bits (65), Expect = 0.12
 Identities = 8/26 (30%), Positives = 15/26 (57%)

Query: 13  QVVNIPSFVVRLDSQKHIDFSLNSPF 38
           + V  PS++V ++ +  ID+   SP 
Sbjct: 135 RRVTSPSYLVSVEEEDLIDYYPTSPL 160


>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
          Length = 323

 Score = 28.0 bits (62), Expect = 0.24
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 33  SLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDEE 67
           +L    GGGG+   +      AA+SAAA  EE+E 
Sbjct: 278 ALEGLLGGGGSAAAEAAAAAPAAASAAAKEEEEES 312


>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
           dihydrolipoamide succinyltransferase.  This model
           represents an Actinobacterial clade of E2 enzyme, a
           component of the 2-oxoglutarate dehydrogenase complex
           involved in the TCA cycle. These proteins have multiple
           domains including the catalytic domain (pfam00198), one
           or two biotin domains (pfam00364) and an E3-component
           binding domain (pfam02817).
          Length = 579

 Score = 26.5 bits (58), Expect = 1.1
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 21  VVRLDSQKHIDFSLNSPFGGGGAGRVKRKNLRKAASSAAAPAE 63
           V +L   K +D  L++  G G  GR++++++  AA +A     
Sbjct: 272 VRKLAKDKGVD--LSTVKGTGVGGRIRKQDVLAAAKAAEEARA 312


>gnl|CDD|99978 cd03806, GT1_ALG11_like, This family is most closely related to the
           GT1 family of glycosyltransferases. ALG11 in yeast is
           involved in adding the final 1,2-linked Man to the
           Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of
           the ER. The deletion analysis of ALG11 was shown to
           block the early steps of core biosynthesis that takes
           place on the cytoplasmic face of the ER and lead to a
           defect in the assembly of lipid-linked oligosaccharides.
          Length = 419

 Score = 24.9 bits (55), Expect = 4.0
 Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 5/37 (13%)

Query: 7   IGRVR-----KQVVNIPSFVVRLDSQKHIDFSLNSPF 38
           IG  R     K+V ++      L  +  ++F +N+PF
Sbjct: 279 IGSCRNEDDEKRVEDLKLLAKELGLEDKVEFVVNAPF 315


>gnl|CDD|215233 PLN02424, PLN02424, ketopantoate hydroxymethyltransferase.
          Length = 332

 Score = 24.3 bits (53), Expect = 6.4
 Identities = 11/25 (44%), Positives = 18/25 (72%)

Query: 43  AGRVKRKNLRKAASSAAAPAEEDEE 67
           A  ++++ L KAA +AAA AE++E 
Sbjct: 301 AEALQKRGLDKAAEAAAAAAEKEES 325


>gnl|CDD|236246 PRK08344, PRK08344, V-type ATP synthase subunit K; Validated.
          Length = 157

 Score = 24.0 bits (52), Expect = 6.7
 Identities = 11/34 (32%), Positives = 15/34 (44%)

Query: 33 SLNSPFGGGGAGRVKRKNLRKAASSAAAPAEEDE 66
          +L +    G AG      +  A S+AA    EDE
Sbjct: 4  ALGAALAAGLAGAASSFGVGIAGSAAAGAVAEDE 37


  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
   0.315    0.134    0.383 

Gapped
Lambda     K      H
   0.267   0.0786    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,499,646
Number of extensions: 257217
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 15
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
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: 41 (21.6 bits)
S2: 53 (24.1 bits)