GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Dinoroseobacter shibae DFL-12

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate 3610069 Dshi_3450 shikimate 5-dehydrogenase (RefSeq)

Query= BRENDA::A0A1K3RIC7
         (272 letters)



>FitnessBrowser__Dino:3610069
          Length = 278

 Score =  149 bits (377), Expect = 5e-41
 Identities = 108/273 (39%), Positives = 144/273 (52%), Gaps = 27/273 (9%)

Query: 6   VFGHPIAHSQSPFIHQEFAGQFGIELSYERILSPLDGFRDSVSAFFAAGGLGANVTLPFK 65
           V G+PI HS+SP +H+ +   +GIE  Y  +        +   A    G  G NVTLPFK
Sbjct: 11  VIGNPITHSRSPHLHRHWLHVYGIEGYYVPLHVQGQDLAEVFHALPKLGFKGVNVTLPFK 70

Query: 66  EQAHALADELSERAQVCGAVNTLYLTEDKRLAGDNTDGEGLVIDLQRLMFIRPGDS---- 121
           E+A  LAD +S+RA + GA NT+    D  +  DNTDG G + +L+      PG S    
Sbjct: 71  ERAIELADRVSDRAALIGAANTITFQPDGTIHADNTDGYGFIENLRN---GAPGWSPRAA 127

Query: 122 -ILLIGAGGAARGALLSLLQAGC-AVTVTNRTFSKAQSLAERFA-------GHGKVSAMP 172
            I+++GAGGAARG L +LL+AG   V + NRT +KA++L   F         HG    M 
Sbjct: 128 AIVVLGAGGAARGVLSALLEAGAPEVRLANRTRAKAEALRSDFGPRVTVVDWHGVSGTME 187

Query: 173 VSETGMTGFSLIINATSSGVDGAVPQIPLSL--LNPSVACYDMFYRSGLTPFLQLAADNG 230
            +ET       ++N TS G+ G  P + L+L  L  S    D+ YR  +TP L+ A   G
Sbjct: 188 DAET-------LVNTTSLGMTGQ-PDLELNLDALPRSAVVTDIVYRPLMTPLLEQAVARG 239

Query: 231 VTRYADGLGMLAGQAAFAFRLWHGVLPDIAPVL 263
                DGLGML  QAA  F  W GV P+I P L
Sbjct: 240 -NPVVDGLGMLLFQAAPGFERWFGVRPEITPEL 271


Lambda     K      H
   0.322    0.137    0.400 

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: 200
Number of extensions: 10
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: 272
Length of database: 278
Length adjustment: 25
Effective length of query: 247
Effective length of database: 253
Effective search space:    62491
Effective search space used:    62491
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate 3610069 Dshi_3450 (shikimate 5-dehydrogenase (RefSeq))
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.31920.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31920.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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