GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Bacteroides thetaiotaomicron VPI-5482

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 351385 BT1857 3-isopropylmalate dehydrogenase (NCBI ptt file)

Query= BRENDA::P54354
         (353 letters)



>FitnessBrowser__Btheta:351385
          Length = 353

 Score =  679 bits (1751), Expect = 0.0
 Identities = 335/353 (94%), Positives = 341/353 (96%)

Query: 1   MDFKIAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETY 60
           MDFKIAVLAGDGIGPEISVQGV+VMSAVCEKFGHKV+YEYAICGADAIDKVGDPFPEETY
Sbjct: 1   MDFKIAVLAGDGIGPEISVQGVDVMSAVCEKFGHKVSYEYAICGADAIDKVGDPFPEETY 60

Query: 61  RVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSP 120
            VCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCL+HKSP
Sbjct: 61  EVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLIHKSP 120

Query: 121 LRAELVEGADFLCIRELTGGMYFGEKYQDNDKAYDTNMYTRPEIERILKVGFEYAMKRRK 180
           LRAELVE ADF+CIRELTGGMYFGEKYQDNDKAYDTN YTRPEIERILKV FEYAMKRRK
Sbjct: 121 LRAELVENADFICIRELTGGMYFGEKYQDNDKAYDTNYYTRPEIERILKVAFEYAMKRRK 180

Query: 181 HLTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVTENT 240
           HLTVVDKANVLASSRLWRQIAQEMAP YPEVTTDYMFVDNAAMKMIQEP FFDVMVTENT
Sbjct: 181 HLTVVDKANVLASSRLWRQIAQEMAPNYPEVTTDYMFVDNAAMKMIQEPAFFDVMVTENT 240

Query: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300
           FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF
Sbjct: 241 FGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVAMLF 300

Query: 301 EYFDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYIRKA 353
           EYFDCK EGALIRKAVDASLD NVRTPEIQV  G K+GTKEVG WIVDYI+KA
Sbjct: 301 EYFDCKEEGALIRKAVDASLDENVRTPEIQVADGAKYGTKEVGQWIVDYIKKA 353


Lambda     K      H
   0.319    0.136    0.403 

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: 626
Number of extensions: 20
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: 353
Length of database: 353
Length adjustment: 29
Effective length of query: 324
Effective length of database: 324
Effective search space:   104976
Effective search space used:   104976
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 351385 BT1857 (3-isopropylmalate dehydrogenase (NCBI ptt file))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.30777.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30777.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.