RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5045
         (407 letters)



>gnl|CDD|218330 pfam04925, SHQ1, SHQ1 protein.  S. cerevisiae SHQ1 protein is
           required for SnoRNAs of the box H/ACA Quantitative
           accumulation (unpublished).
          Length = 185

 Score =  138 bits (349), Expect = 5e-39
 Identities = 50/116 (43%), Positives = 74/116 (63%), Gaps = 2/116 (1%)

Query: 234 RQAQDDRTQMTPSELDTMKQLGNREYLLSSEEKCAVLLSLVNILYAYCYDVRTTMGEHTV 293
           +   +   + T  E + ++ L  + YL+  +++  V L LV+IL+AYCYD R T GEH V
Sbjct: 5   KSKFNLPVEFTDEEQEQLRNLPKKSYLIDDKKE--VYLGLVDILFAYCYDQRVTEGEHNV 62

Query: 294 ESGWTVNKLSSALCWLQSFTSLKQVLISSMRRSLCYPLYREWRLSCAIQQDVNTIL 349
           ES WT+ KLS  L WL SF+++K  LI+ +RR+L YPLYR + L+  + +DV  IL
Sbjct: 63  ESAWTIGKLSPQLSWLDSFSNVKDALIAFIRRALTYPLYRNFDLAQKVWKDVYYIL 118


>gnl|CDD|107220 cd06463, p23_like, Proteins containing this p23_like domain
          include p23 and its Saccharomyces cerevisiae (Sc)
          homolog Sba1. Both are co-chaperones for the heat shock
          protein (Hsp) 90.  p23 binds Hsp90 and participates in
          the folding of a number of Hsp90 clients, including the
          progesterone receptor. p23 also has a passive
          chaperoning activity and in addition may participate in
          prostaglandin synthesis.  Both p23 and Sba1p can
          regulate telomerase activity. This group includes
          domains similar to the C-terminal CHORD-SGT1 (CS)
          domain of suppressor of G2 allele of Skp1 (Sgt1). Sgt1
          interacts with multiple protein complexes and has the
          features of a co-chaperone. Human (h) Sgt1 interacts
          with both Hsp70 and Hsp90, and has been shown to bind
          Hsp90 through its CS domain.  Saccharomyces cerevisiae
          (Sc) Sgt1 is a subunit of both core kinetochore and SCF
          (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is
          required for pathogen resistance in plants.  This group
          also includes the p23_like domains of human
          butyrate-induced transcript 1 (hB-ind1), NUD (nuclear
          distribution) C, Melusin, and NAD(P)H cytochrome b5
          (NCB5) oxidoreductase (OR). hB-ind1 plays a role in the
          signaling pathway mediated by the small GTPase Rac1,
          NUDC is needed for nuclear movement, Melusin interacts
          with two splice variants of beta1 integrin, and NCB5OR
          plays a part in maintaining viable pancreatic beta
          cells.
          Length = 84

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 10 QSEEDVTIIIKAPYANIADTEVYVEDTDFRFS-----SSPYYLRLNFPGPIKETDHTSGK 64
          Q+ ++VTI I        D +V         S        Y L     GPI   D    K
Sbjct: 3  QTLDEVTITIPLKDVTKKDVKVEFTPKSLTVSVKGGGGKEYLLEGELFGPI---DPEESK 59

Query: 65 YDSDKGQFTFTVIKVNTGEHFPDL 88
          +  +  +   T+ K   GE +P L
Sbjct: 60 WTVEDRKIEITLKKKEPGEWWPRL 83


>gnl|CDD|240251 PTZ00063, PTZ00063, histone deacetylase; Provisional.
          Length = 436

 Score = 32.1 bits (73), Expect = 0.56
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 80  NTGEHFPDLDLISKLLIPPVKHRVAKPGIEVMSEPNNVSDEDEDEDDDTMW 130
           N+ EH   L+ I   ++  +++    PG++    P +  D D D++D+   
Sbjct: 353 NSPEH---LEKIKVKILENLRYLEHAPGVQFAYVPPDFFDRDIDDEDEKNQ 400


