GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pseudomonas fluorescens GW456-L13

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate PfGW456L13_3945 3-isopropylmalate dehydrogenase (EC 1.1.1.85)

Query= BRENDA::P96197
         (360 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3945
          Length = 360

 Score =  518 bits (1335), Expect = e-152
 Identities = 280/372 (75%), Positives = 305/372 (81%), Gaps = 24/372 (6%)

Query: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60
           MSKQIL+LPGDGIGPEIMAEAVKVL+LA++K+ LGF L +D +GGAA+DK+GVPLADETL
Sbjct: 1   MSKQILILPGDGIGPEIMAEAVKVLELASDKFALGFELSHDVIGGAAIDKHGVPLADETL 60

Query: 61  ERARR------------RCHPARRRRRSEMGRHRPGHPPGARPAENPFATGPVRQPAPGV 108
           ERAR             +     R  R E G  +     G          G +R   P +
Sbjct: 61  ERARAADAVLLGAVGGPKWDAIERDIRPERGLLKIRAQLGL--------FGNLR---PAI 109

Query: 109 LYPQLAEASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYSESEI 168
           LYPQLAEAS+L+PE+VAGLDILIVRELTGGIYFGAPR +R L NGER +YDTLPYSESEI
Sbjct: 110 LYPQLAEASSLKPEIVAGLDILIVRELTGGIYFGAPRGTRTLENGERQSYDTLPYSESEI 169

Query: 169 RRIAKVGFDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDNAAMQ 228
           RRIA+VGFDMA VRGKKLCSVDKANVLASSQLWR VVE+VAKDYP+V LSHMYVDNAAMQ
Sbjct: 170 RRIARVGFDMAMVRGKKLCSVDKANVLASSQLWREVVEQVAKDYPEVELSHMYVDNAAMQ 229

Query: 229 LVRAPKQFDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRRPDIA 288
           LVRAPKQFDVIVTDNMFGDILSD+ASMLTGSIGMLPSASLD +NKGMYEPCHGS  PDIA
Sbjct: 230 LVRAPKQFDVIVTDNMFGDILSDQASMLTGSIGMLPSASLDTNNKGMYEPCHGS-APDIA 288

Query: 289 GKGIANPLATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKVGTAE 348
           GKGIANPLATILSVSMMLRYSF Q  AA+AIE+AVS VLDQGLRTGDIWS GC KVGT E
Sbjct: 289 GKGIANPLATILSVSMMLRYSFNQQAAADAIEKAVSLVLDQGLRTGDIWSAGCTKVGTQE 348

Query: 349 MGDAVVAALATL 360
           MGDAVVAAL  L
Sbjct: 349 MGDAVVAALRNL 360


Lambda     K      H
   0.318    0.135    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: 472
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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 PfGW456L13_3945 (3-isopropylmalate dehydrogenase (EC 1.1.1.85))
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.7145.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7145.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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