GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

Align Dihydrolipoyl dehydrogenase 1, mitochondrial; AtmLPD1; mtLPD1; Dihydrolipoamide dehydrogenase 1; Glycine cleavage system L protein 1; Pyruvate dehydrogenase complex E3 subunit 1; E3-1; PDC-E3 1; EC 1.8.1.4 (characterized)
to candidate Echvi_0770 Echvi_0770 dihydrolipoamide dehydrogenase

Query= SwissProt::Q9M5K3
         (507 letters)



>FitnessBrowser__Cola:Echvi_0770
          Length = 494

 Score =  482 bits (1240), Expect = e-140
 Identities = 239/464 (51%), Positives = 338/464 (72%), Gaps = 2/464 (0%)

Query: 45  DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+++IG GPGGYVAAI+ +QLG+KT  +EK   LGGTCLNVGCIPSKALL SS  YH A 
Sbjct: 32  DLIVIGSGPGGYVAAIRGAQLGMKTAIVEKYPTLGGTCLNVGCIPSKALLDSSEHYHNAA 91

Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164
           H+F  HGI +  ++V+L  M+++KD+ VK    GI  L KKNK+   +G G F+  N V 
Sbjct: 92  HTFKTHGIDLKDLKVNLKQMISRKDDVVKQNVDGISYLMKKNKIDVHQGVGSFVDKNTVK 151

Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLSEVPKKLIVIGAGY 224
           V   DG +T + G++II+ATGS   SLP I ID+K++++ST AL + EVPK++IVIG G 
Sbjct: 152 VTKDDGKSTEITGENIIIATGSKPASLPFIEIDKKRVITSTEALKMKEVPKRMIVIGGGV 211

Query: 225 IGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVDSS 284
           IG+E+GSV+ R+G++V+VVEF   ++PSMD  + K+ Q+SL+K   +F LK KV +V S+
Sbjct: 212 IGMELGSVYARMGAKVSVVEFMDSLIPSMDKTMGKELQKSLKKLGFEFYLKHKVTAVKST 271

Query: 285 SDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRFLS 344
           +  V +T E ++G E  + + D VLVS GR P+T GL+ E  GV+ +  G++ V++   +
Sbjct: 272 AKEVTVTAENSKGEEVQV-KGDYVLVSIGRKPYTEGLNPEAAGVKVNDRGQVEVDEHLKT 330

Query: 345 NVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVGKT 404
           +   +YAIGDV+ G MLAHKAEE+GV   E +AG+  H++Y+ +PGVVYT PEVA+VG +
Sbjct: 331 SADNIYAIGDVVKGAMLAHKAEEEGVLVAEQLAGQKPHINYNLIPGVVYTWPEVAAVGYS 390

Query: 405 EEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGELIH 464
           EEQLK++G+ Y+ GKFPFMA+ RA+A  + +GLVK+LAD ETD+ILGVH++ P   ++I 
Sbjct: 391 EEQLKEKGIKYKTGKFPFMASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIA 450

Query: 465 EAVLAINYDASSEDIARVCHAHPTMSEALKEAAM-ATYDKPIHI 507
           EAV+A+ Y AS+EDIAR+ HAHPT +EA KEA + AT ++ +H+
Sbjct: 451 EAVVAMEYRASAEDIARMSHAHPTYTEAFKEACLAATENRALHV 494


Lambda     K      H
   0.315    0.133    0.375 

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: 600
Number of extensions: 21
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: 507
Length of database: 494
Length adjustment: 34
Effective length of query: 473
Effective length of database: 460
Effective search space:   217580
Effective search space used:   217580
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate Echvi_0770 Echvi_0770 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.3133.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3133.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.