GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Pseudomonas fluorescens FW300-N2E3

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate AO353_09035 AO353_09035 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_09035
          Length = 415

 Score =  317 bits (811), Expect = 5e-91
 Identities = 166/383 (43%), Positives = 246/383 (64%), Gaps = 2/383 (0%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEI 72
           TP Y+Y    I+  +L + +A  G   L+C+A+KANSNL +L++LA L +G D VS GE+
Sbjct: 27  TPTYVYSRAHIEAQYLAFADALAGTPHLVCFAVKANSNLGVLNVLARLGAGFDIVSGGEL 86

Query: 73  QRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARI 132
           +R L AG +P +IVFSGVGK+  ++ +AL++ +   NVES  EL+ ++ +A  LG++A I
Sbjct: 87  ERVLAAGGQPDKIVFSGVGKTREDMRRALEVGVHCFNVESTDELERLQVVAAELGVRAPI 146

Query: 133 SIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLD 192
           S+R+NP++DA THPYISTGLKENKFG+   +A ++++ A +   LE V V  HIGSQL  
Sbjct: 147 SLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYVRAAQLPNLEVVGVDCHIGSQLTT 206

Query: 193 LEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL 252
           L P ++A  ++  +   L   GI LR  D+GGG+GV Y +EE     DY + +   + G 
Sbjct: 207 LPPFLDALDRLLALIDRLGDCGIYLRHIDLGGGLGVRYRDEEPPLAADYIKAVRERIDGR 266

Query: 253 DLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIRVIT 312
           DLT++ EPGR IVA +G L+T+V Y K  ++K F IVDA MND +RP+LY A   +  + 
Sbjct: 267 DLTLVFEPGRFIVANAGVLLTEVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAVR 326

Query: 313 PSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKL 372
           P +       D+VGP+CE+ D   KD  L  LE GD +A+   GAYG  M+S YN+R + 
Sbjct: 327 P-RATPARAYDIVGPICETGDFLAKDRQL-ALEEGDLLAVHSAGAYGFVMSSNYNTRGRA 384

Query: 373 LELALEDHKIRVIRKREALEDLW 395
            E+ ++  +   +R+RE + +L+
Sbjct: 385 AEVLVDGDQAIEVRRRETVAELF 407


Lambda     K      H
   0.319    0.138    0.389 

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: 383
Number of extensions: 12
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: 405
Length of database: 415
Length adjustment: 31
Effective length of query: 374
Effective length of database: 384
Effective search space:   143616
Effective search space used:   143616
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 AO353_09035 AO353_09035 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.7678.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7678.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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