GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Pseudomonas fluorescens FW300-N2E3

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate AO353_05640 AO353_05640 4-hydroxy-tetrahydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05640
          Length = 268

 Score =  331 bits (849), Expect = 9e-96
 Identities = 173/265 (65%), Positives = 205/265 (77%), Gaps = 1/265 (0%)

Query: 7   RVAIAGAGGRMGRQLIQAALALEGVQ-LGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           R+A+ GA GRMG+ LI+A      +  L AA+ R GS+L+G DAGELA  G+ GV +  +
Sbjct: 3   RIAVMGAAGRMGKILIEAVQQRAPLTGLTAAIVRPGSTLIGVDAGELAALGRIGVPLSGN 62

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           L+ V  +FDV IDFT PE  L +LAFCR+ GK MVIGTTG D A KQ + +A  DI IVF
Sbjct: 63  LEMVAAEFDVLIDFTLPEVMLKNLAFCRKVGKAMVIGTTGLDAAQKQLLAEAGKDIPIVF 122

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           AANFSVGVN+ LKLL+ AA+V+GD  DIEIIEAHHR+K+DAPSGTAL MGE IA ALD+D
Sbjct: 123 AANFSVGVNLSLKLLDMAARVLGDDADIEIIEAHHRNKIDAPSGTALRMGEVIASALDRD 182

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L+  AVY REGHTG R   TIGFATVR GD+VG+HT +FA  GERLEITHKASSRMTFA 
Sbjct: 183 LQKVAVYGREGHTGVRERETIGFATVRGGDVVGDHTVLFACEGERLEITHKASSRMTFAK 242

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GAVR+ALWL G+E GL+DM+DVLDL
Sbjct: 243 GAVRAALWLDGREPGLYDMQDVLDL 267


Lambda     K      H
   0.319    0.135    0.383 

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: 275
Number of extensions: 10
Number of successful extensions: 2
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: 273
Length of database: 268
Length adjustment: 25
Effective length of query: 248
Effective length of database: 243
Effective search space:    60264
Effective search space used:    60264
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: 47 (22.7 bits)

Align candidate AO353_05640 AO353_05640 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.23270.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23270.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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