GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Burkholderia phytofirmans PsJN

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate BPHYT_RS01665 BPHYT_RS01665 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>FitnessBrowser__BFirm:BPHYT_RS01665
          Length = 299

 Score =  282 bits (721), Expect = 7e-81
 Identities = 149/283 (52%), Positives = 182/283 (64%), Gaps = 9/283 (3%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KMHG GNDF+V+D  TQ V  +P  +R LADRH GVG DQLL+VE P    +DF Y
Sbjct: 3   LKFTKMHGAGNDFVVLDGYTQPVNLTPAQVRALADRHFGVGADQLLLVEKPTVAGVDFRY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
           RIFN DG EV  CGNGARCF +FVR  GLT++R +RV    G + LT+ ++  V V+MG 
Sbjct: 63  RIFNCDGGEVEHCGNGARCFVKFVRDSGLTDQRSVRVQVQKGTITLTMQENGEVLVDMGT 122

Query: 121 PNFEPSAVPF-------RANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVE 173
           P F+P  VPF       R   A+  + +     T    VVSMGNPH V  VDDV+   V 
Sbjct: 123 PVFDPERVPFATKGLQGRGEGADTLWPLDVNGTTRWISVVSMGNPHAVQVVDDVEAFPVL 182

Query: 174 TLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGL 233
             GPV+E H RFP+R N GFMQ+V R  I+LRVYERGAGET ACG+GACAAVA GI++GL
Sbjct: 183 VEGPVIERHARFPQRVNAGFMQIVGRSEIKLRVYERGAGETLACGTGACAAVAAGIRRGL 242

Query: 234 LAEEVRVELPGGRLDIAWKG--PGHPLYMTGPAVHVYDGFIHL 274
           L   V V   GG+L I W       PL M GPA  V++G I L
Sbjct: 243 LDAPVLVHTHGGKLTITWDAAQADQPLLMAGPAATVFEGEIEL 285


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: 254
Number of extensions: 6
Number of successful extensions: 4
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: 299
Length adjustment: 26
Effective length of query: 248
Effective length of database: 273
Effective search space:    67704
Effective search space used:    67704
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 BPHYT_RS01665 BPHYT_RS01665 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.23761.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23761.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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