GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Phaeobacter inhibens BS107

Align Acetylornithine deacetylase; AO; Acetylornithinase; EC 3.5.1.16; N-acetylornithinase; NAO (uncharacterized)
to candidate GFF997 PGA1_c10140 acetylornithine deacetylase ArgE

Query= curated2:O68873
         (380 letters)



>FitnessBrowser__Phaeo:GFF997
          Length = 388

 Score =  185 bits (470), Expect = 2e-51
 Identities = 134/383 (34%), Positives = 194/383 (50%), Gaps = 38/383 (9%)

Query: 1   MSDTLPALRATLTELVAMDTTSFRPNVPLIDYAQARLEAAGFSAERQKFLDDAGVEKVNL 60
           M+D L  L   +T+L++  T S   N+PL+D+ +  L + G +A R  ++D     K  +
Sbjct: 1   MADQLTPLEI-MTKLISFPTVSSETNLPLVDWVEGYLASHGITAHR--WVDPDQPHKAAV 57

Query: 61  VAVKGGSGSGRAALALVGHSDCVPYDAA-W-TDALRLTEKDGRLYARGACDTKGFIACAL 118
            A  G    G  A+ L GH+D VP +   W +D   + E+DG+ + RG CD KGF A A+
Sbjct: 58  FAHVGPDVEG--AVVLSGHTDVVPIEGQPWDSDPFTVVERDGKYFGRGTCDMKGFDALAI 115

Query: 119 HAALNAEQ--LKAPLMVVLTADEEVGLTGAKKLVEAG---LGRARHAIVGEPTRLIPVRA 173
            A + A    +  PL + L+ DEEVG TGA  ++ A    L +    IVGEP+ + PV  
Sbjct: 116 WALVAAHHRGVARPLQLALSFDEEVGCTGAPPMIVAMQDVLPKGSCVIVGEPSVMRPVTG 175

Query: 174 NKGYCLAEVEVRGKEGHSAYPDSGASAIFRAGRFL-----QRLEHLALTVLREDLDEGFQ 228
           +KG       + G E HS+   +G SAI +  R +     +  E++A T   +D+   F 
Sbjct: 176 HKGGIGYSTHLVGFEVHSSLMHTGVSAIMQGARLIDWANARNAENMAKTP--DDVAALFT 233

Query: 229 PPFTTVNVGVIQGGKAKNVIPGACRFVVEWRPIPGQPPERVSQLLETIRQELVRDEPAFE 288
           PPFTT +VG+I GG A N+    CRFV+++R +PG+         E      VRD    E
Sbjct: 234 PPFTTCHVGMINGGTAHNITAKDCRFVMDFRVVPGESAAE----WEAAYLAKVRD---IE 286

Query: 289 AQIRVVRTDRGVNTRADAEVVRFLAEASG------------NAPETVSFGTEAPQMTELG 336
           A+++VV  D  ++      V   + E  G            N    VS+GTEA Q  E G
Sbjct: 287 AEMQVVHPDTRIDVSKKFNVPGLVPEVEGEAETLVRALTGDNGTHVVSYGTEAGQFQEAG 346

Query: 337 AEAVVFGPGDIRVAHQTGEYVPV 359
             AV+ GPGDI  AHQ  EY+ V
Sbjct: 347 YSAVICGPGDIAQAHQPNEYIDV 369


Lambda     K      H
   0.319    0.136    0.396 

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: 394
Number of extensions: 19
Number of successful extensions: 6
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: 380
Length of database: 388
Length adjustment: 30
Effective length of query: 350
Effective length of database: 358
Effective search space:   125300
Effective search space used:   125300
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 GFF997 PGA1_c10140 (acetylornithine deacetylase ArgE)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.13556.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13556.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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