GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens FW300-N2C3

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate AO356_04930 AO356_04930 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_04930
          Length = 400

 Score =  715 bits (1846), Expect = 0.0
 Identities = 359/400 (89%), Positives = 385/400 (96%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           MRDV+ICDAIRTPIGRFGG L+ VRADDLAAVP+KAL+E NP+V W+ VDEVF GCANQA
Sbjct: 1   MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMERNPSVDWNAVDEVFLGCANQA 60

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           GEDNRNVARMALLLAGLP+SIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM
Sbjct: 61  GEDNRNVARMALLLAGLPQSIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           SRAPFVMGKA++ +SRNMKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD
Sbjct: 121 SRAPFVMGKADTAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYAVSRAD 180

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QDAFALRSQQ+ AAAQAAGFFAEEIVPVRIAHKKGET+VE+DEH R +TTLE L+KLKPV
Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVPVRIAHKKGETVVEQDEHPRADTTLETLSKLKPV 240

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
           NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPR +VLGMAS GVAPRVMGIGPVP
Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRGKVLGMASAGVAPRVMGIGPVP 300

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           AVRKLTERLG+AV+DFDVIELNEAFASQGLAVLR+LG+ADDAPQVNPNGGAIALGHPLGM
Sbjct: 301 AVRKLTERLGLAVADFDVIELNEAFASQGLAVLRDLGLADDAPQVNPNGGAIALGHPLGM 360

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGARLV+TALH LEK+GG+KGLATMCVGVGQGLALAIERV
Sbjct: 361 SGARLVMTALHHLEKTGGKKGLATMCVGVGQGLALAIERV 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: 668
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: 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 AO356_04930 AO356_04930 (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.26088.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26088.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.