GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate H281DRAFT_00468 H281DRAFT_00468 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Burk376:H281DRAFT_00468
          Length = 590

 Score =  887 bits (2291), Expect = 0.0
 Identities = 455/599 (75%), Positives = 509/599 (84%), Gaps = 14/599 (2%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MS++EVKVPDIGDF  V+VIEV +K GD +E EQ+L+ LESDKAS++VPS  AG V EV+
Sbjct: 1   MSLVEVKVPDIGDFKDVDVIEVNIKPGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60

Query: 61  VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAP--APAAAAP---APAPAAASHSG 115
           VK GDKV QG +I  +E   A AAPA     APA+ P  AP  A P   APAP A S SG
Sbjct: 61  VKAGDKVSQGTIIALVETS-ADAAPAKDAPKAPAKEPEKAPTEAKPQAAAPAPQAGSFSG 119

Query: 116 GADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAA 175
            ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIPSKALLH A 
Sbjct: 120 SADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIPSKALLHTAL 179

Query: 176 VIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLD 235
           VIDEA+AL AHGI F + +IDLD LR +K+ VV KLTGGLAGMAK RKV+VV G G+F+D
Sbjct: 180 VIDEAEALGAHGITFAKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEVVTGTGSFVD 239

Query: 236 PHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEV 295
           P+HMEV+ TEG      GKK V++F++AIIAAGS+AVKLPFIPEDPR+VDSTGALEL ++
Sbjct: 240 PNHMEVQ-TEG------GKK-VVKFKQAIIAAGSEAVKLPFIPEDPRVVDSTGALELRQI 291

Query: 296 PNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVM 355
           P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK N  RF  VM
Sbjct: 292 PQRMLVIGGGIIGLEMATVYATLGAKIDVVEMLDGLMAGADRDLVKVWEKYNSKRFANVM 351

Query: 356 LKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERG 415
           LKTKT   EAK DGIYV FEGE AP E QRYDLVLV+VGRSPNGK+I A+KAGV V++RG
Sbjct: 352 LKTKTTAAEAKDDGIYVSFEGEKAPPEAQRYDLVLVAVGRSPNGKKIGADKAGVTVTDRG 411

Query: 416 FINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFT 475
           FI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHE HVAAEAAHGEKAYFDA QIPSVA+T
Sbjct: 412 FIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEGHVAAEAAHGEKAYFDALQIPSVAYT 471

Query: 476 DPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGI 535
           DPEVAWAG TED+ K +G+KY K VFPWAASGRAIANGRDEGFTKL+FDEETHRVIGGGI
Sbjct: 472 DPEVAWAGKTEDQLKAEGVKYGKAVFPWAASGRAIANGRDEGFTKLLFDEETHRVIGGGI 531

Query: 536 VGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           VG +AGDLISEVCLAIEMGADA DIGKTIHPHPTLGESIGMAAE+YEG CTD+PP +K+
Sbjct: 532 VGLNAGDLISEVCLAIEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCTDLPPQKKK 590


Lambda     K      H
   0.316    0.134    0.387 

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: 1101
Number of extensions: 35
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: 594
Length of database: 590
Length adjustment: 37
Effective length of query: 557
Effective length of database: 553
Effective search space:   308021
Effective search space used:   308021
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: 53 (25.0 bits)

Align candidate H281DRAFT_00468 H281DRAFT_00468 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.28690.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28690.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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