RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17864
         (151 letters)



>gnl|CDD|236263 PRK08425, flgE, flagellar hook protein FlgE; Validated.
          Length = 731

 Score = 29.3 bits (66), Expect = 0.82
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 9   PSRRISDDFIEKA-VAEARASFKVSFKFQVNSGLNLDVTST 48
            +  I +  I+   V  ARAS +VS K  +NSG ++   S 
Sbjct: 150 STGPIQNIRIDPGMVMPARASTEVSIKANLNSGRHIGTQSA 190


>gnl|CDD|162489 TIGR01690, ICE_RAQPRD, integrative conjugative element protein,
           RAQPRD family.  This model represents a small family of
           proteins about 100 amino acids in length, including a
           predicted signal sequence and a perfectly conserved
           motif RAQPRD towards the C-terminus. Members are found
           in the Pseudomonas putida TOL plasmid pWW0 and in
           cryptic plasmid regions of Salmonella enterica subsp.
           enterica serovar Typhi and Pseudomonas syringae DC3000.
           The function is unknown [Mobile and extrachromosomal
           element functions, Plasmid functions].
          Length = 94

 Score = 27.7 bits (62), Expect = 0.96
 Identities = 12/33 (36%), Positives = 16/33 (48%)

Query: 89  SQMALDWIAREQENPGALGRELDQAERELETAR 121
           +  AL   A E+E   A  R+LD  ER  + A 
Sbjct: 12  AASALADQASEREQLAAAIRQLDALERSAQRAA 44


>gnl|CDD|220597 pfam10139, Virul_Fac, Putative bacterial virulence factor.  Members
           of this family of prokaryotic proteins include various
           putative virulence factor effector proteins. Their exact
           function is, as yet, unknown.
          Length = 852

 Score = 28.2 bits (63), Expect = 1.9
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 92  ALDWIAREQENPGALGRELDQAERELETARLAGREL 127
           A+DW+   ++N   L RE D    +L  +R   R L
Sbjct: 1   AIDWVNETRQNAPRLDREADSLTVKLRRSRNRARRL 36


>gnl|CDD|226865 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
           putative virulence factor [Function unknown].
          Length = 821

 Score = 27.9 bits (62), Expect = 2.3
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 89  SQMALDWIAREQENPGALGRELDQAERELETARLAGREL 127
           +Q A+DW+   + N   L  E D  E+ L  +R A R+L
Sbjct: 16  AQDAIDWVGNTRANAVRLDDEADSLEQHLRRSRNAARKL 54


>gnl|CDD|236538 PRK09483, PRK09483, response regulator; Provisional.
          Length = 217

 Score = 27.4 bits (61), Expect = 3.0
 Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 10/52 (19%)

Query: 72  QEVV-----AHYSNRALDDDMRSQMALDWIAREQENPGALGRELDQAERELE 118
           QEVV      H   R +  D+  QMAL  I    ENP A       +EREL+
Sbjct: 109 QEVVSAIRSVHSGQRYIASDIAQQMALSQIEPATENPFA-----SLSERELQ 155


>gnl|CDD|211418 cd11577, GH71, Glycoside hydrolase family 71.  This family of
          glycoside hydrolases 71 (following the CAZY
          nomenclature) function as alpha-1,3-glucanases
          (mutanases, EC 3.2.1.59). They appear to have an
          endo-hydrolytic mode of enzymatic activity and
          bacterial members are investigated as candidates for
          the development of dental caries treatments.The member
          from fission yeast, endo-alpha-1,3-glucanase Agn1p,
          plays a vital role in daughter cell separation, while
          Agn2p has been associated with endolysis of the ascus
          wall.
          Length = 283

 Score = 26.5 bits (59), Expect = 6.1
 Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 15 DDFIEKAVAEARAS-FKVSFKFQVNSGLNLDVTSTIGKKLATYWN 58
             +  A   A A+ FK+   F ++ G +    + +   +ATY  
Sbjct: 51 PTQLALAYQAAEATGFKLFLSFDMSGGWSASDVAEVIALIATYAA 95


>gnl|CDD|206768 cd11363, RNase_PH_PNPase_1, Polyribonucleotide
           nucleotidyltransferase, repeat 1.  Polyribonucleotide
           nucleotidyltransferase (PNPase) is a member of the
           RNase_PH family, named after the bacterial Ribonuclease
           PH, a 3'-5' exoribonuclease. Structurally, all members
           of this family form hexameric rings. In the case of
           PNPase the complex is a trimer, since each monomer
           contains two tandem copies of the domain. PNPase is
           involved in mRNA degradation in a 3'-5' direction and in
           quality control of ribosomal RNA precursors. It is part
           of the RNA degradosome complex and binds to the
           scaffolding domain of the endoribonuclease RNase E.
          Length = 229

 Score = 25.9 bits (58), Expect = 7.4
 Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)

Query: 108 RELDQAERELETARLAGRELR--FPK 131
           RE   +E+E+ T+RL  R +R  FPK
Sbjct: 76  REGRPSEKEILTSRLIDRPIRPLFPK 101


>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
           enzyme [Cell wall/membrane/envelope biogenesis].
          Length = 418

 Score = 26.2 bits (58), Expect = 8.8
 Identities = 10/48 (20%), Positives = 20/48 (41%)

Query: 101 ENPGALGRELDQAERELETARLAGRELRFPKEKKDILMLAHTQINGGS 148
           E    L +EL +   E+E  + A +E    ++ ++ L     Q+    
Sbjct: 246 EYLKKLNQELAKLAAEIERVQEALKESPKSEKAQNKLNRLQMQLEAFE 293


  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
   0.316    0.129    0.360 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,648,147
Number of extensions: 688683
Number of successful extensions: 812
Number of sequences better than 10.0: 1
Number of HSP's gapped: 812
Number of HSP's successfully gapped: 25
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
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: 54 (24.6 bits)