GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Dechlorosoma suillum PS

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Dsui_1977 Dsui_1977 dihydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__PS:Dsui_1977
          Length = 292

 Score =  388 bits (996), Expect = e-113
 Identities = 193/292 (66%), Positives = 233/292 (79%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MI GS+VA+VTP    GRLD+DSL KL+DFH+QEGT+ IV VGT+GES T++V+EH ++I
Sbjct: 1   MITGSIVAIVTPMSDDGRLDYDSLKKLIDFHVQEGTDGIVIVGTSGESPTVNVDEHAELI 60

Query: 61  RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120
           R  V    GRIPVIAGTGANST EA+ LT  AKS GADA L V PYYNKPTQEG+YQHFR
Sbjct: 61  RTTVKHAAGRIPVIAGTGANSTSEAIELTRFAKSVGADAALSVVPYYNKPTQEGLYQHFR 120

Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180
            IAEAV IP ILYNVPGRT  DM  +T  RL+++ N++GIK+ATG+L+R  ++I R   D
Sbjct: 121 SIAEAVDIPVILYNVPGRTVADMSNDTALRLAQIDNVVGIKDATGNLERGADLIARAPAD 180

Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240
           F VYSGDDA+AV L+LLGGKG+ISVTANVAPR M ++CAAA+ GD A AR I+ +L+ LH
Sbjct: 181 FAVYSGDDASAVALILLGGKGDISVTANVAPRLMHEMCAAALAGDVAKAREIHFKLLGLH 240

Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVLA 292
           + LF E+NPIPVKWA+ ++GLIP GIRLPLT LSP CHE +R AMRQ GVLA
Sbjct: 241 RHLFCEANPIPVKWAVQQLGLIPGGIRLPLTTLSPECHERVRSAMRQAGVLA 292


Lambda     K      H
   0.319    0.134    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 292
Number of extensions: 7
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 292
Length of database: 292
Length adjustment: 26
Effective length of query: 266
Effective length of database: 266
Effective search space:    70756
Effective search space used:    70756
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: 48 (23.1 bits)

Align candidate Dsui_1977 Dsui_1977 (dihydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.11504.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11504.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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