RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3566
         (105 letters)



>gnl|CDD|201165 pfam00338, Ribosomal_S10, Ribosomal protein S10p/S20e.  This family
           includes small ribosomal subunit S10 from prokaryotes
           and S20 from eukaryotes.
          Length = 97

 Score = 44.8 bits (107), Expect = 2e-07
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 38  VNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPPQKFNITRMEPNSSVVDA---- 93
           + ++LK YD  +LESY KF+ + A  L I+      LP ++  +T +   S  VD     
Sbjct: 1   IRIKLKSYDHKLLESYVKFIVEAAKRLGIKVSGPIPLPTKRLRVTVL--RSPHVDKKSRE 58

Query: 94  NYHLRIYERNVQ 105
            + +R ++R + 
Sbjct: 59  QFEMRTHKRLID 70


>gnl|CDD|222889 PHA02583, 11, baseplate wedge subunit and tail pin; Provisional.
          Length = 218

 Score = 27.7 bits (62), Expect = 1.0
 Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 1/36 (2%)

Query: 2   KFNAFSSVSDSGSKTTNLFEPDYLDHLNPEIPLYDE 37
           K   F+ VS  G+    L E  Y+D     +  Y +
Sbjct: 138 KSIYFAEVSRKGTDGPKL-EVKYIDSQEHILENYSQ 172


>gnl|CDD|236920 PRK11511, PRK11511, DNA-binding transcriptional activator MarA;
           Provisional.
          Length = 127

 Score = 27.0 bits (59), Expect = 1.4
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 37  EVNVQLKGYDFPVLESYQKFVYKIAASLSIQSDESWALPPQKFNITRM 84
           E+  +LK  + P+L   +++ ++   +L+      + +PP K+ +T M
Sbjct: 65  EIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPPHKYRMTNM 112


>gnl|CDD|143423 cd07105, ALDH_SaliADH, Salicylaldehyde dehydrogenase, DoxF-like.
           Salicylaldehyde dehydrogenase (DoxF, SaliADH,
           EC=1.2.1.65) involved in the upper naphthalene catabolic
           pathway of Pseudomonas strain C18 and other similar
           sequences are present in this CD.
          Length = 432

 Score = 25.6 bits (57), Expect = 5.9
 Identities = 7/27 (25%), Positives = 13/27 (48%)

Query: 11  DSGSKTTNLFEPDYLDHLNPEIPLYDE 37
              S +     P  LD++ P++ +Y E
Sbjct: 310 ADESPSGTSMPPTILDNVTPDMDIYSE 336


>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
          Length = 487

 Score = 25.5 bits (56), Expect = 6.1
 Identities = 7/15 (46%), Positives = 10/15 (66%)

Query: 45  YDFPVLESYQKFVYK 59
            D PVLES + ++ K
Sbjct: 106 VDAPVLESEELYIRK 120


>gnl|CDD|131140 TIGR02085, meth_trns_rumB, 23S rRNA (uracil-5-)-methyltransferase
           RumB.  This family consists of RNA methyltransferases
           designated RumB, formerly YbjF. Members act on 23S rRNA
           U747 and the equivalent position in other
           proteobacterial species. This family is homologous to
           the other 23S rRNA methyltransferase RumA and to the
           tRNA methyltransferase TrmA [Protein synthesis, tRNA and
           rRNA base modification].
          Length = 374

 Score = 25.6 bits (56), Expect = 6.5
 Identities = 12/32 (37%), Positives = 14/32 (43%)

Query: 23  DYLDHLNPEIPLYDEVNVQLKGYDFPVLESYQ 54
           DYL  + P+  LY   N Q    D   L  YQ
Sbjct: 319 DYLSQMAPKFILYSSCNAQTMAKDIAELSGYQ 350


>gnl|CDD|224101 COG1180, PflA, Pyruvate-formate lyase-activating enzyme
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 260

 Score = 25.0 bits (55), Expect = 8.0
 Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 4/31 (12%)

Query: 17  TNLF-EPDYLDHLNPEIPLYDEVNVQLKGYD 46
           TN F  P+ L+ L   +PL D V + LK +D
Sbjct: 119 TNGFLPPEALEEL---LPLLDAVLLDLKAFD 146


>gnl|CDD|178320 PLN02718, PLN02718, Probable galacturonosyltransferase.
          Length = 603

 Score = 25.2 bits (55), Expect = 9.2
 Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)

Query: 62  ASLSIQSDESWALPPQKFNITRMEPNSS---VVDANYHLRIY 100
           A++ I + +   + P  +N   M+ NS     + A  H R Y
Sbjct: 369 ATIQILNIDDMNVLPADYNSLLMKQNSHDPRYISALNHARFY 410


  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    0.132    0.382 

Gapped
Lambda     K      H
   0.267   0.0723    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,217,950
Number of extensions: 416262
Number of successful extensions: 302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 302
Number of HSP's successfully gapped: 14
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (24.2 bits)