RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3121
         (190 letters)



>gnl|CDD|215467 PLN02866, PLN02866, phospholipase D.
          Length = 1068

 Score = 30.1 bits (68), Expect = 0.68
 Identities = 17/32 (53%), Positives = 19/32 (59%), Gaps = 1/32 (3%)

Query: 81  LLIYDYQICLMGILCLKVPRY-LKEFRVEQCP 111
           L+I DYQIC +G L L   RY   E RV  CP
Sbjct: 451 LVIVDYQICFIGGLDLCFGRYDTPEHRVGDCP 482


>gnl|CDD|107323 cd06328, PBP1_SBP_like_2, Periplasmic solute-binding domain of
           active transport proteins found in gram-negative and
           gram-positive bacteria.  Periplasmic solute-binding
           domain of active transport proteins found in
           gram-negative and gram-positive bacteria. Members of
           this group are initial receptors in the process of
           active transport across cellular membrane, but their
           substrate specificities are not known in detail.
           However, they closely resemble the group of AmiC and
           active transport systems for short-chain amides and urea
           (FmdDEF), and thus are likely to exhibit a
           ligand-binding mode similar to that of the amide sensor
           protein AmiC from Pseudomonas aeruginosa. Moreover, this
           binding domain has high sequence identity to the family
           of hydrophobic amino acid transporters (HAAT), and thus
           it may also be involved in transport of amino acids.
          Length = 333

 Score = 29.7 bits (67), Expect = 0.95
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 7   KLSFSVNDPRGYVDKAMHALSSTIVEINVEVLEHSNIGLVSQATTYALLKIAQPREILAL 66
            +   V D  G  + A+      I +  V++L    +G  S     A+L +A+  + + +
Sbjct: 41  PIEVIVKDDAGNPEVAVSLARELIGDDGVDIL----VGSTSSGVALAVLPVAEENKKILI 96

Query: 67  VD---GPSI 72
           V+     SI
Sbjct: 97  VEPAAADSI 105


>gnl|CDD|233272 TIGR01099, galU, UTP-glucose-1-phosphate uridylyltransferase.
          Built to distinquish between the highly similar genes
          galU and galF [Cell envelope, Biosynthesis and
          degradation of surface polysaccharides and
          lipopolysaccharides].
          Length = 260

 Score = 28.8 bits (65), Expect = 1.5
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 58 AQPREILALVDGPSIQF 74
          A P+E+L +VD P IQ+
Sbjct: 20 AIPKEMLPIVDKPLIQY 36


>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase.  Benzyl
           alcohol dehydrogenase is similar to liver alcohol
           dehydrogenase, but has some amino acid substitutions
           near  the active site, which may determine the enzyme's
           specificity of oxidizing aromatic substrates.  Also
           known as aryl-alcohol dehydrogenases, they catalyze the
           conversion of an aromatic alcohol + NAD+ to an aromatic
           aldehyde + NADH + H+.  NAD(P)(H)-dependent
           oxidoreductases are the major enzymes in the
           interconversion of alcohols and aldehydes, or ketones.
           Alcohol dehydrogenase in the liver converts ethanol and
           NAD+ to acetaldehyde and NADH, while in yeast and some
           other microorganisms ADH catalyzes the conversion
           acetaldehyde to ethanol in alcoholic fermentation.   ADH
           is a member of the medium chain alcohol dehydrogenase
           family (MDR), which has a NAD(P)(H)-binding domain in a
           Rossmann fold of a beta-alpha form.  The NAD(H)-binding
           region is comprised of 2 structurally similar halves,
           each of which contacts a mononucleotide.  A GxGxxG motif
           after the first mononucleotide contact half allows the
           close contact of the coenzyme with the ADH backbone.
           The N-terminal catalytic domain has a distant homology
           to GroES.  These proteins typically form dimers
           (typically higher plants, mammals) or tetramers (yeast,
           bacteria), and have 2 tightly bound zinc atoms per
           subunit, a catalytic zinc at the active site and a
           structural zinc in a lobe of the catalytic domain.
           NAD(H) binding occurs in the cleft between the catalytic
            and coenzyme-binding domains at the active site, and
           coenzyme binding induces a conformational closing of
           this cleft. Coenzyme binding typically precedes and
           contributes to substrate binding.  In human  ADH
           catalysis, the zinc ion helps coordinate the alcohol,
           followed by deprotonation of  a histidine, the ribose of
           NAD, a serine, then the alcohol, which allows the
           transfer of a hydride to NAD+, creating NADH and a
           zinc-bound aldehyde or ketone. In yeast and some
           bacteria, the active site zinc binds an aldehyde,
           polarizing it, and leading to the reverse reaction.
          Length = 365

 Score = 27.5 bits (62), Expect = 4.1
 Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 4/35 (11%)

Query: 116 HKCTQHRPFTCFHWHFMNQRRRRPVRKRDGSFNYS 150
             C    P  C ++  +N   RRP    DGS   S
Sbjct: 94  ANCLSGHPAYCENFFPLNFSGRRP----DGSTPLS 124


>gnl|CDD|234528 TIGR04264, hyperosmo_Ebh, hyperosmolarity resistance protein Ebh,
            N-terminal domain.  Staphylococcal protein Ebh
            (extracellular matrix-binding protein homolog) is a giant
            protein, sometimes over 10,000 amino acids long as
            reported. This model describes a non-repetitive
            amino-terminal domain of about 2400 amino acids.
          Length = 2354

 Score = 27.5 bits (61), Expect = 5.3
 Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 2/27 (7%)

Query: 139  PVRKRDGSFNYSPD--TYCTKYDETTG 163
            P R  DG F +SPD  +   +YD TTG
Sbjct: 1115 PGRGTDGGFEWSPDHKSLIYRYDATTG 1141


>gnl|CDD|217441 pfam03232, COQ7, Ubiquinone biosynthesis protein COQ7.  Members of
           this family contain two repeats of about 90 amino acids,
           that contains two conserved motifs. One of these DXEXXH
           may be part of an enzyme active site.
          Length = 170

 Score = 26.4 bits (59), Expect = 8.3
 Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 3/36 (8%)

Query: 24  HALSSTIVEINVEVLEHSNIGL---VSQATTYALLK 56
             L  TI +   E LEH +  +     QA  Y LL 
Sbjct: 118 KELKETIAKFRDEELEHRDTAIEHGAEQAPAYPLLS 153


>gnl|CDD|224131 COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope
          biogenesis, outer membrane].
          Length = 291

 Score = 26.7 bits (60), Expect = 8.7
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 58 AQPREILALVDGPSIQF 74
          A P+E+L +VD P IQ+
Sbjct: 24 AIPKEMLPIVDKPLIQY 40


>gnl|CDD|182231 PRK10086, PRK10086, DNA-binding transcriptional regulator DsdC;
           Provisional.
          Length = 311

 Score = 26.5 bits (59), Expect = 9.2
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 24  HALSSTIVEINVEVLEHSNIGLVSQATTYALLKIAQ 59
            AL S++  +N E+L+  N  L    T Y+   IAQ
Sbjct: 79  WALKSSLDTLNQEILDIKNQELSGTLTVYSRPSIAQ 114


  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
   0.324    0.140    0.446 

Gapped
Lambda     K      H
   0.267   0.0806    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,666,032
Number of extensions: 870526
Number of successful extensions: 616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 14
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.2 bits)