RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10872
         (259 letters)



>gnl|CDD|150982 pfam10400, Vir_act_alpha_C, Virulence activator alpha C-term.  This
           structure is homo-dimeric, and the domain here is the
           C-terminal half of the structure, often associated with
           PadR upstream, (pfam03551), which is a transcriptional
           regulator.
          Length = 90

 Score = 27.6 bits (62), Expect = 2.1
 Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 9/59 (15%)

Query: 150 IDPLALVQAIERYLVVRG-----YARIRDKDSGESDEDNSEEDIDDTLAAVVITHGARH 203
           +DP AL+  +E  L +       Y RI  +D      D SE D +     + +  G R 
Sbjct: 17  LDPEALIAELEERLALHEEKLATYERIEKRDF----ADPSELDRERRGQYLTLRRGIRF 71


>gnl|CDD|182319 PRK10226, PRK10226, isoaspartyl peptidase; Provisional.
          Length = 313

 Score = 29.1 bits (65), Expect = 2.2
 Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 7/52 (13%)

Query: 187 DIDDTLAAVVITHGARHKLQFLIGDHPLP----YNMTVYQAIRQFSCVGHGE 234
           D+D  LAA   T G  +KL   +GD PL     Y      A+   SC G GE
Sbjct: 186 DLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAV---SCTGTGE 234


>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
          Length = 5163

 Score = 28.0 bits (62), Expect = 6.7
 Identities = 13/39 (33%), Positives = 19/39 (48%)

Query: 30  AKCPLESNVIVEHKDCSAEPLAALIAKLNGCVSQLEQLP 68
           A+ PL+  + VE +DCS  P A   A+L     +    P
Sbjct: 116 AQVPLDRPLEVEFEDCSGLPEAEQEARLRDEAQRESLQP 154


>gnl|CDD|233254 TIGR01059, gyrB, DNA gyrase, B subunit.  This model describes the
           common type II DNA topoisomerase (DNA gyrase). Two
           apparently independently arising families, one in the
           Proteobacteria and one in Gram-positive lineages, are
           both designated toposisomerase IV. Proteins scoring
           above the noise cutoff for this model and below the
           trusted cutoff for topoisomerase IV models probably
           should be designated GyrB [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 654

 Score = 27.7 bits (62), Expect = 7.6
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 7/43 (16%)

Query: 154 ALVQAIERYLVVRGYARIRDKDSGESDEDNSEEDIDDTLAAVV 196
           AL + I  Y       +       ES  + + EDI + L AV+
Sbjct: 284 ALTRVINSYAKNNKLLK-------ESKPNLTGEDIREGLTAVI 319


>gnl|CDD|216303 pfam01112, Asparaginase_2, Asparaginase. 
          Length = 296

 Score = 27.4 bits (61), Expect = 7.6
 Identities = 15/48 (31%), Positives = 20/48 (41%)

Query: 187 DIDDTLAAVVITHGARHKLQFLIGDHPLPYNMTVYQAIRQFSCVGHGE 234
           D +  LAA   T G  +K+   +GD P+P            S  G GE
Sbjct: 168 DANGNLAAATSTGGMVNKMPGRVGDSPIPGAGAYANNFAGASATGKGE 215


>gnl|CDD|220740 pfam10416, IBD, Transcription-initiator DNA-binding domain IBD.  In
           Trichomonas vaginalis, thought to be the earliest extant
           eukaryote, the sole initiator element for control of the
           start of transcription is Inr, and this is recognised by
           the initiator binding protein IBP39. IBP39 contains an
           N-terminal Inr binding domain, IBD, connected via a
           flexible, proteolytically sensitive, linker (residues
           127-145) to a C-terminal domain. The IBD structure
           reveals a winged-helix-wing conformation with each
           element binding to DNA, the central helix-turn-helix
           contributing the majority of the specificity-determining
           contacts with the Inr core motif TCAPy(T/A). The binding
           of IBP39 to the Inr directly recruits RNA polymerase II
           and in this way initiates transcription.
          Length = 125

 Score = 26.5 bits (59), Expect = 8.3
 Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 5/61 (8%)

Query: 121 MCNTHQLKCHLQRHPSC--TSLKQWKGGTVKIDPLALVQAIERYLVVRGYAR---IRDKD 175
             NT QLK  L +  S    +L++     +      L++ I          R   +R  D
Sbjct: 65  AINTRQLKLLLGKCKSSINGNLQKLGFEELPSKAEELIKKIPFLKDNPSELRQWTVRRVD 124

Query: 176 S 176
           S
Sbjct: 125 S 125


>gnl|CDD|213403 cd12208, septicolysin_like, putative septicolysin,
          cholesterol-dependent cytolysin family and related
          proteins.  This group contains some members identified
          as septicolysin. While septolysin is poorly
          characterized, it has been identified as a a
          cholesterol-dependent cytolysin, and acts to facilitate
          the infection of certain pathogenic bacteria to cells.
          Cholesterol-dependent cytolysins are pore-forming
          toxins that aid in bacterial pathogenesis of various
          gram positive species. Pores are formed by
          oligomerization into ring-like structures. Related
          proteins in eukaryotic immune systems use this
          pore-forming mechanism.
          Length = 150

 Score = 26.8 bits (60), Expect = 9.4
 Identities = 10/39 (25%), Positives = 22/39 (56%)

Query: 34 LESNVIVEHKDCSAEPLAALIAKLNGCVSQLEQLPVKVH 72
          + +N  V+  D  AE    L+ +L   + +LE+L ++++
Sbjct: 24 INNNAKVQEGDEPAEDPNELLKELEELLDELEELIIRIN 62


  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
   0.318    0.133    0.412 

Gapped
Lambda     K      H
   0.267   0.0749    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,835,191
Number of extensions: 1187317
Number of successful extensions: 1103
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1103
Number of HSP's successfully gapped: 15
Length of query: 259
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 164
Effective length of database: 6,723,972
Effective search space: 1102731408
Effective search space used: 1102731408
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 (21.7 bits)
S2: 58 (26.1 bits)