GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Magnetospirillum magneticum AMB-1

Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate WP_011386317.1 AMB_RS20050 dihydrolipoyl dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>NCBI__GCF_000009985.1:WP_011386317.1
          Length = 469

 Score =  580 bits (1496), Expect = e-170
 Identities = 285/462 (61%), Positives = 352/462 (76%)

Query: 39  DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98
           DVVIIGGGPGGYVAAI+AAQLG KT CIEKRG+LGGTCLNVGCIPSKALL +SH YH A 
Sbjct: 7   DVVIIGGGPGGYVAAIRAAQLGLKTACIEKRGSLGGTCLNVGCIPSKALLTASHHYHAAA 66

Query: 99  HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158
           H   + G+KV+ VE+D+A MMG KDK VS+ T+GIE LFKKNKVTY+ G G   +P +I 
Sbjct: 67  HELGSFGIKVAKVEMDVAGMMGHKDKVVSDNTKGIEFLFKKNKVTYIVGAGAITAPGQIE 126

Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218
           V   +G  + V  KHI+IATGSDV  LPGV IDE+ I+SSTGALALS+ PK +VVIG G 
Sbjct: 127 VTAKDGAKSNVAAKHIVIATGSDVTPLPGVEIDEEVIISSTGALALSKTPKHMVVIGGGV 186

Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278
           IGLE+G+VWGR+G++VTVVEF   I+P  D E+ KQ QR L KQGM+FKL TKV G+   
Sbjct: 187 IGLELGTVWGRLGAKVTVVEFLDRILPFNDGEVSKQMQRLLAKQGMEFKLGTKVTGIAKK 246

Query: 279 GDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFST 338
           G    +TVEP+AGG    IEAD VLV+ GR P+T GL LDK+GV  DK G + ++  F T
Sbjct: 247 GKTATVTVEPAAGGAAEKIEADSVLVAIGRKPYTEGLGLDKVGVALDKRGFVQIDGHFRT 306

Query: 339 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGKT 398
           NV G+YAIGDV+ G MLAHKAEE+GVA  E LAG+ GHV+Y+ +P VVYT PEVASVGKT
Sbjct: 307 NVPGIYAIGDVVGGAMLAHKAEEEGVALAEILAGQHGHVNYEAIPAVVYTWPEVASVGKT 366

Query: 399 EEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELIH 458
           EEQ+K  G+ Y+ GKFPF AN RA++++  +G VK++A   TDK+LG HI+ PNAG+LI 
Sbjct: 367 EEQLKAEGIAYKAGKFPFTANGRARSMNEVDGFVKVLACATTDKVLGAHIVGPNAGDLIA 426

Query: 459 EAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIH 500
           E  +A+++ A+SEDIAR CHAHP + EA+KEA +A   +P+H
Sbjct: 427 EVVLAMEFGAASEDIARTCHAHPGLGEAVKEACLAVDGRPLH 468


Lambda     K      H
   0.315    0.133    0.370 

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: 719
Number of extensions: 27
Number of successful extensions: 1
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: 501
Length of database: 469
Length adjustment: 34
Effective length of query: 467
Effective length of database: 435
Effective search space:   203145
Effective search space used:   203145
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 WP_011386317.1 AMB_RS20050 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.6666.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6666.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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