Alignments for a candidate for dapF in Polaromonas naphthalenivorans CJ2

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_041376778.1 PNAP_RS17155 diaminopimelate epimerase

Query= SwissProt::P0A6K1
         (274 letters)



>NCBI__GCF_000015505.1:WP_041376778.1
          Length = 292

 Score =  255 bits (652), Expect = 7e-73
 Identities = 144/286 (50%), Positives = 171/286 (59%), Gaps = 12/286 (4%)

Query: 1   MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHY 60
           ++F+KM G GNDF+++D     +  SP   R LADRH GVG DQ+L V P     +DF Y
Sbjct: 3   IRFTKMQGAGNDFVMLDETRGPLGLSPAHYRFLADRHFGVGADQILTVRPSPGEGIDFEY 62

Query: 61  RIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGE 120
            I NADG EV QCGNGARCF RFVR +GLT K  ++V T  G +   +  D  V VNMG 
Sbjct: 63  VIHNADGGEVEQCGNGARCFVRFVREQGLTTKDAVKVKTLGGIIEPCMQPDGRVTVNMGA 122

Query: 121 PNFEPSAVPFR--------ANKAEKTYIM---RAAEQTILCGVVSMGNPHCVIQVDDVDT 169
           P FE   +PF         A   +K  +     A    +   VVSMGNPH V  VDDVDT
Sbjct: 123 PVFELERIPFNPAGLTPQTAGSWQKWPLALDGHAQAAPVFVAVVSMGNPHAVQLVDDVDT 182

Query: 170 AAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGI 229
           A V   GP++E H  FP R N GFMQVV R  IRLRVYERGAGET ACG+GACAAV  GI
Sbjct: 183 APVLEAGPLIEHHPSFPRRVNAGFMQVVSRSQIRLRVYERGAGETLACGTGACAAVVAGI 242

Query: 230 QQGLLAEEVRVELPGGRLDIAWKGP-GHPLYMTGPAVHVYDGFIHL 274
           + GLL   V V   GG+L I W G    P+ MTGPA  V++  I +
Sbjct: 243 RLGLLDSRVDVLTRGGQLTIEWAGTLDAPVMMTGPATTVFESEIEV 288


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: 270
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: 292
Length adjustment: 26
Effective length of query: 248
Effective length of database: 266
Effective search space:    65968
Effective search space used:    65968
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 WP_041376778.1 PNAP_RS17155 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.23736.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.23736.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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