RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14833
         (63 letters)



>gnl|CDD|181774 PRK09311, PRK09311, bifunctional 3,4-dihydroxy-2-butanone
           4-phosphate synthase/GTP cyclohydrolase II protein;
           Provisional.
          Length = 402

 Score = 27.2 bits (61), Expect = 0.47
 Identities = 8/12 (66%), Positives = 11/12 (91%)

Query: 34  GSVFGTRKCECG 45
           G VFG+R+C+CG
Sbjct: 261 GDVFGSRRCDCG 272


>gnl|CDD|223956 COG1025, Ptr, Secreted/periplasmic Zn-dependent peptidases,
          insulinase-like [Posttranslational modification,
          protein turnover, chaperones].
          Length = 937

 Score = 27.0 bits (60), Expect = 0.64
 Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 3/21 (14%)

Query: 6  SESYPVENDFHPFAWWVSRNN 26
          SE YP E  F  F   +S++ 
Sbjct: 78 SEKYPDEGGFSEF---LSKHG 95


>gnl|CDD|238348 cd00641, GTP_cyclohydro2, GTP cyclohydrolase II (RibA).  GTP
          cyclohydrolase II catalyzes the conversion of GTP to
          2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'
          phosphate, formate, pyrophosphate (APy), and GMP in the
          biosynthetic pathway of riboflavin. Riboflavin is the
          precursor molecule for the synthesis of  the coenzymes
          flavin mononucleotide (FMN) and flavin adenine
          dinucleotide (FAD) which are essential to cell
          metabolism. The enzyme is present in plants and
          numerous pathogenic bacteria, especially gram negative
          organisms, who are dependent on endogenous synthesis of
          the vitamin because they lack an appropriate uptake
          system.  For animals and humans, which lack this
          biosynthetic pathway, riboflavin is the essential
          vitamin B2. GTP cyclohydrolase II requires magnesium
          ions for activity and has a bound catalytic zinc. The
          functionally active form is thought to be a homodimer.
          A paralogous protein is encoded in the genome of
          Streptomyces coelicolor, which converts GTP to
          2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone
          5'-phosphate (FAPy), an activity that has otherwise
          been reported for unrelated GTP cyclohydrolases III.
          Length = 193

 Score = 26.3 bits (59), Expect = 0.82
 Identities = 7/13 (53%), Positives = 10/13 (76%)

Query: 33 GGSVFGTRKCECG 45
           G VFG+ +C+CG
Sbjct: 55 TGDVFGSLRCDCG 67


>gnl|CDD|119418 cd00892, PIKKc_ATR, ATR (Ataxia telangiectasia and Rad3-related),
           catalytic domain; The ATR catalytic domain subfamily is
           part of a larger superfamily that includes the catalytic
           domains of other kinases such as the typical
           serine/threonine/tyrosine protein kinases (PKs),
           aminoglycoside phosphotransferase, choline kinase, and
           RIO kinases. ATR is also referred to as Mei-41
           (Drosophila), Esr1/Mec1p (Saccharomyces cerevisiae),
           Rad3 (Schizosaccharomyces pombe), and FRAP-related
           protein (human). ATR is a member of the phosphoinositide
           3-kinase-related protein kinase (PIKK) subfamily. PIKKs
           have intrinsic serine/threonine kinase activity and are
           distinguished from other PKs by their unique catalytic
           domain, similar to that of lipid PI3K, and their large
           molecular weight (240-470 kDa). ATR contains a UME
           domain of unknown function, a FAT (FRAP, ATM and TRRAP)
           domain, a catalytic domain, and a FATC domain at the
           C-terminus. Together with its downstream effector
           kinase, Chk1, ATR plays a central role in regulating the
           replication checkpoint. ATR stabilizes replication forks
           by promoting the association of DNA polymerases with the
           fork. Preventing fork collapse is essential in
           preserving genomic integrity. ATR plays a role in normal
           cell growth and in response to DNA damage.
          Length = 237

 Score = 26.1 bits (58), Expect = 1.1
 Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 7/33 (21%)

Query: 1   MRDTCSESYP-------VENDFHPFAWWVSRNN 26
           +R    E YP       +EN   P AW  +RN 
Sbjct: 94  LRSILLEIYPPVFHEWFLENFPDPSAWLKARNA 126


>gnl|CDD|226280 COG3757, Acm, Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell
          envelope biogenesis, outer membrane].
          Length = 269

 Score = 24.3 bits (53), Expect = 4.8
 Identities = 11/51 (21%), Positives = 14/51 (27%), Gaps = 17/51 (33%)

Query: 6  SESYPVENDFHPFAWWVSRNNHKMDYWGGSVFGTRKCECGILGTCIDPTKW 56
              P  NDF P   +       +D  G                 ID +KW
Sbjct: 38 GNPVPAANDFIPAKDFAPDKPMALDIHG-----------------IDVSKW 71


  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
   0.323    0.139    0.538 

Gapped
Lambda     K      H
   0.267   0.0768    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,991,959
Number of extensions: 185591
Number of successful extensions: 126
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 6
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)