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_RS05100 RR42_RS05100 acetaldehyde dehydrogenase

Query= SwissProt::Q9KWS1
         (316 letters)



>FitnessBrowser__Cup4G11:RR42_RS05100
          Length = 321

 Score =  445 bits (1144), Expect = e-130
 Identities = 225/305 (73%), Positives = 256/305 (83%)

Query: 2   SDDRLSVAIIGSGNIGTDLMIKIMRNSKLLKVGAMVGIDPKSDGLARAQRLGVPTTAEGV 61
           S  RL  AIIGSGNIGTDLMIKI+R+ + L+VGAMVGID  SDGLARAQRLGVPTT EG+
Sbjct: 5   SRTRLRAAIIGSGNIGTDLMIKILRHGQHLEVGAMVGIDAASDGLARAQRLGVPTTHEGI 64

Query: 62  DGLLDMPAFRDIKIAFDATSAGAQAIHNQKLQAHGVRVIDLTPAAIGPYVIPVVNFDQHV 121
           +GLL MP F DI++AFDATSAGA   HN  LQ HG++VIDLTPAAIGPYV+PVVN D H+
Sbjct: 65  EGLLGMPGFADIRVAFDATSAGAHMHHNAVLQKHGIQVIDLTPAAIGPYVVPVVNLDAHL 124

Query: 122 DAPNINMVTCGGQATIPIVHAVSKVSPVHYAEIVASISSKSAGPGTRANIDEFTETTSKA 181
           DAPN+NMVTCGGQATIPIV AVS+V+PV YAEIVASI+S+SAGPGTRANIDEFTETTS A
Sbjct: 125 DAPNLNMVTCGGQATIPIVRAVSQVAPVSYAEIVASIASRSAGPGTRANIDEFTETTSNA 184

Query: 182 ILEVGGAAQGRAIIILNPAEPPLIMRDTVYCFVSAEANIDAITDSVEQMVKSVQEYVPGY 241
           I++VGGAA G+AII+LNPAEPPL+MRDTV+C  +A+A  DAI  SVE+MV  V  YVPGY
Sbjct: 185 IVQVGGAAHGKAIIVLNPAEPPLLMRDTVFCLTAADAGQDAIRASVERMVAQVAAYVPGY 244

Query: 242 RLKQKVQFEKIVAGNEQNIPGLGWSTGLKVSVFLEVEGAGHYLPSYAGNLDIMTSAGLTV 301
           RLKQ VQFE+I       +PG+G   GLKVSVFLEVEGA HYLP+YAGNLDIMTSA L  
Sbjct: 245 RLKQHVQFERIDPACPLTLPGIGRLAGLKVSVFLEVEGAAHYLPAYAGNLDIMTSAALAA 304

Query: 302 AERIA 306
           AER+A
Sbjct: 305 AERVA 309


Lambda     K      H
   0.317    0.134    0.380 

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: 392
Number of extensions: 13
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: 316
Length of database: 321
Length adjustment: 27
Effective length of query: 289
Effective length of database: 294
Effective search space:    84966
Effective search space used:    84966
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: 48 (23.1 bits)

Align candidate RR42_RS05100 RR42_RS05100 (acetaldehyde dehydrogenase)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.27976.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27976.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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