GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Shewanella amazonensis SB2B

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 6936188 Sama_0377 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__SB2B:6936188
          Length = 476

 Score =  844 bits (2181), Expect = 0.0
 Identities = 419/475 (88%), Positives = 450/475 (94%), Gaps = 1/475 (0%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MS +IKTQVVVLGAGPAGYSAAFR ADLGLETVI+ER++TLGGVCLNVGCIPSKALLH+A
Sbjct: 1   MSNQIKTQVVVLGAGPAGYSAAFRAADLGLETVIIERFSTLGGVCLNVGCIPSKALLHIA 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAK  AEHG+VFGEP  DIDK+R +KEKVI QLTGGL GMAK RKV+VVNGLGKFT
Sbjct: 61  KVIEEAKTAAEHGVVFGEPSIDIDKLRGYKEKVIGQLTGGLGGMAKMRKVQVVNGLGKFT 120

Query: 121 GANTLEVEGENGK-TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLL 179
           G N++EV G +G  TVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVP++LL
Sbjct: 121 GPNSIEVTGADGAATVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPKKLL 180

Query: 180 VMGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVT 239
           VMGGGIIGLEMGTVYHALGS IDVVEMFDQVIPAADKD+VKV+T++ISKKFNLMLETKVT
Sbjct: 181 VMGGGIIGLEMGTVYHALGSDIDVVEMFDQVIPAADKDVVKVYTRKISKKFNLMLETKVT 240

Query: 240 AVEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDK 299
           AVEAKEDGIYV+MEGKKAP EP RYDAVLVAIGR PNGK +DA KAG+ VD+RGFI+VDK
Sbjct: 241 AVEAKEDGIYVSMEGKKAPTEPVRYDAVLVAIGRTPNGKLIDADKAGINVDERGFIKVDK 300

Query: 300 QLRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAW 359
           QLRTNVPHIFA+GDIVGQPMLAHKGVHEGHVAAEVI+G KH+FDPKVIPSIAYT+PEVAW
Sbjct: 301 QLRTNVPHIFAVGDIVGQPMLAHKGVHEGHVAAEVISGLKHFFDPKVIPSIAYTDPEVAW 360

Query: 360 VGLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGG 419
           VGLTEKEAKEKGI+YETATFPWAASGRAIASD +DGMTKLIFDKE+HRVIGGAIVG NGG
Sbjct: 361 VGLTEKEAKEKGIAYETATFPWAASGRAIASDASDGMTKLIFDKETHRVIGGAIVGVNGG 420

Query: 420 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEV+EGSITDLPNPKAKKK
Sbjct: 421 ELLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVYEGSITDLPNPKAKKK 475


Lambda     K      H
   0.317    0.137    0.396 

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: 858
Number of extensions: 23
Number of successful extensions: 3
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: 474
Length of database: 476
Length adjustment: 33
Effective length of query: 441
Effective length of database: 443
Effective search space:   195363
Effective search space used:   195363
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 6936188 Sama_0377 (dihydrolipoamide dehydrogenase (RefSeq))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.14871.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14871.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.