RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4066
         (69 letters)



>gnl|CDD|190481 pfam02935, COX7C, Cytochrome c oxidase subunit VIIc.  Cytochrome
          c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
          terminal oxidase in the mitochondrial electron
          transport chain. This family is composed of cytochrome
          c oxidase subunit VIIc. The yeast member of this family
          is called COX VIII.
          Length = 67

 Score = 65.1 bits (159), Expect = 3e-16
 Identities = 29/61 (47%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 9  TVRCFSTSAARASHAY--SGPGQNLPFDTHNRYKLTLYFGLFMMTGFGVPFIAVRHQLLK 66
          T R  +TSA R SH++   GPG N+PF   N+Y+L      F  +GF  PF+ VRHQLLK
Sbjct: 7  TARRSTTSAVRFSHSHFKEGPGSNIPFSVTNKYRLAAMMTGFFGSGFAAPFVIVRHQLLK 66

Query: 67 S 67
           
Sbjct: 67 K 67


>gnl|CDD|238469 cd00929, Cyt_c_Oxidase_VIIc, Cytochrome c oxidase subunit VIIc.
          Cytochrome c oxidase (CcO), the terminal oxidase in the
          respiratory chains of eukaryotes and most bacteria, is
          a multi-chain transmembrane protein located in the
          inner membrane of mitochondria and the cell membrane of
          prokaryotes. It catalyzes the reduction of O2 and
          simultaneously pumps protons across the membrane. The
          number of subunits varies from three to five in
          bacteria and up to 13 in mammalian mitochondria.
          Subunits I, II, and III of mammalian CcO are encoded
          within the mitochondrial genome and the remaining 10
          subunits are encoded within the nuclear genome. The
          VIIc subunit is found only in eukaryotes and its
          specific function remains unclear. Peroxide
          inactivation of bovine CcO coincides with the direct
          oxidation of tryptophan (W19) within subunit VIIc,
          along with other structural changes in other subunits.
          Length = 46

 Score = 60.0 bits (146), Expect = 2e-14
 Identities = 27/46 (58%), Positives = 31/46 (67%)

Query: 21 SHAYSGPGQNLPFDTHNRYKLTLYFGLFMMTGFGVPFIAVRHQLLK 66
          SH   GPG NLPF   N+++LT  F LF  +GF  PFI VRHQLLK
Sbjct: 1  SHYGEGPGSNLPFSVTNKWRLTALFHLFFGSGFSAPFIVVRHQLLK 46


>gnl|CDD|183528 PRK12440, PRK12440, acetate kinase; Reviewed.
          Length = 397

 Score = 26.0 bits (57), Expect = 1.4
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 3/57 (5%)

Query: 12 CFSTSAARASHAYSGPGQNLPF---DTHNRYKLTLYFGLFMMTGFGVPFIAVRHQLL 65
          CF    AR S  Y G    +     D H++  +    GL    GF    +AV H+++
Sbjct: 36 CFGLEDARMSWKYQGEKTEIAIEGEDNHHKIAIGRLVGLTEELGFTQDIVAVGHRIV 92


>gnl|CDD|234324 TIGR03712, acc_sec_asp2, accessory Sec system protein Asp2.  This
           protein is designated Asp2 because, along with SecY2,
           SecA2, and other proteins it is part of the accessory
           secretory protein system. The system is involved in the
           export of serine-rich glycoproteins important for
           virulence in a number of Gram-positive species,
           including Streptococcus gordonii and Staphylococcus
           aureus. This protein family is assigned to transport
           rather than glycosylation function, but the specific
           molecular role is unknown [Protein fate, Protein and
           peptide secretion and trafficking, Cellular processes,
           Pathogenesis].
          Length = 511

 Score = 25.4 bits (56), Expect = 2.5
 Identities = 10/28 (35%), Positives = 12/28 (42%), Gaps = 10/28 (35%)

Query: 41  LTLYF----------GLFMMTGFGVPFI 58
           L +YF          G FMM   G PF+
Sbjct: 291 LNVYFSGYRPAEGFEGYFMMKRLGAPFL 318


>gnl|CDD|131504 TIGR02451, anti_sig_ChrR, anti-sigma factor, putative, ChrR family.
            The member of this family from Rhodobacter sphaeroides
           has been shown both to form a complex with sigma(E) and
           to negatively regulate tetrapyrrole biosynthesis. This
           protein likely contains (at least) two distinct
           functional domains; several smaller homologs (excluded
           by the model) show homology only to the C-terminal,
           including a motif PxHxHxGxE [Regulatory functions,
           Other].
          Length = 215

 Score = 24.3 bits (53), Expect = 5.2
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 18  ARASHAYSGPGQNLPFDTHNRYKLTL 43
           AR    Y   GQ++P  TH  ++LTL
Sbjct: 127 ARVRLLYIEAGQSIPQHTHKGFELTL 152


>gnl|CDD|240550 cd13145, MATE_like_5, Uncharacterized subfamily of the multidrug
           and toxic compound extrusion (MATE) proteins.  The
           integral membrane proteins from the MATE family are
           involved in exporting metabolites across the cell
           membrane and are responsible for multidrug resistance
           (MDR) in many bacteria and animals. A number of family
           members are involved in the synthesis of peptidoglycan
           components in bacteria.
          Length = 440

 Score = 23.7 bits (52), Expect = 8.7
 Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 5/35 (14%)

Query: 28  GQNLPFDTHNR----YKLTLYFGLFMMTGFGVPFI 58
           GQN     ++R    YK  L +G  +M      F+
Sbjct: 298 GQNFGAKKYDRVRETYKKALKYGFVIMV-VATVFL 331


  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
   0.328    0.139    0.427 

Gapped
Lambda     K      H
   0.267   0.0688    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,410,505
Number of extensions: 240850
Number of successful extensions: 281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 8
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
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 (21.8 bits)
S2: 53 (24.3 bits)