GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2E2

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate Pf6N2E2_5857 Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5857
          Length = 481

 Score =  836 bits (2160), Expect = 0.0
 Identities = 432/481 (89%), Positives = 449/481 (93%), Gaps = 3/481 (0%)

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

Query: 61  LDSSWKYKEAKESFNVHGI---STGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTS 117
           LDSSWK+ EA++   +HGI   +   V +DV AMVGRKA IVK LT GVATLFKANGVTS
Sbjct: 61  LDSSWKFHEAQDGLAIHGIGGVNRENVTIDVPAMVGRKANIVKGLTSGVATLFKANGVTS 120

Query: 118 IQGHGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEF 177
           IQGHGKLL GKKVEVTK DG+ EVIEAENVILA GSRPIDIPPAPVDQNVIVDSTGALEF
Sbjct: 121 IQGHGKLLMGKKVEVTKPDGSVEVIEAENVILAPGSRPIDIPPAPVDQNVIVDSTGALEF 180

Query: 178 QAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGL 237
           Q+VPKRLGVIGAGVIGLELGSVW+RLGA+VTVLEALDTFLMAAD AVSKEA KTLTKQGL
Sbjct: 181 QSVPKRLGVIGAGVIGLELGSVWSRLGAQVTVLEALDTFLMAADAAVSKEALKTLTKQGL 240

Query: 238 DIKLGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDE 297
           DIKLGARVTGSKVNG EV V YT+A GEQ ITFDKLIVAVGRRPVTTDLLAADSGV +DE
Sbjct: 241 DIKLGARVTGSKVNGEEVVVNYTDANGEQTITFDKLIVAVGRRPVTTDLLAADSGVELDE 300

Query: 298 RGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVI 357
           RG+I VDD+CAT+VPGV+AIGDVVRGMMLAHKASEEGIMVVERIKGHKAQ+NYDLIPSVI
Sbjct: 301 RGFIKVDDFCATTVPGVFAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQINYDLIPSVI 360

Query: 358 YTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV 417
           YTHPEIAWVGKTEQ LKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV
Sbjct: 361 YTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGV 420

Query: 418 HVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK 477
           HVIGPSAAELVQQGAI MEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK
Sbjct: 421 HVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKK 480

Query: 478 R 478
           R
Sbjct: 481 R 481


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: 901
Number of extensions: 20
Number of successful extensions: 3
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: 481
Length adjustment: 34
Effective length of query: 444
Effective length of database: 447
Effective search space:   198468
Effective search space used:   198468
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 Pf6N2E2_5857 (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.16641.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16641.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.