GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Azospirillum brasilense Sp245

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase

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



>FitnessBrowser__azobra:AZOBR_RS31030
          Length = 398

 Score =  173 bits (438), Expect = 9e-48
 Identities = 125/375 (33%), Positives = 177/375 (47%), Gaps = 31/375 (8%)

Query: 6   PPFIEIYRALIATPSISATEEALDQSNADLITLLADWFKDLG------FNVEVQPVPGTR 59
           P  +E+ R LIA  + S        SN DLI  + D   +LG      FN E       R
Sbjct: 15  PRTLELLRDLIAFDTTSRN------SNLDLIHYIRDHLAELGVSSTLVFNEE-------R 61

Query: 60  NKFNMLASIG-QGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFA 118
            K N+ A+IG    GG+ L+GHTD VP DD  W+ DPFTLTE DGKL+G GTADMKGF A
Sbjct: 62  TKANLYATIGPMDRGGVCLSGHTDVVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIA 121

Query: 119 FILDALRDVDVTKLKKPLYILATADEETSMAGARYFAET---TALRPDCAIIGEPTSLQP 175
             L    D     L  P++   + DEE    G           A++P   I+GEPT ++ 
Sbjct: 122 AALAMAPDFLAANLTTPVHYAFSYDEELGCLGVPGLLTQLAGMAVKPRLCIVGEPTRMRV 181

Query: 176 VRAHKGHISNAIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYE-AFTV 234
           +  HKG ++   R+ G + HSS   +GVNA+E   + +  +  +     E+  ++  + +
Sbjct: 182 IVGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLRGMGRRFAEQGPFDHDYDI 241

Query: 235 PYPTLNLGHIHGGDASNRICACCELHMDIRPLP----GMTLNELNGLLNDALAPVSERWP 290
           PY T++ G + GG A N + +      +IR L        L EL          +    P
Sbjct: 242 PYTTVHTGVMEGGTARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVRP 301

Query: 291 GRLTVDELHPPIPGYECPPNHQLVEVVEKLLGAKTE-VVNYCTEAPFIQTLC--PTLVLG 347
                 E     P  + PP  + V +V+ L        V + TE     ++   P +V G
Sbjct: 302 DAGFSWETLSDSPALDTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVCG 361

Query: 348 PGSINQAHQPDEYLE 362
           PG I QAH+PDEY+E
Sbjct: 362 PGDIEQAHKPDEYVE 376


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: 382
Number of extensions: 17
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 352
Effective length of database: 367
Effective search space:   129184
Effective search space used:   129184
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 AZOBR_RS31030 AZOBR_RS31030 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.26987.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26987.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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