GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas simiae WCS417

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate GFF3753 PS417_19210 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__WCS417:GFF3753
          Length = 394

 Score =  341 bits (875), Expect = 2e-98
 Identities = 189/395 (47%), Positives = 247/395 (62%), Gaps = 10/395 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M+E VIV   RT + K+ +G     RPDD+ A CV   L R G     ++D I+G  + E
Sbjct: 1   MREVVIVDSVRTGLAKSFRGKFNQTRPDDMAAHCVNALLTRNGIDPATVEDCIVGAGSNE 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
             QG N+ RN+  L+ L      +T+NR+CSSGLQ+IA AA +I  G  D  +AGG ES+
Sbjct: 61  GAQGYNIGRNVAVLSQLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120

Query: 121 SQVPMMGHVTRPNLA---LAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           S    +  V   NL    L E+ P  Y  MG TAE VA++Y VSRE+QD +A++S Q  A
Sbjct: 121 SLT--LKSVNTDNLINPLLKEQVPGLYFPMGQTAEIVARRYSVSREEQDMYALQSQQRTA 178

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQF---VFSQDEGVRPQTTADILSTLRPAF 234
           +A A+G F DEIVP+ V      ED    E Q    V  +D+  RP TT   L  L+P F
Sbjct: 179 QAQADGLFDDEIVPMAVKYKV--EDKNTGEAQVLDGVVDRDDCNRPDTTLASLQGLKPVF 236

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           + DG+VTAGNSSQ SDGA+  ++M  EKA ALGL P   FR F V G  P+ MGIGPV +
Sbjct: 237 AEDGSVTAGNSSQLSDGASMTLVMSLEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFS 296

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           +P+ LK  GLQ+ DI L+ELNEAFASQ +     L ID  K NVNGG+I++GHP G TG+
Sbjct: 297 VPKLLKAKGLQVADIDLWELNEAFASQCLYARNRLEIDNAKYNVNGGSISIGHPFGMTGS 356

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           +    L+ E++RRN ++G+VTMC+GGGMGA G+FE
Sbjct: 357 RQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFE 391


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: 412
Number of extensions: 16
Number of successful extensions: 3
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: 394
Length adjustment: 31
Effective length of query: 360
Effective length of database: 363
Effective search space:   130680
Effective search space used:   130680
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 GFF3753 PS417_19210 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.2262.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2262.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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