GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Paraburkholderia bryophila 376MFSha3.1

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate H281DRAFT_05615 H281DRAFT_05615 3-dehydroquinate synthase

Query= SwissProt::U3KRF2
         (445 letters)



>FitnessBrowser__Burk376:H281DRAFT_05615
          Length = 361

 Score =  376 bits (965), Expect = e-109
 Identities = 191/335 (57%), Positives = 242/335 (72%), Gaps = 3/335 (0%)

Query: 84  VDVDLGDRSYPIYIGSGLLDQPDLLQRHVHGKRVLVVTNSTVAPIYLDKVVGALTNENPN 143
           V+V+LGDR+YPI+IG+ L+ Q  L   H+ G  V +VTN+TV P+Y D +  +L      
Sbjct: 7   VNVELGDRAYPIHIGADLIGQTALFAPHIAGNSVTIVTNTTVDPLYGDTLRASLAPLGKQ 66

Query: 144 VSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASFLRG 203
           VS  +V+LPDGE +KN++TL  +FD  + SR DR+ T +ALGGGVIGDM G+AAA ++RG
Sbjct: 67  VS--TVVLPDGEAHKNLETLNLIFDALLGSRADRKTTLIALGGGVIGDMTGFAAACYMRG 124

Query: 204 VNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLPDRELASG 263
           V FIQ+PTT+++QVDSSVGGKTGINH LGKN+IGAFYQPQ V+ D   L TLP RELA+G
Sbjct: 125 VPFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPQAVIADIGALRTLPARELAAG 184

Query: 264 LAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDEKESGLRA 323
           +AEV+K G I DA FF W E N+ AL   +P ALA A+KRSCE KA VV+ DE+E GLRA
Sbjct: 185 VAEVIKTGAIADAGFFRWIEANVEALNRCEPEALAEAVKRSCEIKASVVAQDEREGGLRA 244

Query: 324 TLNLGHTFGHAIETGFGYGQWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRAHNILQQAK 383
            LN GHTFGHAIE G GYG+WLHGEAV  GMVMA D+S RLG++DE+   R  +++  A 
Sbjct: 245 ILNFGHTFGHAIEAGLGYGEWLHGEAVGCGMVMAADLSVRLGYLDEASRKRLVDVIVAAH 304

Query: 384 LPTAPPETMTVEMFKSVMAVDKKVADGLLRLILLK 418
           LPT  P  +    +  +M VDKK   G ++ ILLK
Sbjct: 305 LPTRAP-ALGESRYVELMQVDKKAEAGAIKFILLK 338


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: 410
Number of extensions: 11
Number of successful extensions: 2
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: 361
Length adjustment: 31
Effective length of query: 414
Effective length of database: 330
Effective search space:   136620
Effective search space used:   136620
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 H281DRAFT_05615 H281DRAFT_05615 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.14900.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14900.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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