RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13979
         (78 letters)



>gnl|CDD|220650 pfam10247, Romo1, Reactive mitochondrial oxygen species modulator
          1.  This is a family of small, approximately 100 amino
          acid, proteins found from yeasts to humans. The
          majority of endogenous reactive oxygen species (ROS) in
          cells are produced by the mitochondrial respiratory
          chain. An increase or imbalance in ROS alters the
          intracellular redox homeostasis, triggers DNA damage,
          and may contribute to cancer development and
          progression. Members of this family are mitochondrial
          reactive oxygen species modulator 1 (Romo1) proteins
          that are responsible for increasing the level of ROS in
          cells. Increased Romo1 expression can have a number of
          other effects including: inducing premature senescence
          of cultured human fibroblasts and increased resistance
          to 5-fluorouracil.
          Length = 67

 Score = 67.7 bits (166), Expect = 4e-17
 Identities = 37/67 (55%), Positives = 49/67 (73%)

Query: 12 PSCFDRMKVGFMIGFSVGMATGGLFGGFNALRYGLRGAELLKNVGKVMVQGGGSFGTFMA 71
          PSCFD++K+GFM+G +VG A G LFGG+ A RYG+    LL+ +GK M+   G+FG FM 
Sbjct: 1  PSCFDKIKMGFMMGAAVGGAFGFLFGGYAAFRYGMGPRGLLRTLGKSMLGSAGTFGFFMG 60

Query: 72 IGAGIRC 78
          IG+ IRC
Sbjct: 61 IGSVIRC 67


>gnl|CDD|218189 pfam04646, DUF604, Protein of unknown function, DUF604.  This
          family includes a conserved region found in several
          uncharacterized plant proteins.
          Length = 256

 Score = 27.3 bits (61), Expect = 0.67
 Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 4/29 (13%)

Query: 26 FSVGMATGGLFGGFNALRYGLRGAELLKN 54
          FS GMA GG  GGF A+ Y L  A L + 
Sbjct: 5  FSYGMAFGG--GGF-AISYPL-AAALARM 29


>gnl|CDD|221355 pfam11981, DUF3482, Domain of unknown function (DUF3482).  This
           presumed domain is functionally uncharacterized. This
           domain is found in bacteria and eukaryotes. This domain
           is typically between 289 to 301 amino acids in length.
           This domain is found associated with pfam01926. THe
           central region of these proteins contains a hydrophobic
           region that is similar to pfam05433.
          Length = 293

 Score = 25.7 bits (57), Expect = 2.7
 Identities = 6/13 (46%), Positives = 8/13 (61%)

Query: 62  GGGSFGTFMAIGA 74
           GG + G   A+GA
Sbjct: 168 GGLTLGAAAALGA 180


>gnl|CDD|233130 TIGR00797, matE, putative efflux protein, MATE family.  The Multi
           Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The
           MATE family consists of probable efflux proteins
           including a functionally characterized multi drug efflux
           system from Vibrio parahaemolyticus, a putative
           ethionine resistance protein of Saccharomyces
           cerevisiae, and the functionally uncharacterized DNA
           damage-inducible protein F (DinF) of E. coli. These
           proteins have 12 probable TMS [Transport and binding
           proteins, Other].
          Length = 342

 Score = 25.3 bits (56), Expect = 3.1
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 22  FMIGFSVGMATGGLFGGFNALRYGLRGAELLKNVGKVMVQGGGSFGTFMAI 72
           FM  F  G+A   L G       G    +  K V +V ++     G  +AI
Sbjct: 265 FMPAFGFGIAVSILVGQ----ALGAGDPKRAKEVARVALKLSLLLGLVLAI 311


>gnl|CDD|191194 pfam05111, Amelin, Ameloblastin precursor (Amelin).  This family
           consists of several mammalian Ameloblastin precursor
           (Amelin) proteins. Matrix proteins of tooth enamel
           consist mainly of amelogenin but also of non-amelogenin
           proteins, which, although their volumetric percentage is
           low, have an important role in enamel mineralisation.
           One of the non-amelogenin proteins is ameloblastin, also
           known as amelin and sheathlin. Ameloblastin (AMBN) is
           one of the enamel sheath proteins which is though to
           have a role in determining the prismatic structure of
           growing enamel crystals.
          Length = 410

 Score = 24.9 bits (54), Expect = 4.5
 Identities = 10/19 (52%), Positives = 11/19 (57%)

Query: 30  MATGGLFGGFNALRYGLRG 48
           MA G LF GF  +R  LR 
Sbjct: 237 MAYGALFPGFGGMRPTLRR 255


>gnl|CDD|223148 COG0070, GltB, Glutamate synthase domain 3 [Amino acid transport
           and metabolism].
          Length = 301

 Score = 25.0 bits (55), Expect = 4.6
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 4/39 (10%)

