GapMind for catabolism of small carbon sources

 

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

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate PfGW456L13_4830 N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4830
         (368 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4830
          Length = 368

 Score =  743 bits (1917), Expect = 0.0
 Identities = 368/368 (100%), Positives = 368/368 (100%)

Query: 1   MSEDNILTAHGWVRGRLVHEHGKVVSIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60
           MSEDNILTAHGWVRGRLVHEHGKVVSIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM
Sbjct: 1   MSEDNILTAHGWVRGRLVHEHGKVVSIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60

Query: 61  EGAPAFETITRTHVRFGTTSLLATTMTAPSEEISSVLQAVGEFCELRPQGCARVLGVHLE 120
           EGAPAFETITRTHVRFGTTSLLATTMTAPSEEISSVLQAVGEFCELRPQGCARVLGVHLE
Sbjct: 61  EGAPAFETITRTHVRFGTTSLLATTMTAPSEEISSVLQAVGEFCELRPQGCARVLGVHLE 120

Query: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDTLIRDLSSRGIRMQ 180
           GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDTLIRDLSSRGIRMQ
Sbjct: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDTLIRDLSSRGIRMQ 180

Query: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240
           IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH
Sbjct: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240

Query: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300
           PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD
Sbjct: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300

Query: 301 QALRNLVKIGLPIAEASQRLSQFPADYLGITERGRLQPGAWADCVRLDRSLKLTAVMVEG 360
           QALRNLVKIGLPIAEASQRLSQFPADYLGITERGRLQPGAWADCVRLDRSLKLTAVMVEG
Sbjct: 301 QALRNLVKIGLPIAEASQRLSQFPADYLGITERGRLQPGAWADCVRLDRSLKLTAVMVEG 360

Query: 361 EDIDFKNA 368
           EDIDFKNA
Sbjct: 361 EDIDFKNA 368


Lambda     K      H
   0.320    0.137    0.412 

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: 690
Number of extensions: 15
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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: 49 (23.5 bits)

Align candidate PfGW456L13_4830 (N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.9374.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9374.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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