GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Shewanella sp. ANA-3

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 7022768 Shewana3_0023 3-ketoacyl-CoA thiolase (RefSeq)

Query= reanno::ANA3:7022768
         (387 letters)



>FitnessBrowser__ANA3:7022768
          Length = 387

 Score =  759 bits (1959), Expect = 0.0
 Identities = 387/387 (100%), Positives = 387/387 (100%)

Query: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60
           MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ
Sbjct: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60

Query: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120
           TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH
Sbjct: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120

Query: 121 MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAHAAT 180
           MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAHAAT
Sbjct: 121 MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAHAAT 180

Query: 181 VEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVFDPANGTVTAGTSSA 240
           VEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVFDPANGTVTAGTSSA
Sbjct: 181 VEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVFDPANGTVTAGTSSA 240

Query: 241 LSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN 300
           LSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN
Sbjct: 241 LSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN 300

Query: 301 DLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLGCSGARISTTLINLM 360
           DLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLGCSGARISTTLINLM
Sbjct: 301 DLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLGCSGARISTTLINLM 360

Query: 361 EHKDATLGLATMCIGLGQGIATVFERV 387
           EHKDATLGLATMCIGLGQGIATVFERV
Sbjct: 361 EHKDATLGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.320    0.134    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: 707
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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 7022768 Shewana3_0023 (3-ketoacyl-CoA thiolase (RefSeq))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.18425.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18425.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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