GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Pseudomonas fluorescens FW300-N1B4

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate Pf1N1B4_2173 Diaminopimelate epimerase (EC 5.1.1.7)

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2173
          Length = 276

 Score =  315 bits (806), Expect = 9e-91
 Identities = 150/274 (54%), Positives = 192/274 (70%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHGLGNDFMV+D V+Q+    P+  ++  DRH G+GFDQLL+VE P +P++DF Y
Sbjct: 3   LRFTKMHGLGNDFMVLDLVSQHAHILPKHAKQWGDRHTGIGFDQLLIVEAPSNPDVDFRY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFNADGSEV QCGNGARCFARFV  K LT KR IRV T +G + L + +D  + VNMG 
Sbjct: 63  RIFNADGSEVEQCGNGARCFARFVLDKRLTAKRLIRVETKSGIIELDIRNDGQISVNMGA 122

Query: 121 PNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLE 180
           P   P+ +PF A     +Y +     T+    VSMGNPH V++V D++ A V  LGP +E
Sbjct: 123 PRLVPAEIPFDAPNQALSYQVDVDGTTVELAAVSMGNPHAVLRVSDINNAPVHELGPKIE 182

Query: 181 SHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRV 240
            H RFP R N+GF+QV+ R   +LRV+ERGAGETQACG+GACAA    I QG +   + +
Sbjct: 183 HHPRFPARVNVGFLQVIDRSRAQLRVWERGAGETQACGTGACAAAVAAISQGWMDSPLLI 242

Query: 241 ELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL 274
           +LPGGRL I W GPG P+ MTGPAV VY+G + L
Sbjct: 243 DLPGGRLSIEWAGPGQPVMMTGPAVRVYEGQVRL 276


Lambda     K      H
   0.323    0.140    0.425 

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: 256
Number of extensions: 8
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: 274
Length of database: 276
Length adjustment: 25
Effective length of query: 249
Effective length of database: 251
Effective search space:    62499
Effective search space used:    62499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)

Align candidate Pf1N1B4_2173 (Diaminopimelate epimerase (EC 5.1.1.7))
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.31506.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31506.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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