RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8096
         (118 letters)



>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
           domain.  Putative methyl transferase, based on outlier
           plant homologues.
          Length = 124

 Score =  107 bits (268), Expect = 3e-31
 Identities = 43/91 (47%), Positives = 54/91 (59%), Gaps = 1/91 (1%)

Query: 14  VIRASVSDKREKQYMDKGI-GCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEI 72
           +I +  +++R K Y   G    Y+F ID    IDA  KGN ARFINHSC+PNC    VE+
Sbjct: 34  IITSEEAEERPKAYDTDGAKAFYLFDIDSDLCIDARRKGNLARFINHSCEPNCELLFVEV 93

Query: 73  MGKPHIIIFALRKINKGEELTYDYKFPIEDD 103
            G   I+IFALR I  GEELT DY     ++
Sbjct: 94  NGDDRIVIFALRDIKPGEELTIDYGSDYANE 124


>gnl|CDD|216155 pfam00856, SET, SET domain.  SET domains are protein lysine
           methyltransferase enzymes. SET domains appear to be
           protein-protein interaction domains. It has been
           demonstrated that SET domains mediate interactions with
           a family of proteins that display similarity with
           dual-specificity phosphatases (dsPTPases). A subset of
           SET domains have been called PR domains. These domains
           are divergent in sequence from other SET domains, but
           also appear to mediate protein-protein interaction. The
           SET domain consists of two regions known as SET-N and
           SET-C. SET-C forms an unusual and conserved knot-like
           structure of probably functional importance.
           Additionally to SET-N and SET-C, an insert region
           (SET-I) and flanking regions of high structural
           variability form part of the overall structure.
          Length = 113

 Score = 92.2 bits (229), Expect = 1e-25
 Identities = 37/84 (44%), Positives = 51/84 (60%)

Query: 13  AVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDATMKGNAARFINHSCDPNCYSRVVEI 72
           A  R  + +K E + +   +  ++ ++D  + IDAT  GN ARFINHSC+PNC  R V +
Sbjct: 29  AEERELLYNKEELRGLLSDLELFLSRLDSEYDIDATGLGNVARFINHSCEPNCEVRFVFV 88

Query: 73  MGKPHIIIFALRKINKGEELTYDY 96
            G   I++ ALR I  GEELT DY
Sbjct: 89  NGGDRIVVRALRDIKPGEELTIDY 112


>gnl|CDD|225491 COG2940, COG2940, Proteins containing SET domain [General function
           prediction only].
          Length = 480

 Score = 77.2 bits (190), Expect = 9e-18
 Identities = 42/116 (36%), Positives = 59/116 (50%), Gaps = 13/116 (11%)

Query: 14  VIRASVSDKREKQYMDKGIGCYMFK---IDDRFVIDATMKGNAARFINHSCDPNCYSRVV 70
           +IR   + +RE+ Y    +G         D   V D+   G+ ARFINHSC PNC +  +
Sbjct: 365 IIRRKEAREREENYDL--LGNEFSFGLLEDKDKVRDSQKAGDVARFINHSCTPNCEASPI 422

Query: 71  EIMGKPHIIIFALRKINKGEELTYDYKFPIEDDN--------KISCHCLAMRCTNN 118
           E+ G   I I+A+R I  GEELTYDY   +ED+         +  C C   RC++ 
Sbjct: 423 EVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478


>gnl|CDD|236530 PRK09466, metL, bifunctional aspartate kinase II/homoserine
          dehydrogenase II; Provisional.
          Length = 810

 Score = 28.7 bits (65), Expect = 0.79
 Identities = 6/12 (50%), Positives = 7/12 (58%)

Query: 62 DPNCYSRVVEIM 73
          D  CY RV  I+
Sbjct: 24 DAKCYRRVAGIL 35


>gnl|CDD|239924 cd04478, RPA2_DBD_D, RPA2_DBD_D: A subfamily of OB folds
           corresponding to the OB fold of the central
           ssDNA-binding domain (DBD)-D of human RPA2 (also called
           RPA32). RPA2 is a subunit of Replication protein A
           (RPA). RPA is a nuclear ssDNA-binding protein (SSB)
           which appears to be involved in all aspects of DNA
           metabolism including replication, recombination, and
           repair. RPA also mediates specific interactions of
           various nuclear proteins. In animals, plants, and fungi,
           RPA is a heterotrimer with subunits of 70KDa (RPA1),
           32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding
           activity of RPA is associated with RPA1 DBD-A and DBD-B;
           RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is
           also involved in trimerization. The ssDNA binding
           mechanism is believed to be multistep and to involve
           conformational change. N-terminal to human RPA2 DBD-D is
           a domain containing all the known phosphorylation sites
           of RPA. Human RPA2 is phosphorylated in a cell cycle
           dependent manner in response to DNA damage. RPA2
           interacts physically with menin; the gene encoding menin
           is a tumor suppressor gene disrupted in multiple
           endocrine neoplasia type I. This subfamily also includes
           RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an
           SSB, which can be phosphorylated by DNA-PK in vitro.
          Length = 95

