GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2E2

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339
          Length = 394

 Score =  195 bits (496), Expect = 2e-54
 Identities = 133/381 (34%), Positives = 191/381 (50%), Gaps = 15/381 (3%)

Query: 13  RALIATPSISATEEALDQSNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGA 72
           RAL+A     AT      SN  LI  + D+ + LG N E+      R K N+LASIG   
Sbjct: 12  RALLAELVSFATVSR--DSNLALIEFVRDYLQGLGVNSELI-YNAERTKANLLASIGPAV 68

Query: 73  -GGLLLAGHTDTVPFDDGRWTRDPFTLTEHDGKLYGLGTADMKGFFAFILDALRDVDVTK 131
            GG++L+GHTD VP D   WT DPF LTE DGK +G GTADMKG+ A +L A+     + 
Sbjct: 69  PGGVVLSGHTDVVPVDGQAWTVDPFCLTEMDGKWFGRGTADMKGYLASVLAAVPVFLSSP 128

Query: 132 LKKPLYILATADEETSMAGARYFAETTALR---PDCAIIGEPTSLQPVRAHKGHISNAIR 188
           L++P+++  + DEE    G     E    R   P   +IGEPT L+PV  HKG ++    
Sbjct: 129 LRRPVHLAFSYDEEVGCLGVHSLLEVLVRRIAQPALCLIGEPTQLRPVLGHKGKLAMRCH 188

Query: 189 IQGQSGHSSDPARGVNAIELMHDAIGHILQLRDNLKE-RYHYEAFTVPYPTLNLGHIHGG 247
           ++G + HS+    GVNAIE     IG + ++   L E   H   F     T+ +G +HGG
Sbjct: 189 VRGAACHSAYAPYGVNAIEQAARLIGRLGEIGAQLAEPSRHDPRFDPACSTVQVGVVHGG 248

Query: 248 DASNRICACCELHMDIRPLPG----MTLNELNGLLNDALAPVSERWPGRLTVD-ELHPPI 302
            A N + A C    ++R LP     + + +L G     L P  +   G   +  E     
Sbjct: 249 TALNIVPADCRFDFEVRALPDFDPLVVVEQLQGYAEQTLLPAMQAVAGDTAIRFEPLSAY 308

Query: 303 PGYECPPNHQLVEVVEKLLGAKT-EVVNYCTEAP-FIQTLCPTLVLGPGSINQAHQPDEY 360
           PG    P+     ++ +L G+     V + TE   F Q   PT+V GPGS++Q H+PDEY
Sbjct: 309 PGLATSPDSAAARLIAQLCGSDAFGTVAFGTEGGLFHQAGVPTVVCGPGSMDQGHKPDEY 368

Query: 361 LETRFIKPTRELITQVIHHFC 381
           +    +     L+ ++  + C
Sbjct: 369 VSVEQMAACDRLMDRLASYLC 389


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: 378
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: 394
Length adjustment: 30
Effective length of query: 353
Effective length of database: 364
Effective search space:   128492
Effective search space used:   128492
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 Pf6N2E2_1339 (Acetylornithine deacetylase (EC 3.5.1.16))
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.19870.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19870.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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