RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4741
         (62 letters)



>gnl|CDD|214838 smart00827, PKS_AT, Acyl transferase domain in polyketide
          synthase (PKS) enzymes. 
          Length = 298

 Score = 51.6 bits (125), Expect = 8e-10
 Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 2  GSQWPGMARELM-WFAPFRQAIFECDRVYRP-LGLDIVKIITSDDPTT 47
          GSQW GM REL      FR+A+ ECD   +P LG  ++ ++  +D   
Sbjct: 6  GSQWAGMGRELYETEPVFREALDECDAALQPLLGWSLLDVLLGEDGAA 53


>gnl|CDD|144338 pfam00698, Acyl_transf_1, Acyl transferase domain. 
          Length = 319

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 1  MGSQWPGMARELMWFAP-FRQAIFECDRVYRP-LGLDIVKIITSDDPTTFDDILNSFVA 57
           GSQW GM  +L+  +P F  AI  CD  ++P  G  ++ ++ ++     + +     A
Sbjct: 7  QGSQWAGMGMDLLKTSPVFAAAIARCDEAFKPQYGFSVLDVLRNNPEGLLERVDVVQPA 65


>gnl|CDD|223408 COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid
          metabolism].
          Length = 310

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 2  GSQWPGMARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTC 61
          GSQ  GM ++L  +    +A    D     LG D+  ++        +   N+  A++  
Sbjct: 12 GSQSLGMGKDL--YENSPEAKETFDEADEALGFDLWALVFEGPEEELNLTQNTQPALLLV 69


>gnl|CDD|225858 COG3321, COG3321, Polyketide synthase modules and related proteins
           [Secondary metabolites biosynthesis, transport, and
           catabolism].
          Length = 1061

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 2   GSQWPGMARELMWFAP-FRQAIFECDRVYRPL-GLDIVKIITSDD 44
           GSQW GM REL    P F  A    + +   L G  + ++I + D
Sbjct: 535 GSQWAGMGRELYALEPVFASAFDALEALLHRLLGFSLPEVIFAPD 579


>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator
           of transcription [Cell division and chromosome
           partitioning / Transcription].
          Length = 2005

 Score = 26.5 bits (58), Expect = 0.83
 Identities = 16/62 (25%), Positives = 20/62 (32%), Gaps = 10/62 (16%)

Query: 3   SQWPGMARELM---WFA-----PFRQAIFECD-RVYRPLGLDIVKIITSDDPTTFDDILN 53
           S W      ++   WF            F    +  R   L I   I SD+  TF D  N
Sbjct: 267 SIWTLEPLYVIIDCWFYISGIITVPYEFFFKRWKNERAQILFIRLHIESDEKRTF-DYSN 325

Query: 54  SF 55
            F
Sbjct: 326 VF 327


>gnl|CDD|233708 TIGR02072, BioC, biotin biosynthesis protein BioC.  This enzyme,
           which is found in biotin biosynthetic gene clusters in
           proteobacteria, firmicutes, green-sulfur bacteria,
           fusobacterium and bacteroides, is believed to carry out
           an enzymatic step prior to the formation of pimeloyl-CoA
           (although attribution of this annotation is not
           traceable). The enzyme appears related to
           methyltransferases by homology [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Biotin].
          Length = 240

 Score = 24.9 bits (55), Expect = 2.5
 Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 3/48 (6%)

Query: 12  LMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIV 59
           L W     QA+ E  RV +P GL            T  ++  SF    
Sbjct: 108 LQWCDDLSQALSELARVLKPGGLLAFSTFGPG---TLHELRQSFGQHG 152


>gnl|CDD|216526 pfam01487, DHquinase_I, Type I 3-dehydroquinase.  Type I
           3-dehydroquinase, (3-dehydroquinate dehydratase or
           DHQase.) catalyzes the cis-dehydration of
           3-dehydroquinate via a covalent imine intermediate
           giving dehydroshikimate. Dehydroquinase functions in the
           shikimate pathway which is involved in the biosynthesis
           of aromatic amino acids. Type II 3-dehydroquinase
           catalyzes the trans-dehydration of 3-dehydroshikimate
           see pfam01220.
          Length = 222

 Score = 24.8 bits (55), Expect = 3.1
 Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)

Query: 32  LGLDIVKIITSDDPTTFDDILN 53
           LG DIVKI       + +D+L 
Sbjct: 141 LGADIVKIAVM--ANSIEDVLR 160


>gnl|CDD|218837 pfam05981, CreA, CreA protein.  This family consists of several
          bacterial CreA proteins, the function of which is
          unknown.
          Length = 130

 Score = 24.5 bits (54), Expect = 3.1
 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 9/41 (21%)

Query: 22 IFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTCH 62
          + +   V++ LG D + +   DDP          V  VTCH
Sbjct: 1  VGKVSTVFKFLGKDKIVVEAFDDPK---------VPGVTCH 32


>gnl|CDD|182253 PRK10123, wcaM, putative colanic acid biosynthesis protein;
          Provisional.
          Length = 464

 Score = 24.8 bits (54), Expect = 3.4
 Identities = 10/21 (47%), Positives = 11/21 (52%)

Query: 14 WFAPFRQAIFECDRVYRPLGL 34
          W A F+QA  E   V  P GL
Sbjct: 45 WIASFKQAFSEGQTVVVPAGL 65


>gnl|CDD|181561 PRK08818, PRK08818, prephenate dehydrogenase; Provisional.
          Length = 370

 Score = 24.4 bits (53), Expect = 3.9
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 9/49 (18%)

Query: 11  ELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDIL--NSFVA 57
           EL    P+R A FE D         ++  I S +P+ ++DI   N +V 
Sbjct: 189 ELRALMPYRSASFELDTA-------VIARILSLNPSIYEDIQFGNPYVG 230


>gnl|CDD|233265 TIGR01085, murE, UDP-N-acetylmuramyl-tripeptide synthetase.  Most
           members of this family are EC 6.3.2.13,
           UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,
           6-diaminopimelate ligase. An exception is Staphylococcus
           aureus, in which diaminopimelate is replaced by lysine
           in the peptidoglycan and MurE is EC 6.3.2.7. The
           Mycobacteria, part of the closest neighboring branch
           outside of the low-GC Gram-positive bacteria, use
           diaminopimelate. A close homolog, scoring just below the
           trusted cutoff, is found (with introns) in Arabidopsis
           thaliana. Its role is unknown [Cell envelope,
           Biosynthesis and degradation of murein sacculus and
           peptidoglycan].
          Length = 464

 Score = 24.2 bits (53), Expect = 4.4
 Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 14/50 (28%)

Query: 21  AIFEC----DRVYRPL-------GLDIVKIITSDDPTTFD--DILNSFVA 57
            +F C    DR  RPL         D+V I+TSD+P   D   I+   +A
Sbjct: 362 VVFGCGGDRDRGKRPLMGAIAEQLADLV-ILTSDNPRGEDPEQIIADILA 410


  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
   0.330    0.143    0.482 

Gapped
Lambda     K      H
   0.267   0.0893    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,308,229
Number of extensions: 237394
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 11
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (23.9 bits)