GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate Echvi_2060 Echvi_2060 3-isopropylmalate dehydratase, small subunit

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__Cola:Echvi_2060
          Length = 197

 Score =  158 bits (400), Expect = 5e-44
 Identities = 86/193 (44%), Positives = 120/193 (62%), Gaps = 5/193 (2%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           +KF      VVPL   NVDTD IIP +FL+   R GFG +LF DWR+ D +G  P  +FV
Sbjct: 4   DKFNILKSTVVPLPTENVDTDQIIPARFLKATERKGFGDNLFRDWRY-DSEGN-PKADFV 61

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN   Y G  +L+A +NFG GSSREHA WA+ DYGF+ V++  FADIF  N+ N  +LPV
Sbjct: 62  LNDATYSG-KVLVAGKNFGSGSSREHAAWAIYDYGFRCVVSSFFADIFKNNALNIGILPV 120

Query: 123 TLSDAQVDELFALVKANPGIKFEVDLEAQVVK--AGDKTYSFKIDDFRRHCMLNGLDSIG 180
           T++   ++E+FA V+ +P  + EVD+E Q +   +   + SF I+ +++  M NG D I 
Sbjct: 121 TVTPEFLEEIFAEVEKDPATEVEVDIEKQTITLLSTGNSESFDINSYKKQNMQNGFDDID 180

Query: 181 LTLQHEDAIAAYE 193
             L  +D I  +E
Sbjct: 181 YLLNMKDQIVEFE 193


Lambda     K      H
   0.321    0.138    0.416 

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: 146
Number of extensions: 8
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: 201
Length of database: 197
Length adjustment: 21
Effective length of query: 180
Effective length of database: 176
Effective search space:    31680
Effective search space used:    31680
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 Echvi_2060 Echvi_2060 (3-isopropylmalate dehydratase, small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.5999.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5999.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.