RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13496
         (249 letters)



>gnl|CDD|109297 pfam00233, PDEase_I, 3'5'-cyclic nucleotide phosphodiesterase. 
          Length = 237

 Score =  121 bits (304), Expect = 1e-33
 Identities = 52/184 (28%), Positives = 96/184 (52%), Gaps = 13/184 (7%)

Query: 16  NTSVLENHHWRSANTSVLENHHWRSAVGCLLESNVAEQLGSIRPELEQQISSLILATDIT 75
           + SVLENHH  +    +L++         + ++   +   ++R      +  +ILATD++
Sbjct: 67  DESVLENHH-LAQAFKLLQDEECN-----IFQNLSKKDFQTLR----DLVIEMILATDMS 116

Query: 76  RQQEFLTRFKAYLDSGSLDLSKAEDRHFILQIALKCADISNPCRPWDVSKKWSQKVCEEF 135
              + L   K  ++         + +  +L + +  AD+SNP +PW + ++W++ + EEF
Sbjct: 117 LHFQKLKDLKTMVEQKKRLD--LDHKILLLSLLMHAADLSNPTKPWKLHRRWAELIMEEF 174

Query: 136 FRQGDYERQLNLPVTSLCDRHSTSIPKIQTGFFKFVVSPLFEEWHRFLDTKLSTSMMGHL 195
           F QGD ER+L LP + +CDR S  +PK Q GF  F+V P+F+     ++ K    ++  +
Sbjct: 175 FDQGDLERELGLPPSPMCDRTSAYVPKSQVGFIDFIVEPIFKLLADVVE-KDIQPLLDTI 233

Query: 196 RGNQ 199
             N+
Sbjct: 234 EDNR 237


>gnl|CDD|238032 cd00077, HDc, Metal dependent phosphohydrolases with conserved 'HD'
           motif.
          Length = 145

 Score = 29.2 bits (65), Expect = 0.98
 Identities = 20/115 (17%), Positives = 38/115 (33%), Gaps = 18/115 (15%)

Query: 24  HWRSANTSVLENHHWRSAVGCLLESNVAEQLGSIRPELEQQISSLILATDITRQQEFLTR 83
              +   S LE  H            +  +L  +  E+ + I  LILA D +  +     
Sbjct: 47  DAITEEESELEKDHAIVGA------EILREL--LLEEVIKLIDELILAVDASHHE----- 93

Query: 84  FKAYLDSGSLDLSKAEDRHFILQIALKCADISNPCR--PWDVSKKWSQKVCEEFF 136
               LD          +   +    +K AD  +  R    +  ++ +++  EE  
Sbjct: 94  ---RLDGLGYPDGLKGEEITLEARIVKLADRLDALRRDSREKRRRIAEEDLEELL 145


>gnl|CDD|214679 smart00471, HDc, Metal dependent phosphohydrolases with conserved
           'HD' motif.  Includes eukaryotic cyclic nucleotide
           phosphodiesterases (PDEc). This profile/HMM does not
           detect HD homologues in bacterial glycine aminoacyl-tRNA
           synthetases (beta subunit).
          Length = 124

 Score = 28.8 bits (64), Expect = 1.3
 Identities = 23/99 (23%), Positives = 33/99 (33%), Gaps = 26/99 (26%)

Query: 29  NTSVLENHHWRSAVGCLLESNVAEQLGSIRPELEQQISSLILATDITRQQEFLTRFKAYL 88
            TSVLE+HH+  A               +  E E +I   IL T I    E         
Sbjct: 52  KTSVLEDHHFIGAE-------------ILLEEEEPRILEEILRTAILSHHERP------- 91

Query: 89  DSGSLDLSKAEDRHFILQIALKCADISNPCRPWDVSKKW 127
                D  + E      +I +K AD  +  R     ++ 
Sbjct: 92  -----DGLRGEPITLEARI-VKVADRLDALRADRRYRRV 124


>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 535

 Score = 28.8 bits (65), Expect = 3.3
 Identities = 15/48 (31%), Positives = 20/48 (41%)

