GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas simiae WCS417

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__WCS417:GFF1320
          Length = 400

 Score =  717 bits (1852), Expect = 0.0
 Identities = 363/400 (90%), Positives = 383/400 (95%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDVFICDAIRTPIGRFGG L+ VRADDLAA+P+KALIE NP+V W  VDEVF GCANQA
Sbjct: 1   MRDVFICDAIRTPIGRFGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA++ +SR MKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD
Sbjct: 121 SRAPFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYHVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQ+ AAAQAAGFFAEEIVPVR+AHKKGET+VE+DEH R +TTLEALTKLKPV
Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVPVRVAHKKGETVVEQDEHPRADTTLEALTKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLT RARVLGMAS GVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKL ERLG+AV+DFDVIELNEAFASQGLAVLRELG+ADDAPQVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLVLTALHQLEK+GG KGLATMCVGVGQGLALAIER+
Sbjct: 361 SGARLVLTALHQLEKTGGSKGLATMCVGVGQGLALAIERI 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: 655
Number of extensions: 16
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 GFF1320 PS417_06710 (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.19430.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19430.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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