GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Paraburkholderia bryophila 376MFSha3.1

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate H281DRAFT_05115 H281DRAFT_05115 dihydrolipoamide dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>FitnessBrowser__Burk376:H281DRAFT_05115
          Length = 476

 Score =  516 bits (1328), Expect = e-151
 Identities = 267/477 (55%), Positives = 346/477 (72%), Gaps = 6/477 (1%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           M+++FDVVVIGAGPGGY+AAI+AAQLG   ACIEK+ +  G L LGGTCLNVGCIPSKAL
Sbjct: 1   MSKEFDVVVIGAGPGGYIAAIRAAQLGKTVACIEKWKNPAGTLKLGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           L SS +++ A      HGIS   VK+D++ M+ RK GIV+ +T G+  LF+ N +T ++G
Sbjct: 61  LASSEEFENASHHLADHGISVENVKVDISKMMARKDGIVEKMTKGIEFLFRKNKITWLKG 120

Query: 121 HGKLL----AGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALE 176
           HGK      AG ++EV+  +G TEV+ A+NVI+A+GS+   +P  PVD  ++ D+ GAL 
Sbjct: 121 HGKFTGKTDAGVQIEVS-GEGETEVVTAKNVIIATGSKARHLPNIPVDNKIVADNEGALA 179

Query: 177 FQAVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQG 236
           F   PK+L VIGAGVIGLELGSVW RLGAEVTVLEAL  FL AAD A++KEA K   KQG
Sbjct: 180 FDTAPKKLAVIGAGVIGLELGSVWRRLGAEVTVLEALPEFLGAADQALAKEAAKQFKKQG 239

Query: 237 LDIKLGARVTGSKVNGNEVEVTYTNAEGE-QKITFDKLIVAVGRRPVTTDLLAADSGVTI 295
           LDI +G +V       N V + YT+ +G  QK+  D+LIV++GR P T +L     G+  
Sbjct: 240 LDIHVGVKVGEVSTTENSVTINYTDKDGNAQKLEADRLIVSIGRVPNTDNLGLEAIGLKA 299

Query: 296 DERGYIFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPS 355
           +ERG+I VDD+CAT+VP VYAIGDVVRG MLAHKA +EG++V E I G K  ++Y+ IP 
Sbjct: 300 NERGFIDVDDHCATAVPNVYAIGDVVRGPMLAHKAEDEGVLVAEIIDGQKPHIDYNCIPW 359

Query: 356 VIYTHPEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVL 415
           VIYT PEIAWVGKTEQ LKAEG EV  G FPF A+GRA+  N   GFVK+IADAKTD +L
Sbjct: 360 VIYTEPEIAWVGKTEQQLKAEGREVKTGQFPFMANGRALGINKADGFVKMIADAKTDELL 419

Query: 416 GVHVIGPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHV 472
           GVH+I  +A++L+ +  +AMEF  ++ED+G +   HP+LSE + EAALAV+  A+++
Sbjct: 420 GVHIISANASDLIAEAVVAMEFKAASEDIGRICHPHPSLSEVMREAALAVDKRALNM 476


Lambda     K      H
   0.316    0.133    0.374 

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: 714
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: 478
Length of database: 476
Length adjustment: 33
Effective length of query: 445
Effective length of database: 443
Effective search space:   197135
Effective search space used:   197135
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: 51 (24.3 bits)

Align candidate H281DRAFT_05115 H281DRAFT_05115 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.16523.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16523.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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