GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas putida KT2440

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate PP_1377 PP_1377 beta-ketoadipyl-CoA thiolase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Putida:PP_1377
          Length = 400

 Score =  759 bits (1961), Expect = 0.0
 Identities = 389/400 (97%), Positives = 392/400 (98%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M DVFICDAIRTPIGRFGGALA VRADDLAAVPLKALIE NP VQWDQVDEVFFGCANQA
Sbjct: 1   MHDVFICDAIRTPIGRFGGALASVRADDLAAVPLKALIERNPGVQWDQVDEVFFGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDA+GTAFRAIASGEMEL IAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAVGTAFRAIASGEMELVIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKAES YSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD
Sbjct: 121 SRAPFVMGKAESAYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE IVERDEHLRPETTLEALTKLKPV
Sbjct: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGEIIVERDEHLRPETTLEALTKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAA+ILASA AVKKHGLTPRARVLGMASGGVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAAMILASAAAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKLTERLG+AVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLTERLGIAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV
Sbjct: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 671
Number of extensions: 18
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 PP_1377 PP_1377 (beta-ketoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.20849.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20849.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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