Alignments for a candidate for dapE in Pseudomonas simiae WCS417

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate GFF1211 PS417_06155 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__WCS417:GFF1211
          Length = 383

 Score =  458 bits (1178), Expect = e-133
 Identities = 230/375 (61%), Positives = 277/375 (73%), Gaps = 2/375 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQS-PL 62
           SP L LA +LI R SVTP DA CQ LM++RL   GF +E M  ED  NFWA  G    P+
Sbjct: 8   SPTLQLAIDLIRRPSVTPIDADCQKLMMQRLGDAGFALEPMRIEDVDNFWATHGKHDGPV 67

Query: 63  FVFAGHTDVVPAGPLSQWHTPPFEPTVID-GFLHGRGAADMKGSLACMIVAVERFIAEHP 121
             FAGHTDVVP GP+  W   PF+  + + G L GRGAADMKGSLA M+VA ERF+ ++P
Sbjct: 68  LCFAGHTDVVPTGPVQAWQNDPFDALIDENGMLCGRGAADMKGSLAAMLVAAERFVTDYP 127

Query: 122 DHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRG 181
           DH+GS+ FLITSDEEGP  +GT  V+E L AR E +D CIVGEPSST  VGDVVKNGRRG
Sbjct: 128 DHKGSVAFLITSDEEGPAHHGTKAVIERLAARKERLDWCIVGEPSSTTLVGDVVKNGRRG 187

Query: 182 SITGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAG 241
           S+   L V+G QGHVAYPHLA NP+H A PALAELAA  WD+GNA+FPPTSFQI NL +G
Sbjct: 188 SLGATLTVRGIQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFPPTSFQISNLNSG 247

Query: 242 TGASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGE 301
           TGA+NVIPG+    FNFRFSTE T E +++RV  +LD HGLD+ V+W LSG PFLT+ G 
Sbjct: 248 TGATNVIPGDLKAVFNFRFSTESTVEGLQQRVAEILDKHGLDWHVEWALSGLPFLTEPGA 307

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL AV A+++ +  +     T+GGTSDGRFIA +G QVVELGPVNATIH+VNE +  +DL
Sbjct: 308 LLDAVSASIKAITGRETQASTSGGTSDGRFIATLGTQVVELGPVNATIHQVNERILASDL 367

Query: 362 EKLTDMYQKTLNHLL 376
           + LT++Y +TL  LL
Sbjct: 368 DVLTEIYYQTLIKLL 382


Lambda     K      H
   0.318    0.135    0.403 

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: 517
Number of extensions: 24
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: 377
Length of database: 383
Length adjustment: 30
Effective length of query: 347
Effective length of database: 353
Effective search space:   122491
Effective search space used:   122491
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1211 PS417_06155 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.27456.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.27456.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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