GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Pseudomonas fluorescens FW300-N2E3

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate AO353_05480 AO353_05480 1-phosphofructokinase

Query= reanno::pseudo5_N2C3_1:AO356_07330
         (313 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05480
          Length = 313

 Score =  510 bits (1313), Expect = e-149
 Identities = 260/313 (83%), Positives = 279/313 (89%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALDLTV+L  LEPGQVNRSDAMH HAAGKG+NVAQVLADLGH LTVSGF
Sbjct: 1   MAKILTLTLNPALDLTVQLPHLEPGQVNRSDAMHTHAAGKGINVAQVLADLGHQLTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGEDN Q FE LFA+RGFVDAFIRVPGETRSNIKLAE DGRITD+NGPGP+V AAAQQAL
Sbjct: 61  LGEDNLQAFEALFAKRGFVDAFIRVPGETRSNIKLAEADGRITDINGPGPVVSAAAQQAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L RL+QI  GHD VVVAGSLPRGVS QWL  L+ R+K+ GL VALDTSGEALR  L+AGP
Sbjct: 121 LDRLDQITLGHDAVVVAGSLPRGVSAQWLHGLLLRLKSRGLKVALDTSGEALRAGLSAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WLIKPNTEEL++AL CE +S  AQA+AA RLHA GIEHVVISHGA+GVNWFSVG+A+HA+
Sbjct: 181 WLIKPNTEELSEALDCEAISVAAQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHAT 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PP+VSV STVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGI D A LA 
Sbjct: 241 PPRVSVVSTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIGDAAQLAQ 300

Query: 301 LEQGVRVRPLTEQ 313
           LEQ VRVR LTEQ
Sbjct: 301 LEQEVRVRLLTEQ 313


Lambda     K      H
   0.317    0.132    0.373 

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: 422
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: 313
Length of database: 313
Length adjustment: 27
Effective length of query: 286
Effective length of database: 286
Effective search space:    81796
Effective search space used:    81796
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate AO353_05480 AO353_05480 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

Software error:

../bin/blast/fastacmd -i /tmp/list.23243.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23243.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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