GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Marinobacter adhaerens HP15

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate GFF248 HP15_247 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>FitnessBrowser__Marino:GFF248
          Length = 416

 Score =  325 bits (832), Expect = 2e-93
 Identities = 168/381 (44%), Positives = 245/381 (64%), Gaps = 1/381 (0%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEI 72
           TP Y+Y    +++ +  Y +A +    L+CYA+KANSNL++L++LA L +G D VS GE+
Sbjct: 27  TPAYVYSRATLERHYRAYDDALRDHPHLVCYAVKANSNLAVLNVLARLGAGFDIVSAGEL 86

Query: 73  QRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARI 132
           +R L+AG  P R+VFSGVGK  +E+++AL++ +   NVES  EL  +  +A  LG+KA I
Sbjct: 87  ERVLRAGGDPSRVVFSGVGKQEWEMKRALEVGVRCFNVESDTELDRLNAVAGELGVKAPI 146

Query: 133 SIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLD 192
           S+R+NP++DA THPYISTGLKENKFG+   EA +++  A     L+   V  HIGSQL  
Sbjct: 147 SLRVNPDVDAGTHPYISTGLKENKFGIDIAEASQVYARAAGMPNLDVKGVDCHIGSQLTS 206

Query: 193 LEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL 252
           + P ++A  +V  +  SL   GI +   D+GGG+GV+Y  E+  +  DY + +   L   
Sbjct: 207 VSPFLDALDRVLALIDSLADQGIHIHHLDMGGGLGVTYNQEQPPQPSDYVKALAERLGDR 266

Query: 253 DLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIRVIT 312
            L +I EPGRSI A +G L+T+V + K  +++ F I+DA MND +RP+LY A  AI  + 
Sbjct: 267 KLELILEPGRSIAANAGILVTRVEFLKCTEHRNFAIIDAAMNDLIRPALYSAWQAIIPVK 326

Query: 313 PSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKL 372
           P +  E    D+VGPVCE+ D   KD HL  L+ GD +A+   GAYG  M+S YN+R + 
Sbjct: 327 PHQDGEEKAWDLVGPVCETGDFLGKDRHL-RLQAGDLLAVRSAGAYGFVMSSNYNTRNRP 385

Query: 373 LELALEDHKIRVIRKREALED 393
            EL ++  ++ V+R+RE LED
Sbjct: 386 PELMVDGDQVHVVRRRETLED 406


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: 404
Number of extensions: 15
Number of successful extensions: 2
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: 416
Length adjustment: 31
Effective length of query: 374
Effective length of database: 385
Effective search space:   143990
Effective search space used:   143990
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 GFF248 HP15_247 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

Software error:

../bin/blast/fastacmd -i /tmp/list.13202.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13202.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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