GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Phaeobacter inhibens BS107

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE

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



>FitnessBrowser__Phaeo:GFF769
          Length = 384

 Score =  202 bits (514), Expect = 1e-56
 Identities = 131/359 (36%), Positives = 194/359 (54%), Gaps = 19/359 (5%)

Query: 15  LIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGA-G 73
           LIA P++SA       SN ++I  LA+  +D G  V+V    G + K N+ A++G    G
Sbjct: 12  LIAYPTVSA------DSNLEMIAYLANRLEDCGARVDVMFDAGGQ-KANLFATLGPDTDG 64

Query: 74  GLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTKLK 133
           G++L+GH+D VP  D  WT DPFT+ E DG+LYG GT DMKGF A  L           +
Sbjct: 65  GIVLSGHSDVVPVTDQDWTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKFAEQISR 124

Query: 134 KPLYILATADEETSMAGARYFAET---TALRPDCAIIGEPTSLQPVRAHKGHISNAIRIQ 190
           +P++   T DEE    GA +  +      L+P  A+IGEPTS++ V  HKG    + R Q
Sbjct: 125 RPIHFAFTYDEEVGCIGAGHLVQALRERGLKPRLALIGEPTSMRVVEGHKGCHEYSTRFQ 184

Query: 191 GQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKERYHYEA-FTVPYPTLNLGHIHGGDA 249
           G  GH S+P RGVNA+E     +  +L LR +L++R   ++ F  P+ TLN+G ++GG A
Sbjct: 185 GLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPPWTTLNIGALNGGSA 244

Query: 250 SNRICACCELHMDIRPLPGMTLNELNGLL----NDALAPVSER-WPGRLTVDELHPPIPG 304
            N I +  ++  ++RP+     + +   +     D L P  +  +P      E+   + G
Sbjct: 245 HNVIASKAQVDWEMRPVQPSDADHVKDTMARYCRDTLLPAMQAIYPEASIETEVVGEVAG 304

Query: 305 YECPPNHQLVEVVEKLLGAK-TEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYL 361
                 ++  E++  LLG+   E+V + TEA   Q L    +V GPGSI QAH+ DEYL
Sbjct: 305 LTPTTQNEARELMADLLGSNAAELVPFGTEAGLFQELGMDVVVCGPGSIAQAHKADEYL 363


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: 376
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: 383
Length of database: 384
Length adjustment: 30
Effective length of query: 353
Effective length of database: 354
Effective search space:   124962
Effective search space used:   124962
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 GFF769 PGA1_c07830 (acetylornithine deacetylase ArgE)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.32760.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32760.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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