GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Marinobacter adhaerens HP15

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate GFF3782 HP15_3724 1-phosphofructokinase

Query= reanno::psRCH2:GFF3290
         (312 letters)



>FitnessBrowser__Marino:GFF3782
          Length = 321

 Score =  271 bits (694), Expect = 1e-77
 Identities = 147/309 (47%), Positives = 189/309 (61%)

Query: 1   MARVLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGF 60
           MAR+LT+TLNPALDL+V+   L LGEVNR+    +  AGKG+NVA+VLA LGH +TV G 
Sbjct: 1   MARILTITLNPALDLSVETAPLALGEVNRTGHTLMEPAGKGINVARVLARLGHSVTVAGL 60

Query: 61  LGEGNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAEL 120
           LG+ N   FE+LF A G  D FVRV G+ R+N+K+AEA GRVTD+NGPG    E     L
Sbjct: 61  LGDANAAPFERLFEAEGLQDSFVRVPGQNRNNIKIAEAGGRVTDLNGPGFRAPEDALQRL 120

Query: 121 LARLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRP 180
             RLK L+P  + VV+ GSLP G        L+         V LDTSGA L+ G+   P
Sbjct: 121 QLRLKSLLPECDAVVIGGSLPDGFPPSGLAILVEQASRADKPVWLDTSGAGLKAGIKAGP 180

Query: 181 WLIKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240
           + IKPN +EL++  G  L   +++AA    ++  G+ HVVVS GADGV W SP   L + 
Sbjct: 181 YAIKPNTDELSDWAGTPLKDLASVAATVDGIRAGGVSHVVVSMGADGVFWSSPAGILRSR 240

Query: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAE 300
            P V +VSTV AGD+LLAGMLHG+L     +  L  ATA++A+ V  +G G         
Sbjct: 241 VPPVSLVSTVCAGDTLLAGMLHGVLGEQSEDTVLAFATALSAECVQHIGVGDPGAPDFHS 300

Query: 301 LQAAVRLQP 309
           L    R+QP
Sbjct: 301 LLQQTRVQP 309


Lambda     K      H
   0.316    0.132    0.371 

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: 292
Number of extensions: 6
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: 312
Length of database: 321
Length adjustment: 27
Effective length of query: 285
Effective length of database: 294
Effective search space:    83790
Effective search space used:    83790
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate GFF3782 HP15_3724 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

Software error:

../bin/blast/fastacmd -i /tmp/list.3934.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3934.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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