GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Burkholderia phytofirmans PsJN

Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate BPHYT_RS06555 BPHYT_RS06555 ketol-acid reductoisomerase

Query= metacyc::MONOMER-18814
         (338 letters)



>FitnessBrowser__BFirm:BPHYT_RS06555
          Length = 338

 Score =  617 bits (1590), Expect = 0.0
 Identities = 308/338 (91%), Positives = 322/338 (95%)

Query: 1   MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60
           MKVFYDKDADLSLIKGK VTIIGYGSQGHAHALNLK+SGVN+TVGLRK GASW+KA NAG
Sbjct: 1   MKVFYDKDADLSLIKGKQVTIIGYGSQGHAHALNLKESGVNITVGLRKGGASWSKAENAG 60

Query: 61  LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120
           LQVKEVAEAVKGADVVM+LLPDEQIA+VY  EVH NIK+GAALAFAHGFNVHYG VIPRA
Sbjct: 61  LQVKEVAEAVKGADVVMMLLPDEQIAEVYAKEVHANIKQGAALAFAHGFNVHYGQVIPRA 120

Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180
           DLDVIMIAPKAPGHTVR TY+QGGGVPHLIAV Q+KSGAARDIALSYA ANGGGRAGIIE
Sbjct: 121 DLDVIMIAPKAPGHTVRGTYSQGGGVPHLIAVAQDKSGAARDIALSYAAANGGGRAGIIE 180

Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240
           TNFREETETDLFGEQAVLCGGTV+LIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE
Sbjct: 181 TNFREETETDLFGEQAVLCGGTVDLIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240

Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300
           GGIANMNYSISNNAEYGEYVTGPR+VT ETKKAMK  LTDIQTGEYAKSF++ENKAGAPT
Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTAETKKAMKAVLTDIQTGEYAKSFIIENKAGAPT 300

Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338
           L SRRRLTAEHQIE VGAKLR+MMPWIA NK+VDQSKN
Sbjct: 301 LQSRRRLTAEHQIETVGAKLRSMMPWIAANKLVDQSKN 338


Lambda     K      H
   0.316    0.133    0.379 

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: 547
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate BPHYT_RS06555 BPHYT_RS06555 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

Software error:

../bin/blast/fastacmd -i /tmp/list.30352.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30352.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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