GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Shewanella loihica PV-4

Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate 5211315 Shew_3727 shikimate 5-dehydrogenase (RefSeq)

Query= SwissProt::Q9KVT3
         (278 letters)



>FitnessBrowser__PV4:5211315
          Length = 304

 Score =  311 bits (797), Expect = 1e-89
 Identities = 156/275 (56%), Positives = 196/275 (71%), Gaps = 1/275 (0%)

Query: 1   MASQI-DQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGG 59
           M  Q+ D+YAVFG+PI HSKSP IH  FA+ T +S+ Y A   P+DGF E+ + FF  GG
Sbjct: 26  MTQQVQDRYAVFGHPIGHSKSPAIHQAFAKSTGESLQYEAILAPLDGFAESLRAFFEHGG 85

Query: 60  RGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQV 119
           +G NVT+PFKE+AY   D L + A+LAGAVNTL +L DG I GDNTDG GLV DL     
Sbjct: 86  KGANVTLPFKEQAYALCDCLGDEAKLAGAVNTLTRLADGRIKGDNTDGLGLVADLERHLG 145

Query: 120 LLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFE 179
            L G ++LLIGAGGAARG + PLL+    S+T+ NRT +KAEQLAE   AYG+VKA   +
Sbjct: 146 SLCGKSVLLIGAGGAARGAILPLLNAGIDSLTIHNRTHSKAEQLAEAFKAYGQVKASTLD 205

Query: 180 QLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAI 239
           +L  S+D++INSTSASL GELP++   I ++ SVCYDMMYG+  T FN WA   G +Q I
Sbjct: 206 ELTHSFDIVINSTSASLSGELPSLPKAIIAAHSVCYDMMYGRELTAFNHWALDQGASQTI 265

Query: 240 DGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNL 274
           DGLGMLVGQAA+SF +WRG+ P  + +L +LR  L
Sbjct: 266 DGLGMLVGQAAKSFAIWRGVEPAVEPVLAKLRSEL 300


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: 250
Number of extensions: 7
Number of successful extensions: 1
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: 304
Length adjustment: 26
Effective length of query: 252
Effective length of database: 278
Effective search space:    70056
Effective search space used:    70056
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 5211315 Shew_3727 (shikimate 5-dehydrogenase (RefSeq))
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.29081.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29081.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.