GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Marinobacter adhaerens HP15

Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate GFF3278 HP15_3220 dehydroquinase, class II

Query= SwissProt::P43877
         (154 letters)



>FitnessBrowser__Marino:GFF3278
          Length = 133

 Score =  174 bits (440), Expect = 6e-49
 Identities = 83/133 (62%), Positives = 103/133 (77%), Gaps = 1/133 (0%)

Query: 14  MLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINRIHQA-FQNTDFII 72
           MLG REP +YG +TL+DI+  L+  A  QG+ L + Q+N E  LI R+H+A  +  DFII
Sbjct: 1   MLGTREPEVYGYETLADIDDRLRSLAAEQGHHLLHLQSNAEYELIERVHEARAEGVDFII 60

Query: 73  INPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDVAKGVICGLGAKGY 132
           INP AFTHTSVA+RDA+LA  IPFIEVHLSNVHAREPFRHHSY SD+A+GVICGLG++GY
Sbjct: 61  INPAAFTHTSVALRDAMLASGIPFIEVHLSNVHAREPFRHHSYFSDIAEGVICGLGSQGY 120

Query: 133 DYALDFAISELQK 145
           D AL  A+  + +
Sbjct: 121 DLALQAALKRIHR 133


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: 128
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: 133
Length adjustment: 16
Effective length of query: 138
Effective length of database: 117
Effective search space:    16146
Effective search space used:    16146
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: 42 (20.8 bits)

Align candidate GFF3278 HP15_3220 (dehydroquinase, class II)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.32369.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32369.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.