GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Dinoroseobacter shibae DFL-12

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate 3606580 Dshi_0012 succinyl-diaminopimelate desuccinylase (RefSeq)

Query= curated2:Q5LN80
         (380 letters)



>FitnessBrowser__Dino:3606580
          Length = 379

 Score =  557 bits (1436), Expect = e-163
 Identities = 278/377 (73%), Positives = 306/377 (81%)

Query: 4   DAARLTADLIRCASVTPADDGALDVLERVLSQAGFSCTRVDRGGICNLFARWGDKGHARS 63
           D   LTADLIRC SVTP + GAL +LE  LS AGF+CTRVDR GI NLFARWG+KGHARS
Sbjct: 3   DPVALTADLIRCPSVTPEEGGALSLLEARLSAAGFACTRVDRNGIANLFARWGEKGHARS 62

Query: 64  FGFNGHTDVVPVGDAAAWTVAPFGAEEKDGFLYGRGATDMKSGVAAFVAAAVDLVTTTPP 123
           FGFNGHTDVVPVG  A W   PFGA+ +  ++YGRGA DMKS VAAF AAA+D V  TPP
Sbjct: 63  FGFNGHTDVVPVGARADWRFDPFGAQVEGDWMYGRGAVDMKSAVAAFAAAAMDFVADTPP 122

Query: 124 EGAVIVTITGDEEGDALDGTKALLDYMAASGERMSVCLVGEPTCPDRMGEMIKIGRRGSM 183
           +GAVI+ ITGDEEGDA DGT ALLD+MAA GE M VCLVGEPTCPD MGEM+KIGRRGSM
Sbjct: 123 DGAVILAITGDEEGDAKDGTVALLDWMAAQGEAMDVCLVGEPTCPDEMGEMMKIGRRGSM 182

Query: 184 TAWFTVTGVQGHSAYPHRAKNPLPAMARLMDRLASHGLDQGTDHFDPSTLAVVTIDTGNT 243
           T +F   GVQGHSAYPHRAKNPLPA+A+L+DRLA   LD GTDHFDPSTLAV T DTGN 
Sbjct: 183 TFFFEALGVQGHSAYPHRAKNPLPALAKLVDRLAGLELDTGTDHFDPSTLAVTTFDTGNP 242

Query: 244 ATNVIPAQCRGAVNIRFNDLHSGASLTGWMQGEADRVAEEFGVAVEMKVKISGESFLTPP 303
           A NVIPA CR  VNIRFND HS  SLT  ++G A  VA E G+ +  +V +SGESF+TPP
Sbjct: 243 ANNVIPAACRATVNIRFNDAHSSESLTAMVRGIAAEVAAETGIEITDRVSVSGESFITPP 302

Query: 304 GELSDLVAAAVEAETGVTPVLSTSGGTSDARFVKDHCPVVEFGLVGRTMHQVDERVEIAQ 363
           G LSDLVAAAVE ETG  PVLSTSGGTSDARFV+ HCPVVEFGLVG++MHQVDERV IAQ
Sbjct: 303 GRLSDLVAAAVETETGRVPVLSTSGGTSDARFVQHHCPVVEFGLVGKSMHQVDERVAIAQ 362

Query: 364 IHQLKAIYGRILRDFFA 380
           I QLKAIY RILRD+FA
Sbjct: 363 IPQLKAIYTRILRDYFA 379


Lambda     K      H
   0.319    0.135    0.405 

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: 562
Number of extensions: 17
Number of successful extensions: 1
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: 380
Length of database: 379
Length adjustment: 30
Effective length of query: 350
Effective length of database: 349
Effective search space:   122150
Effective search space used:   122150
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: 50 (23.9 bits)

Align candidate 3606580 Dshi_0012 (succinyl-diaminopimelate desuccinylase (RefSeq))
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.1193.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1193.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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