GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ac3H11_178 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_178
          Length = 394

 Score =  608 bits (1567), Expect = e-178
 Identities = 305/394 (77%), Positives = 338/394 (85%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVS VRTAIGTFGGSLKD+AP +LGALVV+E+LARA V G DVGHVVFG+V+ T
Sbjct: 1   MTREVVVVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EP+DMYL RVAA+NGG     PA  VNRLCGSGLQAIVSAAQ I LGD DV IG GAE M
Sbjct: 61  EPKDMYLSRVAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAP+ +   RWGARMGD  +VDMM+GALHDPFH IHMGVTAEN+A ++ ISR  QD+ A
Sbjct: 121 SRAPFASLNMRWGARMGDTKMVDMMIGALHDPFHTIHMGVTAENIAAKWGISREDQDKLA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           +ESH RA  A  AGYFKDQIVPV  K +KGDV + TDEH R  AT+DD  KL+PVFVKEN
Sbjct: 181 VESHNRAERATAAGYFKDQIVPVTLKSKKGDVQYATDEHFRPGATLDDFAKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+NDAAAAVV+M+ A A+ RG KPLARLV+Y HAGVDPK MGIGPVPAT++
Sbjct: 241 GTVTAGNASGINDAAAAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGPVPATQL 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           AL++AGL V+DLDVIEANEAFAAQACAVTK LGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALKKAGLTVADLDVIEANEAFAAQACAVTKDLGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKA+HEL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKAIHELQRVQGRYALVTMCIGGGQGIAAIFERL 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: 569
Number of extensions: 7
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 Ac3H11_178 (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.23924.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23924.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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