GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__azobra:AZOBR_RS14130
          Length = 371

 Score =  472 bits (1214), Expect = e-138
 Identities = 235/368 (63%), Positives = 291/368 (79%), Gaps = 2/368 (0%)

Query: 4   RSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEK 63
           + L  LPGDGIGPE M +VR++I++++   N  F V+EGLVGG+A DA+GV + D  +  
Sbjct: 5   KKLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLAD 64

Query: 64  ALAADAILFGAVGGPKWDG-VPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLK 122
           ALAADA++ GAVGGPKWD    Y  RPEAGLL LRK+L LFANLRPA+ + AL  AS+LK
Sbjct: 65  ALAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLK 124

Query: 123 PELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELAR 182
            ++++GLDILIVRELTGGVYFGEP+ I D+GNG++RG++TQ+Y T EI R+A VAFELAR
Sbjct: 125 ADVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVAFELAR 184

Query: 183 SRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVI 242
            R N++ SMEK NVM+SG+LW Q VT+ H  ++ DV LEHM AD G MQL++ PKQFDVI
Sbjct: 185 KRGNKLHSMEKANVMESGLLWRQEVTKLHQEEFSDVTLEHMYADNGAMQLLKNPKQFDVI 244

Query: 243 VTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIAN 302
           VTDNLFGD+LSD AAM+TGSLGMLPSASLGAPDA  G+RKA+YEPVHGSAPDIAG+ +AN
Sbjct: 245 VTDNLFGDILSDEAAMMTGSLGMLPSASLGAPDA-NGQRKALYEPVHGSAPDIAGRDLAN 303

Query: 303 PIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVL 362
           P A + SFAMCLRYSFNM +EA  LE A+ NVL  G+RTADIMA G  +  T+ MGD++L
Sbjct: 304 PCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCSTTVMGDSIL 363

Query: 363 AEFKALSA 370
            E   L++
Sbjct: 364 RELDKLAS 371


Lambda     K      H
   0.319    0.135    0.387 

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: 450
Number of extensions: 11
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: 370
Length of database: 371
Length adjustment: 30
Effective length of query: 340
Effective length of database: 341
Effective search space:   115940
Effective search space used:   115940
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 AZOBR_RS14130 AZOBR_RS14130 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

Software error:

../bin/blast/fastacmd -i /tmp/list.15592.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15592.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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