 Score = 25.6 bits (57), Expect = 3.6
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 18/53 (33%)

Query: 63  PNCYSRVV----EIMGKPHIIIFALRKINKGEELTYDYKFPIEDDNKISCHCL 111
              Y RV        GK  I+ F++R              P+ D N+++ H L
Sbjct: 50  EGTYVRVFGNLKSFQGKKSIMAFSIR--------------PVTDFNEVTYHLL 88


>gnl|CDD|200387 TIGR04136, rSAM_FibroRumin, radical SAM peptide maturase,
           FibroRumin system.  Members of this protein family are
           radical SAM enzymes proposed to act on small, Cys-rich
           peptides encoded by tandem gene pairs. Members occur in
           enzymes Fibrobacter succinogenes subsp. succinogenes S85
           (genes for their target peptides missed) and in
           Ruminococcus albus 8. This enzyme family is similar in
           sequence to the SCIFF (Six Cysteines in Forty-Five)
           system maturase (TIGR03974).
          Length = 458

 Score = 26.5 bits (58), Expect = 4.4
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 6   SVSVTLM--AVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDATMKGNAARFI 57
           S+S+TL    +           +Y  KG+G  +   DDRF + A     AA+FI
Sbjct: 258 SLSITLSEETIKDQQDVIDLIDEYGIKGLGFNIMMGDDRFPLPADYNDKAAQFI 311


>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
          Members of this group possess KH domains in a tandem
          arrangement. Most members, similar to the poly(C)
          binding proteins (PCBPs) and Nova, containing three KH
          domains, with the first and second domains, which are
          represented here, in tandem arrangement, followed by a
          large spacer region, with the third domain near the
          C-terminal end of the protein. The poly(C) binding
          proteins (PCBPs) can be divided into two groups, hnRNPs
          K/J and the alphaCPs, which share a triple KH domain
          configuration and  poly(C) binding specificity. They
          play roles in mRNA stabilization, translational
          activation, and translational silencing. Nova-1 and
          Nova-2 are nuclear RNA-binding proteins that regulate
          splicing. This group also contains plant proteins that
          seem to have two tandem repeat arrrangements, like
          Hen4, a protein that plays a role in  AGAMOUS (AG)
          pre-mRNA processing and important step in plant
          development. In general, KH binds single-stranded RNA
          or DNA. It is found in a wide variety of proteins
          including ribosomal proteins, transcription factors and
          post-transcriptional modifiers of mRNA.
          Length = 65

 Score = 24.4 bits (54), Expect = 6.6
 Identities = 12/27 (44%), Positives = 13/27 (48%)

Query: 60 SCDPNCYSRVVEIMGKPHIIIFALRKI 86
          S  P    RVV I GKP  +  AL  I
Sbjct: 38 SVLPGSTERVVTISGKPSAVQKALLLI 64


>gnl|CDD|223238 COG0160, GabT, 4-aminobutyrate aminotransferase and related
          aminotransferases [Amino acid transport and
          metabolism].
          Length = 447

 Score = 25.6 bits (57), Expect = 8.2
 Identities = 6/36 (16%), Positives = 13/36 (36%)

Query: 13 AVIRASVSDKREKQYMDKGIGCYMFKIDDRFVIDAT 48
            +  S    R    + +  G Y++ +D    +D  
Sbjct: 27 EALARSYGRFRFPLVIVRAEGAYLYDVDGNEYLDFL 62


>gnl|CDD|233100 TIGR00713, hemL, glutamate-1-semialdehyde-2,1-aminomutase.  This
          enzyme, glutamate-1-semialdehyde-2,1-aminomutase
          (glutamate-1-semialdehyde aminotransferase, GSA
          aminotransferase), contains a pyridoxal phosphate
          attached at a Lys residue at position 283 of the seed
          alignment. It is in the family of class III
          aminotransferases [Biosynthesis of cofactors,
          prosthetic groups, and carriers, Heme, porphyrin, and
          cobalamin].
          Length = 423

 Score = 25.4 bits (56), Expect = 8.4
 Identities = 9/32 (28%), Positives = 16/32 (50%)

Query: 15 IRASVSDKREKQYMDKGIGCYMFKIDDRFVID 46
          +RA  S      ++ +G G Y++ +D    ID
Sbjct: 21 VRAFKSVGPTPFFVARGKGAYLYDVDGNEYID 52


>gnl|CDD|223759 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein
           [Amino acid transport and metabolism].
          Length = 363

 Score = 25.5 bits (56), Expect = 9.5
 Identities = 9/25 (36%), Positives = 10/25 (40%), Gaps = 2/25 (8%)

Query: 41  DRFVIDATMKG--NAARFINHSCDP 63
           D   I    K    A +FIN   DP
Sbjct: 271 DNLAIPKGAKNVDAAYKFINFLLDP 295


  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    0.138    0.425 

Gapped
Lambda     K      H
   0.267   0.0717    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,860,641
Number of extensions: 510387
Number of successful extensions: 501
Number of sequences better than 10.0: 1
Number of HSP's gapped: 500
Number of HSP's successfully gapped: 25
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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 (24.2 bits)