GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaC in Pseudomonas fluorescens GW456-L13

Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate PfGW456L13_4584 4-carboxymuconolactone decarboxylase (EC 4.1.1.44)

Query= BRENDA::Q6SJB9
         (125 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4584
          Length = 130

 Score =  115 bits (287), Expect = 3e-31
 Identities = 52/120 (43%), Positives = 74/120 (61%)

Query: 3   ERYDNGMKVRRRVLGDAYVDRAEAGKTAFEAPFQTLITEGAWGTVWASDGISDRERSMLT 62
           +RYD GMKVRR VLGDA+VDR+    T F + FQ +IT  AWG +W  +G+    RS++T
Sbjct: 5   QRYDEGMKVRRAVLGDAHVDRSLTTLTEFNSEFQEMITRHAWGDIWTREGLPRHTRSLIT 64

Query: 63  LALLAALGNFDEIPMHIRATARTGASKQDVLEAFQHVAIYAGVPRANQALKLARQTYDEM 122
           +A+L  +    E+ +H+RA A  G S+ ++ E     AIY G+P AN    LA   +DE+
Sbjct: 65  IAMLIGMNREGELKLHLRAAANNGVSRGEIKEVIMQSAIYCGIPAANATFHLAESVWDEL 124


Lambda     K      H
   0.318    0.131    0.376 

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: 66
Number of extensions: 2
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: 125
Length of database: 130
Length adjustment: 14
Effective length of query: 111
Effective length of database: 116
Effective search space:    12876
Effective search space used:    12876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 41 (20.4 bits)

Align candidate PfGW456L13_4584 (4-carboxymuconolactone decarboxylase (EC 4.1.1.44))
to HMM TIGR02425 (pcaC: 4-carboxymuconolactone decarboxylase (EC 4.1.1.44))

Software error:

../bin/blast/fastacmd -i /tmp/list.13060.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13060.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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