GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Burkholderia phytofirmans PsJN

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BPHYT_RS12830 BPHYT_RS12830 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__BFirm:BPHYT_RS12830
          Length = 600

 Score =  897 bits (2317), Expect = 0.0
 Identities = 460/608 (75%), Positives = 515/608 (84%), Gaps = 22/608 (3%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           MS++EVKVPDIGDF  V+VIEV +KAGD +E EQ+L+ LESDKAS++VPS  AG V EV+
Sbjct: 1   MSLVEVKVPDIGDFKDVDVIEVNIKAGDVIENEQALMTLESDKASIEVPSDTAGTVKEVR 60

Query: 61  VKVGDKVGQGAVICTIE-------AQQAAAAPA--PAQAPAPAQA-PAPAAAAPA----P 106
           VK GDKV QG VI  +E       A+ A  APA  P +APA A+A P  A AAPA    P
Sbjct: 61  VKAGDKVSQGTVIALVETSADAAPAKDAPKAPAKEPEKAPAQAEAKPQAAQAAPAKAATP 120

Query: 107 APAAASHSGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIP 166
           AP A S SG ADI+C+MLVLG+GPGGYSAAFR+ADLGM TVLVERY+TLGGVCLNVGCIP
Sbjct: 121 APQAGSFSGNADIECDMLVLGSGPGGYSAAFRSADLGMKTVLVERYATLGGVCLNVGCIP 180

Query: 167 SKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQV 226
           SKALLH A VIDEA+AL +HGI FG+ +IDLD LR +K+ VV KLTGGLAGMAK RKV+V
Sbjct: 181 SKALLHTALVIDEAEALRSHGITFGKPQIDLDKLRDFKSGVVKKLTGGLAGMAKMRKVEV 240

Query: 227 VRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDS 286
           V G G+F+DPHHMEV++  G        K V++F++AIIAAGS+AVKLPFIPEDPR+VDS
Sbjct: 241 VTGTGSFVDPHHMEVQVEGG--------KKVVKFKQAIIAAGSEAVKLPFIPEDPRVVDS 292

Query: 287 TGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKK 346
           TGALEL ++P +MLVIGGGIIGLEMATVY+TLGA IDVVEMLDGLM GADRDLVKVWEK 
Sbjct: 293 TGALELRQIPQRMLVIGGGIIGLEMATVYATLGAQIDVVEMLDGLMAGADRDLVKVWEKY 352

Query: 347 NKDRFGKVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEK 406
           N  RF  VMLKTKT   EAK DGIYV FEGE APAE QRYDLVLV+VGRSPNGK+I A+K
Sbjct: 353 NSKRFANVMLKTKTTAAEAKDDGIYVSFEGEKAPAEAQRYDLVLVAVGRSPNGKKIGADK 412

Query: 407 AGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDA 466
           AGVAV+ERGFI+VDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAE AHGEKAYFDA
Sbjct: 413 AGVAVTERGFIDVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEVAHGEKAYFDA 472

Query: 467 KQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEE 526
            QIPSVA+TDPEVAWAG TED+ K +GIKY K VFPWAASGRAIANGRDEGFTKL+FDEE
Sbjct: 473 LQIPSVAYTDPEVAWAGKTEDQLKAEGIKYGKAVFPWAASGRAIANGRDEGFTKLLFDEE 532

Query: 527 THRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCT 586
           THRVIGGGIVG +AGDLISEVCLA+EMGADA DIGKTIHPHPTLGESIGMAAE+YEG CT
Sbjct: 533 THRVIGGGIVGLNAGDLISEVCLAVEMGADATDIGKTIHPHPTLGESIGMAAELYEGVCT 592

Query: 587 DVPPPRKR 594
           D+PP +K+
Sbjct: 593 DLPPQKKK 600


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: 1111
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: 594
Length of database: 600
Length adjustment: 37
Effective length of query: 557
Effective length of database: 563
Effective search space:   313591
Effective search space used:   313591
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 BPHYT_RS12830 BPHYT_RS12830 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.11539.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11539.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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