RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10770
         (253 letters)



>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
          Length = 813

 Score = 30.5 bits (69), Expect = 0.95
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 5/43 (11%)

Query: 11  SKHNYLTFTPQTLAHTLQGMGQDEGMYQQYIPLALHIAEDHFL 53
           S H  LT+T   + H LQG   D+ + +QY PL  H+ E H L
Sbjct: 376 SSHARLTYT--KVWHILQG---DQDLREQYAPLVKHLEELHNL 413


>gnl|CDD|216094 pfam00747, Viral_DNA_bp, ssDNA binding protein.  This protein is
           found in herpesviruses and is needed for replication.
          Length = 1111

 Score = 29.3 bits (66), Expect = 2.2
 Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 18/103 (17%)

Query: 69  ADVLRVYAPEAPYKDPDQVKTIFLFLIKQLNGLKDPKDPAFKRYFYLLENLAYVKSFNM- 127
            DVL  +A     +  D  +            ++D    + +RY YLLE L Y    ++ 
Sbjct: 519 CDVLGNFARRYALEKKDDGEA-------AKADMQDTYRASVERYKYLLEILDYCDKNSLI 571

Query: 128 -CFELEDSQEI-----FCALFSLMFKIVNDEHSGKVKSFMLDV 164
            C   ED+  I     F  + S + ++V+DE    V  FM ++
Sbjct: 572 DCSTGEDTSNIHGKRDFVKVVSDLNQVVDDE----VVQFMREL 610


>gnl|CDD|190951 pfam04356, DUF489, Protein of unknown function (DUF489).  Protein
           of unknown function, cotranscribed with purB in
           Escherichia coli, but with function unrelated to purine
           biosynthesis.
          Length = 190

 Score = 28.3 bits (64), Expect = 3.4
 Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 2/50 (4%)

Query: 65  ACCIADVLRVYA--PEAPYKDPDQVKTIFLFLIKQLNGLKDPKDPAFKRY 112
              +  +L+         Y   + +K     L+ QLN     KD    RY
Sbjct: 31  ETSLNSLLQTNPASTLDVYGGKENLKLGLETLLSQLNSDSQGKDAELTRY 80


>gnl|CDD|129323 TIGR00219, mreC, rod shape-determining protein MreC.  MreC (murein
           formation C) is involved in the rod shape determination
           in E. coli, and more generally in cell shape
           determination of bacteria whether or not they are
           rod-shaped. Cells defective in MreC are round. Species
           with MreC include many of the Proteobacteria,
           Gram-positives, and spirochetes [Cell envelope,
           Biosynthesis and degradation of murein sacculus and
           peptidoglycan].
          Length = 283

 Score = 27.1 bits (60), Expect = 9.3
 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 177 HELLDIILMNIVDPQKTQRKNAYLLAKELIVKTNDTLEPYIQNL 220
            E+ D I  N+ D    + +N Y L +EL+ K N  LE   QNL
Sbjct: 55  REVFDGISENLKDVNNLEYEN-YKLRQELLKK-NQQLEILTQNL 96


>gnl|CDD|222094 pfam13387, DUF4105, Domain of unknown function (DUF4105).  This is
           a family of uncharacterized bacterial proteins. There is
           a highly conserved histidine residue and a
           well-conserved NCT motif.
          Length = 172

 Score = 26.8 bits (60), Expect = 9.4
 Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 5/40 (12%)

Query: 83  DPDQVKTIFLFLIKQLNGLKDPKDPAFKRYFYLLENLAYV 122
            P++ + +FL L +  N L  P      RY +  +N A  
Sbjct: 106 TPEEKRALFLHLWELANPLNRP-----YRYNFFTDNCATR 140


>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
           (vWA) domain [General function prediction only].
          Length = 4600

 Score = 27.3 bits (60), Expect = 9.9
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 192 KTQRKNAYLLAKELIVKTNDTLEPYIQNLTRLANAVF-PNLGDIAPLGAMEIFM--GAMK 248
           K  R   +LL  E+ + + +TLE     L +  + +     GD+ P+     F   G M 
Sbjct: 631 KCMRNGEWLLLDEINLASEETLELIDGLLGKKESGILLSESGDLRPIRIHPGFRLFGCMN 690

Query: 249 PLRD 252
           P  D
Sbjct: 691 PGTD 694


  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
   0.324    0.140    0.411 

Gapped
Lambda     K      H
   0.267   0.0766    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,002,530
Number of extensions: 1252273
Number of successful extensions: 1269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1269
Number of HSP's successfully gapped: 24
Length of query: 253
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 158
Effective length of database: 6,723,972
Effective search space: 1062387576
Effective search space used: 1062387576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.0 bits)