RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16436
         (94 letters)



>gnl|CDD|213980 TIGR04367, HpnR_B12_rSAM, hopanoid C-3 methylase HpnR.  Members of
           this are family are a B12-binding domain/radical SAM
           domain protein required for 3-methylhopanoid production.
           Activity was confirmed by mutant phenotype by disrupting
           this gene in Methylococcus capsulatus strain Bath. This
           protein family should only occur in genomes that encode
           a squalene-hopene cyclase (see TIGR01507) [Fatty acid
           and phospholipid metabolism, Biosynthesis].
          Length = 490

 Score = 30.1 bits (68), Expect = 0.11
 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 28  WYFYGTRLYREDYPKVDGEDMLPIPCTNIAIV 59
           W FYG R YR   P+V GE++  I    I IV
Sbjct: 205 WTFYG-RSYRTLSPEVAGEELARIREPGIFIV 235


>gnl|CDD|173632 cd05051, PTKc_DDR, Catalytic domain of the Protein Tyrosine
           Kinases, Discoidin Domain Receptors.  Protein Tyrosine
           Kinase (PTK) family; Discoidin Domain Receptor (DDR)
           subfamily; catalytic (c) domain. The DDR subfamily
           consists of homologs of mammalian DDR1, DDR2, and
           similar proteins. The PTKc family is part of a larger
           superfamily that includes the catalytic domains of other
           kinases such as protein serine/threonine kinases, RIO
           kinases, and phosphoinositide 3-kinase (PI3K). PTKs
           catalyze the transfer of the gamma-phosphoryl group from
           ATP to tyrosine (tyr) residues in protein substrates.
           DDR subfamily members are receptor tyr kinases (RTKs)
           containing an extracellular discoidin homology domain, a
           transmembrane segment, an extended juxtamembrane region,
           and an intracellular catalytic domain. The binding of
           the ligand, collagen, to DDRs results in a slow but
           sustained receptor activation. DDRs regulate cell
           adhesion, proliferation, and extracellular matrix
           remodeling. They have been linked to a variety of human
           cancers including breast, colon, ovarian, brain, and
           lung. There is no evidence showing that DDRs act as
           transforming oncogenes. They are more likely to play a
           role in the regulation of tumor growth and metastasis.
          Length = 296

 Score = 26.9 bits (60), Expect = 1.4
 Identities = 9/17 (52%), Positives = 10/17 (58%)

Query: 35  LYREDYPKVDGEDMLPI 51
           LY  DY +V G   LPI
Sbjct: 180 LYSSDYYRVQGRAPLPI 196


>gnl|CDD|143413 cd07094, ALDH_F21_LactADH-like, ALDH subfamily: NAD+-dependent,
           lactaldehyde dehydrogenase, ALDH family 21 A1, and
           related proteins.  ALDH subfamily which includes Tortula
           ruralis aldehyde dehydrogenase ALDH21A1 (RNP123), and
           NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22)
           and like sequences.
          Length = 453

 Score = 26.6 bits (59), Expect = 2.3
 Identities = 6/24 (25%), Positives = 15/24 (62%)

Query: 52  PCTNIAIVGLSVEANSPKGWVKLL 75
           P + + +  + VEA  P+G ++++
Sbjct: 163 PLSALELAKILVEAGVPEGVLQVV 186


>gnl|CDD|223111 COG0033, Pgm, Phosphoglucomutase [Carbohydrate transport and
           metabolism].
          Length = 524

 Score = 26.2 bits (58), Expect = 3.4
 Identities = 7/24 (29%), Positives = 9/24 (37%)

Query: 23  NQSAFWYFYGTRLYREDYPKVDGE 46
                +   G    R DY +VD E
Sbjct: 405 IPQEHYAELGRNFGRPDYERVDAE 428


>gnl|CDD|215424 PLN02790, PLN02790, transketolase.
          Length = 654

 Score = 25.8 bits (57), Expect = 3.6
 Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 4/34 (11%)

Query: 46  EDMLPIPCTNIAIVGLSVEANSPKGWVKLLESSH 79
           E +LP   T      +SVEA S  GW K + S  
Sbjct: 589 ESVLPSSVTAR----VSVEAGSTFGWEKYVGSKG 618


>gnl|CDD|140326 PTZ00305, PTZ00305, NADH:ubiquinone oxidoreductase; Provisional.
          Length = 297

 Score = 25.4 bits (55), Expect = 6.0
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 9/54 (16%)

Query: 42  KVDGEDMLPIPCTNIAIVGLSVEANS------PKGWVKLLESSH---CCITKQA 86
           +VDG   L + C  +A+ G+S+  +S       +G V+L+  +H   C I +QA
Sbjct: 119 QVDGTQNLVVSCATVALPGMSIITDSRLVRDAREGNVELILINHPNDCPICEQA 172


>gnl|CDD|133180 cd05049, PTKc_Trk, Catalytic domain of the Protein Tyrosine
           Kinases, Tropomyosin Related Kinases.  Protein Tyrosine
           Kinase (PTK) family; Tropomyosin Related Kinase (Trk)
           subfamily; catalytic (c) domain. The Trk subfamily
           consists of TrkA, TrkB, TrkC, and similar proteins. The
           PTKc family is part of a larger superfamily that
           includes the catalytic domains of other kinases such as
           protein serine/threonine kinases, RIO kinases, and
           phosphoinositide 3-kinase (PI3K). PTKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           tyrosine (tyr) residues in protein substrates. Trk
           subfamily members are receptor tyr kinases (RTKs)
           containing an extracellular region with arrays of
           leucine-rich motifs flanked by two cysteine-rich
           clusters followed by two immunoglobulin-like domains, a
           transmembrane segment, and an intracellular catalytic
           domain. Binding to their ligands, the nerve growth
           factor (NGF) family of neutrotrophins, leads to Trk
           receptor oligomerization and activation of the catalytic
           domain. Trk receptors are mainly expressed in the
           peripheral and central nervous systems. They play
           important roles in cell fate determination, neuronal
           survival and differentiation, as well as in the
           regulation of synaptic plasticity. Altered expression of
           Trk receptors is associated with many human diseases.
          Length = 280

 Score = 25.1 bits (55), Expect = 7.0
 Identities = 9/17 (52%), Positives = 11/17 (64%)

Query: 35  LYREDYPKVDGEDMLPI 51
           +Y  DY +V G  MLPI
Sbjct: 172 VYTTDYYRVGGHTMLPI 188


>gnl|CDD|238429 cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty
          acids into a large variety of different products,
          called polyketides, by successive decarboxylating
          Claisen condensations. PKSs can be divided into 2
          groups, modular type I PKSs consisting of one or more
          large multifunctional proteins and iterative type II
          PKSs, complexes of several monofunctional subunits.
          Length = 421

 Score = 24.8 bits (55), Expect = 8.1
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 7/39 (17%)

Query: 56 IAIVGLSV---EANSPKGWVKLLESSHCCITKQAGPVPP 91
          IAIVG++     A  P  + + L      I+     +P 
Sbjct: 3  IAIVGMACRFPGAADPDEFWENLLEGRDAIS----EIPE 37


  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
   0.320    0.139    0.447 

Gapped
Lambda     K      H
   0.267   0.0670    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,672,139
Number of extensions: 364401
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 10
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
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 (21.8 bits)
S2: 53 (24.3 bits)