GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Shewanella amazonensis SB2B

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 6936759 Sama_0946 N-acetylglucosamine-6-phosphate deacetylase (RefSeq)

Query= reanno::SB2B:6936759
         (377 letters)



>FitnessBrowser__SB2B:6936759
          Length = 377

 Score =  748 bits (1930), Expect = 0.0
 Identities = 377/377 (100%), Positives = 377/377 (100%)

Query: 1   MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG 60
           MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG
Sbjct: 1   MKTTLIAERLFDGEQFHHNVPLTVEDGQVLALDTVAGCAEVRLQGTLVPGFIDVQVNGGG 60

Query: 61  GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG 120
           GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG
Sbjct: 61  GVLFNDTPTVAAIEAIGAAHARFGTTGYLPTLITDKVETMARAADAAAEAIAKGSTGVLG 120

Query: 121 VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV 180
           VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV
Sbjct: 121 VHFEGPHLSVPKKGVHPESHIRRIGDRELEIFARQDLGLKVVTLAPENVSPEVICALVDV 180

Query: 181 GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV 240
           GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV
Sbjct: 181 GVKVCLGHSNADYATTVAALEAGATGFTHLYNAMSALTSREPGVVGAAIDSDEAWCGLIV 240

Query: 241 DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE 300
           DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE
Sbjct: 241 DGHHVHSAAARIAIKAKPRGKVMLVTDAMPPVGMDDNASFELFGIQVVRQGDKLNALTGE 300

Query: 301 LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD 360
           LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD
Sbjct: 301 LAGCVLDMAGAVQNTVDMLGLPQAEAIRMASLYPAAFLGIDNRVGTLSVGKQADMVLLDD 360

Query: 361 NGRCRGTWIGGRQVFGL 377
           NGRCRGTWIGGRQVFGL
Sbjct: 361 NGRCRGTWIGGRQVFGL 377


Lambda     K      H
   0.320    0.137    0.402 

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: 593
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: 377
Length of database: 377
Length adjustment: 30
Effective length of query: 347
Effective length of database: 347
Effective search space:   120409
Effective search space used:   120409
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: 50 (23.9 bits)

Align candidate 6936759 Sama_0946 (N-acetylglucosamine-6-phosphate deacetylase (RefSeq))
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.29521.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29521.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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