GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas putida KT2440

Align FadA (EC 2.3.1.16) (characterized)
to candidate PP_2137 PP_2137 beta-ketoadipyl CoA thiolase, beta component

Query= metacyc::G1G01-2278-MONOMER
         (391 letters)



>FitnessBrowser__Putida:PP_2137
          Length = 391

 Score =  780 bits (2014), Expect = 0.0
 Identities = 391/391 (100%), Positives = 391/391 (100%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG 60
           MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG
Sbjct: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG
Sbjct: 61  CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120

Query: 121 GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA 180
           GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG 240
           HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG
Sbjct: 181 HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG 300
           TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG
Sbjct: 241 TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG 300

Query: 301 LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL 360
           LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTLGVATMCVGLGQGITTVFERV 391
           LNVMKQNGGTLGVATMCVGLGQGITTVFERV
Sbjct: 361 LNVMKQNGGTLGVATMCVGLGQGITTVFERV 391


Lambda     K      H
   0.319    0.134    0.392 

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: 716
Number of extensions: 17
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate PP_2137 PP_2137 (beta-ketoadipyl CoA thiolase, beta component)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.30185.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30185.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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