GapMind for Amino acid biosynthesis

 

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

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_13080 AO356_13080 acetylornithine deacetylase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_13080
          Length = 385

 Score =  362 bits (930), Expect = e-105
 Identities = 190/379 (50%), Positives = 247/379 (65%), Gaps = 5/379 (1%)

Query: 5   LPPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPV-PGTRNKFN 63
           LP   + + ALIATPS+S T+  LDQSN+ +I LLA W  +LGF+ +VQ V PG   KFN
Sbjct: 3   LPSMKDQFAALIATPSVSCTQPGLDQSNSAVIELLAGWLTELGFSCDVQQVSPG---KFN 59

Query: 64  MLASIGQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDA 123
           +LAS G G GGL+LAGH+DTVPFD   W  DP  LTE DG+  GLG+ DMKGFFA  ++A
Sbjct: 60  LLASFGSGPGGLVLAGHSDTVPFDGALWQTDPLKLTEVDGRWVGLGSCDMKGFFALAIEA 119

Query: 124 LRDVDVTKLKKPLYILATADEETSMAGARYFAETTALRPDCAIIGEPTSLQPVRAHKGHI 183
           ++ +     K+PL ILAT DEE+SMAGAR  A+        A+IGEPT L+P+R HKG +
Sbjct: 120 VKPLLDQPFKQPLLILATCDEESSMAGARALADAGRPLGRAAVIGEPTGLRPIRLHKGVM 179

Query: 184 SNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGH 243
              I I G+SGHSSDP+ G +A+E MHDA+G +  LR   +  +    F+VP PTLN G 
Sbjct: 180 MERIDILGRSGHSSDPSLGRSALEAMHDAMGELRGLRLQWQREFRNPQFSVPQPTLNFGC 239

Query: 244 IHGGDASNRICACCELHMDIRPLPGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIP 303
           IHGGD  NRIC  C +  D+RPLPGM    L   +   L P++ER   ++    L P +P
Sbjct: 240 IHGGDNPNRICGQCSMEFDLRPLPGMDPQVLRAAIRQKLEPIAERHQVKIDYAPLFPEVP 299

Query: 304 GYECPPNHQLVEVVEKLLGAKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYLE 362
            +E   + +LV V E+L G + E V + TEAP++Q L C TLVLGPG I  AHQP EYLE
Sbjct: 300 PFEQAEDAELVRVAERLTGHRAEAVAFGTEAPYLQRLGCETLVLGPGDIACAHQPGEYLE 359

Query: 363 TRFIKPTRELITQVIHHFC 381
              ++PT +L+ Q+I H+C
Sbjct: 360 MSRLQPTVQLLRQLIGHYC 378


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: 471
Number of extensions: 16
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: 383
Length of database: 385
Length adjustment: 30
Effective length of query: 353
Effective length of database: 355
Effective search space:   125315
Effective search space used:   125315
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 AO356_13080 AO356_13080 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.1097.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1097.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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