RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16824
         (85 letters)



>gnl|CDD|217867 pfam04062, P21-Arc, ARP2/3 complex ARPC3 (21 kDa) subunit.  The
           seven component ARP2/3 actin-organising complex is
           involved in actin assembly and function.
          Length = 175

 Score =  154 bits (392), Expect = 5e-50
 Identities = 45/79 (56%), Positives = 63/79 (79%)

Query: 1   MYSLALAKFDLPGEAGFPLNSVYAKPQSQNEADLMKNYLTQVRQETGLRVCERVFNTPDG 60
           + +LAL  F +PG+ GFPLNS+YA P ++ EA+L++ YL Q+RQE  +R+ ERV+   DG
Sbjct: 97  LNNLALDNFAIPGDPGFPLNSLYAPPANRQEAELLRQYLQQLRQELAIRLLERVYADEDG 156

Query: 61  KPSKWWLCFSKKRFMDKSL 79
           KPSKWWLCF+K++FM+KSL
Sbjct: 157 KPSKWWLCFTKRKFMNKSL 175


>gnl|CDD|222424 pfam13862, BCIP, p21-C-terminal region-binding protein.  This
           family of p21-binding proteins is important as a
           modulator of p21 activity. The domain binds the
           C-terminal region of p21 in a ternary complex with CDK2,
           which results in inhibition of the kinase activity of
           CDK2.
          Length = 189

 Score = 28.3 bits (64), Expect = 0.35
 Identities = 8/35 (22%), Positives = 15/35 (42%)

Query: 24  AKPQSQNEADLMKNYLTQVRQETGLRVCERVFNTP 58
            K   +     ++  L+   ++ GL + ER  N P
Sbjct: 92  KKSADKEVLAKLEKLLSDSDKKVGLLINERFINMP 126


>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
           Provisional.
          Length = 1331

 Score = 27.3 bits (61), Expect = 1.00
 Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 15/37 (40%)

Query: 18  PLNSVYAKPQSQNEADLMKNY-----LTQVRQETGLR 49
           PLNSVY          +M        ++QVRQ  G+R
Sbjct: 118 PLNSVY----------MMAFSGARGNMSQVRQLVGMR 144


>gnl|CDD|239168 cd02767, MopB_ydeP, The MopB_ydeP CD includes a group of related
           uncharacterized bacterial molybdopterin-binding
           oxidoreductase-like domains with a putative
           molybdopterin cofactor binding site. These members
           belong to the molybdopterin_binding (MopB) superfamily
           of proteins.
          Length = 574

 Score = 26.1 bits (58), Expect = 2.4
 Identities = 8/11 (72%), Positives = 8/11 (72%)

Query: 51  CERVFNTPDGK 61
            ER FNTP GK
Sbjct: 561 RERKFNTPSGK 571


>gnl|CDD|227787 COG5500, COG5500, Predicted integral membrane protein [Function
           unknown].
          Length = 159

 Score = 26.0 bits (57), Expect = 2.5
 Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 2/26 (7%)

Query: 18  PLNSVYA--KPQSQNEADLMKNYLTQ 41
           PLN   A   P S + A L  +YLT 
Sbjct: 109 PLNDALAAANPASTDGAKLWTSYLTN 134


>gnl|CDD|173839 cd01150, AXO, Peroxisomal acyl-CoA oxidase.  Peroxisomal acyl-CoA
           oxidases (AXO) catalyze the first set in the peroxisomal
           fatty acid beta-oxidation, the alpha,beta
           dehydrogenation of the corresponding trans-enoyl-CoA by
           FAD, which becomes reduced. In a second oxidative
           half-reaction, the reduced FAD is reoxidized by
           molecular oxygen. AXO is generally a homodimer, but it
           has been reported to form a different type of oligomer
           in yeast. There are several subtypes of AXO's, based on
           substrate specificity. Palmitoyl-CoA oxidase acts on
           straight-chain fatty acids and prostanoids; whereas, the
           closely related Trihydroxycoprostanoly-CoA oxidase has
           the greatest activity for  2-methyl branched side chains
           of bile precursors. Pristanoyl-CoA oxidase, acts on
           2-methyl branched fatty acids.  AXO has an additional
           domain, C-terminal to the region with similarity to
           acyl-CoA dehydrogenases, which is included in this
           alignment.
          Length = 610

 Score = 25.4 bits (56), Expect = 4.3
 Identities = 9/15 (60%), Positives = 10/15 (66%)

Query: 52  ERVFNTPDGKPSKWW 66
           E V NTPD   +KWW
Sbjct: 164 EFVINTPDFTATKWW 178


>gnl|CDD|241403 cd13249, PH_anillin_2, Anillin Pleckstrin homology (PH) domain.
          Anillin is an actin binding protein involved in
          cytokinesis. It has a C-terminal PH domain, which has
          been shown to be necessary, but not sufficient for
          targetting of anillin to ectopic septin containing
          foci. PH domains have diverse functions, but in general
          are involved in targeting proteins to the appropriate
          cellular location or in the interaction with a binding
          partner. They share little sequence conservation, but
          all have a common fold, which is electrostatically
          polarized. Less than 10% of PH domains bind
          phosphoinositide phosphates (PIPs) with high affinity
          and specificity. PH domains are distinguished from
          other PIP-binding domains by their specific
          high-affinity binding to PIPs with two vicinal
          phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
          PtdIns(3,4,5)P3 which results in targeting some PH
          domain proteins to the plasma membrane. A few display
          strong specificity in lipid binding. Any specificity is
          usually determined by loop regions or insertions in the
          N-terminus of the domain, which are not conserved
          across all PH domains. PH domains are found in cellular
          signaling proteins such as serine/threonine kinase,
          tyrosine kinases, regulators of G-proteins, endocytotic
          GTPases, adaptors, as well as cytoskeletal associated
          molecules and in lipid associated enzymes.
          Length = 111

 Score = 24.6 bits (54), Expect = 5.7
 Identities = 7/23 (30%), Positives = 14/23 (60%)

Query: 33 DLMKNYLTQVRQETGLRVCERVF 55
          ++M  YL+Q +   GL+   R++
Sbjct: 2  EMMSGYLSQQQSVEGLQSWTRLY 24


>gnl|CDD|215342 PLN02636, PLN02636, acyl-coenzyme A oxidase.
          Length = 686

 Score = 25.2 bits (55), Expect = 5.8
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 52  ERVFNTPDGKPSKWWL 67
           E V NTP+    KWW+
Sbjct: 203 EFVINTPNDGAIKWWI 218


>gnl|CDD|225634 COG3092, COG3092, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 149

 Score = 24.4 bits (53), Expect = 7.5
 Identities = 12/29 (41%), Positives = 15/29 (51%)

Query: 14  EAGFPLNSVYAKPQSQNEADLMKNYLTQV 42
           EAG  L  V  KP  Q  AD++K    Q+
Sbjct: 113 EAGQALAPVEEKPTYQALADVLKRAFKQL 141


  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    0.132    0.408 

Gapped
Lambda     K      H
   0.267   0.0793    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,156,008
Number of extensions: 303512
Number of successful extensions: 230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 10
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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: 53 (24.1 bits)