RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12014
         (78 letters)



>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
          composed of two C4-type zinc fingers.  DNA-binding
          domain of Tailless (TLX) is composed of two C4-type
          zinc fingers. Each zinc finger contains a group of four
          Cys residues which co-ordinates a single zinc atom. TLX
          interacts with specific DNA sites upstream of the
          target gene and modulates the rate of transcriptional
          initiation.  TLX is an orphan receptor that is
          expressed by neural stem/progenitor cells in the adult
          brain of the subventricular zone (SVZ) and the dentate
          gyrus (DG). It plays a key role in neural development
          by promoting cell cycle progression and preventing
          apoptosis in the developing brain. Like other members
          of the nuclear receptor (NR) superfamily of
          ligand-activated transcription factors, TLX has a
          central well conserved DNA-binding domain (DBD), a
          variable N-terminal domain, a flexible hinge and a
          C-terminal ligand binding domain (LBD).
          Length = 92

 Score = 28.2 bits (63), Expect = 0.20
 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 16 GLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPL 51
          G+++C  CS  +K+  S+ R++ Y C  + +  CP+
Sbjct: 22 GIYACDGCSGFFKR--SIRRNRQYVCKSKGQGGCPV 55


>gnl|CDD|173487 PTZ00236, PTZ00236, mitochondrial import inner membrane
          translocase subunit tim17; Provisional.
          Length = 164

 Score = 28.1 bits (63), Expect = 0.28
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 15 GGLFSCSDCSRVY 27
          GGLFS  DC+  Y
Sbjct: 70 GGLFSTFDCTLQY 82


>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
           transition [Transcription / Cell division and chromosome
           partitioning].
          Length = 423

 Score = 27.8 bits (61), Expect = 0.55
 Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 23  CSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLTTHMAIRHH 71
            ++   +  S  +   +    +P YRC +C  R K    L  H    H 
Sbjct: 376 QNQKLHENPSPEKMNIFSAKDKP-YRCEVCDKRYKNLNGLKYHRKHSHD 423


>gnl|CDD|150045 pfam09237, GAGA, GAGA factor.  Members of this family bind to a
          5'-GAGAG-3' DNA consensus binding site, and contain a
          Cys2-His2 zinc finger core as well as an N-terminal
          extension containing two highly basic regions. The zinc
          finger core binds in the DNA major groove and
          recognises the first three GAG bases of the consensus
          in a manner similar to that seen in other classical
          zinc finger-DNA complexes. The second basic region
          forms a helix that interacts in the major groove
          recognising the last G of the consensus, while the
          first basic region wraps around the DNA in the minor
          groove and recognises the A in the fourth position of
          the consensus sequence.
          Length = 54

 Score = 26.5 bits (58), Expect = 0.56
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 8/50 (16%)

Query: 34 TRHQTYECGQQPKYR--------CPLCSYRAKQKIHLTTHMAIRHHKKLG 75
           R +     ++ K +        CP+C    +Q  +L  H+ +RH KK G
Sbjct: 4  KRAKHPPGTEKIKSKSQSEQPATCPICQAVIRQSRNLRRHLELRHFKKPG 53


>gnl|CDD|185698 cd09021, Aldose_epim_Ec_YphB, aldose 1-epimerase, similar to
           Escherichia coli YphB.  Proteins similar to Escherichia
           coli YphB are uncharacterized members of the
           aldose-1-epimerase superfamily. Aldose 1-epimerases or
           mutarotases are key enzymes of carbohydrate metabolism,
           catalyzing the interconversion of the alpha- and
           beta-anomers of hexose sugars such as glucose and
           galactose. This interconversion is an important step
           that allows anomer specific metabolic conversion of
           sugars. Studies of the catalytic mechanism of the best
           known member of the family, galactose mutarotase, have
           shown a glutamate and a histidine residue to be critical
           for catalysis; the glutamate serves as the active site
           base to initiate the reaction by removing the proton
           from the C-1 hydroxyl group of the sugar substrate, and
           the histidine as the active site acid to protonate the
           C-5 ring oxygen.
          Length = 273

 Score = 26.9 bits (60), Expect = 0.89
 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 5/27 (18%)

Query: 49  CPLCSYRAKQKIHLTTH-----MAIRH 70
            P  +YRA+Q+ HL        +++ +
Sbjct: 104 DPPWAYRAEQRFHLAGDGLSITLSVTN 130


>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain. 
          Length = 24

 Score = 24.9 bits (55), Expect = 1.1
 Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 1/25 (4%)

Query: 47 YRCPLCSYRAKQKIHLTTHMAIRHH 71
          Y+C  C Y +  K  L  H+ + H 
Sbjct: 1  YKCSHCPYSSTPK-KLERHLKLHHG 24


>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
           Zn-ribbon domain [General function prediction only].
          Length = 421

 Score = 25.4 bits (56), Expect = 3.3
 Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 9/51 (17%)

Query: 13  KGGGLFSCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLCSYRAKQKIHLT 63
            G   F C  C      +A  T  +      +P    P  + R     HL+
Sbjct: 363 AGRNGFRCKKCGT----RARETLIKEVPRDLEPGVEVPPVARR-----HLS 404


>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger. 
          Length = 23

 Score = 23.6 bits (51), Expect = 3.8
 Identities = 10/22 (45%), Positives = 10/22 (45%)

Query: 47 YRCPLCSYRAKQKIHLTTHMAI 68
          YRCP C    K K  L  HM  
Sbjct: 1  YRCPECGKVFKSKSALREHMRT 22


>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family.  This family represents a
           domain found in eukaryotes and prokaryotes. The domain
           contains a characteristic motif of the zinc
           metallopeptidases. This family includes the bacterial
           SprT protein.
          Length = 153

 Score = 24.6 bits (54), Expect = 5.2
 Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 9/34 (26%)

Query: 19  SCSDCSRVYKKKASLTRHQTYECGQQPKYRCPLC 52
            C  C ++Y +K  + RH         KYRC  C
Sbjct: 121 RCGSCGQLYPRKRRIRRH---------KYRCGRC 145


  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
   0.325    0.136    0.439 

Gapped
Lambda     K      H
   0.267   0.0655    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,620,820
Number of extensions: 242010
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 350
Number of HSP's successfully gapped: 27
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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: 40 (21.6 bits)
S2: 53 (24.3 bits)