GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N1B4

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_3904 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904
          Length = 383

 Score =  732 bits (1889), Expect = 0.0
 Identities = 362/383 (94%), Positives = 376/383 (98%)

Query: 9   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWGCVNQTLEQ 68
           VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISK+LERN KVDP EVEDVIWGCVNQTLEQ
Sbjct: 1   VIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQ 60

Query: 69  GWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 128
           GWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV
Sbjct: 61  GWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHV 120

Query: 129 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLAHKATVEGK 188
           SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+REQQDAF VRSHQLAHKAT+EGK
Sbjct: 121 SMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQLAHKATLEGK 180

Query: 189 FKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAGTSSQITDG 248
           FKDEIIPMQGYDENGFLK+FDYDETIRP+TTLESLAALKPAFNPKGGTVTAGTSSQITDG
Sbjct: 181 FKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAFNPKGGTVTAGTSSQITDG 240

Query: 249 ASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLNMADIDF 308
           ASCMIVMSAQRA+DLG++P+AVIRSMAVAGVDPAIMGYGPVPATQKALKRAGL + DIDF
Sbjct: 241 ASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLGINDIDF 300

Query: 309 IELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 368
            ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG
Sbjct: 301 FELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNG 360

Query: 369 GTFGLSTMCIGLGQGIATVFERV 391
           GTFG++TMCIGLGQGI+TVFERV
Sbjct: 361 GTFGVATMCIGLGQGISTVFERV 383


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: 662
Number of extensions: 15
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: 383
Length adjustment: 30
Effective length of query: 361
Effective length of database: 353
Effective search space:   127433
Effective search space used:   127433
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 Pf1N1B4_3904 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.27523.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27523.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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