>gnl|CDD|107219 cd00298, ACD_sHsps_p23-like, This domain family includes the
          alpha-crystallin domain (ACD) of alpha-crystallin-type
          small heat shock proteins (sHsps) and a similar domain
          found in p23-like proteins.  sHsps are small stress
          induced proteins with monomeric masses between 12 -43
          kDa, whose common feature is this ACD. sHsps are
          generally active as large oligomers consisting of
          multiple subunits, and are believed to be
          ATP-independent chaperones that prevent aggregation and
          are important in refolding in combination with other
          Hsps. p23 is a cochaperone of the Hsp90 chaperoning
          pathway. It binds Hsp90 and participates in the folding
          of a number of Hsp90 clients including the progesterone
          receptor. p23 also has a passive chaperoning activity.
          p23 in addition may act as the cytosolic prostaglandin
          E2 synthase. Included in this family is the p23-like
          C-terminal CHORD-SGT1 (CS) domain of suppressor of G2
          allele of Skp1 (Sgt1) and  the p23-like domains of
          human butyrate-induced transcript 1 (hB-ind1), NUD
          (nuclear distribution) C, Melusin, and NAD(P)H
          cytochrome b5 (NCB5) oxidoreductase (OR).
          Length = 80

 Score = 29.1 bits (66), Expect = 0.77
 Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 15/81 (18%)

Query: 10 QSEEDVTIIIKAPYANIADTEVYVEDTDFRFS------------SSPYYLRLNFPGPIKE 57
          Q++++V + +  P     D +V VED     S               +      P  +  
Sbjct: 3  QTDDEVVVTVDLPGVKKEDIKVEVEDNVLTISGKREEEEERERSYGEFERSFELPEDVDP 62

Query: 58 TDHTSGKYDSDKGQFTFTVIK 78
           + +    ++  G    T+ K
Sbjct: 63 -EKSKASLEN--GVLEITLPK 80


>gnl|CDD|234279 TIGR03607, TIGR03607, patatin-related protein.  This bacterial
           protein family contains an N-terminal patatin domain,
           where patatins are plant storage proteins capable of
           phospholipase activity (see pfam01734). Regions of
           strong sequence conservation are separated by regions of
           significant sequence and length variability. Members of
           the family are distributed sporadically among bacteria.
           The function is unknown [Unknown function, General].
          Length = 739

 Score = 29.7 bits (67), Expect = 3.0
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 10/47 (21%)

Query: 29  TEVYVEDTDFRFSSSPYYLRLNFPGPIKETDHTSGKYDSDKGQFTFT 75
            +++V  TD R  S+   L  +    ++E +H         G F FT
Sbjct: 161 LDLFVTATDLRGRSTR--LFDDDGTVVEEREHR--------GVFRFT 197


>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D.  This
           model represents one of two ATPase subunits of the
           trimeric magnesium chelatase responsible for insertion
           of magnesium ion into protoporphyrin IX. This is an
           essential step in the biosynthesis of both chlorophyll
           and bacteriochlorophyll. This subunit is found in green
           plants, photosynthetic algae, cyanobacteria and other
           photosynthetic bacteria. Unlike subunit I (TIGR02030),
           this subunit is not found in archaea [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Chlorophyll
           and bacteriochlorphyll].
          Length = 589

 Score = 29.0 bits (65), Expect = 4.7
 Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 87  DLDLISKLLIPPVKHRV----AKPGIEVMSEPNNVSDEDEDEDDDTMWFIEQEPQHQPEE 142
           DL L  +L++ P   R+     +P            +E+ DE D T     +E    PEE
Sbjct: 250 DLKLAVELVLLPRATRLPEPEPQPPPPPPPPEPPEPEEEPDEPDQTDPDDGEETDQIPEE 309


>gnl|CDD|239625 cd03568, VHS_STAM, VHS domain family, STAM subfamily; members
           include STAM (Signal Transducing Adaptor Molecule), EAST
           (EGFR-associated protein with SH3 and TAM domains) and
           Hbp (Hrs-binding protein). Collectively, they are
           referred to as STAM. All STAMs have at their N-termini a
           VHS domain, which is involved in cytokine-mediated
           intracellular signal transduction and has a superhelical
           structure similar to the structure of ARM (Armadillo)
           repeats, followed by a SH3 (Src homology 3) domain, a
           well-established protein-protein interaction domain. At
           the C-termini of most vertebrate STAMS, an ITAM
           (Immunoreceptor Tyrosine-based Activation) motif is
           present, which mediates the binding of HRS (hepatocyte
           growth factor-regulated tyrosine kinase substrate) in
           endocytic and exocytic machineries.
          Length = 144

