Alignments for a candidate for dapF in Desulfovibrio oxyclinae DSM 11498

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_018126068.1 B149_RS0115400 diaminopimelate epimerase

Query= curated2:O67693
         (279 letters)



>NCBI__GCF_000375485.1:WP_018126068.1
          Length = 286

 Score =  222 bits (566), Expect = 6e-63
 Identities = 133/278 (47%), Positives = 166/278 (59%), Gaps = 14/278 (5%)

Query: 3   FWKLQGSGNDFVVIDDRDEKLESFLKERGVSKEDFVRKVCAFHTGVGADGLILIKN-PDN 61
           F+K+QG GNDFVVID+R+  L           +D+V K+CA   GV ADGL  I N P  
Sbjct: 11  FFKMQGCGNDFVVIDNRELGLPE------AEMKDWVTKICARAFGVYADGLFFIDNAPKG 64

Query: 62  PENDFKWEFFNSDGSVAEMCGNGSRCAVRFAYERGIVGNKVRFETLAGVIKAEVYENGRK 121
              D++W FFNSDGS AEMCGN SRC  R AYE G    +  F T AG IKAEV   G K
Sbjct: 65  SGLDYRWHFFNSDGSRAEMCGNASRCMGRLAYELGAAPREHTFGTDAGPIKAEVILEGEK 124

Query: 122 ---VKVQLTPPSKPEEKT-LTVDGEEVIGVFINTGVPHFVVPVEDVEKVNVIKLGRAIRF 177
              VK+QLTP       T L VDG+ +    ++TGVPH VV ++DV  +++ +LG AIR+
Sbjct: 125 AGEVKIQLTPAQGMTLNTELEVDGQTLTVHHVDTGVPHAVVFLDDVNAIDIKRLGAAIRY 184

Query: 178 HEEFQPKGTNVNFVQPVSEDTIKVRTYERGVESETLACGTGATACAIVSYLKGLVKKKPV 237
           H+ F P G N NF Q + +DT+ +RTYERGVE ET ACGTGA A  IV++  GL   +  
Sbjct: 185 HDHFAPAGCNANFAQVLDKDTMLLRTYERGVEDETYACGTGAAATQIVAHELGLTNAEAA 244

Query: 238 NVLTRSGEVLTIDFSEDLKEVFLTGSVYKVFEGRLSEE 275
            + T  GEVLTI         FL G+   VF+G L  E
Sbjct: 245 -LTTSGGEVLTIALENG--NAFLQGAATLVFKGELYPE 279


Lambda     K      H
   0.317    0.138    0.399 

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: 246
Number of extensions: 16
Number of successful extensions: 5
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: 286
Length adjustment: 26
Effective length of query: 253
Effective length of database: 260
Effective search space:    65780
Effective search space used:    65780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate WP_018126068.1 B149_RS0115400 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.438.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.438.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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