GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Shewanella loihica PV-4

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 5211055 Shew_3471 3-isopropylmalate dehydrogenase (RefSeq)

Query= BRENDA::D2YZL2
         (364 letters)



>FitnessBrowser__PV4:5211055
          Length = 364

 Score =  647 bits (1669), Expect = 0.0
 Identities = 318/362 (87%), Positives = 343/362 (94%)

Query: 1   MSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATL 60
           MSYQ+AVLAGDGIGPEVMAEARKVL AVE+RF L IEYSEYDVGGAAID+HGCPLPE+TL
Sbjct: 1   MSYQVAVLAGDGIGPEVMAEARKVLKAVEERFSLDIEYSEYDVGGAAIDHHGCPLPESTL 60

Query: 61  KGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSP 120
           KGCE ADA+LFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLH GLEHMSP
Sbjct: 61  KGCEEADAILFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHVGLEHMSP 120

Query: 121 LRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFES 180
           LRSDIS +GFD+LCVRELTGGIYFGKPKGRQGEGE EEAFDTMRYSR+E+RRIAKIAFE+
Sbjct: 121 LRSDISAQGFDVLCVRELTGGIYFGKPKGRQGEGEQEEAFDTMRYSRREVRRIAKIAFEA 180

Query: 181 AQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDV 240
           A+GRRKKVTSVDKANVLACSVLWREVVEEVAK++PDV LEHIYIDNATMQLLRRP +FDV
Sbjct: 181 ARGRRKKVTSVDKANVLACSVLWREVVEEVAKEFPDVALEHIYIDNATMQLLRRPFDFDV 240

Query: 241 MLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQI 300
           MLCSNLFGDI+SDEIAMLTGSMGLL+S+S+NS GFG+YEPAGGSAPDIAGQGIANP+AQI
Sbjct: 241 MLCSNLFGDIISDEIAMLTGSMGLLSSVSLNSDGFGLYEPAGGSAPDIAGQGIANPIAQI 300

Query: 301 LSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAI 360
           LSAALLLRHSLK E AA AIE AV+KALSDGYLT ELLPA +R +AKST +MGDYIAQA+
Sbjct: 301 LSAALLLRHSLKEEAAAKAIEDAVAKALSDGYLTGELLPADQRDKAKSTREMGDYIAQAV 360

Query: 361 AE 362
            E
Sbjct: 361 RE 362


Lambda     K      H
   0.317    0.135    0.390 

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: 609
Number of extensions: 17
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 5211055 Shew_3471 (3-isopropylmalate dehydrogenase (RefSeq))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.21557.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21557.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.