GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Sphingomonas koreensis DSMZ 15582

Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate Ga0059261_4225 Ga0059261_4225 3-isopropylmalate dehydratase, small subunit

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



>FitnessBrowser__Korea:Ga0059261_4225
          Length = 209

 Score =  148 bits (374), Expect = 6e-41
 Identities = 82/189 (43%), Positives = 107/189 (56%), Gaps = 12/189 (6%)

Query: 7   KHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPDFVLNFP 66
           K  G   P  A N+DTD IIP  +L+ ++R G G   F   R          PD + +  
Sbjct: 6   KVEGRAYPWGAKNIDTDIIIPAHWLKTISREGLGKGAFESVR--------AEPDNIFDDA 57

Query: 67  QYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVKLSD 126
           +Y G+ IL+A ENFGCGSSREHA WAL D G   VIAPS++DIF GN+F N ++ V L  
Sbjct: 58  RYAGSPILIAGENFGCGSSREHAAWALKDMGVTAVIAPSYSDIFSGNAFKNGIVAVVLPQ 117

Query: 127 AEVDELFALVKANPGIHFDVDLEAQEVKAG-EKTYRFTIDAFRRHCMMNGLDSIGLTLQH 185
             VD L  + K +P     +DLE   V    +  + F +D FRR C+M GLD +GLTL  
Sbjct: 118 DAVDRLVEVAKTDP---VTIDLETMTVTTPYQDRFAFEMDPFRRDCLMQGLDEVGLTLAK 174

Query: 186 DDAIAAYEA 194
           D  I+ YE+
Sbjct: 175 DTVISKYES 183


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: 111
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: 201
Length of database: 209
Length adjustment: 21
Effective length of query: 180
Effective length of database: 188
Effective search space:    33840
Effective search space used:    33840
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 Ga0059261_4225 Ga0059261_4225 (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.15538.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15538.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.