GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Desulfovibrio vulgaris Hildenborough

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate 209045 DVU0115 shikimate 5-dehydrogenase

Query= curated2:Q30VD9
         (279 letters)



>MicrobesOnline__882:209045
          Length = 301

 Score =  296 bits (759), Expect = 3e-85
 Identities = 156/271 (57%), Positives = 185/271 (68%), Gaps = 2/271 (0%)

Query: 5   RIPRQLYGIIGYPLGHSMSPLLHNWGFELLGEQAAYMAFPVAPEKLAEFICCARMLPVSG 64
           RIP +LYGI+G+PLGH++SPLLHNWGF L    A YMA+PV P + A F+   R LPV G
Sbjct: 31  RIPERLYGIVGHPLGHTLSPLLHNWGFALHSLPAVYMAWPVPPGRFASFMEAVRTLPVHG 90

Query: 65  LSVTIPHKQAVMPLLDAVTPRAQAAGAVNTLFYDDGKLTGDNTDVYGFLHPLDSCGTAHA 124
            SVTIPHK+  + L D VT RA+A GAVNTLF +DG + G+NTDV GFL PL + G    
Sbjct: 91  ASVTIPHKEEALRLCDRVTDRARAVGAVNTLFLEDGVVCGENTDVTGFLAPLRARGVRID 150

Query: 125 AALVLGAGGAANAVLAALTARGMCNVTVTNRNGDRARILAERFGVRCVAWEERHAVDADL 184
            ALVLGAGGAA AVLA L   G+  V ++NR  D+A  LA  FG   V W+ER +  A L
Sbjct: 151 EALVLGAGGAARAVLAGLVELGVRRVRISNRTHDKAMELAGAFGADVVPWDERGSAAAGL 210

Query: 185 VVNTTPLGMAGDRQAQTPLDPAFFSSRPAGLAYDLIYNPAQTFFLASAQAAGWRVLNGLD 244
           VVNTTP GM G R  ++PL    FS R  G+AYDL+YNP  T FLA A+AAGW   +GL 
Sbjct: 211 VVNTTPCGMQGARMGESPLPEGAFSGR--GMAYDLVYNPLTTRFLADARAAGWETQDGLG 268

Query: 245 MFVAQGAEQFRIWRGRELPFAQARALIADAL 275
           MFV QG EQFRIW G +LP   AR LIA+AL
Sbjct: 269 MFVEQGREQFRIWTGLDLPAEGARRLIAEAL 299


Lambda     K      H
   0.324    0.137    0.427 

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: 247
Number of extensions: 9
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: 279
Length of database: 301
Length adjustment: 26
Effective length of query: 253
Effective length of database: 275
Effective search space:    69575
Effective search space used:    69575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate 209045 DVU0115 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.16889.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16889.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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