RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5514
         (124 letters)



>gnl|CDD|219316 pfam07162, B9-C2, Ciliary basal body-associated, B9 protein.  The
           B9-C2 domain is found in proteins associated with the
           ciliary basal body. B9 domains were identified as a
           specific family of C2 domains. There are three
           sub-families represented by this family, notably,
           Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins.
           Mutations in human Mks1 result in the developmental
           disorder Mechler-Gruber syndrome; mutations in mouse
           Stumpy lead to perinatal hydrocephalus and severe
           polycystic kidney disease. All the three distinct types
           of B9-C2 proteins cooperatively localise to the basal
           body or centrosome of cilia.
          Length = 165

 Score = 90.0 bits (224), Expect = 5e-24
 Identities = 25/69 (36%), Positives = 42/69 (60%)

Query: 52  GIEEGISQISKHTAGCPQFVWNFPIEIVFKSNNPHGWPQLILCVYGLDGFGNDVIRGYGL 111
           G+  G +Q ++        V+N P ++  K+ NP GWPQL++ V+ LD +G + + GYG 
Sbjct: 36  GLTSGQTQTARSAGNDDVAVFNHPFDLHLKTTNPFGWPQLVVTVWSLDSWGRERLEGYGA 95

Query: 112 CHLPISSGT 120
           CH+P++ G 
Sbjct: 96  CHVPLTPGK 104


>gnl|CDD|203694 pfam07600, DUF1564, Protein of unknown function (DUF1564).  A
           family of paralogous proteins in Leptospira interrogans.
           Several have been annotated as possible CopG-like
           transcriptional regulators (see pfam01402).
          Length = 167

 Score = 28.1 bits (63), Expect = 0.95
 Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 7/39 (17%)

Query: 41  LGVSR-----YLRKLFGIEEGISQISKHTAGCPQFVWNF 74
            GVSR     YL  L G+ +  S +     G P F  ++
Sbjct: 103 HGVSRCYLFNYLLWLDGVGD--SIVKTLNRGVPTFHRSY 139


>gnl|CDD|223022 PHA03248, PHA03248, DNA packaging tegument protein UL25;
           Provisional.
          Length = 583

 Score = 28.1 bits (63), Expect = 1.4
 Identities = 6/22 (27%), Positives = 13/22 (59%)

Query: 1   MFAQYTVNVYGSCKQLHITQLF 22
           +  +Y   +Y +  ++ +TQLF
Sbjct: 445 LCERYVAPLYRADPRVELTQLF 466


>gnl|CDD|224627 COG1713, COG1713, Predicted HD superfamily hydrolase involved in
           NAD metabolism [Coenzyme metabolism].
          Length = 187

 Score = 27.3 bits (61), Expect = 1.8
 Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 3/31 (9%)

Query: 43  VSRY-LRKLFGI--EEGISQISKHTAGCPQF 70
           V  Y L++ FGI  EE +S I  HT G  Q 
Sbjct: 86  VGAYLLKEEFGIKDEEVLSAIEYHTTGRKQM 116


>gnl|CDD|215189 PLN02330, PLN02330, 4-coumarate--CoA ligase-like 1.
          Length = 546

 Score = 27.3 bits (60), Expect = 2.5
 Identities = 12/26 (46%), Positives = 13/26 (50%)

Query: 99  DGFGNDVIRGYGLCHLPISSGTTAKQ 124
           D   N+ I    LC LP SSGTT   
Sbjct: 174 DTSDNEEILQTDLCALPFSSGTTGIS 199


>gnl|CDD|185724 cd08983, GH43_4, Glycosyl hydrolase family 43.  This glycosyl
           hydrolase family 43 (GH43) includes enzymes with
           beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
           3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
           alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
           (EC 3.2.1.99), xylanase (EC 3.2.1.8),
           endo-alpha-L-arabinanase and galactan
           1,3-beta-galactosidase (EC 3.2.1.145) activities. These
           are inverting enzymes (i.e. they invert the
           stereochemistry of the anomeric carbon atom of the
           substrate) that have an aspartate as the catalytic
           general base, a glutamate as the catalytic general acid
           and another aspartate that is responsible for pKa
           modulation and orienting the catalytic acid. Many of the
           enzymes in this family display both
           alpha-L-arabinofuranosidase and beta-D-xylosidase
           activity using aryl-glycosides as substrates. A common
           structural feature of GH43 enzymes is a 5-bladed
           beta-propeller domain that contains the catalytic acid
           and catalytic base. A long V-shaped groove, partially
           enclosed at one end, forms a single extended
           substrate-binding surface across the face of the
           propeller.
          Length = 276

 Score = 26.9 bits (60), Expect = 2.7
 Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 11/48 (22%)

Query: 64  TAGCPQFVWNFPIE--IVFKSNNPHGWPQLILCVYGLDGFGNDVIRGY 109
             G     W   +E   VFK NN  GW      +YG D +      GY
Sbjct: 174 IVGTGDAGWGGAVEGPTVFKLNNGGGW-----YLYG-DNYSG---GGY 212


