GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Klebsiella michiganensis M5al

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate BWI76_RS04460 BWI76_RS04460 4-hydroxy-tetrahydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__Koxy:BWI76_RS04460
          Length = 273

 Score =  489 bits (1259), Expect = e-143
 Identities = 247/273 (90%), Positives = 261/273 (95%)

Query: 1   MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGV 60
           MHDA IRVAIAGAGGRMGRQLIQA   ++G  LGAALEREGSSLLGSDAGELAGAGK GV
Sbjct: 1   MHDAQIRVAIAGAGGRMGRQLIQAVQQMDGAALGAALEREGSSLLGSDAGELAGAGKAGV 60

Query: 61  TVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAAD 120
            VQSSL+AVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD+AGKQAIR+A+ +
Sbjct: 61  VVQSSLEAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDDAGKQAIREASQE 120

Query: 121 IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAH 180
           IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIA 
Sbjct: 121 IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAG 180

Query: 181 ALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSR 240
           ALDKDLK CAVYSREG+TGERVPGTIGFATVRAGDIVGEHTAMFADIGER+EI+HKASSR
Sbjct: 181 ALDKDLKACAVYSREGYTGERVPGTIGFATVRAGDIVGEHTAMFADIGERIEISHKASSR 240

Query: 241 MTFANGAVRSALWLSGKESGLFDMRDVLDLNNL 273
           MTFANGAVRSALWL GK++GLFDMRDVL+LN+L
Sbjct: 241 MTFANGAVRSALWLKGKKNGLFDMRDVLELNSL 273


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: 387
Number of extensions: 10
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: 273
Length adjustment: 25
Effective length of query: 248
Effective length of database: 248
Effective search space:    61504
Effective search space used:    61504
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 BWI76_RS04460 BWI76_RS04460 (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.20882.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20882.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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