GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dyella japonica UNC79MFTsu3.2

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate N515DRAFT_2778 N515DRAFT_2778 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2778
          Length = 474

 Score =  568 bits (1465), Expect = e-166
 Identities = 293/474 (61%), Positives = 348/474 (73%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS KFDV+VIGAGP GYVAAIRAAQLGLKTACI+ + GK+GK ALGGTCLNVGCIPSKAL
Sbjct: 1   MSDKFDVIVIGAGPAGYVAAIRAAQLGLKTACIDAFTGKDGKQALGGTCLNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           LDSS ++H     F VHGI A    IDV   + RK  IVK  TGGI  LFKAN VT+F G
Sbjct: 61  LDSSKQFHNLTHNFAVHGITADNAKIDVATFIGRKDKIVKQFTGGIGQLFKANKVTAFYG 120

Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180
            GKLL    VE+T  DG  Q + A NVI+ASGS P+E+P A   +  IVD+ GAL+F  V
Sbjct: 121 TGKLLKGNSVEITANDGSKQTISATNVILASGSVPIELPFAKFDNKFIVDNAGALDFPEV 180

Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240
           PK+LGVIGAGVIGLELGSVW RLGA+VT+LEAL  FL  AD  +AK A K   KQGL I+
Sbjct: 181 PKRLGVIGAGVIGLELGSVWGRLGADVTILEALPDFLSVADADVAKIAAKEFAKQGLKIK 240

Query: 241 LGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300
           LGA++T +E+K  +V +T+ D +G  + T DKL+VAVGRR  T  LLA D+GV LDERG 
Sbjct: 241 LGAKLTKAEIKGNEVALTYEDKDGAHELTVDKLLVAVGRRAYTAGLLADDTGVKLDERGR 300

Query: 301 IYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTH 360
           I VD+H  T V GV+AIGD VRG MLAHK SEEGV VAE IAG    +N+D IP VIYT 
Sbjct: 301 IVVDEHNHTGVDGVWAIGDAVRGPMLAHKGSEEGVAVAEWIAGKAGHVNFDTIPWVIYTE 360

Query: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVI 420
           PEIAW GKTE+ LK  G+   VGTFPFAA GRA+A N+  G VK++A A+TDR+LGVH++
Sbjct: 361 PEIAWAGKTEKELKDAGIPYKVGTFPFAAIGRAVAMNEAVGQVKMLAHAETDRLLGVHMV 420

Query: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIAN 474
           GP  +EL+ +  + MEF  SAEDL  +V +HPTLSEA+HEAAL+V+  AIH  N
Sbjct: 421 GPGVSELIAEAVVTMEFKGSAEDLARIVHAHPTLSEAVHEAALSVDKRAIHKGN 474


Lambda     K      H
   0.316    0.134    0.375 

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: 667
Number of extensions: 25
Number of successful extensions: 1
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: 478
Length of database: 474
Length adjustment: 33
Effective length of query: 445
Effective length of database: 441
Effective search space:   196245
Effective search space used:   196245
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 N515DRAFT_2778 N515DRAFT_2778 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.10534.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10534.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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