GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Pseudomonas putida KT2440

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate PP_0794 PP_0794 1-phosphofructokinase monomer

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



>FitnessBrowser__Putida:PP_0794
          Length = 315

 Score =  412 bits (1059), Expect = e-120
 Identities = 214/313 (68%), Positives = 242/313 (77%), Gaps = 3/313 (0%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MAKILTLTLNPALD+T+ L  L PGQVNRS A H+HAAGKG+NVAQVLADLGH++TV GF
Sbjct: 1   MAKILTLTLNPALDITIGLDTLRPGQVNRSQAQHSHAAGKGLNVAQVLADLGHSVTVGGF 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LG DN Q FE L   RGF D F+RVPGETRSNIKL E DGR+TD+NG GP VD AA+ AL
Sbjct: 61  LGGDNLQPFEALIDGRGFTDCFVRVPGETRSNIKLVEADGRVTDINGQGPEVDEAARSAL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
           L RLEQIAPGHD VVVAGSLPRG+S  W + L+ R+KA GL V LD+SGEALRV L + P
Sbjct: 121 LHRLEQIAPGHDAVVVAGSLPRGISADWFRQLLERLKAQGLKVVLDSSGEALRVGLQSAP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
           WL+KPNTEEL + LG  V + T Q  AA+RL   G+EHVV+S G  GV+WFS   AL A 
Sbjct: 181 WLVKPNTEELGEVLGLAVDNLTQQRAAAKRLLDSGVEHVVVSAGEQGVSWFSRDLALQAR 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLAS 300
           PPKV VASTVGAGDSL+AGM+HGLL A+ P QTL  ATAIAA AVTQ+GFGIHD   LA 
Sbjct: 241 PPKVRVASTVGAGDSLVAGMVHGLLLAEAPAQTLTRATAIAAQAVTQVGFGIHDREHLAQ 300

Query: 301 LEQGVRVRPLTEQ 313
           LE  V+   LTEQ
Sbjct: 301 LEAAVQ---LTEQ 310


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: 340
Number of extensions: 12
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: 315
Length adjustment: 27
Effective length of query: 286
Effective length of database: 288
Effective search space:    82368
Effective search space used:    82368
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 PP_0794 PP_0794 (1-phosphofructokinase monomer)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

Software error:

../bin/blast/fastacmd -i /tmp/list.18896.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18896.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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