GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Marinobacter adhaerens HP15

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF65 HP15_65 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0H2ZB32
         (464 letters)



>FitnessBrowser__Marino:GFF65
          Length = 461

 Score =  514 bits (1324), Expect = e-150
 Identities = 268/466 (57%), Positives = 337/466 (72%), Gaps = 9/466 (1%)

Query: 1   MSQILKTSLLIVGGGPGGYVAAIRAGQLGIPTVLVEGAALGGTCLNVGCIPSKALIHAAE 60
           MS+++KT +L+VGGGPGGYVAAIR GQLG+ TVLVE   LGGTCL  GCIPSKA+IHAA 
Sbjct: 1   MSEVIKTKVLVVGGGPGGYVAAIRCGQLGLDTVLVEADQLGGTCLTRGCIPSKAMIHAAS 60

Query: 61  EYLKARHYAGRSALGIQV-QAPSIDIARTVEWKDAIVDRLTSGVAALLKKHGVDVVQGWA 119
           E+      A +  LGI + + P +D+A TV+WKD+IV RL +GVAALLK+  V VV+GW 
Sbjct: 61  EFSAMMKAASKPHLGISLSEPPKVDLAATVDWKDSIVKRLNTGVAALLKRAKVKVVKGWG 120

Query: 120 RILDGKSVAVELAGGGSQRIECEHLLLAAGSQSVELPILPLGGKVISSTEALAPGSLPKR 179
              D K+  VE A G    I+ EH++LA GS  VELP LPLGGKVISSTEAL+   +P +
Sbjct: 121 TFSDAKTCNVETADGVIT-IQSEHVILATGSAPVELPFLPLGGKVISSTEALSLPDVPSK 179

Query: 180 LVVVGGGYIGLELGTAYRKLGVEVAVVEAQPRILPGYDEELTKPVAQALRKLGVELYLGH 239
           LVV+G GYIGLELG AY KLG +V +VE+  RILP YDE L +PV + L +  V+L+L  
Sbjct: 180 LVVIGAGYIGLELGIAYAKLGSDVTIVESSDRILPLYDEALVEPVRRWLDESAVKLHLNA 239

Query: 240 SLLGPSENGVRVRDGAGEEREIAADQVLVAVGRKPRSEGWNLESLGLDMNGRAVKVDDQC 299
             LG  + G+ V    G E  + AD +LV VGRKP ++GW LE++ LDM+GR V+VD+QC
Sbjct: 240 RALGERDGGLAVELEGGSETVLPADNILVTVGRKPVTQGWGLENMALDMDGRYVRVDEQC 299

Query: 300 RTSMRNVWAIGDLAGEPMLAHRAMAQGEMVAELIAGKRRQFAPVAIPAVCFTDPEVVVAG 359
            TSM+NVWAIGDL GEPMLAH+A AQGE+VAE+IAGKRR+F PVAIPAVCFT+PE+V  G
Sbjct: 300 ATSMKNVWAIGDLVGEPMLAHKASAQGEVVAEVIAGKRRRFDPVAIPAVCFTEPEIVSVG 359

Query: 360 LSPEQAKDAGLDCLVASFPFAANGRAMTLEA--NEGFVRVVARRDNHLVVGWQAVGKAVS 417
             P  A       +   FP AANGRA++++A  N GFVRVVA  + H ++G QAVG  +S
Sbjct: 360 AEPSLA-----GTVTGVFPVAANGRALSMDAGDNGGFVRVVAHSETHRILGVQAVGTHIS 414

Query: 418 ELSTAFAQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALH 463
           EL+ AF  ++EMGA ++DI G I AHPTLGE   EA+L+ LGHA+H
Sbjct: 415 ELTAAFVTAVEMGATVDDIEGMIQAHPTLGEMFHEASLKILGHAIH 460


Lambda     K      H
   0.318    0.136    0.393 

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: 670
Number of extensions: 36
Number of successful extensions: 8
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: 464
Length of database: 461
Length adjustment: 33
Effective length of query: 431
Effective length of database: 428
Effective search space:   184468
Effective search space used:   184468
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF65 HP15_65 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.4531.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4531.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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