RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12387
         (98 letters)



>gnl|CDD|216332 pfam01151, ELO, GNS1/SUR4 family.  Members of this family are
          involved in long chain fatty acid elongation systems
          that produce the 26-carbon precursors for ceramide and
          sphingolipid synthesis. Predicted to be integral
          membrane proteins, in eukaryotes they are probably
          located on the endoplasmic reticulum. Yeast ELO3
          affects plasma membrane H+-ATPase activity, and may act
          on a glucose-signaling pathway that controls the
          expression of several genes that are transcriptionally
          regulated by glucose such as PMA1.
          Length = 244

 Score = 53.4 bits (129), Expect = 5e-10
 Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 29 FWTGSLWRPFLLMCFYYYFVKFLGPWFMKNRQPYNLDTVLKVYNVFQILYSAFGVY 84
              S W   L++  Y  FV FLGP  M+NR+P++L  +L V+N+F +L S +G Y
Sbjct: 1  PLLSSPWPVILIIVLYLVFV-FLGPKIMRNRKPFDLKRLLIVHNLFLVLLSLYGFY 55


>gnl|CDD|219638 pfam07914, DUF1679, Protein of unknown function (DUF1679).  The
           region featured in this family is found in a number of
           C. elegans proteins, in one case as a repeat. In many of
           the family members, this region is associated with the
           CHK region described by SMART as being found in ZnF_C4
           and HLH domain-containing kinases. In fact, one member
           of this family is annotated as being a member of the
           nuclear hormone receptor family, and contains regions
           typical of such proteins (Interpro:IPR000536,
           Interpro:IPR008946, and Interpro:IPR001628).
          Length = 413

 Score = 29.9 bits (68), Expect = 0.13
 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 4/38 (10%)

Query: 37  PFLLMCFYYYFVKFLGPWFMKNRQPYNLDTVLKVYNVF 74
             LL  +Y  F K LG     N +PY L+ +   YN++
Sbjct: 328 EELLEQYYETFTKVLGD----NEEPYTLEQLKDSYNLY 361


>gnl|CDD|184100 PRK13509, PRK13509, transcriptional repressor UlaR; Provisional.
          Length = 251

 Score = 30.0 bits (68), Expect = 0.16
 Identities = 8/20 (40%), Positives = 13/20 (65%)

Query: 3   QVITGVVNITNYLIETDHTD 22
           Q+IT  + + NYLI+ +H  
Sbjct: 118 QIITNYLPLANYLIDQEHDS 137


>gnl|CDD|221660 pfam12600, DUF3769, Protein of unknown function (DUF3769).  This
           family of proteins is found in bacteria and eukaryotes.
           Proteins in this family are typically between 560 and
           931 amino acids in length.
          Length = 403

 Score = 28.0 bits (63), Expect = 0.75
 Identities = 8/25 (32%), Positives = 15/25 (60%), Gaps = 3/25 (12%)

Query: 69  KVYNV---FQILYSAFGVYIVSPGI 90
           +++N     Q +YS++G  + SP I
Sbjct: 215 RLFNGSLGEQTVYSSYGAVLESPVI 239


>gnl|CDD|213306 cd05940, FATP_FACS, Fatty acid transport proteins (FATP) play dual
           roles as fatty acid transporters and its activation
           enzymes.  Fatty acid transport protein (FATP) transports
           long-chain or very-long-chain fatty acids across the
           plasma membrane. FATPs also have fatty acid CoA
           synthetase activity, thus playing dual roles as fatty
           acid transporters and its activation enzymes. At least
           five copies of FATPs are identified in mammalian cells.
           This family also includes prokaryotic FATPs. FATPs are
           the key players in the trafficking of exogenous fatty
           acids into the cell and in intracellular fatty acid
           homeostasis.
          Length = 444

 Score = 26.8 bits (60), Expect = 1.7
 Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 2/28 (7%)

Query: 28  WFWTGSLWRPFLLMCFYYYFVKFLGPWF 55
           +F TG L R       Y+YFV  LG  F
Sbjct: 319 YFNTGDLVRRDGFG--YFYFVDRLGDTF 344


>gnl|CDD|184271 PRK13717, PRK13717, conjugal transfer protein TrbI; Provisional.
          Length = 128

 Score = 26.3 bits (57), Expect = 2.0
 Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 2/39 (5%)

Query: 17 ETDHTDPRTRDWFWT--GSLWRPFLLMCFYYYFVKFLGP 53
           TD T PR   W+WT  G L    L     Y  V+   P
Sbjct: 7  TTDVTAPRRSHWWWTVPGCLAMVLLNAAVSYGIVRLNAP 45


>gnl|CDD|237262 PRK12997, PRK12997, PTS system ascorbate-specific transporter
           subunit IIC; Reviewed.
          Length = 466

