GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate GFF2539 Psest_2589 3-isopropylmalate dehydrogenase

Query= BRENDA::P96197
         (360 letters)



>FitnessBrowser__psRCH2:GFF2539
          Length = 360

 Score =  538 bits (1387), Expect = e-158
 Identities = 294/365 (80%), Positives = 307/365 (84%), Gaps = 10/365 (2%)

Query: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANEKYQLGFVLGYDELGGAAVDKYGVPLADETL 60
           MSKQILVLPGDGIGPEIMAEAVKVLQLAN+K+QL F L YDELGGAAVDKYGVPLADETL
Sbjct: 1   MSKQILVLPGDGIGPEIMAEAVKVLQLANDKFQLDFELSYDELGGAAVDKYGVPLADETL 60

Query: 61  ERARRRCHPARRRRRSEMGRHR-PGHPPGARPAENPFAT----GPVRQPAPGVLYPQLAE 115
           ERAR     A       +G  +     P  RP           G      P +LYPQLAE
Sbjct: 61  ERARA----ADAILLGAVGGPKWDTIDPAIRPERGLLKIRSQLGLFGNLRPALLYPQLAE 116

Query: 116 ASTLRPEVVAGLDILIVRELTGGIYFGAPRESRLLANGERMAYDTLPYSESEIRRIAKVG 175
           AS+L+PE+VAGLDILIVRELTGGIYFG PRES++L +GERMAYDTLPYSESEIRRIAKVG
Sbjct: 117 ASSLKPEIVAGLDILIVRELTGGIYFGQPRESKVLESGERMAYDTLPYSESEIRRIAKVG 176

Query: 176 FDMARVRGKKLCSVDKANVLASSQLWRAVVEEVAKDYPDVVLSHMYVDNAAMQLVRAPKQ 235
           FDMA VR KKLCSVDKANVLASSQLWRAVVEEVAK YPDV LSHMYVDNAAMQLVRAPKQ
Sbjct: 177 FDMAMVRNKKLCSVDKANVLASSQLWRAVVEEVAKYYPDVELSHMYVDNAAMQLVRAPKQ 236

Query: 236 FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDADNKGMYEPCHGSRRPDIAGKGIANP 295
           FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDA NKGMYEPCHGS  PDIAG+GIANP
Sbjct: 237 FDVIVTDNMFGDILSDEASMLTGSIGMLPSASLDAGNKGMYEPCHGS-APDIAGQGIANP 295

Query: 296 LATILSVSMMLRYSFGQVEAANAIEQAVSKVLDQGLRTGDIWSEGCRKVGTAEMGDAVVA 355
           LATILSVSMMLRYSF QV AA+AIEQAVS VLDQGLRTGDIWSEGC KVGT  MGDAVVA
Sbjct: 296 LATILSVSMMLRYSFNQVAAADAIEQAVSDVLDQGLRTGDIWSEGCTKVGTQAMGDAVVA 355

Query: 356 ALATL 360
           ALA L
Sbjct: 356 ALAKL 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: 499
Number of extensions: 12
Number of successful extensions: 3
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: 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 GFF2539 Psest_2589 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.30592.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30592.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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