GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Herbaspirillum seropedicae SmR1

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate HSERO_RS01990 HSERO_RS01990 shikimate 5-dehydrogenase

Query= SwissProt::Q9KVT3
         (278 letters)



>FitnessBrowser__HerbieS:HSERO_RS01990
          Length = 271

 Score =  291 bits (744), Expect = 1e-83
 Identities = 153/271 (56%), Positives = 193/271 (71%), Gaps = 3/271 (1%)

Query: 5   IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNV 64
           +D+Y V GNPI HSKSP IH  FA QT QSM Y    VP+ GF  A + F  +GGRG N+
Sbjct: 1   MDEYVVIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLHGFKAAVQVFQRRGGRGANI 60

Query: 65  TVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQ-VLLKG 123
           TVPFK EA+  AD+LTERARLAGAVNT K  ++G ILGDNTDG GLV D++      L+G
Sbjct: 61  TVPFKLEAHALADQLTERARLAGAVNTFK-FEEGCILGDNTDGAGLVTDIMVNAGQALQG 119

Query: 124 ATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQ 183
             ILL+GAGGA+RG L PLL Q+PA + V NRT ++AE+LA   AAYG V++  F  L+ 
Sbjct: 120 RRILLLGAGGASRGALLPLLQQRPAELVVVNRTASRAEELATQFAAYGPVRSTTFAGLEG 179

Query: 184 SYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLG 243
           ++DVI+N+TSASL  +LP + P ++ S ++ YDMMYG+G TVF Q A+QHG A   DGLG
Sbjct: 180 AFDVIVNATSASLSDDLPPLPPSVYGSETLAYDMMYGRGPTVFMQSAQQHG-AHVRDGLG 238

Query: 244 MLVGQAAESFMLWRGLRPGTKQILRELRKNL 274
           MLV QAAE+F  WRG+RP T ++   LR+ L
Sbjct: 239 MLVEQAAEAFQWWRGVRPATAEVFASLRQQL 269


Lambda     K      H
   0.320    0.135    0.392 

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: 211
Number of extensions: 8
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: 278
Length of database: 271
Length adjustment: 25
Effective length of query: 253
Effective length of database: 246
Effective search space:    62238
Effective search space used:    62238
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate HSERO_RS01990 HSERO_RS01990 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.12001.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12001.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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