GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Phaeobacter inhibens BS107

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF2287 PGA1_c23190 dihydrolipoyl dehydrogenase LpdA

Query= BRENDA::P0A9P0
         (474 letters)



>FitnessBrowser__Phaeo:GFF2287
          Length = 459

 Score =  464 bits (1194), Expect = e-135
 Identities = 238/459 (51%), Positives = 314/459 (68%), Gaps = 8/459 (1%)

Query: 9   VVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVAKVIEEAKA 68
           ++VLGAGP GY+ AFR ADLG   +IV+   TLGGVCLNVGCIPSKALLH A++I E + 
Sbjct: 8   LIVLGAGPGGYACAFRAADLGRSVIIVDPRATLGGVCLNVGCIPSKALLHAAEMIRETRH 67

Query: 69  LAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFTGANTLEVE 128
               GI+ G    D++K+R  K+ ++ QLT GL G+AK RKV+ + G  +FT   +LE++
Sbjct: 68  GGGWGILTGNVSVDLNKLRAKKDSIVEQLTTGLVGLAKRRKVQTIRGSAQFTSDKSLEID 127

Query: 129 GENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLVMGGGIIGL 188
           GE+      FD A+IA GS P++LP  P ED RIWDSTDALEL+E+P+RL ++GGGIIGL
Sbjct: 128 GESW----TFDQAVIAVGSAPVRLPGWP-EDDRIWDSTDALELREIPKRLSIVGGGIIGL 182

Query: 189 EMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRI-SKKFNLMLETKVTAVEAKEDG 247
           EM TVY ALGS++ V+E  DQ+ P AD D V +    + ++   +   TKVT V+A +  
Sbjct: 183 EMATVYAALGSKVTVIEFMDQIAPGADADAVTILRAALETEDVTIHTGTKVTEVKASKTA 242

Query: 248 IYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQLRTNVPH 307
           + +T EG        + DA + A+GR  NG  +D   AGVE DDRG I VD   RTNV  
Sbjct: 243 LTLTCEGGFEGTI--KADAAIQAVGRRSNGSLVDPAAAGVEADDRGIIPVDASCRTNVAT 300

Query: 308 IFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWVGLTEKEA 367
           +FAIGD+ G PMLAH+  H+GHVAAEV +G     D  +IPS+AYT PE+AW GLT+ +A
Sbjct: 301 VFAIGDVTGNPMLAHRATHQGHVAAEVASGHATALDTDLIPSVAYTAPELAWAGLTQAKA 360

Query: 368 KEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGELLGEIGL 427
            E+GI +  A FPWAASGR ++S   +G+TKL++  +SHR++G  IVG N GELL E  L
Sbjct: 361 TERGIPHRVANFPWAASGRNLSSGGGEGLTKLVYCPDSHRLLGATIVGRNAGELLAECVL 420

Query: 428 AIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDL 466
           A+EMG   ED++L +HAHPTL E+VG AAE   G++TDL
Sbjct: 421 AMEMGATLEDMSLAVHAHPTLSETVGFAAERALGTLTDL 459


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: 562
Number of extensions: 18
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 474
Length of database: 459
Length adjustment: 33
Effective length of query: 441
Effective length of database: 426
Effective search space:   187866
Effective search space used:   187866
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 GFF2287 PGA1_c23190 (dihydrolipoyl dehydrogenase LpdA)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.12356.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12356.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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