Alignments for a candidate for dapF in Pseudomonas simiae WCS417

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate GFF3002 PS417_15365 diaminopimelate epimerase

Query= curated2:Q3IZB6
         (279 letters)



>FitnessBrowser__WCS417:GFF3002
          Length = 267

 Score =  244 bits (624), Expect = 1e-69
 Identities = 126/261 (48%), Positives = 165/261 (63%), Gaps = 2/261 (0%)

Query: 10  LGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQEGADCALD 69
           L F+KMH  G+DF++ID RG     +TA +AR LG+RH G+GF+QLA + D + A   + 
Sbjct: 3   LPFVKMHAHGDDFIIIDRRGLHDP-ITAKVARQLGNRHTGIGFNQLAVLLDCDDAAARIK 61

Query: 70  FWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVAVNMGAPQL 129
           FWN +G+   TCG+ATR V+D LM + G D V L T RG L   R     ++VNMG P L
Sbjct: 62  FWNPNGTLLATCGSATRGVADRLMHEAGTDSVVLRTDRGLLTCARAAGRQISVNMGEPSL 121

Query: 130 LWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVETDPLFPER 189
            WS +PLA AM+T +LP++G P+A  MGNPHC +FVED  AVD+A  G A+E  PLFP +
Sbjct: 122 DWSAVPLAEAMDTLTLPIDGNPAACSMGNPHCTFFVEDLTAVDVATVGPALEIHPLFPAK 181

Query: 190 TNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRLEMDGGVLE 249
           TNV F  ++    +RLR+WERG G+ L  GS  C   V   RRGL    V++  DGG + 
Sbjct: 182 TNVHFVQVLDRGHIRLRIWERGGGVPLGSGSCCCGAVVNGIRRGLLDATVQVHCDGGTVT 241

Query: 250 VDWRDEG-VWLSGPVARVFEG 269
           V W  EG V L+G V  V +G
Sbjct: 242 VHWAGEGAVVLTGSVEPVMQG 262


Lambda     K      H
   0.321    0.138    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: 280
Number of extensions: 5
Number of successful extensions: 2
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: 279
Length of database: 267
Length adjustment: 25
Effective length of query: 254
Effective length of database: 242
Effective search space:    61468
Effective search space used:    61468
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 GFF3002 PS417_15365 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.18493.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.18493.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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