RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14662
         (237 letters)



>gnl|CDD|176262 cd08367, P53, P53 DNA-binding domain.  P53 is a tumor suppressor
           gene product; mutations in p53 or lack of expression are
           found associated with a large fraction of all human
           cancers. P53 is activated by DNA damage and acts as a
           regulator of gene expression that ultimatively blocks
           progression through the cell cycle. P53 binds to DNA as
           a tetrameric transcription factor. In its inactive form,
           p53 is bound to the ring finger protein Mdm2, which
           promotes its ubiquitinylation and subsequent proteosomal
           degradation. Phosphorylation of p53 disrupts the
           Mdm2-p53 complex, while the stable and active p53 binds
           to regulatory regions of its target genes, such as the
           cyclin-kinase inhibitor p21, which complexes and
           inactivates cdk2 and other cyclin complexes.
          Length = 179

 Score =  142 bits (361), Expect = 6e-43
 Identities = 62/186 (33%), Positives = 93/186 (50%), Gaps = 42/186 (22%)

Query: 50  QYSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHV 109
            YS +LNK+F+ + K  PIQ K+    +   PP L++RA  +Y   +H   PVERCP H 
Sbjct: 17  TYSPKLNKLFVKMAKTCPIQFKV----NPSPPPGLYVRAMLVYKDPEHVKEPVERCPNHR 72

Query: 110 CRDPPPLFLRATPIYSQDDHRGRPVERCPLHVSDALCNEINKGFEAVVKHIVRCTSAHCQ 169
             D                                       G  A   H++RC +   +
Sbjct: 73  QGDD--------------------------------------GHTAPNSHVIRCENPQAE 94

Query: 170 YPMDERSGRHTCVTPLSPPQPGADTVTLMYSFVCKTSCLGGMDRRPVLLLLTLENQHGQI 229
           Y  D  +GR + V PL PPQ G++ VT++  F+C+ SC GG++RRP+ L+ TLE+++G +
Sbjct: 95  YVGDAFTGRLSVVVPLEPPQVGSEYVTVLLQFMCQNSCPGGINRRPIQLVFTLEDENGNV 154

Query: 230 LGRRSL 235
           LGRR +
Sbjct: 155 LGRRVI 160


>gnl|CDD|201481 pfam00870, P53, P53 DNA-binding domain.  This family contains one
           anomalous member, viz: Zea mays (Q6JAD8). This sequence
           is identical to human P53 and would appear to be a a
           human contaminant within the Zea mays sampling effort.
          Length = 196

 Score =  118 bits (297), Expect = 4e-33
 Identities = 65/185 (35%), Positives = 94/185 (50%), Gaps = 41/185 (22%)

Query: 51  YSYELNKVFIDIGKVLPIQVKLLYKHDEPAPPPLFLRATPIYSQDDHRGRPVERCPLHVC 110
           YS +LNK+F  + K  P+QVK+    D P PP   +RA  IY + +H    V RCP H  
Sbjct: 32  YSPDLNKLFCQLAKTCPVQVKV----DSPPPPGTIVRAMAIYKKSEHVAEVVRRCPHH-- 85

Query: 111 RDPPPLFLRATPIYSQDDHRGRPVERCPLHVSDALCNEINKGFEAVVKHIVRCT-SAHCQ 169
                                               +E N+G      H++R   +   Q
Sbjct: 86  ---------------------------------ERSSEHNEGLAPP-SHLIRVEGNQLAQ 111

Query: 170 YPMDERSGRHTCVTPLSPPQPGADTVTLMYSFVCKTSCLGGMDRRPVLLLLTLENQHGQI 229
           Y  D  +GRH+ + P  PPQ G++  T++Y+F+C +SC+GGM+RRP+L ++TLE Q GQ+
Sbjct: 112 YMEDPNTGRHSVLVPYEPPQVGSEWTTILYNFMCNSSCMGGMNRRPILTIITLETQEGQL 171

Query: 230 LGRRS 234
           LGRRS
Sbjct: 172 LGRRS 176


>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3.  the
           380 kDa motor unit of dynein belongs to the AAA class of
           chaperone-like ATPases. The core of the 380 kDa motor
           unit contains a concatenated chain of six AAA modules,
           of which four correspond to the ATP binding sites with
           P-loop signatures described previously, and two are
           modules in which the P loop has been lost in evolution.
           This particular family is the D3 and is an ATP binding
           site.
          Length = 272

 Score = 28.0 bits (62), Expect = 4.0
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 8/52 (15%)

Query: 157 VKHIVRCTSAHCQYP------MDERSGRHTCVTPLSPPQPGADTVTLMYSFV 202
           +K I  C    C  P      ++ R  RH CV  LS   PG D ++ +Y+ +
Sbjct: 143 LKEIHNCQYVSCMNPTAGSFTINSRLQRHFCVFALS--FPGQDALSTIYNII 192


>gnl|CDD|217061 pfam02482, Ribosomal_S30AE, Sigma 54 modulation protein / S30EA
           ribosomal protein.  This Pfam family contains the
           sigma-54 modulation protein family and the S30AE family
           of ribosomal proteins which includes the light-
           repressed protein (lrtA).
          Length = 94

 Score = 26.3 bits (59), Expect = 6.3
 Identities = 9/29 (31%), Positives = 15/29 (51%)

Query: 139 LHVSDALCNEINKGFEAVVKHIVRCTSAH 167
           + V+DAL   + +  E + K+  R  SA 
Sbjct: 9   VEVTDALREYVEEKLEKLEKYFDRIISAD 37


>gnl|CDD|192243 pfam09287, CEP1-DNA_bind, CEP-1, DNA binding.  Members of this
           family of DNA-binding domains are found the
           transcription factor CEP-1. They adopt a beta sandwich
           structure, with nine strands in two beta-sheets, in a
           Greek-key topology.
          Length = 198

 Score = 26.9 bits (59), Expect = 8.6
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 190 PGADTVTLMYSFVCKTSCLGGMDRRPVLLL-LTLENQHG 227
           PGA        F C+  CL   DRR  + L + L++++G
Sbjct: 128 PGATQALFDIIFKCQEKCLDLADRRKRMCLAVFLDDENG 166


  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    0.141    0.452 

Gapped
Lambda     K      H
   0.267   0.0702    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,163,035
Number of extensions: 1127481
Number of successful extensions: 654
Number of sequences better than 10.0: 1
Number of HSP's gapped: 650
Number of HSP's successfully gapped: 16
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 41 (22.0 bits)
S2: 57 (25.8 bits)