GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Cupriavidus basilensis 4G11

Align Acetaldehyde dehydrogenase; Acetaldehyde dehydrogenase [acetylating]; EC 1.2.1.10 (characterized)
to candidate RR42_RS32630 RR42_RS32630 acetaldehyde dehydrogenase

Query= SwissProt::Q52060
         (312 letters)



>FitnessBrowser__Cup4G11:RR42_RS32630
          Length = 314

 Score =  456 bits (1172), Expect = e-133
 Identities = 237/309 (76%), Positives = 267/309 (86%), Gaps = 2/309 (0%)

Query: 4   KLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASDGLARAQRMGVTTTYAGVEGL 63
           K KVAIIGSGNIGTDLMIKV+RN + LEMGAMVGIDAASDGLARA R+GV TT  G+EGL
Sbjct: 8   KHKVAIIGSGNIGTDLMIKVMRNGRQLEMGAMVGIDAASDGLARAARLGVPTTAEGIEGL 67

Query: 64  IKLPEFADIDFVFDATSASAHVQNEALLRQAKPGIRLIDLTPAAIGPYCVPVVNLEEHLG 123
           +++  F DI   FDATSA AH  +  +L+Q   GI++IDLTPAAIGPY VPVVNL++ LG
Sbjct: 68  VRMAGFGDIRIAFDATSAGAHAHHNQILQQH--GIQVIDLTPAAIGPYVVPVVNLDQQLG 125

Query: 124 KLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSKAI 183
             N+NMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTS+AI
Sbjct: 126 ASNINMVTCGGQATIPMVAAVSRVAKVHYAEIVASISSKSAGPGTRANIDEFTETTSQAI 185

Query: 184 EVIGGAAKGKAIIIMNPAEPPLIMRDTVYVLSAAADQAAVAASVAEMVQAVQAYVPGYRL 243
             +GGAA+GKAII++NPAEPPL+MRDTV+ LS  AD+AA+ ASV  M +AVQAYVPGYRL
Sbjct: 186 CSVGGAARGKAIIVLNPAEPPLMMRDTVFTLSEDADEAAIEASVQAMAKAVQAYVPGYRL 245

Query: 244 KQQVQFDVIPESAPLNIPGLGRFSGLKTSVFLEVEGAAHYLPAYAGNLDIMTSAALATAE 303
           KQ+VQF+ I  SAPLNIPGLG  SGLKTS+FLEVEGAAHYLPAYAGNLDIMTSAALA AE
Sbjct: 246 KQRVQFERIDPSAPLNIPGLGLMSGLKTSIFLEVEGAAHYLPAYAGNLDIMTSAALACAE 305

Query: 304 RMAQSMLNA 312
           R+AQ+ L A
Sbjct: 306 RLAQTRLAA 314


Lambda     K      H
   0.317    0.132    0.362 

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: 320
Number of extensions: 3
Number of successful extensions: 2
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: 312
Length of database: 314
Length adjustment: 27
Effective length of query: 285
Effective length of database: 287
Effective search space:    81795
Effective search space used:    81795
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: 48 (23.1 bits)

Align candidate RR42_RS32630 RR42_RS32630 (acetaldehyde dehydrogenase)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.4069.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4069.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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