GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc02487 SMc02487 dihydrolipoamide dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>FitnessBrowser__Smeli:SMc02487
          Length = 468

 Score =  550 bits (1418), Expect = e-161
 Identities = 270/465 (58%), Positives = 347/465 (74%), Gaps = 2/465 (0%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           D+++IG GPGGYV AIKAAQLG+K   +EKR   GGTCLNVGCIPSKALLH+S M+H+A+
Sbjct: 4   DLIVIGSGPGGYVCAIKAAQLGMKVAVVEKRSTYGGTCLNVGCIPSKALLHASEMFHQAQ 63

Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164
           H     GV+V++ +++L  M+A KD  VK+   GV  LFKKNK++  +G GK L   +VS
Sbjct: 64  HGLEALGVEVANPKLNLQKMMAHKDATVKSNVDGVSFLFKKNKIDGFQGTGKVLGQGKVS 123

Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGITI--DEKKIVSSTGALSLTEIPKKLIVIGA 222
           V    GE  V++ K++++ATGSDV  +PG+ +  DEK IVSSTGAL+L ++P  +IV+G 
Sbjct: 124 VTNEKGEEQVLEAKNVVIATGSDVAGIPGVEVAFDEKTIVSSTGALALEKVPASMIVVGG 183

Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVD 282
           G IGLE+GSVW RLG++VTVVEF   I+  MDGE+ KQ QR L KQ + F L  KV G  
Sbjct: 184 GVIGLELGSVWARLGAKVTVVEFLDTILGGMDGEVAKQLQRMLTKQGIDFKLGAKVTGAV 243

Query: 283 SSGDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERF 342
            SGDG K+  EP +GGE TTL+A+VVL++ GR P T GL L K GV  D  GR+ ++  F
Sbjct: 244 KSGDGAKVTFEPVKGGEATTLDAEVVLIATGRKPSTDGLGLAKAGVVLDSRGRVEIDRHF 303

Query: 343 STNVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVG 402
            T+++GVYAIGDV+ GPMLAHKAE++GVA  E IAG+ GHV+YD +PGVVYT PEVASVG
Sbjct: 304 QTSIAGVYAIGDVVRGPMLAHKAEDEGVAVAEIIAGQAGHVNYDVIPGVVYTQPEVASVG 363

Query: 403 KTEEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGEL 462
           KTEE+LK  GV+Y +GKFPF AN RA+A+   +G VKILADKETD++LG HI+   AGE+
Sbjct: 364 KTEEELKAAGVAYKIGKFPFTANGRARAMLQTDGFVKILADKETDRVLGGHIIGFGAGEM 423

Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507
           IHE  + + +  SSED+ R CHAHPTMSEA+KEAA++T+ KPIHM
Sbjct: 424 IHEIAVLMEFGGSSEDLGRTCHAHPTMSEAVKEAALSTFFKPIHM 468


Lambda     K      H
   0.315    0.134    0.376 

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: 666
Number of extensions: 31
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: 507
Length of database: 468
Length adjustment: 34
Effective length of query: 473
Effective length of database: 434
Effective search space:   205282
Effective search space used:   205282
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: 52 (24.6 bits)

Align candidate SMc02487 SMc02487 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.14572.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14572.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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