GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Azospirillum brasilense Sp245

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate AZOBR_RS03220 AZOBR_RS03220 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__azobra:AZOBR_RS03220
          Length = 378

 Score =  289 bits (739), Expect = 1e-82
 Identities = 167/360 (46%), Positives = 227/360 (63%), Gaps = 11/360 (3%)

Query: 81  PTIVD---VDLGDRSYPIYIGSGLLDQPD-LLQRHVHGKRVLVVTNSTVAPIYLDKVVGA 136
           PT +D   +DLG RSY I +G  +LD     +     GK  +VVT+  VAP +L  +   
Sbjct: 7   PTAIDTVRLDLGPRSYDILVGDRVLDGAGPRIAAITRGKAPIVVTDENVAPRHLPTLERT 66

Query: 137 LTNENPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYA 196
           L +     + ++++LP GEK K++    ++ D  +   ++R    +ALGGGVIGD+ G+A
Sbjct: 67  LRDAGIEPT-QAIVLPAGEKTKDIAHFERLMDAVLARGIERSAVLLALGGGVIGDITGFA 125

Query: 197 AASFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLP 256
           AAS LRG++FIQ+PTT+++QVDSSVGGKTGIN   GKNLIGAF+QP+ V+ DT TL+TLP
Sbjct: 126 AASALRGIDFIQVPTTLLSQVDSSVGGKTGINSPHGKNLIGAFHQPRLVIADTATLDTLP 185

Query: 257 DRELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDE 316
            RE+ +G AEVVKYGLIR   FF W E+N   ++A D  A  +A+  SC  KA +V +DE
Sbjct: 186 RREVLAGYAEVVKYGLIRLPGFFAWLEENGERVVAGDSDARRHAVTESCRAKAAIVGVDE 245

Query: 317 KESGLRATLNLGHTFGHAIETGFGYG-QWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRA 375
           +ESG RA LNLGHTFGHA+E   G+G + LHGEAV+ GMV+A D+S RLG    +   +A
Sbjct: 246 RESGDRALLNLGHTFGHALEAATGFGSRLLHGEAVSIGMVLAFDLSVRLGLCPAADAEKA 305

Query: 376 HNILQQAKLPTAPPETMTVEM----FKSVMAVDKKVADGLLRLILLKGPLGNCVFTGDYD 431
              L +  LP  P +   VE         MA DKKV DG +  +L++  LG+     D D
Sbjct: 306 RAHLARVGLPVRPTDVPGVEWDIDGLILSMAKDKKVKDGRITFVLVRA-LGDAFTQRDVD 364


Lambda     K      H
   0.317    0.133    0.382 

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: 396
Number of extensions: 15
Number of successful extensions: 4
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: 445
Length of database: 378
Length adjustment: 31
Effective length of query: 414
Effective length of database: 347
Effective search space:   143658
Effective search space used:   143658
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate AZOBR_RS03220 AZOBR_RS03220 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.17403.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17403.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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