Alignments for a candidate for dapF in Paraburkholderia phymatum STM815

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_012399501.1 BPHY_RS00375 diaminopimelate epimerase

Query= SwissProt::P44859
         (274 letters)



>NCBI__GCF_000020045.1:WP_012399501.1
          Length = 286

 Score =  288 bits (737), Expect = 9e-83
 Identities = 146/282 (51%), Positives = 190/282 (67%), Gaps = 8/282 (2%)

Query: 1   MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHY 60
           ++F+KMHG GNDFVV+DG TQ +  T   +R LANRH G+G DQLL+VE P    +DF Y
Sbjct: 3   LKFTKMHGAGNDFVVLDGYTQPLNLTETQVRALANRHFGVGADQLLVVEKPTVDGVDFRY 62

Query: 61  RIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGE 120
           RIFN DG EV  CGNGARCF +FV    LT+K+ + V  QKG + LT++D+ ++ V+MG 
Sbjct: 63  RIFNCDGGEVEHCGNGARCFVKFVRDSRLTDKRSVRVQVQKGVITLTMQDNGEVVVDMGA 122

Query: 121 PIWEPAKIPFTANKFEKN-------YILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVE 173
           P++EP ++PF A+  E         Y L  + +T     VSMGNPH V  VDD++   V 
Sbjct: 123 PVFEPVQVPFDASGVEARREGNDTLYALEVNGETRWVSVVSMGNPHAVQVVDDVEAFPVL 182

Query: 174 QLGPLLESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGL 233
             GP++E+H RFP+RVNAGFMQI+ +  +KLRVYERGAGET ACG+GACAAVA GI +GL
Sbjct: 183 VDGPVIETHPRFPQRVNAGFMQIVGRSEVKLRVYERGAGETLACGTGACAAVAAGIRRGL 242

Query: 234 LNNNVQVDLPGGSLMIEWNG-VGHPLYMTGEATHIYDGFITL 274
           L+  V+V   GG+L I WNG     L M G A  +++G I L
Sbjct: 243 LDAPVKVHTHGGTLTITWNGESASSLMMAGPAATVFEGEIEL 284


Lambda     K      H
   0.321    0.139    0.423 

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: 278
Number of extensions: 8
Number of successful extensions: 3
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: 286
Length adjustment: 26
Effective length of query: 248
Effective length of database: 260
Effective search space:    64480
Effective search space used:    64480
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_012399501.1 BPHY_RS00375 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.20216.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.20216.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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