GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Marinobacter adhaerens HP15

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF3373 HP15_3315 acetylornithine deacetylase (ArgE)

Query= ecocyc::ACETYLORNDEACET-MONOMER
         (383 letters)



>FitnessBrowser__Marino:GFF3373
          Length = 389

 Score =  372 bits (955), Expect = e-108
 Identities = 189/378 (50%), Positives = 249/378 (65%), Gaps = 1/378 (0%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNM 64
           +P   ++   LI+ PSIS+     D SN  ++  LA+W + LGF+VE+  VPG   KFN+
Sbjct: 11  VPGIRDMLARLISLPSISSASAKWDHSNEPVVRTLAEWLEALGFSVEILEVPGMPGKFNL 70

Query: 65  LASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDAL 124
           + ++G G GGL+L+GHTDTVPFDD RW  DPFTLTE D + YGLGT DMKGFF   ++A 
Sbjct: 71  IGTLGSGPGGLVLSGHTDTVPFDDKRWQSDPFTLTERDNRWYGLGTCDMKGFFPLAIEAA 130

Query: 125 RDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHIS 184
           R      LK+PL ILATADEE+SM GAR  AE    +   A+IGEPTSL+PVR HKG + 
Sbjct: 131 RAFVDEDLKQPLIILATADEESSMDGARALAEAGKPKARYAVIGEPTSLKPVRMHKGIMM 190

Query: 185 NAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHI 244
             ++ +GQSGHSS+PA G NA+E MH+A+  +L LR   +E+Y    F V +PTLNLG I
Sbjct: 191 ERLKFEGQSGHSSNPALGRNAMEGMHEALTELLALRSGWQEKYRNPNFEVQFPTLNLGCI 250

Query: 245 HGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPG 304
           HGGD  NRICA CELH D+RPLPGM +  L   +   + P+++R    L  + L   +P 
Sbjct: 251 HGGDNPNRICAQCELHFDLRPLPGMNMETLRQAILSKVQPIADRRELSLEFEPLFDGVPP 310

Query: 305 YECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLET 363
           +E P +  LV+  EKL G     V + TEAP++Q L   TLV+GPGSI+QAHQPDE++E 
Sbjct: 311 FETPADAALVKACEKLTGHTAHAVAFATEAPWLQKLGLETLVMGPGSIDQAHQPDEFIEL 370

Query: 364 RFIKPTRELITQVIHHFC 381
             I PT +++  +I  FC
Sbjct: 371 SQIDPTVKVLRGLIRQFC 388


Lambda     K      H
   0.320    0.139    0.430 

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: 440
Number of extensions: 12
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: 383
Length of database: 389
Length adjustment: 30
Effective length of query: 353
Effective length of database: 359
Effective search space:   126727
Effective search space used:   126727
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate GFF3373 HP15_3315 (acetylornithine deacetylase (ArgE))
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.16424.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16424.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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