RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5411
         (88 letters)



>gnl|CDD|214560 smart00210, TSPN, Thrombospondin N-terminal -like domains.
           Heparin-binding and cell adhesion domain of
           thrombospondin.
          Length = 184

 Score = 26.6 bits (59), Expect = 1.5
 Identities = 15/51 (29%), Positives = 24/51 (47%)

Query: 28  TGKYFKFALKVTLDGVTAFVNCEEIESTRVVRNPQELLFDSASTLYLGQAG 78
            G++ K AL V+    T +V+C EI+S  + R  Q  +      +   QA 
Sbjct: 116 DGQWHKLALSVSGSSATLYVDCNEIDSRPLDRPGQPPIDTDGIEVRGAQAA 166


>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding
          protein 34 (RBM34) and similar proteins.  This
          subfamily corresponds to the RRM2 of RBM34, a putative
          RNA-binding protein containing two RNA recognition
          motifs (RRMs), also termed RBDs (RNA binding domains)
          or RNPs (ribonucleoprotein domains). Although the
          function of RBM34 remains unclear currently, its RRM
          domains may participate in mRNA processing. RBM34 may
          act as an mRNA processing-related protein. .
          Length = 73

 Score = 25.6 bits (57), Expect = 1.6
 Identities = 6/19 (31%), Positives = 13/19 (68%)

Query: 44 TAFVNCEEIESTRVVRNPQ 62
            F +C ++E+ R+VR+ +
Sbjct: 18 KHFEDCGDVEAVRIVRDRK 36


>gnl|CDD|234278 TIGR03606, non_repeat_PQQ, dehydrogenase, PQQ-dependent, s-GDH
           family.  PQQ, or pyrroloquinoline-quinone, serves as a
           cofactor for a number of sugar and alcohol
           dehydrogenases in a limited number of bacterial species.
           Most characterized PQQ-dependent enzymes have multiple
           repeats of a sequence region described by pfam01011 (PQQ
           enzyme repeat), but this protein family in unusual in
           lacking that repeat. Below the noise cutoff are related
           proteins mostly from species that lack PQQ biosynthesis.
          Length = 454

 Score = 26.8 bits (59), Expect = 1.7
 Identities = 13/30 (43%), Positives = 16/30 (53%)

Query: 59  RNPQELLFDSASTLYLGQAGPIIKGALDIL 88
           RNPQ L F    TLY  + GP     L+I+
Sbjct: 230 RNPQGLAFTPDGTLYASEQGPNSDDELNII 259


>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 504

 Score = 26.0 bits (57), Expect = 3.4
 Identities = 10/24 (41%), Positives = 12/24 (50%)

Query: 61  PQELLFDSASTLYLGQAGPIIKGA 84
           PQE L   A+ L  G A   + GA
Sbjct: 241 PQERLRGIAAALAQGDAAEALSGA 264


>gnl|CDD|238766 cd01489, Uba2_SUMO, Ubiquitin activating enzyme (E1) subunit UBA2.
           UBA2 is part of the heterodimeric activating enzyme
           (E1), specific for the SUMO family of ubiquitin-like
           proteins (Ubls). E1 enzymes are part of a conjugation
           cascade to attach Ub or Ubls, covalently to substrate
           proteins consisting of activating (E1), conjugating
           (E2), and/or ligating (E3) enzymes. E1 activates
           ubiquitin by C-terminal adenylation, and subsequently
           forms a highly reactive thioester bond between its
           catalytic cysteine and Ubls C-terminus. The E1 also
           associates with E2 and promotes ubiquitin transfer to
           the E2's catalytic cysteine. Post-translational
           modification by SUMO family of ubiquitin-like proteins
           (Ublps) is involved in cell division, nuclear transport,
           the stress response and signal transduction. UBA2
           contains both the nucleotide-binding motif involved in
           adenylation and the catalytic cysteine involved in the
           thioester intermediate and Ublp transfer to E2.
          Length = 312

 Score = 25.0 bits (55), Expect = 6.6
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 65  LFDSASTLYLGQAGPIIKG 83
           L +S +T +LGQ   I KG
Sbjct: 118 LIESGTTGFLGQVQVIKKG 136


  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
   0.321    0.138    0.390 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,300,079
Number of extensions: 337863
Number of successful extensions: 223
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 8
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)