GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Shewanella amazonensis SB2B

Align 3-ketoacyl-CoA thiolase FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__SB2B:6938035
          Length = 436

 Score =  625 bits (1613), Expect = 0.0
 Identities = 305/426 (71%), Positives = 366/426 (85%)

Query: 11  QGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQM 70
           +G+RIAIVSGLRTPFA+QATAFHG+ A+D+GKMVV ELL+RSE+  +++EQLV+GQVVQM
Sbjct: 11  RGERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQM 70

Query: 71  PEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSS 130
           P APNIAREIVLGTGMNV TDAYSV+RACATSFQ+  N+AES+M G I  GIAGGADSSS
Sbjct: 71  PAAPNIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSS 130

Query: 131 VLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYSTGLRMGDTAEQ 190
           VLPIGVSKKLA  LVD+ KART  Q+L +F RL ++DL+PVPPAVAEYSTGL MG TAEQ
Sbjct: 131 VLPIGVSKKLAHALVDLTKARTFGQKLAIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQ 190

Query: 191 MAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNNIRGNSSL 250
           MAKT+GI+R  QDA+AHRSH  AAQ W+ G +K EVM A +PPY Q + +DNNIR +S L
Sbjct: 191 MAKTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPYNQFIEKDNNIRESSDL 250

Query: 251 ADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAID 310
           A YAKLRP FDRKHG+VTAANSTPLTDGA+A++LM+E RAK LG  P+GY++SYAF AID
Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310

Query: 311 VWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRA 370
           VW+DML+GP+++TP+AL+RAG+ + DLTLI+MHEAFAAQ LAN+++  S++FA E LG+ 
Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370

Query: 371 HATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVTACAAGGLGAA 430
            A GE+D SKFNVLGGS+AYGHPFAATGAR+ITQ  +EL+RRGGG GL TACAAGGLGAA
Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAA 430

Query: 431 MVLEAE 436
           M+LE E
Sbjct: 431 MILEVE 436


Lambda     K      H
   0.319    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: 573
Number of extensions: 9
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 6938035 Sama_2168 (3-ketoacyl-CoA thiolase (RefSeq))
to HMM TIGR02446 (fadI: acetyl-CoA C-acyltransferase FadI (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.25688.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25688.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.