GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Pseudomonas fluorescens FW300-N2E3

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate AO353_05305 AO353_05305 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1110
         (303 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05305
          Length = 303

 Score =  582 bits (1501), Expect = e-171
 Identities = 291/303 (96%), Positives = 300/303 (99%)

Query: 1   MNPQELKSILSSGLLSFPVTDFNAQGDFHRAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60
           MNPQELKSILSSGLLSFPVTDFNAQGDFHRAGYIKRLEWLAPYGASALFAAGGTGEFFSL
Sbjct: 1   MNPQELKSILSSGLLSFPVTDFNAQGDFHRAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60

Query: 61  AASEYSEIIKTAVDTCATSVPILAGVGGATRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120
           AASEYSE+IKTAVDTCA+SVPILAGVGG+TRQAIEYAQEAERLGAKGLLLLPHYLTEASQ
Sbjct: 61  AASEYSEVIKTAVDTCASSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120

Query: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180
           DGVAAHVEAVCKSVKIGV+VYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR
Sbjct: 121 DGVAAHVEAVCKSVKIGVIVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180

Query: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAREDHATVGK 240
           RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNF+PK AMDFYHAIAR+DHATVGK
Sbjct: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFLPKMAMDFYHAIARDDHATVGK 240

Query: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRAPLTDLTGEEYEMLAALIDKQ 300
           +IDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVR PLTDLT EE+EMLAAL+DKQ
Sbjct: 241 LIDDFFLPYLDIRNRKAGYAVSIVKAGAKIAGYDAGPVRTPLTDLTPEEFEMLAALMDKQ 300

Query: 301 GAQ 303
           GAQ
Sbjct: 301 GAQ 303


Lambda     K      H
   0.320    0.137    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: 482
Number of extensions: 8
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: 303
Length of database: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
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: 48 (23.1 bits)

Align candidate AO353_05305 AO353_05305 (5-dehydro-4-deoxyglucarate dehydratase)
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))

Software error:

../bin/blast/fastacmd -i /tmp/list.7899.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7899.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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