RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12129
         (154 letters)



>gnl|CDD|238077 cd00132, CRIB, PAK (p21 activated kinase) Binding Domain (PBD),
          binds Cdc42p- and/or Rho-like small GTPases; also known
          as the Cdc42/Rac interactive binding (CRIB) motif; has
          been shown to inhibit transcriptional activation and
          cell transformation mediated by the Ras-Rac pathway.
          CRIB-containing effector proteins are functionally
          diverse and include serine/threonine kinases, tyrosine
          kinases, actin-binding proteins, and adapter molecules.
          Length = 42

 Score = 42.8 bits (101), Expect = 1e-06
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 53 SMIGEPTNFQHTGHIGSGDVEL-GNSRLRAIQNQMQSKGGYE 93
            I  PT+F+H  H+G   V   G +    +Q+  Q+ G   
Sbjct: 1  MEISTPTDFKHISHVGWDGVGFDGANLPPDLQSLFQTAGISA 42


>gnl|CDD|144398 pfam00786, PBD, P21-Rho-binding domain.  Small domains that bind
          Cdc42p- and/or Rho-like small GTPases. Also known as
          the Cdc42/Rac interactive binding (CRIB).
          Length = 59

 Score = 35.9 bits (83), Expect = 6e-04
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 54 MIGEPTNFQHTGHIG 68
           I  PTNF+H  H+G
Sbjct: 1  EISTPTNFKHVVHVG 15


>gnl|CDD|197628 smart00285, PBD, P21-Rho-binding domain.  Small domains that bind
          Cdc42p- and/or Rho-like small GTPases. Also known as
          the Cdc42/Rac interactive binding (CRIB).
          Length = 36

 Score = 33.7 bits (78), Expect = 0.003
 Identities = 8/14 (57%), Positives = 10/14 (71%)

Query: 55 IGEPTNFQHTGHIG 68
          I  PTNF+H  H+G
Sbjct: 1  ISTPTNFKHIAHVG 14


>gnl|CDD|238526 cd01093, CRIB_PAK_like, PAK (p21 activated kinase) Binding Domain
          (PBD), binds Cdc42p- and/or Rho-like small GTPases;
          also known as the Cdc42/Rac interactive binding (CRIB)
          motif; has been shown to inhibit transcriptional
          activation and cell transformation mediated by the
          Ras-Rac pathway. This subgroup of CRIB/PBD-domains is
          found N-terminal of Serine/Threonine kinase domains in
          PAK and PAK-like proteins.
          Length = 46

 Score = 27.2 bits (61), Expect = 0.58
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 53 SMIGEPTNFQHTGHIG 68
            I  PTNF+H  H+G
Sbjct: 1  PEISSPTNFKHRVHVG 16


>gnl|CDD|236141 PRK08032, fliD, flagellar capping protein; Reviewed.
          Length = 462

 Score = 28.5 bits (64), Expect = 1.5
 Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 104 QTHTRSQRRYRKEDPNGS-DSSGDVELGNSRLRAIQNQMQS 143
           Q    S  +Y   D      SS    LG+S LR IQ Q++S
Sbjct: 287 QDTFSSLTKYTAVDAGADQSSSNGALLGDSTLRTIQTQLKS 327


>gnl|CDD|235346 PRK05111, PRK05111, acetylornithine deacetylase; Provisional.
          Length = 383

 Score = 26.7 bits (60), Expect = 5.3
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 25/64 (39%)

Query: 51  DRSMIGEPTNFQ----HTGHIG-----------SGDVELGN----------SRLRAIQNQ 85
           D ++IGEPT+ +    H GH+            S D  LG             L  ++++
Sbjct: 162 DCAIIGEPTSLKPVRAHKGHMSEAIRITGQSGHSSDPALGVNAIELMHDVIGELLQLRDE 221

Query: 86  MQSK 89
           +Q +
Sbjct: 222 LQER 225


>gnl|CDD|188431 TIGR03916, rSAM_link_UDG, putative DNA modification/repair radical
           SAM protein.  This uncharacterized protein of about 400
           amino acids in length contains a radical SAM protein in
           the N-terminal half. Members are present in about twenty
           percent of prokaryotic genomes, always paired with a
           member of the conserved hypothetical protein TIGR03915.
           Roughly forty percent of the members of that family
           exist as fusions with a uracil-DNA glycosylase-like
           region, TIGR03914. In DNA, uracil results from
           deamidation of cytosine, forming U/G mismatches that
           lead to mutation, and so uracil-DNA glycosylase is a DNA
           repair enzyme. This indirect connection, and the
           recurring role or radical SAM protein in modification
           chemistries, suggest that this protein may act in DNA
           modification, repair, or both [Unknown function, Enzymes
           of unknown specificity].
          Length = 415

 Score = 26.1 bits (58), Expect = 8.7
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 12/57 (21%)

Query: 8   SEELGYQSGNMAGEMWLQWFSCCINQPT-------APQRKRHQVRRPMRIDRSMIGE 57
           S EL  ++G +A  +     S  +  PT       AP++    + +PMR  ++ I +
Sbjct: 146 SPELIEEAGLLADRL-----SVNLELPTEEGLKLLAPEKSHQSILKPMRFIQNGIIQ 197


  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
   0.314    0.131    0.388 

Gapped
Lambda     K      H
   0.267   0.0783    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,621,939
Number of extensions: 652096
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 17
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 42 (22.0 bits)
S2: 55 (24.9 bits)