GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N1B4

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835
          Length = 393

 Score =  674 bits (1739), Expect = 0.0
 Identities = 337/393 (85%), Positives = 371/393 (94%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQ+VVIVAATRTA+GSFQGSLA++ A +LGAAVIR+LL QTGLDPAQVDEVI+GQVLTAG
Sbjct: 1   MQEVVIVAATRTAIGSFQGSLANVSAVDLGAAVIRQLLAQTGLDPAQVDEVIMGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQA+I AGLP AVP++TLNKVCGSGLKALHL AQAIRCGDAEVIIAGG ENMSL
Sbjct: 61  AGQNPARQAAIKAGLPFAVPAMTLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           + YV+P ARTGLRMGHA+++D+MI+DGLWDAFNDYHMGITAENL +KY ++RE QDAFAA
Sbjct: 121 SNYVMPGARTGLRMGHAQIVDTMISDGLWDAFNDYHMGITAENLAEKYSLTREQQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           ASQQKA AAIEAGRF DEITPILIPQRKGDP++FA DEQPRAGTTA+SL KLK AFKKDG
Sbjct: 181 ASQQKAVAAIEAGRFADEITPILIPQRKGDPLSFATDEQPRAGTTADSLGKLKAAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAV+LMSA+KAKALGLPVLA+IA+YANAGVDPAIMGIGPVSATRRC
Sbjct: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKIAAYANAGVDPAIMGIGPVSATRRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDK GWS+G LDLIEANEAFAAQSLAV K+LEWD  KVNVNGGAIA+GHPIGASGCRVLV
Sbjct: 301 LDKTGWSIGQLDLIEANEAFAAQSLAVAKDLEWDLNKVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393
           TLLHEMIK+DAKKGLATLCIGGGQGVALA+ER+
Sbjct: 361 TLLHEMIKQDAKKGLATLCIGGGQGVALAIERA 393


Lambda     K      H
   0.317    0.133    0.378 

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: 559
Number of extensions: 14
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: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 Pf1N1B4_5835 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.9294.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9294.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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