GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Pseudomonas simiae WCS417

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate GFF5387 PS417_27580 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>FitnessBrowser__WCS417:GFF5387
          Length = 415

 Score =  321 bits (822), Expect = 3e-92
 Identities = 167/387 (43%), Positives = 249/387 (64%), Gaps = 2/387 (0%)

Query: 9   QTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVS 68
           Q   TP Y+Y    I+  + ++ +A  G   L+CYA+KANSNL +L++LA L +G D VS
Sbjct: 23  QRFGTPTYVYSRAHIEAQYRSFTDALDGVSHLVCYAVKANSNLGVLNVLARLGAGFDIVS 82

Query: 69  IGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGI 128
            GE++R L AG K  +IVFSGVGK+  ++ +AL++ +   N+ES  EL+ ++ +A  +G+
Sbjct: 83  RGELERVLAAGGKAEKIVFSGVGKTREDMRRALEVGVHCFNIESTDELERLQVVAAEMGV 142

Query: 129 KARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGS 188
           +A IS+R+NP++DA THPYISTGLKENKFG+   +A ++++ A +   LE + V  HIGS
Sbjct: 143 RAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYIRAAQLPNLEVLGVDCHIGS 202

Query: 189 QLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNA 248
           QL  L P ++A  ++  +   L   GI L   D+GGG+GV Y +EE   + DY + +   
Sbjct: 203 QLTTLPPFLDALDRLLALIDRLGECGIYLHHIDLGGGVGVRYRDEEPPLIADYIKAVRER 262

Query: 249 LQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAI 308
           ++G DLT++ EPGR IVA +G L+TQV Y K  ++K F IVDA MND +RP+LY A   +
Sbjct: 263 IEGRDLTLMFEPGRYIVANAGVLLTQVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMNV 322

Query: 309 RVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNS 368
             +TP +  E    D+VGP+CE+ D   KD  L  LE GD +AI   GAYG  M+S YN+
Sbjct: 323 TAVTP-RASEARAYDIVGPICETGDFLAKDRQL-ALEEGDLLAIHSAGAYGFVMSSNYNT 380

Query: 369 RPKLLELALEDHKIRVIRKREALEDLW 395
           R +  E+ ++  +   +R+RE + +L+
Sbjct: 381 RGRTAEVLVDGDQAFEVRRRETVAELY 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: 10
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 GFF5387 PS417_27580 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.26047.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26047.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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