RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3735
         (91 letters)



>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain. 
          Length = 57

 Score = 49.0 bits (118), Expect = 1e-09
 Identities = 18/31 (58%), Positives = 20/31 (64%)

Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          RR RTTFT  QLEELEK F +  YP    R+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEERE 31


>gnl|CDD|197696 smart00389, HOX, Homeodomain.  DNA-binding factors that are
          involved in the transcriptional regulation of key
          developmental processes.
          Length = 57

 Score = 43.8 bits (104), Expect = 1e-07
 Identities = 17/32 (53%), Positives = 21/32 (65%)

Query: 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          +RR RT+FT  QLEELEK F +  YP    R+
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREERE 32


>gnl|CDD|238039 cd00086, homeodomain, Homeodomain;  DNA binding domains involved
          in the transcriptional regulation of key eukaryotic
          developmental processes; may bind to DNA as monomers or
          as homo- and/or heterodimers, in a sequence-specific
          manner.
          Length = 59

 Score = 43.0 bits (102), Expect = 2e-07
 Identities = 17/31 (54%), Positives = 19/31 (61%)

Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          RR RT FT  QLEELEK F +  YP    R+
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREERE 31


>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
          [Transcription].
          Length = 156

 Score = 32.4 bits (74), Expect = 0.014
 Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 6/53 (11%)

Query: 19 EDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMP 71
          +D +S PK K+RR     T  QL  LE+ F    YP   TR   + S   +MP
Sbjct: 45 QDGSSPPKSKRRR----TTDEQLMVLEREFEINPYPSSITRI--KLSLLLNMP 91


>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
          Length = 1034

 Score = 27.7 bits (62), Expect = 0.74
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 7/53 (13%)

Query: 7   GRGEEDVSE--GEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVF 57
           G  EE   E    ME +A     +   +  +  +FQL     A+ + HYP VF
Sbjct: 659 GHSEEKARELFDRMEKFAGYGFNRSHAFAYSALAFQL-----AYFKAHYPAVF 706


>gnl|CDD|240472 cd12892, SPRY_PRY_TRIM18, PRY/SPRY domain of TRIM18/MID1, also
          known as FXY or RNF59.  This domain, consisting of the
          distinct N-terminal PRY subdomain followed by the SPRY
          subdomain, is at the C-terminus of the overall domain
          architecture of MID1 (also known as FXY, RNF59, TRIM18)
          gene represented by a RING finger domain (RING), two
          B-box motifs (BBOX), coiled-coil C-terminal to Bbox
          domain (BBC) and fibronectin type 3 domain (FN3).
          Mutations in the human MID1 gene result in X-linked
          Opitz G/BBB syndrome (OS), a disorder affecting
          development of midline structures, causing
          craniofacial, urogenital, gastrointestinal and
          cardiovascular abnormalities. A unique MID1 gene
          mutation located in a variable loop in the SPRY domain
          alters conformation of the binding pocket and may
          affect the binding affinity to the PRY/SPRY domain.
          Length = 177

 Score = 26.9 bits (59), Expect = 1.5
 Identities = 10/36 (27%), Positives = 19/36 (52%)

Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          PK   R+ + +  +  +E  E +  ++H P+ FT Q
Sbjct: 6  PKSAHRKLKVSHDNLTVERDETSSKKSHTPERFTSQ 41


>gnl|CDD|239212 cd02846, PAZ_argonaute_like, PAZ domain, argonaute_like subfamily.
           Argonaute is part of the RNA-induced silencing complex
           (RISC), and is an endonuclease that plays a key role in
           the RNA interference pathway. The PAZ domain has been
           named after the proteins Piwi,Argonaut, and Zwille. PAZ
           is found in two families of proteins that are essential
           components of RNA-mediated gene-silencing pathways,
           including RNA interference, the Piwi and Dicer families.
           PAZ functions as a nucleic acid binding domain, with a
           strong preference for single-stranded nucleic acids (RNA
           or DNA) or RNA duplexes with single-stranded 3'
           overhangs. It has been suggested that the PAZ domain
           provides a unique mode for the recognition of the two
           3'-terminal nucleotides in single-stranded nucleic acids
           and buries the 3' OH group, and that it might recognize
           characteristic 3' overhangs in siRNAs within RISC
           (RNA-induced silencing) and other complexes.
          Length = 114

 Score = 26.5 bits (59), Expect = 1.6
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 4/51 (7%)

