GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Pseudomonas fluorescens GW456-L13

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10); propanal dehydrogenase (CoA-propanoylating) (EC 1.2.1.87) (characterized)
to candidate PfGW456L13_2505 Acetaldehyde dehydrogenase, acetylating, (EC 1.2.1.10) in gene cluster for degradation of phenols, cresols, catechol

Query= BRENDA::Q79AF6
         (304 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2505
          Length = 302

 Score =  465 bits (1197), Expect = e-136
 Identities = 223/299 (74%), Positives = 262/299 (87%)

Query: 1   MTKKIKCALIGPGNIGTDLLAKLQRSPVLEPIWMVGIDPESDGLKRAREMGIKTTADGVD 60
           M+KK++ A+IGPGNIGTDLL K+ RS  +EP+WMVG+DP+S+GLKRAREMGIKTTA GVD
Sbjct: 1   MSKKLRAAIIGPGNIGTDLLMKMCRSQWIEPVWMVGVDPDSEGLKRAREMGIKTTAGGVD 60

Query: 61  GLIPHMQADGVQIVFDATSAYVHADNSRKVNALGALMIDLTPAAIGPFCVPTVNLKEHVG 120
           GL+PH+  D ++I FDATSAYVHA+NSRK+N LG +MIDLTPAAIGP+CVP VNLKEH  
Sbjct: 61  GLLPHVLDDDIRIAFDATSAYVHAENSRKLNELGVIMIDLTPAAIGPYCVPPVNLKEHAS 120

Query: 121 KGEMNVNMVTCGGQATIPMVAAVSRVQPVAYGEIVATVSSKSAGPGTRKNIDEFTRTTAG 180
              MNVNMVTCGGQATIPMVAAVSRVQPV+YGEIVATVSS S GPGTR+NIDEFTRTTAG
Sbjct: 121 SLAMNVNMVTCGGQATIPMVAAVSRVQPVSYGEIVATVSSGSVGPGTRQNIDEFTRTTAG 180

Query: 181 AVEKVGGAKKGKAIIILNPAEPPLIMRDTVHCLLESEPDQAKITESIHAMIKEVQKYVPG 240
           AVEK+GGA++GKAII++NPAEPPL+MRDT+HCL + EP+Q  I  S+  M++EVQ+YVPG
Sbjct: 181 AVEKIGGARRGKAIIVINPAEPPLMMRDTIHCLTDDEPNQDAIRTSVLEMVREVQRYVPG 240

Query: 241 YKLVNGPVFDGLRVSVYLEVEGLGDYLPKYAGNLDIMTAAAARTAEMFAEEILAGQLTL 299
           YKL+NGPVFDG +VS+++EVEGLGD+LPK AGNLDIMTAA  RTAEMFAEE   G L L
Sbjct: 241 YKLINGPVFDGRKVSIFIEVEGLGDFLPKSAGNLDIMTAAGLRTAEMFAEEAHKGTLQL 299


Lambda     K      H
   0.317    0.135    0.388 

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: 347
Number of extensions: 7
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: 304
Length of database: 302
Length adjustment: 27
Effective length of query: 277
Effective length of database: 275
Effective search space:    76175
Effective search space used:    76175
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 PfGW456L13_2505 (Acetaldehyde dehydrogenase, acetylating, (EC 1.2.1.10) in gene cluster for degradation of phenols, cresols, catechol)
to HMM TIGR03215 (acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.8742.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8742.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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