GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Shewanella amazonensis SB2B

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 6936139 Sama_0336 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::Q8E9N3
         (364 letters)



>FitnessBrowser__SB2B:6936139
          Length = 364

 Score =  653 bits (1684), Expect = 0.0
 Identities = 326/364 (89%), Positives = 345/364 (94%)

Query: 1   MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATL 60
           MSYQIAVLAGDGIGPEVMAEARKVL  VEARF LNIEY+EYDVGGIAIDNHGCPLP+ATL
Sbjct: 1   MSYQIAVLAGDGIGPEVMAEARKVLAEVEARFDLNIEYSEYDVGGIAIDNHGCPLPDATL 60

Query: 61  KGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSP 120
           KGCEAADAILFGSVGGPKWE LPPNEQPERGALLPLRGHFELFCNLRPA+LH GLEHMSP
Sbjct: 61  KGCEAADAILFGSVGGPKWEHLPPNEQPERGALLPLRGHFELFCNLRPARLHTGLEHMSP 120

Query: 121 LRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEA 180
           LR+DISA+GFDVLCVRELTGGIYFGKPKGRQGEGE EEAFDTMRYSRREI RIA+IAFEA
Sbjct: 121 LRADISAQGFDVLCVRELTGGIYFGKPKGRQGEGEEEEAFDTMRYSRREIRRIAKIAFEA 180

Query: 181 ARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDV 240
           ARGRR KVTSVDKANVLACSVLWR+VVEEVA DFPDV LEHIYIDNATMQLLRRP +FDV
Sbjct: 181 ARGRRGKVTSVDKANVLACSVLWREVVEEVAKDFPDVTLEHIYIDNATMQLLRRPFDFDV 240

Query: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQI 300
           MLCSNLFGDILSDEIAMLTGSMGLLSSASMN +GFGL+EPAGGSAPDIAGKGIANPIAQI
Sbjct: 241 MLCSNLFGDILSDEIAMLTGSMGLLSSASMNGSGFGLYEPAGGSAPDIAGKGIANPIAQI 300

Query: 301 LSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAV 360
           LSAALMLRHSLKQEEAA+ IERAV  AL +G+LTGELLS+DQRH AK+T +MGDFIA+A+
Sbjct: 301 LSAALMLRHSLKQEEAAACIERAVGAALEAGFLTGELLSADQRHNAKSTKEMGDFIANAI 360

Query: 361 KAGV 364
           + GV
Sbjct: 361 REGV 364


Lambda     K      H
   0.318    0.136    0.393 

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: 559
Number of extensions: 16
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: 364
Length of database: 364
Length adjustment: 29
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 6936139 Sama_0336 (3-isopropylmalate dehydrogenase (RefSeq))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.21947.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21947.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.