GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dechlorosoma suillum PS

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Dsui_1576 Dsui_1576 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__PS:Dsui_1576
          Length = 581

 Score =  815 bits (2105), Expect = 0.0
 Identities = 417/593 (70%), Positives = 484/593 (81%), Gaps = 16/593 (2%)

Query: 3   VIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVK 62
           ++EVKVPDIGDF  V VIEV VK GDTV+VE  L+ LESDKA+MDVPSSAAG V E+KVK
Sbjct: 4   LVEVKVPDIGDFKDVPVIEVFVKVGDTVKVEDPLVSLESDKATMDVPSSAAGVVKEIKVK 63

Query: 63  VGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCE 122
           +GDKV +G VI  +EA  AAAAPAP Q  APA APAPAAA P   P A SH GGAD++C+
Sbjct: 64  LGDKVAEGTVIVVVEAGAAAAAPAP-QPAAPAAAPAPAAAPP---PVAGSHGGGADVECD 119

Query: 123 MLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKA 182
           MLVLGAGPGGYSAAFR+ADLG+ TVLVERY TLGGVCLNVGCIPSKALLH AAV++EA+ 
Sbjct: 120 MLVLGAGPGGYSAAFRSADLGLKTVLVERYPTLGGVCLNVGCIPSKALLHVAAVLEEAQH 179

Query: 183 LAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVE 242
           LA  G+ F   ++D+D LR +K +VVGKLTGGLAGMAK RKVQ V+G+G F+DPHH+EV 
Sbjct: 180 LADCGVTFAAPQVDVDKLRAHKEKVVGKLTGGLAGMAKGRKVQHVQGVGQFIDPHHIEVT 239

Query: 243 LTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALELPEVPNKMLV 301
             +G       KK V++F+ AIIAAGSQ V LPF+P +DPR++DSTGALEL  VP KMLV
Sbjct: 240 AADG-------KKQVVKFKNAIIAAGSQPVALPFMPKDDPRVIDSTGALELRSVPKKMLV 292

Query: 302 IGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTV 361
           IGGGIIGLEMATVYS LG  I VVE+  GLM GADRDLVKVWEKKN  RF +++L T   
Sbjct: 293 IGGGIIGLEMATVYSALGTRITVVELGPGLMPGADRDLVKVWEKKNTQRFDRILLATGVT 352

Query: 362 GVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDK 421
             EAK +GI V +    +  E + +DLVLV+VGR+PNGK+I+A+KAGVAV++RGFINVD 
Sbjct: 353 AAEAKAEGIEVTY----STGEKEAFDLVLVAVGRTPNGKKIAADKAGVAVTDRGFINVDA 408

Query: 422 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAW 481
           QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE A GEKA FDA QIPSVA+T PE+AW
Sbjct: 409 QMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAAGEKAAFDALQIPSVAYTHPEIAW 468

Query: 482 AGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAG 541
           AG TED+ K  GIK+ K VFPWAASGRAIANG +EGFTKL+FD E+HR++GGGIVG +AG
Sbjct: 469 AGKTEDQLKNDGIKFEKAVFPWAASGRAIANGAEEGFTKLLFDAESHRLLGGGIVGMNAG 528

Query: 542 DLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           DLI EVCLA+EMG DAVDIGKTIHPHPTL ESIGMAAE+  G+CTD+PP +K+
Sbjct: 529 DLIGEVCLAVEMGCDAVDIGKTIHPHPTLCESIGMAAEVAHGSCTDLPPMKKK 581


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: 1053
Number of extensions: 41
Number of successful extensions: 5
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: 581
Length adjustment: 37
Effective length of query: 557
Effective length of database: 544
Effective search space:   303008
Effective search space used:   303008
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 Dsui_1576 Dsui_1576 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.32498.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32498.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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