GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas fluorescens FW300-N2E3

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate AO353_13685 AO353_13685 3-dehydroquinate dehydratase

Query= SwissProt::P43877
         (154 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13685
          Length = 150

 Score =  191 bits (486), Expect = 3e-54
 Identities = 95/146 (65%), Positives = 116/146 (79%), Gaps = 1/146 (0%)

Query: 1   MKKILLLNGPNLNMLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINR 60
           M  +L+L+GPNLN+LG REP +YG+ TL++I Q L+Q A+  G+ L Y Q+N E  LI+R
Sbjct: 1   MATLLVLHGPNLNLLGTREPGVYGAVTLAEINQDLEQRARNAGHHLLYLQSNAEYELIDR 60

Query: 61  IHQAF-QNTDFIIINPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDV 119
           IH A  +  DFI+INP AFTHTSVA+RDALLAVSIPFIEVHLSNVH REPFRHHSY SDV
Sbjct: 61  IHAARGEGVDFILINPAAFTHTSVALRDALLAVSIPFIEVHLSNVHKREPFRHHSYFSDV 120

Query: 120 AKGVICGLGAKGYDYALDFAISELQK 145
           A GVICGLGA GY  AL+ A+ +L++
Sbjct: 121 AVGVICGLGASGYRLALEAALEQLER 146


Lambda     K      H
   0.320    0.137    0.395 

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: 119
Number of extensions: 5
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: 154
Length of database: 150
Length adjustment: 17
Effective length of query: 137
Effective length of database: 133
Effective search space:    18221
Effective search space used:    18221
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: 43 (21.2 bits)

Align candidate AO353_13685 AO353_13685 (3-dehydroquinate dehydratase)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.13219.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13219.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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