GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Sphingomonas koreensis DSMZ 15582

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Ga0059261_1675 Ga0059261_1675 acetylornithine deacetylase (ArgE)

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



>FitnessBrowser__Korea:Ga0059261_1675
          Length = 395

 Score =  191 bits (484), Expect = 4e-53
 Identities = 126/365 (34%), Positives = 182/365 (49%), Gaps = 19/365 (5%)

Query: 9   IEIYRALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASI 68
           +EI R L+  P++S        SN DLI  + D+    G    V        K N+ A+I
Sbjct: 15  VEILRTLVGFPTVSR------DSNLDLIHWVRDYLASHGV-ASVLTSGKDPGKANLFATI 67

Query: 69  GQGAGGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVD 128
           G G GG++L+GH+D VP D   W  +PF L E DG L+G GT DMKGF A  L  +  + 
Sbjct: 68  GSGEGGIVLSGHSDVVPVDGQDWHSNPFVLEERDGLLFGRGTCDMKGFIAACLAKVPMLA 127

Query: 129 VTKLKKPLYILATADEETSMAGARYFAE---TTALRPDCAIIGEPTSLQPVRAHKGHISN 185
              L +P+++  + DEE    GA +  E      LRP   ++GEPTS++PV  HK   + 
Sbjct: 128 SANLNEPVHLAISFDEEIGCKGAGHMIEELVARGLRPRGCVVGEPTSMEPVIGHKTGSAY 187

Query: 186 AIRIQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLK-ERYHYEAFTVPYPTLNLGHI 244
              + G   HSS    GVNAI      I  I  +   L+ E   +  ++VP+ TL+ G I
Sbjct: 188 GCAVHGLEAHSSLAPYGVNAIFYAARLIARIEAIAARLRAEERRHPGYSVPFSTLSAGVI 247

Query: 245 HGGDASNRICACCELHMDIRPL----PGMTLNELNGLLNDALAPVSERWPGRLTVD-ELH 299
            GG ASN + A C    DIR L    P   + EL   ++  L P          ++  ++
Sbjct: 248 EGGQASNIVPALCRFRFDIRTLPWTDPDAIIAELQTYIDHELLPEMRAVHAGARIEITMN 307

Query: 300 PPIPGYECPPNHQLVEVVEKLLGAKTE--VVNYCTEAPFIQTL-CPTLVLGPGSINQAHQ 356
             +PG+    +  L   V++L G+  E   V + +EA   Q    PT++ GPGSI QAH+
Sbjct: 308 GRVPGFAIDADAPLTRHVQRLAGSNAEPGFVAFGSEAGLFQARGVPTILCGPGSIEQAHK 367

Query: 357 PDEYL 361
           PDE++
Sbjct: 368 PDEFV 372


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: 388
Number of extensions: 20
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: 395
Length adjustment: 30
Effective length of query: 353
Effective length of database: 365
Effective search space:   128845
Effective search space used:   128845
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 Ga0059261_1675 Ga0059261_1675 (acetylornithine deacetylase (ArgE))
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.19483.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19483.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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