GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Pseudomonas fluorescens FW300-N1B4

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Pf1N1B4_2750 3-dehydroquinate dehydratase II (EC 4.2.1.10)

Query= BRENDA::W6JLW3
         (160 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2750
          Length = 146

 Score =  181 bits (458), Expect = 6e-51
 Identities = 81/143 (56%), Positives = 106/143 (74%)

Query: 15  PLITVLNGPNLNMLGLRQPGIYGHATLDDVEQVCIQAAERLDVAIDFRQTNGEGELVSWV 74
           P++ VLNGPNLN+LG R+P  YGH TL D+  +C +AAE   + ++FRQTN EGEL+ W+
Sbjct: 3   PIVLVLNGPNLNLLGTREPATYGHETLADISALCGRAAEEFGLTVEFRQTNHEGELLDWI 62

Query: 75  QECRGRADGIVINPAAYGHTSIALLDALLAVELPVVEVHISNIHRREPFRHHTYVSQAAI 134
              RGR  GIVINPAA+ HTS+A+ DAL+A ELPV+EVH+SN+H REPFRHH++VS  A 
Sbjct: 63  HAARGRCAGIVINPAAWTHTSVAIRDALVASELPVIEVHLSNVHAREPFRHHSFVSSIAA 122

Query: 135 GVICGLGVRGYAHALQAITDMIE 157
            V+CG G  GY  AL+  +  +E
Sbjct: 123 AVMCGFGSHGYRLALEHFSHRLE 145


Lambda     K      H
   0.322    0.139    0.413 

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: 112
Number of extensions: 2
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: 160
Length of database: 146
Length adjustment: 17
Effective length of query: 143
Effective length of database: 129
Effective search space:    18447
Effective search space used:    18447
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 (21.9 bits)
S2: 43 (21.2 bits)

Align candidate Pf1N1B4_2750 (3-dehydroquinate dehydratase II (EC 4.2.1.10))
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.13759.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13759.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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