GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas simiae WCS417

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF3432 PS417_17560 dihydrolipoamide dehydrogenase

Query= reanno::WCS417:GFF3432
         (459 letters)



>FitnessBrowser__WCS417:GFF3432
          Length = 459

 Score =  905 bits (2338), Expect = 0.0
 Identities = 459/459 (100%), Positives = 459/459 (100%)

Query: 1   MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60
           MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE
Sbjct: 1   MTQTLNTTLLIIGGGPGGYVAAIRAGQLGIPTILVEGQALGGTCLNIGCIPSKALIHVAE 60

Query: 61  QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120
           QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK
Sbjct: 61  QFQQTIHHSQGSHLGIEVDVPTLDIRKSVEWKDGIVDRLTTGVAALLKKHKVQVIHGWAK 120

Query: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180
           VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG
Sbjct: 121 VVDGKTVEVGDQRIQCEHLLLATGSKSVNLPMLPIGGPIISSTEALAPTRVPKRLIVVGG 180

Query: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240
           GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT
Sbjct: 181 GYIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTQPVNESLKHLGVKLYLKHSVTGFT 240

Query: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300
           DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN
Sbjct: 241 DGSLQVRDPNGDTVSLATDQVLVAVGRKPNTQGWNLEALNLEMNGAAIKIDSRCQTSMRN 300

Query: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360
           VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA
Sbjct: 301 VYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPAAIPAVCFTDPELVVVGKTPDEA 360

Query: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420
           KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL
Sbjct: 361 KAAGLDCIVSSFPFAANGRAMTLESKTGFVRVVARRDNHLIVGWQAVGVGVSELSTAFGL 420

Query: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459
           SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 SLEMGSRLEDVAGTIHAHPTLGEAVQEAALRALGHALHL 459


Lambda     K      H
   0.318    0.136    0.395 

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: 808
Number of extensions: 13
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: 459
Length of database: 459
Length adjustment: 33
Effective length of query: 426
Effective length of database: 426
Effective search space:   181476
Effective search space used:   181476
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: 51 (24.3 bits)

Align candidate GFF3432 PS417_17560 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.9454.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9454.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.