GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Burkholderia phytofirmans PsJN

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate BPHYT_RS02730 BPHYT_RS02730 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::BFirm:BPHYT_RS02730
         (367 letters)



>FitnessBrowser__BFirm:BPHYT_RS02730
          Length = 367

 Score =  728 bits (1880), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM 60
           MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM
Sbjct: 1   MLTGNILTTDGWIHGTLEYENGRITALTGERADPSTNDAPYILPGFIDLHVHGGGGSDVM 60

Query: 61  EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE 120
           EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE
Sbjct: 61  EGGSAIETITRTHARYGTTSLLATTMTAPRDELMAVVAELGNNARIRTPGGARVLGVHLE 120

Query: 121 GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ 180
           GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ
Sbjct: 121 GPYINPGKLGAQPDAAVSAVMDEVLKYLSIAPIRVVTLAPEIAGHMEIISEMAARGVRVQ 180

Query: 181 LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH 240
           LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH
Sbjct: 181 LGHSLGTYDDAVAALKHGACGFTHLFNAMSPLHHRNPGLVGAALAHAEFAEIIPDLLHVH 240

Query: 241 PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD 300
           PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD
Sbjct: 241 PGAIRAALRAIPRLYVVTDSTSATGMPDGEYRLGSQHVTKCLGGVRLADGTLAGSTLTMD 300

Query: 301 QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG 360
           QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG
Sbjct: 301 QALRNLVSIGLPIADVSNRLSRYAADYLGIEDRGRIARGAWADVVVFDRELALSATYVEG 360

Query: 361 EAIVEYA 367
           EAIVEYA
Sbjct: 361 EAIVEYA 367


Lambda     K      H
   0.319    0.136    0.399 

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: 615
Number of extensions: 23
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS02730 BPHYT_RS02730 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.8368.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8368.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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