Query: 37  GGFNALRYGLRGAELLKNVGKVMVQG--GGSFGTFMAIG 73
            G  A  YGL+G  L ++  ++   G  G SFG F A G
Sbjct: 66  SGEIAKGYGLQG--LPEDTVEINFNGSAGQSFGAFNAKG 102


>gnl|CDD|233175 TIGR00895, 2A0115, benzoate transport.  [Transport and binding
           proteins, Carbohydrates, organic alcohols, and acids].
          Length = 398

 Score = 24.6 bits (54), Expect = 5.6
 Identities = 8/30 (26%), Positives = 12/30 (40%)

Query: 18  MKVGFMIGFSVGMATGGLFGGFNALRYGLR 47
           +       F+ G   G +  G+ A R G R
Sbjct: 286 LAATGGALFNFGGVIGSIIFGWLADRLGPR 315


>gnl|CDD|225143 COG2234, Iap, Predicted aminopeptidases [General function
           prediction only].
          Length = 435

 Score = 24.5 bits (53), Expect = 7.1
 Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 13/54 (24%)

Query: 35  LFGGFNALRYGLRGAE---------LLKNVGKV----MVQGGGSFGTFMAIGAG 75
            F  F A   GL G+E         L K +  V    M+       T +  G G
Sbjct: 253 RFVAFGAEESGLLGSEAYVKRLSKDLDKKIALVINLDMLGSPNPTPTLILYGNG 306


>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
           FMN-binding domain.  DHPD catalyzes the first step in
           pyrimidine degradation: the NADPH-dependent reduction of
           uracil and thymine to the corresponding
           5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
           and eight [4Fe-4S] clusters, arranged in two electron
           transfer chains that pass the dimer interface twice. Two
           of the Fe-S clusters show a hitherto unobserved
           coordination involving a glutamine residue.
          Length = 299

 Score = 24.6 bits (54), Expect = 7.5
 Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 5/45 (11%)

Query: 18  MKVGFMIGFSVGMATGGLFGGFNALRYGLRGAELLKNVGKVMVQG 62
            + G  I        GG+    +A  + L GA +++    VM QG
Sbjct: 249 PEPGLPI-----SGIGGIESWEDAAEFLLLGASVVQVCTAVMNQG 288


>gnl|CDD|184072 PRK13475, PRK13475, ribulose bisphosphate carboxylase; Provisional.
          Length = 443

 Score = 24.3 bits (53), Expect = 8.9
 Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 3/32 (9%)

Query: 37  GGFNALRYGLRG-AELLKNVGKVMVQGGGSFG 67
           GG NALR  L G  + L +   +   GGG+FG
Sbjct: 369 GGMNALR--LPGFFDNLGHGNVINTAGGGAFG 398


>gnl|CDD|217053 pfam02466, Tim17, Tim17/Tim22/Tim23/Pmp24 family.  The
          pre-protein translocase of the mitochondrial outer
          membrane (Tom) allows the import of pre-proteins from
          the cytoplasm. Tom forms a complex with a number of
          proteins, including Tim17. Tim17 and Tim23 are thought
          to form the translocation channel of the inner
          membrane. This family includes Tim17, Tim22 and Tim23.
          This family also includes Pmp24 a peroxisomal protein.
          The involvement of this domain in the targeting of
          PMP24 remains to be proved. PMP24 was known as Pmp27
          in.
          Length = 128

 Score = 23.8 bits (52), Expect = 9.9
 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 13 SCFDRMKVGFMIGFSVGMATGGLFGGFNALR-------YGLRGAELLKNVGKVMVQGGGS 65
           C +R+      GF +G   GG FG  + L          LR   +L   G+     G +
Sbjct: 1  PCPERIVYDTGGGFLMGAVYGGFFGAPHGLVNALRSGPLKLRLNGVLNATGRRGPSHGNN 60

Query: 66 FGTFMAIGAGIRC 78
          F  F  + +GI C
Sbjct: 61 FAVFGGLYSGIEC 73


>gnl|CDD|238483 cd00983, recA, RecA is a  bacterial enzyme which has roles in
           homologous recombination, DNA repair, and the induction
           of the SOS response.  RecA couples ATP hydrolysis to DNA
           strand exchange.
          Length = 325

 Score = 24.1 bits (53), Expect = 9.9
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 12/49 (24%)

Query: 17  RMKVGFMIGFSVGMATGGLFGGFNAL------RYGLRGAELLKNVGKVM 59
           R K+G M G      TGG     NAL      R  +R  E +K+  +V+
Sbjct: 192 REKIGVMFGNP-ETTTGG-----NALKFYSSVRLDIRRIETIKDGDEVI 234


  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    0.148    0.464 

Gapped
Lambda     K      H
   0.267   0.0687    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,174,601
Number of extensions: 347844
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 735
Number of HSP's successfully gapped: 51
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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 (21.7 bits)
S2: 53 (24.3 bits)