RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17721
         (130 letters)



>gnl|CDD|129249 TIGR00144, beta_RFAP_syn, beta-RFAP synthase.  This protein family
           contains several archaeal examples of
           beta-ribofuranosylaminobenzene 5-prime-phosphate
           synthase (beta-RFAP synthase), an enzyme involved in
           methanopterin biosynthesis. In some species, two members
           of this family are found. It is unclear whether both act
           as beta-RFAP synthase. This family is related to the
           GHMP kinases (Galactokinase, Homoserine kinase,
           Mevalonate kinase, Phosphomevalonate kinase). Members
           are found so far only in the Archaea and in
           Methylobacterium extorquens [Unknown function, Enzymes
           of unknown specificity].
          Length = 324

 Score = 31.0 bits (70), Expect = 0.15
 Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 9/61 (14%)

Query: 26  TRLS-RTARAVFQFYPE--NSAQIELVTSQAMRAGF------YGGLVVDYPHSTKAKKFF 76
           T+LS    R V ++Y     + +I  +  +   +G        GG +VD  HS+K K  F
Sbjct: 101 TQLSLAVGRLVSEYYGMKFTAREIAHIVGRGGTSGIGVASFEDGGFIVDGGHSSKEKSDF 160

Query: 77  L 77
           L
Sbjct: 161 L 161


>gnl|CDD|218010 pfam04293, SpoVR, SpoVR like protein.  Bacillus subtilis stage V
          sporulation protein R is involved in spore cortex
          formation. Little is known about cortex biosynthesis,
          except that it depends on several sigma E controlled
          genes, including spoVR.
          Length = 427

 Score = 29.9 bits (68), Expect = 0.33
 Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 12/62 (19%)

Query: 23 RLFTRLSRTARAVFQ--------FYPENSAQIELVTS-QAMRAGFYGGLVVDYPHSTKAK 73
            F  L      + +        FYP    QIE++T+ Q   A    G+   YPH +  K
Sbjct: 4  WTFELLEEADEEIEEIAREYGLDFYPN---QIEVITAEQMYDAYASVGMPTRYPHWSFGK 60

Query: 74 KF 75
           F
Sbjct: 61 HF 62


>gnl|CDD|216427 pfam01308, Chlam_OMP, Chlamydia major outer membrane protein.  The
           major outer membrane protein of Chlamydia contains four
           symmetrically spaced variable domains (VDs I to IV).
           This protein is believed to be an integral part to the
           pathogenesis, possibly adhesion. Along with the
           lipopolysaccharide, the major out membrane protein
           (MOMP) makes up the surface of the elementary body cell.
           The MOMP is the protein used to determine the different
           serotypes.
          Length = 389

 Score = 28.7 bits (64), Expect = 0.81
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 6/57 (10%)

Query: 53  AMRAGFYGGLVVDYPHSTKAKKFFLVLMTGGDLPLPPALGEGEGSQSPWDKPREMYG 109
           ++RAG+YG  V D    T   K F +    G  P   A+       +  D+P   YG
Sbjct: 59  SLRAGYYGDYVFDRVLKTDVNKTFQM----GAAPTGKAV--AADYTTNVDRPNPAYG 109


>gnl|CDD|237348 PRK13320, PRK13320, pantothenate kinase; Reviewed.
          Length = 244

 Score = 27.9 bits (63), Expect = 1.5
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 14/47 (29%)

Query: 50  TSQAMRAGFY-------GGLVVDYPHSTKAKKF--FLVLMTGGDLPL 87
           T + +R+G          GL+  Y       K    LV++TGGD P 
Sbjct: 175 TEECIRSGVVWGCVAEIEGLIEAYKS-----KLPELLVILTGGDAPF 216


>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
          polyadenylation element-binding protein CPEB-2, CPEB-3,
          CPEB-4 and similar protiens.  This subgroup corresponds
          to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
          CPEB-4, all well-conserved in both, vertebrates and
          invertebrates. Due to the high sequence similarity,
          members in this family may share similar expression
          patterns and functions. CPEB-2 is an RNA-binding
          protein that is abundantly expressed in testis and
          localized in cytoplasm in transfected HeLa cells. It
          preferentially binds to poly(U) RNA oligomers and may
          regulate the translation of stored mRNAs during
          spermiogenesis. Moreover, CPEB-2 impedes target RNA
          translation at elongation; it directly interacts with
          the elongation factor, eEF2, to reduce
          eEF2/ribosome-activated GTP hydrolysis in vitro and
          inhibit peptide elongation of CPEB2-bound RNA in vivo.
          CPEB-3 is a sequence-specific translational regulatory
          protein that regulates translation in a
          polyadenylation-independent manner. It functions as a
          translational repressor that governs the synthesis of
          the AMPA receptor GluR2 through binding GluR2 mRNA. It
          also represses translation of a reporter RNA in
          transfected neurons and stimulates translation in
          response to NMDA. CPEB-4 is an RNA-binding protein that
          mediates meiotic mRNA cytoplasmic polyadenylation and
          translation. It is essential for neuron survival and
          present on the endoplasmic reticulum (ER). It is
          accumulated in the nucleus upon ischemia or the
          depletion of ER calcium. CPEB-4 is overexpressed in a
          large variety of tumors and is associated with many
          mRNAs in cancer cells. All family members contain an
          N-terminal unstructured region, two RNA recognition
          motifs (RRMs), also termed RBDs (RNA binding domains)
          or RNPs (ribonucleoprotein domains), and a Zn-finger
          motif. In addition, they do have conserved nuclear
          export signals that are not present in CPEB-1. .
          Length = 92

 Score = 26.6 bits (59), Expect = 2.0
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 59 YGGLVVDYPHSTKAKKFF 76
          +G LVVD+PH  ++K +F
Sbjct: 24 FGPLVVDWPHKAESKSYF 41


>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
          Length = 1229

 Score = 27.4 bits (62), Expect = 2.8
 Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 7/41 (17%)

Query: 12   AQFSLKQISHLRLFTRLSRTARAVFQFYPENSAQ--IELVT 50
            AQ  L +I   +  T     AR V   +P NS    IE+ T
Sbjct: 986  AQAMLDKIIAEKWLT-----ARGVIGLFPANSVGDDIEVYT 1021


>gnl|CDD|236298 PRK08574, PRK08574, cystathionine gamma-synthase; Provisional.
          Length = 385

 Score = 25.8 bits (57), Expect = 9.3
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 10/59 (16%)

Query: 25  FTRLSRTARAVFQFYPENSAQIELVTSQAMRAGFYGGLVVDYPHSTKAKKFFLVLMTGG 83
           F R  R A A+ +F  E+  ++  V        +Y GL    P+   AK+ F   + GG
Sbjct: 252 FERQCRNAMAIAEFLSEHP-KVAEV--------YYPGL-PSDPYHGVAKRLFGKDLYGG 300


  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    0.136    0.400 

Gapped
Lambda     K      H
   0.267   0.0549    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,607,563
Number of extensions: 569955
Number of successful extensions: 400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 399
Number of HSP's successfully gapped: 12
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
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 (24.6 bits)