GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate RR42_RS25455 RR42_RS25455 acetyl-CoA acetyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Cup4G11:RR42_RS25455
          Length = 394

 Score =  708 bits (1827), Expect = 0.0
 Identities = 358/394 (90%), Positives = 379/394 (96%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVSGVRTAIGTFGGSLKD++P ++GA+VVREALARAQVSGDDVGHVVFGNVIQT
Sbjct: 1   MTREVVVVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALARAQVSGDDVGHVVFGNVIQT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EPRDMYLGRVAAV GGVTI+APALTVNRLCGSGLQAIVSAAQTILLGD DVAIGGGAESM
Sbjct: 61  EPRDMYLGRVAAVEGGVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAESM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAPYLA +ARWGARMGDA ++DMMLGALHDPFH IHMGVTAENVAKEYDISR QQDEAA
Sbjct: 121 SRAPYLAQSARWGARMGDAKMLDMMLGALHDPFHGIHMGVTAENVAKEYDISRVQQDEAA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LESHRRASAAI+AG+FKDQI+PV  KGRKGDVTFDTDEHVRHDA ++DMTKL+PVFVKEN
Sbjct: 181 LESHRRASAAIRAGHFKDQILPVTLKGRKGDVTFDTDEHVRHDAVMEDMTKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASGLNDAAAAVV+MERAEAE+RGLKP+ARLVSY HAGVDPK MGIGPVPATK 
Sbjct: 241 GTVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVSYAHAGVDPKTMGIGPVPATKK 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           ALERAGL V+DLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALERAGLTVADLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKAL+EL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKALYELQRVQGRYALVTMCIGGGQGIAAIFERV 394


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: 635
Number of extensions: 8
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 RR42_RS25455 RR42_RS25455 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.31377.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31377.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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