GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Escherichia coli BW25113

Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate 14217 b0071 isopropylmalate isomerase small subunit (NCBI)

Query= ecocyc::LEUD-MONOMER
         (201 letters)



>FitnessBrowser__Keio:14217
          Length = 201

 Score =  413 bits (1061), Expect = e-120
 Identities = 201/201 (100%), Positives = 201/201 (100%)

Query: 1   MAEKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPD 60
           MAEKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPD
Sbjct: 1   MAEKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPD 60

Query: 61  FVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL 120
           FVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL
Sbjct: 61  FVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLL 120

Query: 121 PVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIG 180
           PVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIG
Sbjct: 121 PVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIG 180

Query: 181 LTLQHDDAIAAYEAKQPAFMN 201
           LTLQHDDAIAAYEAKQPAFMN
Sbjct: 181 LTLQHDDAIAAYEAKQPAFMN 201


Lambda     K      H
   0.322    0.138    0.421 

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: 279
Number of extensions: 3
Number of successful extensions: 1
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: 201
Length of database: 201
Length adjustment: 21
Effective length of query: 180
Effective length of database: 180
Effective search space:    32400
Effective search space used:    32400
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: 45 (21.9 bits)

Align candidate 14217 b0071 (isopropylmalate isomerase small subunit (NCBI))
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.32459.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32459.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.