GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Synechococcus elongatus PCC 7942

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (uncharacterized)
to candidate Synpcc7942_2467 Synpcc7942_2467 shikimate 5-dehydrogenase

Query= curated2:Q8YVC1
         (289 letters)



>FitnessBrowser__SynE:Synpcc7942_2467
          Length = 288

 Score =  318 bits (816), Expect = 7e-92
 Identities = 161/287 (56%), Positives = 209/287 (72%), Gaps = 3/287 (1%)

Query: 2   ITGKTKLLGVIGHPVEHSLSPVMHNAAIAQLGLDYVYLPFPIAPDNLEAAIALLATIGVV 61
           +TG+T+LLG+IG P+EHSLSP++ NAAIA+LGLDY Y+PFP+   +L  A+A LA IGV 
Sbjct: 4   LTGRTRLLGIIGDPIEHSLSPLIQNAAIAELGLDYCYVPFPVKGADLATALAGLAAIGVQ 63

Query: 62  GFSVTIPHKQAIIPLLSEISPVAQAIGAVNTVTRQNNQWVGTNTDIEGFIAPLQTTYKRD 121
           GF+VTIPHKQA++PLLS++S +AQ++G+VNTV +    WVGTNTD+ GF+APLQ T + D
Sbjct: 64  GFNVTIPHKQAVMPLLSQVSELAQSVGSVNTVWQTEQGWVGTNTDVLGFLAPLQ-TLRSD 122

Query: 122 WSQQIAVILGNGGAARAVVAGCYQLGFAEIHVVGRNVQRLEEFRHSWENSPIAENLQVHT 181
           WS    V+LG GGAARAVVAGC QLG + I  V R+ Q+ + F+ SW +   A++L +H 
Sbjct: 123 WSGCRVVLLGCGGAARAVVAGCLQLGCSAIATVVRDAQKGDAFQQSWGDR--ADSLTIHD 180

Query: 182 WDYLAKLIPQANLLVNTTPIGMYPQVDESPLSAEELVNLQTGTIAYDLIYIPKPTQFLQK 241
           W  +  ++  A+L+VNTTP+GM P ++ SPL       L+  TIAYDLIY P PT+FLQ+
Sbjct: 181 WSDIPDVLSTADLVVNTTPLGMDPHIERSPLDNSAAQQLRPETIAYDLIYTPSPTRFLQQ 240

Query: 242 AQQQGAIIIDGLEMLVQQGVAALKIWLQQDDIPVDVMRQALIKHLGL 288
           A  QG   IDGLEMLVQQG A LKIW   + +PVD MR  L  HLGL
Sbjct: 241 AIAQGCHAIDGLEMLVQQGAAGLKIWTGAEAVPVDTMRSVLNAHLGL 287


Lambda     K      H
   0.320    0.136    0.403 

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: 291
Number of extensions: 9
Number of successful extensions: 3
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: 289
Length of database: 288
Length adjustment: 26
Effective length of query: 263
Effective length of database: 262
Effective search space:    68906
Effective search space used:    68906
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: 48 (23.1 bits)

Align candidate Synpcc7942_2467 Synpcc7942_2467 (shikimate 5-dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.5711.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5711.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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