GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Herbaspirillum seropedicae SmR1

Align catabolic 3-dehydroquinase (characterized)
to candidate HSERO_RS01935 HSERO_RS01935 3-dehydroquinate dehydratase

Query= CharProtDB::CH_122158
         (153 letters)



>FitnessBrowser__HerbieS:HSERO_RS01935
          Length = 145

 Score =  186 bits (471), Expect = 2e-52
 Identities = 88/140 (62%), Positives = 109/140 (77%), Gaps = 1/140 (0%)

Query: 1   MEKSILLINGPNLNLLGTREPHIYGSTTLSDVEESSKGHAASLGASLQTFQSNHEGAIVD 60
           M K +LL+NGPNLNLLGTREP +YGSTTL+D+E+ ++  A + GASL  FQSNHEGA++D
Sbjct: 1   MAKQLLLLNGPNLNLLGTREPAVYGSTTLADIEQRAQEQARAAGASLVAFQSNHEGALID 60

Query: 61  RIHAARGN-TDAIIINPGAYTHTSVAIRDALLGVEIPFIELHVSNVHAREPFRHHSYFSD 119
           RIH AR    D IIINPG  THTSVA+RDAL GV IPF+E+H+SN+H RE FRH SY S 
Sbjct: 61  RIHQARSEGVDGIIINPGGLTHTSVALRDALAGVAIPFVEVHISNIHQREEFRHFSYLSG 120

Query: 120 KASGIIVGLGVYGYKVAVEH 139
            A  ++ G GV GY++AV+H
Sbjct: 121 IARAVLCGFGVDGYRMAVDH 140


Lambda     K      H
   0.317    0.134    0.382 

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: 90
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: 153
Length of database: 145
Length adjustment: 16
Effective length of query: 137
Effective length of database: 129
Effective search space:    17673
Effective search space used:    17673
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 42 (20.8 bits)

Align candidate HSERO_RS01935 HSERO_RS01935 (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.8321.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8321.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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