GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroD in Bacteroides thetaiotaomicron VPI-5482

Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 352369 BT2842 3-dehydroquinate dehydratase (NCBI ptt file)

Query= BRENDA::Q48255
         (167 letters)



>FitnessBrowser__Btheta:352369
          Length = 140

 Score =  135 bits (339), Expect = 4e-37
 Identities = 69/143 (48%), Positives = 99/143 (69%), Gaps = 7/143 (4%)

Query: 1   MKILVIQGPNLNMLGHRDPRLYGMVTL-DQIHEIMQTFVKQGNLDVELEFFQTNFEGEII 59
           M+I +I GPN+N+LG R+P +YG VT  D + E+ + +      D+E+++FQ+N EGE+I
Sbjct: 1   MRIQIINGPNINLLGKREPSIYGSVTFEDYLAELRKRYA-----DLEIDYFQSNIEGEMI 55

Query: 60  DKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTG 119
           D IQ+ VG + +GII+N GA++HTSIA+ DAI     PVIEVH++N+ +RE FR  S   
Sbjct: 56  DCIQQ-VGFEVDGIILNAGAYTHTSIALQDAIRSVTSPVIEVHISNVHSRESFRHVSMIA 114

Query: 120 AACGGVIMGFGPLGYNMALMAMV 142
            AC GVI GFG   Y +AL A++
Sbjct: 115 CACKGVICGFGLNSYRLALEALL 137


Lambda     K      H
   0.320    0.137    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: 86
Number of extensions: 4
Number of successful extensions: 3
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: 167
Length of database: 140
Length adjustment: 17
Effective length of query: 150
Effective length of database: 123
Effective search space:    18450
Effective search space used:    18450
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 352369 BT2842 (3-dehydroquinate dehydratase (NCBI ptt file))
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))

Software error:

../bin/blast/fastacmd -i /tmp/list.27675.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27675.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.