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_3683 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3683
          Length = 478

 Score =  852 bits (2201), Expect = 0.0
 Identities = 435/478 (91%), Positives = 452/478 (94%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           MTQKFDVVVIGAGPGGYVAAIKAAQLGL TACIEKYTD EGKLALGGTCLNVGCIPSKAL
Sbjct: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLSTACIEKYTDKEGKLALGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDSSWK+ EA++ F +HGI+   V MDV AMVGRKA IVK LT GVATLFKANGVTSIQG
Sbjct: 61  LDSSWKFHEAQDGFAIHGINHAGVTMDVPAMVGRKANIVKGLTSGVATLFKANGVTSIQG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
           HGKLLAGKKVEVTK DG+ E+IEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEFQ+V
Sbjct: 121 HGKLLAGKKVEVTKPDGSVEIIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEFQSV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVW+RLGAEVTVLEALDTFLMAAD AVSKEA KTLTKQGLDIK
Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEALDTFLMAADAAVSKEALKTLTKQGLDIK 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           LGARVTGSKVNG+EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAAD GVT+DERG+
Sbjct: 241 LGARVTGSKVNGDEVVVNYTDANGEQNITFDKLIVAVGRRPVTTDLLAADCGVTLDERGF 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           + VDD+CAT+VPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH
Sbjct: 301 VHVDDHCATTVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIAWVGKTEQ LKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI
Sbjct: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIH+ANRKKR
Sbjct: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHIANRKKR 478


Lambda     K      H
   0.316    0.133    0.374 

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: 886
Number of extensions: 17
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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_3683 (Dihydrolipoamide dehydrogenase of 2-oxoglutarate 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.19091.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19091.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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