GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Herbaspirillum seropedicae SmR1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate HSERO_RS13940 HSERO_RS13940 acetylornithine deacetylase

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



>FitnessBrowser__HerbieS:HSERO_RS13940
          Length = 390

 Score =  174 bits (440), Expect = 5e-48
 Identities = 121/351 (34%), Positives = 172/351 (49%), Gaps = 22/351 (6%)

Query: 31  SNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASI--------GQGAGGLLLAGHTD 82
           SN +LIT + D  +  G    +      + K N+ A++        G   GG++L+GHTD
Sbjct: 20  SNLELITTVRDSLQQQGVASWLAHNKD-KTKANLFATLPATAGPHAGSTEGGIVLSGHTD 78

Query: 83  TVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTKLKKPLYILATA 142
            VP D  +W  DPF LTE DG LY  G+ DMKGF A  L  + +       KP+++  + 
Sbjct: 79  VVPVDGQKWDTDPFKLTEKDGALYARGSCDMKGFIATALALVPEYLAMPRVKPIHLAFSF 138

Query: 143 DEETSMAGARYFAE---TTALRPDCAIIGEPTSLQPVRAHKGHISNAIRIQGQSGHSSDP 199
           DEE    GA    E      ++ D  ++GEPTS+  V AHKG    A ++ G+S HSS  
Sbjct: 139 DEEIGCIGAPVMLEEIVKRGIKVDGCVVGEPTSMNVVVAHKGINVFACKVHGKSAHSSLT 198

Query: 200 ARGVNAIELMHDAIGHILQLRDNLKERYHYEA-FTVPYPTLNLGHIHGGDASNRICACCE 258
            +G NAIE     I  I    D  K    Y+  F VP+ T+    I GG A N I   CE
Sbjct: 199 PQGCNAIEHAARLICAIRDFADGYKANGPYDQFFDVPFSTMTTNQIRGGIAVNTIPELCE 258

Query: 259 LHMDIRPLPGMTLNELNGLLNDALAPV------SERWPGRLTVDELHPPIPGYECPPNHQ 312
              + R LPGM++ ++   ++  +A V      +E    R+ +D      P  E      
Sbjct: 259 FTYEFRNLPGMSVADIQAQIDKYIAEVLLPKMRTEFPDARVEIDNF-AGSPALEAVEQAA 317

Query: 313 LVEVVEKLLG-AKTEVVNYCTEAPFIQTL-CPTLVLGPGSINQAHQPDEYL 361
           + E+V  L G  +T  V Y TEA   Q +  PT+V GPG I  AH+P+E++
Sbjct: 318 ITELVRALTGDRQTRKVAYGTEAGLFQQIGIPTIVCGPGDIGNAHKPNEFV 368


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: 328
Number of extensions: 13
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: 390
Length adjustment: 30
Effective length of query: 353
Effective length of database: 360
Effective search space:   127080
Effective search space used:   127080
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 HSERO_RS13940 HSERO_RS13940 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.30653.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30653.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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