RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1519
         (210 letters)



>gnl|CDD|217118 pfam02578, Cu-oxidase_4, Multi-copper polyphenol oxidoreductase
           laccase.  Laccases are multi-copper oxidoreductases able
           to oxidise a wide variety of phenolic and non-phenolic
           compounds and are widely distributed among both
           prokaryotes and eukaryotes. There are two main active
           catalytic sites with conserved histidines that are
           capable of binding four copper atoms.
          Length = 224

 Score = 28.4 bits (64), Expect = 2.1
 Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)

Query: 176 PADIKIESFFGTPLSPELYEIKPEVAEYFKQKKP 209
           P DI      G  + P  YE+  EVAE F+   P
Sbjct: 125 PEDILA--AIGPSIGPCCYEVGEEVAEAFEAAFP 156


>gnl|CDD|224159 COG1238, COG1238, Predicted membrane protein [Function unknown].
          Length = 161

 Score = 28.0 bits (63), Expect = 2.6
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 11/60 (18%)

Query: 16  TLWEILGNLKGYGVGRLLYRQRFQRYPEPCYFKILKVQPVQHDGNLENPHENYRKVMVYV 75
           TL  +LG L  Y +GR L     +R+            P   +   +   + YR+  V+ 
Sbjct: 59  TLGSVLGGLVNYALGRFLPEFIARRW-----------FPGSEEALEKLQEKWYRRYGVWT 107


>gnl|CDD|224413 COG1496, yfiH, Multicopper polyphenol oxidase (laccase) [Secondary
           metabolites biosynthesis, transport and catabolism].
          Length = 249

 Score = 26.9 bits (60), Expect = 6.7
 Identities = 12/34 (35%), Positives = 14/34 (41%), Gaps = 2/34 (5%)

Query: 176 PADIKIESFFGTPLSPELYEIKPEVAEYFKQKKP 209
           P DI      G  +S   YE+ PEV   F    P
Sbjct: 149 PEDIIA--ALGPAISGCNYEVGPEVLAAFVAADP 180


>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
           fill DNA gaps that arise during DNA repair,
           recombination and replication.  Family A polymerase
           functions primarily to fill DNA gaps that arise during
           DNA repair, recombination and replication. DNA-dependent
           DNA polymerases can be classified in six main groups
           based upon phylogenetic relationships with E. coli
           polymerase I (classA), E. coli polymerase II (class B),
           E.coli polymerase III (class C), euryarchaaeota
           polymerase II (class D), human polymerase  beta (class
           x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma
           pigmentosum variant (class Y). Family A polymerase are
           found primarily in organisms related to prokaryotes and
           include prokaryotic DNA polymerase I ,mitochondrial
           polymerase delta, and several bacteriphage polymerases
           including those from odd-numbered phage (T3, T5, and
           T7). Prokaryotic Pol Is have two functional domains
           located on the same polypeptide; a 5'-3' polymerase and
           5'-3' exonuclease. Pol I uses its 5' nuclease activity
           to remove the ribonucleotide portion of newly
           synthesized Okazaki fragments and DNA polymerase
           activity to fill in the resulting gap. A combination of
           phylogenomic and signature sequence-based (or phonetic)
           approaches is used to understand the evolutionary
           relationships among bacteria. DNA polymerase I is one of
           the conserved proteins that is used to search for
           protein signatures. The structure of these polymerases
           resembles in overall morphology a cupped human right
           hand, with fingers (which bind an incoming nucleotide
           and interact with the single-stranded template), palm
           (which harbors the catalytic amino acid residues and
           also binds an incoming dNTP) and thumb (which binds
           double-stranded DNA) subdomains.
          Length = 429

 Score = 27.0 bits (60), Expect = 7.3
 Identities = 13/39 (33%), Positives = 17/39 (43%)

Query: 80  RGVLEPEVQEIFATSYKPDYRLIPKHEEQEWLRRTGKGE 118
           R  LE E+QE+F   Y  D  +  K      +R   KG 
Sbjct: 17  REDLENELQEVFPPWYVSDGFVPKKRTTNNSVRGYVKGA 55


  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
   0.318    0.139    0.426 

Gapped
Lambda     K      H
   0.267   0.0764    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,338,027
Number of extensions: 1080360
Number of successful extensions: 836
Number of sequences better than 10.0: 1
Number of HSP's gapped: 836
Number of HSP's successfully gapped: 14
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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 (21.7 bits)
S2: 57 (25.7 bits)