RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15613
         (219 letters)



>gnl|CDD|190706 pfam03662, Glyco_hydro_79n, Glycosyl hydrolase family 79,
           N-terminal domain.  Family of endo-beta-N-glucuronidase,
           or heparanase. Heparan sulfate proteoglycans (HSPGs)
           play a key role in the self- assembly, insolubility and
           barrier properties of basement membranes and
           extracellular matrices. Hence, cleavage of heparan
           sulfate (HS) affects the integrity and functional state
           of tissues and thereby fundamental normal and
           pathological phenomena involving cell migration and
           response to changes in the extracellular
           micro-environment. Heparanase degrades HS at specific
           intra-chain sites. The enzyme is synthesised as a latent
           approximately 65 kDa protein that is processed at the
           N-terminus into a highly active approximately 50 kDa
           form. Experimental evidence suggests that heparanase may
           facilitate both tumour cell invasion and
           neovascularization, both critical steps in cancer
           progression. The enzyme is also involved in cell
           migration associated with inflammation and autoimmunity.
          Length = 320

 Score = 31.6 bits (72), Expect = 0.27
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 107 GETGSCVGGGVEGLTDTFAASFLWIDKLG 135
           GE G     G   +++TF  SF ++D+LG
Sbjct: 292 GEAGGAYNSGGNLVSNTFINSFWYLDQLG 320


>gnl|CDD|130605 TIGR01542, A118_put_portal, phage portal protein, putative, A118
           family.  This model represents a family of phage minor
           structural proteins. The protein is suggested to be the
           head-tail connector, or portal protein, on the basis of
           its position in the phage gene order, its presence in
           mature phage, its size, and its conservation across a
           number of complete genomes of tailed phage that lack
           other candidate portal proteins. Several other known
           portal protein families lack clear homology to this
           family and to each other [Mobile and extrachromosomal
           element functions, Prophage functions].
          Length = 476

 Score = 28.0 bits (62), Expect = 4.0
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 155 YSLLDWNTLEPNPDWWLSVLYKRLVDPRVLNISVPLSHRTLRLYVQCSPAHNITVFGINS 214
           Y+LL+++  + + D+ ++    R  DP  +   VPL+     LY    P   +T      
Sbjct: 168 YTLLEFHEWQGHDDYVITNELYRSDDPNEVGTKVPLT----ELYDDLEPVVKLT--DFTR 221

Query: 215 PSFLY 219
           P+F+Y
Sbjct: 222 PTFIY 226


>gnl|CDD|223552 COG0476, ThiF, Dinucleotide-utilizing enzymes involved in
           molybdopterin and thiamine biosynthesis family 2
           [Coenzyme metabolism].
          Length = 254

 Score = 27.0 bits (60), Expect = 7.2
 Identities = 11/58 (18%), Positives = 23/58 (39%)

Query: 111 SCVGGGVEGLTDTFAASFLWIDKLGLAARLGVSVVVRQSLEFGNYSLLDWNTLEPNPD 168
           SC   GV G       S   ++ + L   +G+  ++ + L +    +  + TL+    
Sbjct: 188 SCDEAGVLGPLVGVVGSLQALEAIKLLTGIGLEPLIGRLLLYDALDMERFRTLKLRRR 245


  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
   0.323    0.140    0.451 

Gapped
Lambda     K      H
   0.267   0.0685    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,473,987
Number of extensions: 1074000
Number of successful extensions: 758
Number of sequences better than 10.0: 1
Number of HSP's gapped: 758
Number of HSP's successfully gapped: 7
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.8 bits)