RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15627
         (77 letters)



>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
          factor.  Replicative DNA polymerases are capable of
          polymerising tens of thousands of nucleotides without
          dissociating from their DNA templates. The high
          processivity of these polymerases is dependent upon
          accessory proteins that bind to the catalytic subunit
          of the polymerase or to the substrate. The Epstein-Barr
          virus (EBV) BMRF1 protein is an essential component of
          the viral DNA polymerase and is absolutely required for
          lytic virus replication. BMRF1 is also a
          transactivator. This family is predicted to have a UL42
          like structure.
          Length = 381

 Score = 26.9 bits (60), Expect = 0.83
 Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 8/55 (14%)

Query: 17 IQPEAAYSS-----VSTLGEAGIVQFR--DEERPMCVSSSRVDWNTSHAFRHTPF 64
          IQ     +      +S +G+AGI+ F+  +    +       +   S +FR+T  
Sbjct: 30 IQISGLTTGPVLSVLSNVGDAGILSFKLTNAVAELHNHQEMTE-PVSLSFRNTSL 83


>gnl|CDD|152159 pfam11723, Aromatic_hydrox, Homotrimeric ring hydroxylase.  This
          domain is found on aromatic hydroxylating enzymes such
          as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from
          Pseudomonas putida and carbazole 1,9a-dioxygenase from
          Janthinobacterium. These enzymes are homotrimers and
          are distantly related to the typical oxygenase. This
          domain is found C terminal to the Rieske domain which
          binds an iron-sulphur cluster.
          Length = 240

 Score = 26.3 bits (58), Expect = 1.5
 Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 2/24 (8%)

Query: 54 NTSHAFRH--TPFVKGLGIALPLG 75
          +  H F H  +P V G  +ALPLG
Sbjct: 45 DPGHVFIHKDSPLVYGNDLALPLG 68


>gnl|CDD|114880 pfam06187, DUF993, Protein of unknown function (DUF993).  This
          family consists of several hypothetical bacterial
          proteins of unknown function.
          Length = 382

 Score = 26.1 bits (58), Expect = 1.7
 Identities = 10/22 (45%), Positives = 15/22 (68%)

Query: 50 RVDWNTSHAFRHTPFVKGLGIA 71
           +DW+ + AFRH  +  GLG+A
Sbjct: 54 AIDWDATLAFRHHLWSLGLGVA 75


>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family.  This
          family consists of the 116kDa V-type ATPase (vacuolar
          (H+)-ATPases) subunits, as well as V-type ATP synthase
          subunit i. The V-type ATPases family are proton pumps
          that acidify intracellular compartments in eukaryotic
          cells for example yeast central vacuoles,
          clathrin-coated and synaptic vesicles. They have
          important roles in membrane trafficking processes. The
          116kDa subunit (subunit a) in the V-type ATPase is part
          of the V0 functional domain responsible for proton
          transport. The a subunit is a transmembrane
          glycoprotein with multiple putative transmembrane
          helices it has a hydrophilic amino terminal and a
          hydrophobic carboxy terminal. It has roles in proton
          transport and assembly of the V-type ATPase complex.
          This subunit is encoded by two homologous gene in yeast
          VPH1 and STV1.
          Length = 707

 Score = 25.0 bits (55), Expect = 4.8
 Identities = 9/14 (64%), Positives = 10/14 (71%)

Query: 26 VSTLGEAGIVQFRD 39
          V  LGE G+VQ RD
Sbjct: 1  VDALGELGLVQIRD 14


>gnl|CDD|129652 TIGR00561, pntA, NAD(P) transhydrogenase, alpha subunit.  This
           integral membrane protein is the alpha subunit of alpha
           2 beta 2 tetramer that couples the proton transport
           across the membrane to the reversible transfer of
           hydride ion equivalents between NAD and NADP. An
           alternate name is pyridine nucleotide transhydrogenase
           alpha subunit. The N-terminal region is homologous to
           alanine dehydrogenase. In some species, such as
           Rhodospirillum rubrum, the alpha chain is replaced by
           two shorter chains, both with some homology to the
           full-length alpha chain modeled here. These score below
           the trusted cutoff [Energy metabolism, Electron
           transport].
          Length = 511

 Score = 24.5 bits (53), Expect = 6.9
 Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)

Query: 45  CVSSSRVDWNTSHAFRHTPFV 65
           CV    V WN SHA  HTP +
Sbjct: 434 CVVGYYVVWNVSHAL-HTPLM 453


>gnl|CDD|221406 pfam12070, DUF3550, Protein of unknown function (DUF3550/UPF0682). 
           This family of proteins is functionally uncharacterized.
           This protein is found in eukaryotes. Proteins in this
           family are typically between 249 to 606 amino acids in
           length.
          Length = 512

 Score = 24.3 bits (53), Expect = 7.9
 Identities = 5/17 (29%), Positives = 10/17 (58%)

Query: 51  VDWNTSHAFRHTPFVKG 67
           +D + S AF++   + G
Sbjct: 385 IDSDNSTAFKNFTNLFG 401


  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
   0.322    0.134    0.404 

Gapped
Lambda     K      H
   0.267   0.0656    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,798,170
Number of extensions: 273667
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 7
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
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 (22.0 bits)
S2: 53 (24.3 bits)