GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Burkholderia phytofirmans PsJN

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thiolase

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__BFirm:BPHYT_RS09180
          Length = 394

 Score =  619 bits (1595), Expect = 0.0
 Identities = 312/394 (79%), Positives = 349/394 (88%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           M R+VVVVSGVRTAIG FGGSLKD +P +LGA VVRE LARA VSGD+VGHVVFGNV+ T
Sbjct: 1   MQRDVVVVSGVRTAIGGFGGSLKDFSPTDLGARVVREVLARANVSGDEVGHVVFGNVVHT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EP+DMYL RVAA+NGGV  +APALTVNRLCGSGLQAIVSAAQ++LLGD D+AIGGGAE+M
Sbjct: 61  EPKDMYLARVAAINGGVAQHAPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAPY  PAAR+G RMGDA LVDMM+GAL+DPF  IHMGVTAENVA++YDISR  QD  A
Sbjct: 121 SRAPYSMPAARFGQRMGDARLVDMMVGALNDPFQSIHMGVTAENVARKYDISREAQDALA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LESHRRA+ AI +GYFK+QI+P+    +KGDV FDTDEH R  A+ +D +KL+PVF KEN
Sbjct: 181 LESHRRAANAITSGYFKEQILPITIPSKKGDVVFDTDEHTRMSASPEDFSKLKPVFAKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+NDAAAAVV+MER+ AE+RG+KPLARLVSY HAGVDP  MGIGPVPAT+ 
Sbjct: 241 GTVTAGNASGINDAAAAVVLMERSLAEQRGIKPLARLVSYAHAGVDPAYMGIGPVPATRR 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           ALERAGL V+DLDVIEANEAFAAQACAV+K LG DPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALERAGLTVADLDVIEANEAFAAQACAVSKELGFDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKAL+EL R+ GRYALVTMCIGGGQGIAAIFERI
Sbjct: 361 VKALYELQRIGGRYALVTMCIGGGQGIAAIFERI 394


Lambda     K      H
   0.318    0.134    0.381 

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: 574
Number of extensions: 13
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 BPHYT_RS09180 BPHYT_RS09180 (3-ketoacyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.7030.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7030.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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