GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Burkholderia phytofirmans PsJN

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate BPHYT_RS03230 BPHYT_RS03230 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__BFirm:BPHYT_RS03230
          Length = 399

 Score =  358 bits (920), Expect = e-103
 Identities = 195/395 (49%), Positives = 268/395 (67%), Gaps = 8/395 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+ +RTP+GKA +G     RPD+L    +K  + +  G +   I+D IIGCA P
Sbjct: 5   LQDAYIVAASRTPIGKAPRGMFKNTRPDELLVHAIKSAVAQVPGLDTKVIEDAIIGCAIP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQGLN+AR    LAGLP +V  +TVNR+C+SGL ++A AA++I +G  D  IAGG ES
Sbjct: 65  EAEQGLNVARMGALLAGLPNSVGGVTVNRFCASGLTALAMAADRIRVGESDAMIAGGCES 124

Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           MS VPMMG+    +  + ++  +  ++  MG TAE+VA+++ +SRE QDAF+V SH+ A 
Sbjct: 125 MSMVPMMGNKPSMSPHIFDRNEDVGIAYGMGLTAEKVAERWKISREAQDAFSVESHRRAI 184

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPME---KQFVFSQDEGVRPQTTADILSTLRPAF 234
            A   G+F DEI     T+TE   D    E   K    S DEG R +T+ + L+ LR  F
Sbjct: 185 AAQQAGEFNDEIAAY--TITERFPDLATGEVRVKTREVSLDEGPRAETSLEGLAKLRAVF 242

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           +  G+VTAGNSSQTSDGA A++++  +      L PL +F SFAV GVPPE+MGIGP EA
Sbjct: 243 ANKGSVTAGNSSQTSDGAGALIVVSEKMLKEFNLTPLARFVSFAVRGVPPEIMGIGPKEA 302

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           IP ALK AGL++ D+   ELNEAFA+Q++ VI++LG+D  K+N  GGAIALGHPLG TG 
Sbjct: 303 IPAALKAAGLKIDDLDWIELNEAFAAQSLAVIQDLGLDPAKINPLGGAIALGHPLGATGA 362

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
               +++H ++RRN ++G+VTMC+G GMGAAG+ E
Sbjct: 363 IRASTVVHGLRRRNYKYGMVTMCVGTGMGAAGIIE 397


Lambda     K      H
   0.316    0.133    0.377 

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: 434
Number of extensions: 17
Number of successful extensions: 4
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: 399
Length adjustment: 31
Effective length of query: 360
Effective length of database: 368
Effective search space:   132480
Effective search space used:   132480
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate BPHYT_RS03230 BPHYT_RS03230 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.32112.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32112.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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