GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

Align Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf1N1B4_4477 Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4477
          Length = 460

 Score =  861 bits (2224), Expect = 0.0
 Identities = 435/460 (94%), Positives = 450/460 (97%)

Query: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGIPTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60
           MQTLNTTLLIIGGGPGGYVTAIRAGQLGI TILVEGQSLGGTCLNIGCIPSKALIHVAEQ
Sbjct: 1   MQTLNTTLLIIGGGPGGYVTAIRAGQLGISTILVEGQSLGGTCLNIGCIPSKALIHVAEQ 60

Query: 61  FHQTQHHSQHSALGISVSAPTLDIGKSVEWKDGIVDRLTTGVAALLKKNKVQVVQGWAKV 120
           FHQTQHHSQHSALGISVSAPTL+IGKSVEWKDGIVDRLTTGV+ALLKK+KVQV+QGWAKV
Sbjct: 61  FHQTQHHSQHSALGISVSAPTLNIGKSVEWKDGIVDRLTTGVSALLKKHKVQVIQGWAKV 120

Query: 121 VDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180
           +DGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG
Sbjct: 121 IDGKTVEVGDTRIQCEHLVLATGSKSVNLPMLPIGGPIISSTEALAPTSVPKRLIVVGGG 180

Query: 181 YIGLELGIAYRKLGAEVSVVEAQERILPAYDAELTQPVHDELKKLGVKLYLKHSVQGFDS 240
           YIGLELGIAYRKLGAEVSVVEAQ+RILPAYDAELT PVH+ LK+L VKLYLKHSVQGFDS
Sbjct: 181 YIGLELGIAYRKLGAEVSVVEAQDRILPAYDAELTHPVHEALKQLDVKLYLKHSVQGFDS 240

Query: 241 SNNTLQVLAPNGETLNLETDQVLVAVGRKPNTQGWNLEALNLDMNGSSIKIDNRCQTSMR 300
            NNTLQV+ P+G++LNL+TDQVLVAVGRKPNTQGWNLEALNLDMNGS+IKIDNRCQTSMR
Sbjct: 241 VNNTLQVIDPSGDSLNLKTDQVLVAVGRKPNTQGWNLEALNLDMNGSAIKIDNRCQTSMR 300

Query: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKTREFNPTAIAAVCFTDPELVVVGKTPDE 360
           NVYAIGDLSGEPMLAHRAMAQGEMVAELISGK REFNPTAIAAVCFTDPELVVVGKTPDE
Sbjct: 301 NVYAIGDLSGEPMLAHRAMAQGEMVAELISGKHREFNPTAIAAVCFTDPELVVVGKTPDE 360

Query: 361 AKAAGWDCIVSSFPFAANGRAMTLESKSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFA 420
           AKAAG DCIVSSFPFAANGRAMTLES+SGFVRVVARRDNHVIVGWQAVGVGVSELSTAF 
Sbjct: 361 AKAAGLDCIVSSFPFAANGRAMTLESRSGFVRVVARRDNHVIVGWQAVGVGVSELSTAFG 420

Query: 421 QSLEMGARLEDIGGTIHAHPTLGEAVQEAALRALGHALHL 460
           QSLEMGARLEDI GTIHAHPTLGEAVQEAALRALGHALHL
Sbjct: 421 QSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALHL 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: 765
Number of extensions: 16
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 Pf1N1B4_4477 (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.6108.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6108.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.