GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Bacteroides thetaiotaomicron VPI-5482

Align TPP-dependent acetoin dehydrogenase complex, E3 component, dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 352713 BT3186 dihydrolipoamide dehydrogenase (NCBI ptt file)

Query= CharProtDB::CH_006552
         (578 letters)



>FitnessBrowser__Btheta:352713
          Length = 447

 Score =  333 bits (853), Expect = 1e-95
 Identities = 188/449 (41%), Positives = 270/449 (60%), Gaps = 9/449 (2%)

Query: 118 LVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHSSQLLTEMKEG 177
           +++IGGGP GY AA  A + G  V LIEK +LGG CLN GCIPTK LL+S++     +  
Sbjct: 5   VIIIGGGPAGYTAAEAAGKAGLSVLLIEKNNLGGVCLNEGCIPTKTLLYSAKTYDSARHS 64

Query: 178 DKLGIDIEGSIVVNWKHIQKRKKIVIKKLVSGVSGLLTCNKVKVIKGTAKFESKDTILVT 237
            K  +++   +  +   I  RK  V++KLV GV   LT N V ++ G A+   K+T+   
Sbjct: 65  SKYAVNVS-EVSFDLPKIIARKSKVVRKLVLGVKAKLTSNNVAMVTGEAQIIDKNTVRCG 123

Query: 238 KEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESNPESIAIIGGGVIG 297
           +E       N +N I+ TGS  FIP I G +         AL  +  P S+AI+GGGVIG
Sbjct: 124 EET-----YNAENLILCTGSETFIPPITGVETVNYWTHRDALDSKELPASLAIVGGGVIG 178

Query: 298 VEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININNNCKVTRIEQGED 357
           +EFAS FNSLG +V++IEM+  IL  MD+E+S + +A+  + GI    + KV  + Q E+
Sbjct: 179 MEFASFFNSLGVQVTVIEMMDEILGGMDKELSALLRAEYAKRGIKFLLSTKVVALSQTEE 238

Query: 358 GLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGV-KTEGGSIIVNDKMETNVEG 416
           G  VS+   +G+ S+  EK+L++VGRR   +G  +E + + KT  G+I VN+KM+T++ G
Sbjct: 239 GAVVSYENAEGKGSVIAEKLLMSVGRRPVTKGFGLENLNLDKTGRGAIKVNEKMQTSLSG 298

Query: 417 IYAIGDCTGKIMLAHVASDQGVVAAENIMGQNKKMDYKTVPACVYTKPELASVGLTEEQA 476
           +Y  GD TG  +LAH A  +  VA  +I+G+   M Y+ +P  VYT PE+A VG TEE A
Sbjct: 299 VYVCGDLTGFSLLAHTAVREAEVAVHSILGKEDAMSYRAIPGVVYTNPEIAGVGETEESA 358

Query: 477 KEKGIDYKVGKFQLAANGKSLIMNE-TGGVIKIITDKKYEEILGVHILGPRATDLITEAA 535
             KGI YKV K  +A +G+ +  NE   GV K++ D++ E I+G H+LG  A+++IT A 
Sbjct: 359 SAKGITYKVVKLPMAYSGRFVAENEGVNGVCKVLLDEQ-ERIIGAHVLGNPASEIITLAG 417

Query: 536 LALRLEATLEEIITTVHAHPTVGEAMKEA 564
            A+ L  T       V  HPTVGE  +EA
Sbjct: 418 TAIELGLTAAAWKKVVFPHPTVGEIFREA 446


Lambda     K      H
   0.313    0.134    0.365 

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: 610
Number of extensions: 29
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: 578
Length of database: 447
Length adjustment: 34
Effective length of query: 544
Effective length of database: 413
Effective search space:   224672
Effective search space used:   224672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 352713 BT3186 (dihydrolipoamide dehydrogenase (NCBI ptt file))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.12319.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12319.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.