GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Echinicola vietnamensis KMM 6221, DSM 17526

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Echvi_4609 Echvi_4609 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Cola:Echvi_4609
          Length = 465

 Score =  447 bits (1149), Expect = e-130
 Identities = 232/461 (50%), Positives = 315/461 (68%), Gaps = 2/461 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD+IV+G GPGGYVAAIRA+QL LK A+VE   LGGICLNWGCIPTK+LL+SA+V+  + 
Sbjct: 6   FDVIVVGSGPGGYVAAIRASQLGLKTAVVEAAELGGICLNWGCIPTKALLKSAQVFEYIN 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +A+ YG+T   P  D   ++ RSR VA  ++ G++ LL+KNK+E + G G++   +++ V
Sbjct: 66  HAKDYGITVKDPKADFGGMVKRSRGVADGMSKGIQFLLKKNKIEQLLGWGKVKPGKKVEV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           E  +G++    A +IIIATGAR+R+LP +  D K I  Y  A+     PKK++V+GSGAI
Sbjct: 126 EDKDGKKTTYSADNIIIATGARSRELPAIKIDDKKIIGYRKAMTLEKQPKKMVVVGSGAI 185

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           G+EFA FYA  G EV++VE   +I+P EDAEVS  + + +KK G+ I+T + + ++    
Sbjct: 186 GVEFAYFYAAIGTEVTVVEFMDRIVPNEDAEVSKALERMYKKAGMNIMTSTEVTSVDTKG 245

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
            G    +    G+ T +     + A GVVANVEN GL+ +GI +D+G I VD F +TN+ 
Sbjct: 246 SGCKVTVKTKKGEETID-CDVVLSAAGVVANVENCGLEDVGIVVDKGRIKVDEFYKTNMP 304

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
             +AIGDV   P LAH AS +G+I  E IAG D   PL+  NIPGCTY  P++ASVG TE
Sbjct: 305 GYYAIGDVIPGPALAHVASAEGIICVEKIAGHD-PEPLDYNNIPGCTYCVPEIASVGYTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
           EKA++ GY +K+G FPF A+GKA A GA+DGFVK +FDA  G LLGAHM+GA VTEMI  
Sbjct: 364 EKAKEAGYELKVGKFPFSASGKAKAAGASDGFVKLIFDAKYGELLGAHMIGANVTEMIAE 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
               R LETT  E+++T+ PHPT+SEA+ E+  AAY   +H
Sbjct: 424 IVAVRKLETTGHELIKTVHPHPTMSEAVMEAAAAAYDEVIH 464


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: 585
Number of extensions: 25
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 Echvi_4609 Echvi_4609 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.26087.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26087.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.