GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PfGW456L13_3543 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3543
         (460 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3543
          Length = 460

 Score =  906 bits (2342), Expect = 0.0
 Identities = 460/460 (100%), Positives = 460/460 (100%)

Query: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60
           MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ
Sbjct: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60

Query: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120
           FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV
Sbjct: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120

Query: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180
           VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG
Sbjct: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180

Query: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240
           YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS
Sbjct: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240

Query: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300
           SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR
Sbjct: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300

Query: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360
           NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE
Sbjct: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360

Query: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420
           AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA
Sbjct: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420

Query: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460
           QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460


Lambda     K      H
   0.317    0.134    0.388 

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: 821
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: 460
Length of database: 460
Length adjustment: 33
Effective length of query: 427
Effective length of database: 427
Effective search space:   182329
Effective search space used:   182329
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate PfGW456L13_3543 (Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.13615.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13615.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.