GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Escherichia coli BW25113

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate 15520 b1398 phenylacetyl-CoA ligase (NCBI)

Query= SwissProt::P76085
         (437 letters)



>FitnessBrowser__Keio:15520
          Length = 437

 Score =  888 bits (2294), Expect = 0.0
 Identities = 437/437 (100%), Positives = 437/437 (100%)

Query: 1   MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL 60
           MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL
Sbjct: 1   MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL 60

Query: 61  RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120
           RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS
Sbjct: 61  RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120

Query: 121 LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM 180
           LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM
Sbjct: 121 LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM 180

Query: 181 IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL 240
           IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL
Sbjct: 181 IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL 240

Query: 241 SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI 300
           SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI
Sbjct: 241 SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI 300

Query: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL 360
           RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL
Sbjct: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL 360

Query: 361 EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR 420
           EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR
Sbjct: 361 EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR 420

Query: 421 SEGKACRVFDLRNIVGA 437
           SEGKACRVFDLRNIVGA
Sbjct: 421 SEGKACRVFDLRNIVGA 437


Lambda     K      H
   0.320    0.137    0.411 

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: 825
Number of extensions: 23
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: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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: 51 (24.3 bits)

Align candidate 15520 b1398 (phenylacetyl-CoA ligase (NCBI))
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.21718.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21718.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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