GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Pseudomonas fluorescens GW456-L13

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate PfGW456L13_5101 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101
          Length = 267

 Score =  342 bits (876), Expect = 7e-99
 Identities = 174/264 (65%), Positives = 204/264 (77%)

Query: 7   RVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSL 66
           R+A+ GA GRMG+ LI+A     G  L AA++R  S+L+G+DAGELA  G+ GV +   L
Sbjct: 3   RIAVMGAAGRMGKTLIEAVQQTPGAGLTAAVDRPDSTLVGADAGELAALGRIGVPLSGDL 62

Query: 67  DAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFA 126
           D V D+FDV IDFT P  TL +LAFCR+HGK M+IGTTGF    KQ + +A  DI IVFA
Sbjct: 63  DRVVDEFDVLIDFTHPTVTLKNLAFCRKHGKAMIIGTTGFSVEEKQLLAEAGKDIPIVFA 122

Query: 127 ANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDL 186
           ANFSVGVN+ LKLL+ AA+V+GD  DIEI EAHHRHKVDAPSGTA+ MGE IA AL +DL
Sbjct: 123 ANFSVGVNLCLKLLDTAARVLGDDVDIEITEAHHRHKVDAPSGTAVRMGEVIADALGRDL 182

Query: 187 KDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANG 246
           K  AVY REG TG R   TIGFATVRAGDIVG+HT +FA  GER+EITHKASSRMTFA G
Sbjct: 183 KKVAVYGREGQTGARDRETIGFATVRAGDIVGDHTVLFAADGERVEITHKASSRMTFAKG 242

Query: 247 AVRSALWLSGKESGLFDMRDVLDL 270
           AVR+ALWL G+E GL+DM+DVLDL
Sbjct: 243 AVRAALWLDGREPGLYDMQDVLDL 266


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: 276
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: 273
Length of database: 267
Length adjustment: 25
Effective length of query: 248
Effective length of database: 242
Effective search space:    60016
Effective search space used:    60016
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 PfGW456L13_5101 (4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.23513.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23513.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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