Query: 47  ESNVAEQLGSIRPELEQQISSLILATDITRQQEFLTRFKAYLDSGSLD 94
           ES VA+ LG + P   +     IL  D  +  E L   + Y     LD
Sbjct: 232 ESKVADMLGLLDPSKLEDFFQAILNQDKEKLFELLKELEDYEAEMVLD 279


>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
           only].
          Length = 296

 Score = 27.8 bits (62), Expect = 4.8
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 18/80 (22%)

Query: 93  LDLSKAEDR------HFILQIALKC-----------ADISNPCRPWDVSKKWSQKVCEEF 135
           L L KA+DR       F+  + +             AD + P R WD +        ++F
Sbjct: 122 LWLIKADDRALGTDEDFLRDVIILGLDKRVLFVVTQADRAEPGREWDSAGHQPSPAIKQF 181

Query: 136 FR-QGDYERQLNLPVTSLCD 154
              + +   +L   V  +  
Sbjct: 182 IEEKAEALGRLFQEVKPVVA 201


>gnl|CDD|203679 pfam07544, Med9, RNA polymerase II transcription mediator complex
          subunit 9.  This family of Med9 proteins is conserved
          in yeasts. It forms part of the middle region of
          Mediator. Med9 has two functional domains. The
          species-specific amino-terminal half (aa 1-63) plays a
          regulatory role in transcriptional regulation, whereas
          this well-conserved carboxy-terminal half (aa 64-149)
          has a more fundamental function involved in direct
          binding to the amino-terminal portions of Med4 and Med7
          and the assembly of Med9 into the Middle module. Also,
          some unidentified factor(s) in med9 extracts may impact
          the binding of TFIID to the promoter.
          Length = 83

 Score = 26.4 bits (59), Expect = 4.9
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 10/40 (25%)

Query: 46 LESNVAEQLGSIRPELEQQISSLILATDITRQQEFLTRFK 85
          +  +V EQ   I  ELE+QI          R++E L +FK
Sbjct: 50 ISRSVEEQEAEIE-ELEEQI---------ARKREVLQKFK 79


>gnl|CDD|173954 cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the
           conversion of DAHP to DHQ in shikimate pathway for
           aromatic compounds synthesis.  Dehydroquinate synthase
           (DHQS) catalyzes the conversion of
           3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
           dehydroquinate (DHQ) in the second step of the shikimate
           pathway. This pathway, which involves seven sequential
           enzymatic steps in the conversion of erythrose
           4-phosphate and phosphoenolpyruvate into chorismate for
           subsequent synthesis of aromatic compounds,  is found in
           bacteria, microbial eukaryotes, and plants, but not in
           mammals. Therefore, enzymes of this pathway are
           attractive targets for the development of non-toxic
           antimicrobial compounds, herbicides and anti-parasitic
           agents. The activity of DHQS requires nicotinamide
           adenine dinucleotide (NAD) as cofactor. A single active
           site in DHQS catalyzes five sequential reactions
           involving alcohol oxidation, phosphate elimination,
           carbonyl reduction, ring opening, and intramolecular
           aldol condensation. The binding of substrates and
           ligands induces domain conformational changes. In some
           fungi and protozoa, this domain is fused with the other
           four domains in shikimate pathway and forms a
           penta-domain AROM protein, which catalyzes steps 2-6 in
           the shikimate pathway.
          Length = 345

 Score = 27.4 bits (62), Expect = 7.7
 Identities = 8/31 (25%), Positives = 18/31 (58%)

Query: 41  AVGCLLESNVAEQLGSIRPELEQQISSLILA 71
           A+G +  + ++E+LG +  E  ++I  L+  
Sbjct: 259 AIGMVAAARLSERLGLLSEEDLERIEKLLKK 289


  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
   0.321    0.133    0.417 

Gapped
Lambda     K      H
   0.267   0.0564    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,178,965
Number of extensions: 1092914
Number of successful extensions: 805
Number of sequences better than 10.0: 1
Number of HSP's gapped: 802
Number of HSP's successfully gapped: 13
Length of query: 249
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 155
Effective length of database: 6,768,326
Effective search space: 1049090530
Effective search space used: 1049090530
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 (21.9 bits)
S2: 58 (26.5 bits)