GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate N515DRAFT_2155 N515DRAFT_2155 dihydrolipoamide dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2155
          Length = 594

 Score =  766 bits (1977), Expect = 0.0
 Identities = 399/602 (66%), Positives = 481/602 (79%), Gaps = 19/602 (3%)

Query: 2   SVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKV 61
           + IEVKVPDIG  D+V VIEVLVKAGD+V  +QSLI LESDKA+M++PSSAAG + EVKV
Sbjct: 3   NTIEVKVPDIGGHDSVPVIEVLVKAGDSVTKDQSLITLESDKATMEIPSSAAGTIKEVKV 62

Query: 62  KVGDKVGQGAVICTIEAQQAAAAPAP-------AQAPAPAQAPAPAAAAPAPAPAAASHS 114
           KVGD++ +GAVI  +E    AAAPA        A APAPA APAPA AA APAP AA  S
Sbjct: 63  KVGDELSEGAVIVILEVSGDAAAPAAEAPKAAAAPAPAPASAPAPAKAA-APAPQAAGAS 121

Query: 115 GG-ADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHN 173
           G  ADI+C+++VLG+GPGGY+AAFRAADLG++TVLVERY+TLGGVCLNVGCIPSKALLH 
Sbjct: 122 GRTADIECKLVVLGSGPGGYTAAFRAADLGVDTVLVERYATLGGVCLNVGCIPSKALLHA 181

Query: 174 AAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNF 233
           AAVIDEA+A+AAHG+ FG+ K+DLD LR +KN+VVG+LTGGLAGM++ RKV+ V+G+G+F
Sbjct: 182 AAVIDEAEAMAAHGVSFGKPKLDLDKLRSFKNKVVGQLTGGLAGMSRQRKVRTVQGVGSF 241

Query: 234 LDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRIVDSTGALEL 292
           + PH +EVE  EG        K ++RFE AIIAAGSQ+VKLP  P +D R++DSTGALEL
Sbjct: 242 VSPHELEVETAEG--------KKLVRFEHAIIAAGSQSVKLPAFPWDDERVMDSTGALEL 293

Query: 293 PEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFG 352
            +VP K+LV+GGGIIGLEMATVY+ LG+++ VVE +D L+ GAD DL+K   K+   +  
Sbjct: 294 KDVPGKLLVVGGGIIGLEMATVYAALGSEVTVVEFMDQLIPGADADLIKPLAKRLGGKLK 353

Query: 353 KVMLKTKTVGVEAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVS 412
            V LKTK    +A   GI V +EG++ P E + +D VLV+VGRSPNG +I A+KAGVAV+
Sbjct: 354 GVHLKTKVTEAKATKKGIEVAYEGDSIP-ETKLFDRVLVAVGRSPNGGKIGADKAGVAVT 412

Query: 413 ERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSV 472
           ERGFINVD QMRTNVPHIFAIGD+VGQPMLAHKA HEA VAAE   G K++FDA+ IPSV
Sbjct: 413 ERGFINVDTQMRTNVPHIFAIGDLVGQPMLAHKATHEARVAAEVVAGMKSHFDARVIPSV 472

Query: 473 AFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIG 532
           AFTDPEVAW G+TE E KEKG+K   G FPWAASGRAI   R EGFTKLIFDEETHRV+G
Sbjct: 473 AFTDPEVAWVGVTEREAKEKGLKIGVGKFPWAASGRAIGIDRTEGFTKLIFDEETHRVVG 532

Query: 533 GGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPR 592
           G IVG HAGDLI+E+  AIEMG++A DIG TIHPHPTL ES+GMAAE+YEGT TD+  P+
Sbjct: 533 GAIVGPHAGDLIAEITHAIEMGSEAADIGLTIHPHPTLSESVGMAAEVYEGTITDLYMPK 592

Query: 593 KR 594
           ++
Sbjct: 593 RK 594


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: 1014
Number of extensions: 48
Number of successful extensions: 6
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: 594
Length adjustment: 37
Effective length of query: 557
Effective length of database: 557
Effective search space:   310249
Effective search space used:   310249
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 N515DRAFT_2155 N515DRAFT_2155 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.16566.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16566.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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