GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate GFF2654 HP15_2598 isopropylmalate isomerase small subunit

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



>FitnessBrowser__Marino:GFF2654
          Length = 211

 Score =  210 bits (534), Expect = 2e-59
 Identities = 106/201 (52%), Positives = 138/201 (68%), Gaps = 7/201 (3%)

Query: 3   EKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDE-------KGQ 55
           E F  HTGLVVP D +NVDTDAI+PKQ+L+ + +TGF   LF+D R+LD          +
Sbjct: 2   EAFKTHTGLVVPFDRSNVDTDAILPKQYLKMLEKTGFADFLFDDERYLDPGDVDIPVSER 61

Query: 56  QPNPDFVLNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSF 115
           +P+PDF+LN   Y  ASILLAR NFGCGSSREHA WAL D+G + VIA SF DIF+ N F
Sbjct: 62  RPDPDFILNRAPYDRASILLARANFGCGSSREHAVWALKDFGVRAVIASSFGDIFFNNCF 121

Query: 116 NNQLLPVKLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNG 175
           NN LLPV L ++ +DELF L     G+   VDLE  E+++ +KT+RF +++ RR  +++G
Sbjct: 122 NNGLLPVILDESTIDELFNLASDTDGLELTVDLEQCEIRSPKKTWRFVVESGRRENLLSG 181

Query: 176 LDSIGLTLQHDDAIAAYEAKQ 196
           LD IG TL    +I AYEA +
Sbjct: 182 LDEIGRTLTFSGSIQAYEANR 202


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: 182
Number of extensions: 7
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: 211
Length adjustment: 21
Effective length of query: 180
Effective length of database: 190
Effective search space:    34200
Effective search space used:    34200
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 GFF2654 HP15_2598 (isopropylmalate isomerase small subunit)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.27713.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27713.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.