Query: 25  PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELC 75
             +   +  +    F+    EK   R  YP++   Q GR  +   +P ELC
Sbjct: 65  ELKDGEKEISVADYFK----EKYNIRLKYPNLPCLQVGRKGKPNYLPMELC 111


>gnl|CDD|217833 pfam03997, VPS28, VPS28 protein. 
          Length = 187

 Score = 25.5 bits (56), Expect = 3.9
 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)

Query: 41 LEELEKAFSRTHY-PDVFTRQCGRFSRQ 67
          LE+LEKA+ +    P  +T  C +   Q
Sbjct: 11 LEQLEKAYIKDCVSPSEYTSTCSKLIVQ 38


>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
           recombination, and repair].
          Length = 935

 Score = 25.2 bits (56), Expect = 5.4
 Identities = 10/23 (43%), Positives = 12/23 (52%)

Query: 29  QRRYRTTFTSFQLEELEKAFSRT 51
           +RRY  T +    EELEK  S  
Sbjct: 377 ERRYLETESESIREELEKYMSEK 399


>gnl|CDD|240497 cd13739, SPRY_PRY_TRIM1, PRY/SPRY domain of tripartite
          motif-binding protein 1 (TRIM1) or MID2.  This domain,
          consisting of the distinct N-terminal PRY subdomain
          followed by the SPRY subdomain, is found at the
          C-terminus of TRIM1 (also known as MID2 or midline 2).
          MID2 and its close homolog, TRIM18 (also known as
          MID1), both contain a B30.2-like domain at their
          C-terminus and a single fibronectin type III (FN3)
          motif between it and their N-terminal RBCC domain. MID2
          and MID1 coiled-coil motifs mediate both homo- and
          heterodimerization, a prerequisite for association of
          the rapamycin-sensitive PP2A regulatory subunit Alpha 4
          with microtubules. Mutations in MID1 have shown to
          cause Opitz syndrome, a disorder causing congenital
          anomalies such as cleft lip and palate as well as heart
          defects.
          Length = 168

 Score = 25.0 bits (54), Expect = 6.5
 Identities = 8/34 (23%), Positives = 19/34 (55%)

Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 58
          PK   ++ + +    Q+E+ E +  ++H P+ F+
Sbjct: 5  PKMAHKKLKISNDGLQMEKDESSLKKSHTPERFS 38


>gnl|CDD|176879 cd08870, START_STARD2_7-like, Lipid-binding START domain of
           mammalian STARD2, -7, and related proteins.  This
           subfamily includes the steroidogenic acute regulatory
           protein (StAR)-related lipid transfer (START) domains of
           STARD2 (also known as phosphatidylcholine transfer
           protein/PC-TP), and STARD7 (also known as gestational
           trophoblastic tumor 1/GTT1). The START domain family
           belongs to the SRPBCC
           (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
           superfamily of proteins that bind hydrophobic ligands.
           SRPBCC domains have a deep hydrophobic ligand-binding
           pocket. STARD2 is a cytosolic phosphatidycholine
           (PtdCho) transfer protein, which traffics PtdCho, the
           most common class of phospholipids in eukaryotes,
           between membranes. It represents a minimal START domain
           structure. STARD2 plays roles in hepatic cholesterol
           metabolism, in the development of atherosclerosis, and
           may also have a mitochondrial function. The gene
           encoding STARD7 is overexpressed in choriocarcinoma.
           STARD7 appears to be involved in the intracellular
           trafficking of PtdCho to mitochondria. STARD7 was shown
           to be surface active and to interact differentially with
           phospholipid monolayers. It showed a preference for
           phosphatidylserine, cholesterol, and
           phosphatidylglycerol.
          Length = 209

 Score = 25.0 bits (55), Expect = 6.8
 Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 8/65 (12%)

Query: 19  EDYASLPKRKQRRYRTTFTSFQLEELEKAFSRT-------HYPDV-FTRQCGRFSRQRSM 70
             Y S+P+  ++R     +S  +  ++     +       H PD    R+  + + +R M
Sbjct: 136 VPYPSVPRSGRKRVDDYESSLVIRAVKGDGQGSACEVTYFHNPDGGIPRELAKLAVKRGM 195

Query: 71  PGELC 75
           PG L 
Sbjct: 196 PGFLK 200


  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    0.130    0.394 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,655,576
Number of extensions: 364633
Number of successful extensions: 337
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 13
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
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 (21.8 bits)
S2: 53 (24.1 bits)