 Score = 28.0 bits (63), Expect = 5.2
 Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 224 VVSRDYASDVRQAQDDRTQMTPSE--LDTMKQL 254
           V SRD+  ++++  +DR   T  E   + +KQ 
Sbjct: 76  VASRDFTQELKKLINDRVHPTVKEKLREVVKQW 108


>gnl|CDD|238082 cd00140, beta_clamp, Beta clamp domain.  The beta subunit
           (processivity factor) of DNA polymerase III holoenzyme,
           refered to as the beta clamp, forms a ring shaped dimer
           that encircles dsDNA (sliding clamp) in bacteria.  The
           beta-clamp is structurally similar to the trimeric ring
           formed by PCNA (found in eukaryotes and archaea) and the
           processivity factor (found in bacteriophages T4 and
           RB69).  This structural correspondence further
           substantiates the mechanistic connection between
           eukaryotic and prokaryotic DNA replication that has been
           suggested on biochemical grounds. .
          Length = 365

 Score = 28.2 bits (64), Expect = 7.4
 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 3/25 (12%)

Query: 162 MKVTISKSDLGFDLEELETAARIVE 186
           MK TI++  L   LE L+  +R +E
Sbjct: 1   MKFTINREAL---LEALQKVSRAIE 22


>gnl|CDD|214602 smart00292, BRCT, breast cancer carboxy-terminal domain. 
          Length = 78

 Score = 26.2 bits (58), Expect = 8.0
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 159 LTNMKVTISKSDLGFDLEELETAARIVEEE--EVERALCNHVSTLVLCSNSEQSERSIIF 216
                  I+ S    + +EL+    ++E    +V  +L +  +T V+  + E  +  ++ 
Sbjct: 4   FKGKTFYITGSFDKEERDELK---ELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLK 60

Query: 217 FIGLDFWVVSRDY 229
            I L   +V  ++
Sbjct: 61  AIALGIPIVKEEW 73


>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
           subunit.  This is a family of proteins which are
           subunits of the eukaryotic translation initiation factor
           3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
           cerevisiae protein eIF3j (HCR1) has been shown to be
           required for processing of 20S pre-rRNA and binds to 18S
           rRNA and eIF3 subunits Rpg1p and Prt1p.
          Length = 242

 Score = 27.7 bits (62), Expect = 8.9
 Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 18/77 (23%)

Query: 120 EDEDEDDDTM--WFIEQEPQHQPEENSTTYGYGFANKTKGTLTNMKVTISKSDLGFDLEE 177
           +DEDEDDD    W  E++ + + E+         A K K           K  L   +EE
Sbjct: 25  DDEDEDDDVKDSWDEEEDEEKEEEKAKV------AAKAKA----------KKALKAKIEE 68

Query: 178 LETAARIVEEEEVERAL 194
            E A R  EE+ +    
Sbjct: 69  KEKAKREKEEKGLRELE 85


>gnl|CDD|173022 PRK14557, pyrH, uridylate kinase; Provisional.
          Length = 247

 Score = 27.9 bits (62), Expect = 9.9
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 9/61 (14%)

Query: 346 NTILSQDILGYKVMKQVTISKS-DLG-----FDLDELETAARIVEEEEVERALCNHVSTL 399
           N ++ Q+I   +VM Q  +  + D       F+ DE     RI   E V   + +  S L
Sbjct: 187 NDVVRQNI---QVMDQAALLLARDYNLPAHVFNFDEPGVMRRICLGEHVGTLINDDASLL 243

Query: 400 V 400
           V
Sbjct: 244 V 244


  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
   0.316    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0697    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,191,527
Number of extensions: 1913359
Number of successful extensions: 2069
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2065
Number of HSP's successfully gapped: 22
Length of query: 407
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 308
Effective length of database: 6,546,556
Effective search space: 2016339248
Effective search space used: 2016339248
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 (21.6 bits)
S2: 60 (27.0 bits)