>gnl|CDD|204134 pfam09102, Exotox-A_target, Exotoxin A, targeting.  Members of
          this family are found in Pseudomonas aeruginosa
          exotoxin A, and are responsible for transmembrane
          targeting of the toxin, as well as transmembrane
          translocation of the catalytic domain into the
          cytoplasmic compartment. A furin cleavage site is
          present within the domain: cleavage generates a 37 kDa
          carboxy-terminal fragment, which includes the enzymatic
          domain, which is then is translocated into the
          cytoplasm. The domain adopts a helical structure, with
          six alpha-helices forming a bundle.
          Length = 143

 Score = 26.6 bits (58), Expect = 3.2
 Identities = 5/22 (22%), Positives = 7/22 (31%)

Query: 75 PIEIVFKSNNPHGWPQLILCVY 96
          P+E   +   P        C Y
Sbjct: 17 PLETFARHRKPRDLEDDEQCAY 38


>gnl|CDD|151902 pfam11463, R-HINP1I, R.HinP1I restriction endonuclease.  Hinp1I
          is a type II restriction endonuclease, recognising and
          cleaving a palindromic tetranucleotide sequence (G/CGC)
          resulting in 2 nt 5' overhanging ends. HINP1I has a
          conserved catalytic core domain containing an active
          site motif SDC18QXK and a DNA-binding domain.
          Length = 205

 Score = 26.4 bits (58), Expect = 4.8
 Identities = 12/30 (40%), Positives = 15/30 (50%)

Query: 49 KLFGIEEGISQISKHTAGCPQFVWNFPIEI 78
          KL   + G +QI K      Q +WNFP  I
Sbjct: 43 KLVSNKRGFNQIDKRWLAHYQEMWNFPDNI 72


>gnl|CDD|241245 cd01209, PTB_Shc, Shc-like phosphotyrosine-binding (PTB) domain. 
          Shc is a substrate for receptor tyrosine kinases, which
          can interact with phosphoproteins at NPXY motifs. Shc
          contains an PTB domain followed by an SH2 domain. PTB
          domains have a common PH-like fold and are found in
          various eukaryotic signaling molecules. This domain was
          initially shown to binds peptides with a NPXY motif
          with differing requirements for phosphorylation of the
          tyrosine, although more recent studies have found that
          some types of PTB domains can bind to peptides lack
          tyrosine residues altogether. In contrast to SH2
          domains, which recognize phosphotyrosine and adjacent
          carboxy-terminal residues, PTB-domain binding
          specificity is conferred by residues amino-terminal to
          the phosphotyrosine.  PTB domains are classified into
          three groups: phosphotyrosine-dependent Shc-like,
          phosphotyrosine-dependent IRS-like, and
          phosphotyrosine-independent Dab-like PTB domains. This
          cd is part of the Shc-like subgroup.
          Length = 170

 Score = 26.0 bits (58), Expect = 5.3
 Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 3/21 (14%)

Query: 33 GVC---RYLGCLGVSRYLRKL 50
          GV    RY+GC+ V + +R L
Sbjct: 14 GVSYPVRYMGCIEVLQSMRSL 34


>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
           Every known example of the phenylalanyl-tRNA
          synthetase, except the monomeric form of mitochondrial,
          is an alpha 2 beta 2 heterotetramer. The beta subunits
          break into two subfamilies that are considerably
          different in sequence, length, and pattern of gaps.
          This model represents the subfamily that includes the
          beta subunit from eukaryotic cytosol, the Archaea, and
          spirochetes [Protein synthesis, tRNA aminoacylation].
          Length = 551

 Score = 26.3 bits (58), Expect = 5.4
 Identities = 9/20 (45%), Positives = 12/20 (60%)

Query: 37 YLGCLGVSRYLRKLFGIEEG 56
           L   G++R LR   GIE+G
Sbjct: 55 LLSVEGLARSLRGYLGIEKG 74


>gnl|CDD|222734 pfam14397, ATPgrasp_ST, Sugar-transfer associated ATP-grasp.  A
           member of the ATP-grasp fold predicted to be involved in
           the biosynthesis of cell surface polysaccharides.
          Length = 284

 Score = 25.8 bits (57), Expect = 7.9
 Identities = 9/43 (20%), Positives = 14/43 (32%)

Query: 47  LRKLFGIEEGISQISKHTAGCPQFVWNFPIEIVFKSNNPHGWP 89
             K F ++E I Q    +   P  V    I  ++     H   
Sbjct: 111 NEKGFVVQERIRQHHGMSKLNPSSVNTLRIVTLYDDGKVHILY 153


>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
          Length = 470

 Score = 25.4 bits (56), Expect = 9.2
 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 20  QLFKIGHTEVGTLGVC-RYLGCLGVSRYLRKL 50
           QL K  +T  GTL  C R+L  LG  R+L  L
Sbjct: 393 QLLKHINTNFGTLAFCRRWLDRLGQDRHLLAL 424


  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
   0.326    0.144    0.478 

Gapped
Lambda     K      H
   0.267   0.0696    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,219,584
Number of extensions: 530483
Number of successful extensions: 476
Number of sequences better than 10.0: 1
Number of HSP's gapped: 476
Number of HSP's successfully gapped: 19
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)