GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Cupriavidus basilensis 4G11

Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate RR42_RS22860 RR42_RS22860 l-threonine 3-dehydrogenase

Query= BRENDA::P07913
         (341 letters)



>FitnessBrowser__Cup4G11:RR42_RS22860
          Length = 351

 Score =  559 bits (1441), Expect = e-164
 Identities = 263/340 (77%), Positives = 300/340 (88%)

Query: 1   MKALSKLKAEEGIWMTDVPVPELGHNDLLIKIRKTAICGTDVHIYNWDEWSQKTIPVPMV 60
           MKAL+KL+   G+ +TDVP PE+GHND++I+IR+TAICGTD+HI+ WDEW+Q TIPVPM 
Sbjct: 1   MKALAKLERAPGLTLTDVPEPEVGHNDVMIRIRQTAICGTDIHIWKWDEWAQNTIPVPMQ 60

Query: 61  VGHEYVGEVVGIGQEVKGFKIGDRVSGEGHITCGHCRNCRGGRTHLCRNTIGVGVNRPGC 120
           VGHEYVGE+V IGQEV+G  IGDRVSGEGHITCG CRNCR GR HLCRN++GVGVNR G 
Sbjct: 61  VGHEYVGEIVAIGQEVRGLAIGDRVSGEGHITCGFCRNCRAGRRHLCRNSVGVGVNRAGA 120

Query: 121 FAEYLVIPAFNAFKIPDNISDDLAAIFDPFGNAVHTALSFDLVGEDVLVSGAGPIGIMAA 180
           FAEYLVIPAFNAF+IPD+I D++AAIFDPFGNA HTALSF+LVGEDVL++GAGPIGIMAA
Sbjct: 121 FAEYLVIPAFNAFRIPDDIPDEIAAIFDPFGNATHTALSFNLVGEDVLITGAGPIGIMAA 180

Query: 181 AVAKHVGARNVVITDVNEYRLELARKMGITRAVNVAKENLNDVMAELGMTEGFDVGLEMS 240
           A+A+HVGARNVVITDVNEYRL LARKMG TRAVNV  ENL DV AEL MTEGFDVG+EMS
Sbjct: 181 AIARHVGARNVVITDVNEYRLALARKMGATRAVNVQHENLKDVAAELHMTEGFDVGMEMS 240

Query: 241 GAPPAFRTMLDTMNHGGRIAMLGIPPSDMSIDWTKVIFKGLFIKGIYGREMFETWYKMAA 300
           G P AF TML+ MNHGG+IAMLGIPPS M+IDW +VIFKGL IKGIYGREMFETWYKM A
Sbjct: 241 GVPTAFATMLEHMNHGGKIAMLGIPPSKMAIDWNQVIFKGLEIKGIYGREMFETWYKMVA 300

Query: 301 LIQSGLDLSPIITHRFSIDDFQKGFDAMRSGQSGKVILSW 340
           ++QSGLDL+P+ITHRF + DF+ GF AM SG SGKV+L W
Sbjct: 301 MLQSGLDLTPMITHRFRVGDFEAGFAAMLSGNSGKVVLDW 340


Lambda     K      H
   0.322    0.140    0.433 

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: 502
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: 341
Length of database: 351
Length adjustment: 29
Effective length of query: 312
Effective length of database: 322
Effective search space:   100464
Effective search space used:   100464
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate RR42_RS22860 RR42_RS22860 (l-threonine 3-dehydrogenase)
to HMM TIGR00692 (tdh: L-threonine 3-dehydrogenase (EC 1.1.1.103))

Software error:

../bin/blast/fastacmd -i /tmp/list.29074.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29074.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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