GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Shewanella loihica PV-4

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 5211003 Shew_3429 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__PV4:5211003
          Length = 475

 Score =  828 bits (2140), Expect = 0.0
 Identities = 406/474 (85%), Positives = 447/474 (94%)

Query: 1   MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA 60
           MS EIKTQVVVLGAGPAGYSAAFR ADLGLETVIVER++TLGGVCLNVGCIPSKALLHV+
Sbjct: 1   MSNEIKTQVVVLGAGPAGYSAAFRAADLGLETVIVERFSTLGGVCLNVGCIPSKALLHVS 60

Query: 61  KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT 120
           KVIEEAKA++ HG+VFGEP+ D+DK+R +K+ VI+QLTGGL GM+K RKV VVNGLGKFT
Sbjct: 61  KVIEEAKAISNHGVVFGEPQIDLDKLREFKQSVISQLTGGLGGMSKMRKVNVVNGLGKFT 120

Query: 121 GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV 180
           G NT+EV GE+G  V++F+ AIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVP +LLV
Sbjct: 121 GPNTIEVAGEDGVKVVHFEQAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPGKLLV 180

Query: 181 MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA 240
           MGGGIIGLEMGTVY +LGS+IDVVEMFDQVIPAADKDIV+V+TK+I  KFNL+LETKVTA
Sbjct: 181 MGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDIVRVYTKKIKNKFNLILETKVTA 240

Query: 241 VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ 300
           VEAKEDGIYV+MEGKKAP EP RYDAVLVAIGR PNGK +DA KAGV +D+RGFI VDKQ
Sbjct: 241 VEAKEDGIYVSMEGKKAPTEPVRYDAVLVAIGRTPNGKLIDADKAGVNIDERGFINVDKQ 300

Query: 301 LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV 360
           +RTNVPHI+AIGDIVGQPMLAHKGVHEGHVAAEVIAG KHYFDPKVIPSIAYT+PEVAWV
Sbjct: 301 MRTNVPHIYAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTDPEVAWV 360

Query: 361 GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE 420
           GLTEKEAKE+GI+YETA+FPWAASGRAIASDC++GMTKLIFDKE+HRVIGGAIVG NGGE
Sbjct: 361 GLTEKEAKEQGIAYETASFPWAASGRAIASDCSEGMTKLIFDKETHRVIGGAIVGVNGGE 420

Query: 421 LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK 474
           LLGEIGLAIEMGCDAED+ALTIHAHPTLHESVGLAAE++EGSITDLPNPKAKKK
Sbjct: 421 LLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEIYEGSITDLPNPKAKKK 474


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: 837
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: 474
Length of database: 475
Length adjustment: 33
Effective length of query: 441
Effective length of database: 442
Effective search space:   194922
Effective search space used:   194922
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 5211003 Shew_3429 (dihydrolipoamide dehydrogenase (RefSeq))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.16900.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16900.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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