GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Pseudomonas simiae WCS417

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate GFF781 PS417_03970 1-phosphofructokinase

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



>FitnessBrowser__WCS417:GFF781
          Length = 306

 Score =  447 bits (1149), Expect = e-130
 Identities = 232/313 (74%), Positives = 255/313 (81%), Gaps = 7/313 (2%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MA+ILTLTLNPALDLTV LARLEPG+VNRS+ +  HAAGKGVNVAQVLADLGH LTVSGF
Sbjct: 1   MARILTLTLNPALDLTVRLARLEPGEVNRSETLLTHAAGKGVNVAQVLADLGHELTVSGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LGE N Q FE L AQRGF DAFIRVPGETRSNIK+AEQDGR+TD+N PGP V   AQ AL
Sbjct: 61  LGEGNPQAFEALIAQRGFTDAFIRVPGETRSNIKIAEQDGRVTDINAPGPQVTEQAQNAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L +L QIAPG D VVVAGSLPRGVSPQW + L+ ++K  GL VALDTSGEALR  L AGP
Sbjct: 121 LDKLAQIAPGFDAVVVAGSLPRGVSPQWFKGLLEQLKRYGLKVALDTSGEALRAGLLAGP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WL+KPNTEELA+AL            A  +LH QG+EHVV+S GA GV+W+S  AAL A+
Sbjct: 181 WLVKPNTEELAEAL-------DNATDAVSQLHRQGVEHVVVSDGAAGVSWYSPNAALQAT 233

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKV+VASTVGAGDSLLAGMLHGLL+ DTPEQTLR ATAIAAMAVTQIGFGI D A LA 
Sbjct: 234 PPKVTVASTVGAGDSLLAGMLHGLLTGDTPEQTLRRATAIAAMAVTQIGFGISDHAQLAR 293

Query: 301 LEQGVRVRPLTEQ 313
           LE GV+VR LTEQ
Sbjct: 294 LESGVQVRSLTEQ 306


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: 399
Number of extensions: 8
Number of successful extensions: 2
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: 306
Length adjustment: 27
Effective length of query: 286
Effective length of database: 279
Effective search space:    79794
Effective search space used:    79794
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 GFF781 PS417_03970 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

Software error:

../bin/blast/fastacmd -i /tmp/list.15699.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15699.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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