GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Cupriavidus basilensis 4G11

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate RR42_RS12930 RR42_RS12930 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__Cup4G11:RR42_RS12930
          Length = 478

 Score =  494 bits (1272), Expect = e-144
 Identities = 262/473 (55%), Positives = 340/473 (71%), Gaps = 8/473 (1%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIE--KYTDAEGKLALGGTCLNVGCIPSK 58
           M+++FDV+VIGAGPGGY+AAI+A QLGL  AC E   Y D + +  LGGTCLNVGCIPSK
Sbjct: 1   MSKQFDVLVIGAGPGGYIAAIRAGQLGLNVACCEGNAYDDPKDEPRLGGTCLNVGCIPSK 60

Query: 59  ALLDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSI 118
           ALL SS +++  +     HGI+ G+VK+DVA M+ RK  IV  +T G+  LF+ N VT +
Sbjct: 61  ALLASSEEFENVQHHLGDHGITVGDVKVDVAKMLKRKDDIVGKMTKGIEFLFRKNKVTLL 120

Query: 119 QGHGKLLA----GKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGA 174
           +G+GK +     G +VE+    GT EV+ A+ VI+A+GS+   +P   VD  ++ D+ GA
Sbjct: 121 KGYGKFVGKTAEGFQVEIAGKAGT-EVVTAKQVIVATGSKARHLPGIAVDNVLVSDNEGA 179

Query: 175 LEFQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTK 234
           L+F  VPK+LGVIGAGVIGLELGSVW RLGAEVTVLEAL +FL AAD  V+KEAQK LTK
Sbjct: 180 LKFAGVPKKLGVIGAGVIGLELGSVWRRLGAEVTVLEALPSFLGAADEGVAKEAQKLLTK 239

Query: 235 QGLDIKLGARVTGSKVNGNEVEVTYTNAEGE-QKITFDKLIVAVGRRPVTTDLLAADSGV 293
           QGL   LG +V   K   + V V+YT+ +G  Q +  D+LIV+VGR P T +L     G+
Sbjct: 240 QGLKFSLGVKVNEVKTGKDNVTVSYTDKDGAAQTLEVDRLIVSVGRVPNTDNLGLDAIGL 299

Query: 294 TIDERGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLI 353
             D+RG+I VDD+CATSVPG++AIGDVVRG MLAHKA +EG+ V ERI G K  ++Y+ I
Sbjct: 300 AADQRGFIEVDDHCATSVPGLWAIGDVVRGPMLAHKAEDEGVAVAERIAGQKPHIDYNCI 359

Query: 354 PSVIYTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDR 413
           P VIYT PEIAWVGKTEQ LKAEG E   G FPF A+GRA+    + GFVK++ADAKTD 
Sbjct: 360 PWVIYTFPEIAWVGKTEQQLKAEGREYKSGQFPFMANGRALGMGHSEGFVKMLADAKTDE 419

Query: 414 VLGVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVN 466
           +LGVHV+  +A++L+ +  +AMEF  ++ED+G     HP++SE + EAALAV+
Sbjct: 420 ILGVHVVAANASDLIAEAVVAMEFKAASEDIGRTCHPHPSMSEVMREAALAVD 472


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: 714
Number of extensions: 33
Number of successful extensions: 4
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 RR42_RS12930 RR42_RS12930 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.13686.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13686.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.