GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ga0059261_2888 Ga0059261_2888 acetyl-CoA acetyltransferases

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Korea:Ga0059261_2888
          Length = 393

 Score =  487 bits (1254), Expect = e-142
 Identities = 247/391 (63%), Positives = 303/391 (77%), Gaps = 1/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           +V+++SGVRTAIG FGG+LK+V  A+LGALV+ EA+ARA ++ D VGHVV GNVI + P 
Sbjct: 3   DVLILSGVRTAIGDFGGALKNVPAADLGALVIGEAIARAGIAADAVGHVVMGNVIPSTPS 62

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D YL RVAAV  GV +  PALTVNRLCGSGLQAI+SAAQ I LG+  VA+ GGAE+MS+A
Sbjct: 63  DAYLARVAAVRAGVPVAVPALTVNRLCGSGLQAIISAAQGIALGECGVAVAGGAENMSQA 122

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           P+   +AR+G +MGD  ++D +   L DPF ++HMGVTAENVA +  I RA QDEAA+ES
Sbjct: 123 PHYVASARFGQKMGDIQMLDALTRTLSDPFDQVHMGVTAENVAAQCGIDRAAQDEAAVES 182

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
           HRR + AI  G F+DQIVPV  K R G V FDTDEHVR + T++DM +LRP F + +GTV
Sbjct: 183 HRRGARAIAEGRFRDQIVPVEIKSRGGTVMFDTDEHVRAEVTLEDMARLRPAF-QRDGTV 241

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND AAAVV+    EA+R G KPLAR++ +GHAGV+P+ MG+GPV A  IAL 
Sbjct: 242 TAGNASGINDGAAAVVLGSPEEAQRLGAKPLARILGWGHAGVEPRVMGLGPVEAVPIALR 301

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           RAG+ +  +DVIE+NEAFAAQACAV+  LG DP K N NGSGISLGHP+GATGA+ TVK 
Sbjct: 302 RAGVTLDRIDVIESNEAFAAQACAVSAQLGFDPEKTNVNGSGISLGHPVGATGAINTVKL 361

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           L+EL R  GR  LVTMCIGGGQGIA + ER+
Sbjct: 362 LYELQRSGGRLGLVTMCIGGGQGIALVIERL 392


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: 541
Number of extensions: 19
Number of successful extensions: 2
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: 393
Length adjustment: 31
Effective length of query: 363
Effective length of database: 362
Effective search space:   131406
Effective search space used:   131406
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 Ga0059261_2888 Ga0059261_2888 (acetyl-CoA acetyltransferases)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.14724.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14724.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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