GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas simiae WCS417

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1490 PS417_07580 3-ketoacyl-CoA thiolase

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__WCS417:GFF1490
          Length = 391

 Score =  739 bits (1909), Expect = 0.0
 Identities = 367/391 (93%), Positives = 380/391 (97%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60
           MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERN+KVDP EVEDVIWG
Sbjct: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG
Sbjct: 61  CVNQTLEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+RE QDAF +RSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREAQDAFGLRSHQLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240
           HKAT+EGKFKDEIIPM GYDENGFLK+ DYDETIRPDTTLESLAALKPAFNPKGGTVTAG
Sbjct: 181 HKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSAQRA+DLG++PLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG
Sbjct: 241 TSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L + DIDF ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LTINDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQNGG  G++TMCIGLGQGI+TVFERV
Sbjct: 361 LNVMKQNGGNLGVATMCIGLGQGISTVFERV 391


Lambda     K      H
   0.318    0.133    0.386 

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: 668
Number of extensions: 14
Number of successful extensions: 1
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF1490 PS417_07580 (3-ketoacyl-CoA thiolase)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.6421.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6421.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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