GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dinoroseobacter shibae DFL-12

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 3608411 Dshi_1811 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Dino:3608411
          Length = 465

 Score =  538 bits (1385), Expect = e-157
 Identities = 264/462 (57%), Positives = 345/462 (74%), Gaps = 2/462 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD++V+G GPGGYVAAIRAAQL LKVA+VER H+GGICLNWGCIPTK++LRS+EV+H M 
Sbjct: 6   FDMVVVGAGPGGYVAAIRAAQLGLKVAIVEREHMGGICLNWGCIPTKAMLRSSEVFHLMH 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
            A+ +GL +    +DLD ++ARSR +A +L SGV  L++KNKV V+ G   L     + V
Sbjct: 66  RAKEFGLKADGVGYDLDAVVARSRAIAKQLNSGVSHLMKKNKVTVVMGEASLPAKGTVAV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           +T +G E  L A  +++ATGARAR+LP + +DG  +WTY HAL P  MPKKLLVIGSGAI
Sbjct: 126 KTDKGTET-LRAPHVVLATGARARELPGLEADGDLVWTYKHALTPKRMPKKLLVIGSGAI 184

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           GIEFASFY   G E ++VE   +ILP+EDAE+S +  K F+K+G+ I  ++ +++L    
Sbjct: 185 GIEFASFYNTLGTETTVVEVMDRILPVEDAEISGFAKKQFEKQGMTIREKAMVKSLERGK 244

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
             VTA+I    GK T E F   I A+G+V N E +GL+ LG+++++  +  D + RT V+
Sbjct: 245 GTVTAQIEQG-GKTTAETFDTVISAVGIVGNTEKLGLEALGVRVEKTHVVTDAYCRTGVE 303

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
            ++AIGD+AGAP LAHKASH+GV+ AE IAG + VHP+   +I GCTY +PQ+ASVG+TE
Sbjct: 304 GLYAIGDLAGAPWLAHKASHEGVMVAELIAGRNDVHPVTPDSIAGCTYCQPQIASVGMTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
            +A++ G+ +K+G FPFI NGKAIA G  +G +KTVFDA +G LLGAHMVGAEVTE+IQG
Sbjct: 364 AQAKEAGHKIKVGRFPFIGNGKAIALGEPEGMIKTVFDAGTGELLGAHMVGAEVTELIQG 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           Y V R LETTE ++M T+FPHPTLSE MHESVL AYGRALHF
Sbjct: 424 YVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAYGRALHF 465


Lambda     K      H
   0.319    0.135    0.393 

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: 677
Number of extensions: 26
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 3608411 Dshi_1811 (dihydrolipoamide dehydrogenase (RefSeq))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.25333.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25333.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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