GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Dinoroseobacter shibae DFL-12

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 3606718 Dshi_0149 dihydrodipicolinate synthase (RefSeq)

Query= BRENDA::Q8UGL3
         (294 letters)



>FitnessBrowser__Dino:3606718
          Length = 291

 Score =  374 bits (960), Expect = e-108
 Identities = 195/293 (66%), Positives = 228/293 (77%), Gaps = 3/293 (1%)

Query: 1   MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60
           MFKGS+PAL+TP  D G+VD     A VEWQIAEGS+GLVPVGTTGESPTLSH+EH+ VV
Sbjct: 1   MFKGSMPALVTPMKD-GAVDFATLEALVEWQIAEGSHGLVPVGTTGESPTLSHEEHEAVV 59

Query: 61  ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120
              IEVAA RVPVIAGAGSNNT EA+    HA++AGAD  LVVTPYYNKPTQ G+ AH++
Sbjct: 60  AKVIEVAAGRVPVIAGAGSNNTVEAVRFVRHAKDAGADGALVVTPYYNKPTQGGMIAHYT 119

Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180
           A+AEA  +PIVIYNIP RSVVDM+P TM AL  A   I+GVKDATG L RVS+ R++CG 
Sbjct: 120 ALAEAADIPIVIYNIPGRSVVDMTPATMAALA-ALPTIVGVKDATGDLARVSQTRMACGP 178

Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240
           +F+QLSGED TALGFNAHGGVGCISVTANVAP LC++FQ A LAGD+A AL  QD+LMPL
Sbjct: 179 EFIQLSGEDATALGFNAHGGVGCISVTANVAPALCAQFQEATLAGDFATALALQDKLMPL 238

Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLM 293
           H AIF+EPG+ G KYALS     +  VR PL+  L   T+  I  A+ HAG++
Sbjct: 239 HEAIFVEPGLVGAKYALSLLGKCSEDVRLPLLG-LSDGTKVLIKDAMIHAGIL 290


Lambda     K      H
   0.317    0.133    0.384 

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: 346
Number of extensions: 12
Number of successful extensions: 3
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: 294
Length of database: 291
Length adjustment: 26
Effective length of query: 268
Effective length of database: 265
Effective search space:    71020
Effective search space used:    71020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 3606718 Dshi_0149 (dihydrodipicolinate synthase (RefSeq))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.20922.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20922.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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