GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Pseudomonas fluorescens FW300-N2C3

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate AO356_06090 AO356_06090 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_06090
          Length = 383

 Score =  458 bits (1178), Expect = e-133
 Identities = 233/375 (62%), Positives = 276/375 (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   SPTLQLACDLIRRPSVTPVDADCQKLMMQRLGNAGFTLEPMRIEDVDNFWASHGKHDGPV 67

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

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

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

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

Query: 302 LLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADL 361
           LL AV +++ +V  +     T+GGTSDGRFIA MG QVVELGPVNATIH+VNE V  ADL
Sbjct: 308 LLDAVSSSIRDVTGRETQASTSGGTSDGRFIATMGTQVVELGPVNATIHQVNERVLAADL 367

Query: 362 EKLTDMYQKTLNHLL 376
           + LT++Y KTL  LL
Sbjct: 368 DVLTEIYYKTLIKLL 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: 493
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 AO356_06090 AO356_06090 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.4107.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4107.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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