 Score = 26.4 bits (59), Expect = 2.5
 Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 38  FLLMCFYYYFVKFLGPWFMKNRQPYNLDTVLKVYNVFQILYS---AFGVYIVSPGIKL 92
            +++ F+   +   GP  M N       T  + + ++ I+ +   + GV+I+  G+++
Sbjct: 243 IVMLVFFGIILLAAGPDIMANVDLIAKGTGGQNWFMYIIIQALTFSVGVFILLQGVRM 300


>gnl|CDD|234477 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent, PP_1105 family.
            This model describes a family of ATP-dependent DNA
           ligases present in about 12 % of prokaryotic genomes. It
           occurs as part of a four-gene system with an
           exonuclease, a helicase and a phosphoesterase, with all
           four genes clustered or at least the first two and last
           two paired. This family resembles DNA ligase I (see
           TIGR00574 and pfam01068), and its presumed function may
           be in DNA repair, replication, or recombination.
          Length = 526

 Score = 25.4 bits (56), Expect = 5.5
 Identities = 8/17 (47%), Positives = 10/17 (58%)

Query: 52  GPWFMKNRQPYNLDTVL 68
           GPW+   R P  +D VL
Sbjct: 391 GPWWKWKRDPLTVDAVL 407


>gnl|CDD|236428 PRK09247, PRK09247, ATP-dependent DNA ligase; Validated.
          Length = 539

 Score = 25.6 bits (57), Expect = 5.9
 Identities = 8/17 (47%), Positives = 10/17 (58%)

Query: 52  GPWFMKNRQPYNLDTVL 68
           GPW+   R P  +D VL
Sbjct: 400 GPWWKWKRDPLTIDAVL 416


>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
          Length = 565

 Score = 25.1 bits (56), Expect = 6.7
 Identities = 9/13 (69%), Positives = 11/13 (84%), Gaps = 1/13 (7%)

Query: 3   QVITGVV-NITNY 14
           QV+ GVV NIT+Y
Sbjct: 203 QVVEGVVKNITDY 215


>gnl|CDD|206319 pfam14150, YesK, YesK-like protein.  The YesK-like protein family
          includes the B. subtilis YesK protein, which is
          functionally uncharacterized. Its expression is
          regulated by the sporulation-specific sigma factor
          sigma-E. This family of proteins is found in bacteria.
          Proteins in this family are approximately 100 amino
          acids in length.
          Length = 81

 Score = 24.1 bits (53), Expect = 7.8
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 5/51 (9%)

Query: 38 FLLMCFYYYFVKFLGPWFMKNRQP-----YNLDTVLKVYNVFQILYSAFGV 83
          F L+      + F     ++ + P       L T+L +  +  +LYS F +
Sbjct: 1  FYLLGAITAIIVFAVSALLRKKFPNKHPELILATILILLCLLTVLYSIFLI 51


>gnl|CDD|212566 cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of
           Dedicator of Cytokinesis proteins.  DOCK proteins
           comprise a family of atypical guanine nucleotide
           exchange factors (GEFs) that lack the conventional Dbl
           homology (DH) domain. As GEFs, they activate the small
           GTPases Rac and Cdc42 by exchanging bound GDP for free
           GTP. They are also called the CZH (CED-5, Dock180, and
           MBC-zizimin homology) family, after the first family
           members identified. Dock180 was first isolated as a
           binding partner for the adaptor protein Crk. The
           Caenorhabditis elegans protein, Ced-5, is essential for
           cell migration and phagocytosis, while the Drosophila
           ortholog, Myoblast city (MBC), is necessary for myoblast
           fusion and dorsal closure. DOCKs are divided into four
           classes (A-D) based on sequence similarity and domain
           architecture: class A includes Dock1 (or Dock180), 2 and
           5; class B includes Dock3 and 4; class C includes Dock6,
           7, and 8; and class D includes Dock9, 10 and 11. All
           DOCKs contain two homology domains: the DHR-1 (Dock
           homology region-1), also called CZH1, and DHR-2 (also
           called CZH2 or Docker). This alignment model represents
           the DHR-2 domain of DOCK proteins, which contains the
           catalytic GEF activity for Rac and/or Cdc42.
          Length = 392

 Score = 25.0 bits (55), Expect = 7.9
 Identities = 5/21 (23%), Positives = 10/21 (47%), Gaps = 3/21 (14%)

Query: 43  FYYYFVKFLG---PWFMKNRQ 60
             Y+ V F G   P  ++ ++
Sbjct: 122 PTYFRVGFYGKGFPESLRGKE 142


  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
   0.330    0.145    0.504 

Gapped
Lambda     K      H
   0.267   0.0752    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,083,519
Number of extensions: 415851
Number of successful extensions: 585
Number of sequences better than 10.0: 1
Number of HSP's gapped: 582
Number of HSP's successfully gapped: 39
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
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 (24.1 bits)