GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Phaeobacter inhibens BS107

Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate GFF2932 PGA1_c29790 3-isopropylmalate dehydratase small subunit

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



>FitnessBrowser__Phaeo:GFF2932
          Length = 201

 Score =  196 bits (498), Expect = 2e-55
 Identities = 93/194 (47%), Positives = 131/194 (67%), Gaps = 3/194 (1%)

Query: 3   EKFIKHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPDFV 62
           EKF K  G+  P+   N+DTD IIPK FL+ + RTGFG +LF++ R+   +      DFV
Sbjct: 2   EKFTKIQGIAAPMPLVNIDTDMIIPKVFLKSIQRTGFGKNLFDEMRY--NRDGSEIADFV 59

Query: 63  LNFPQYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN PQY+ A IL+A +NFGCGSSREHAPWA+ D+G + +++ SFADIF+ NSF N +LP+
Sbjct: 60  LNKPQYRDAEILIAGDNFGCGSSREHAPWAIADFGIRCIVSTSFADIFFNNSFKNGILPI 119

Query: 123 KLSDAEVDELFALVKANPGIHFDVDLEAQEVKAGE-KTYRFTIDAFRRHCMMNGLDSIGL 181
            L   +VD L    +        VDLEAQE+   + +  +F +DAF++HC++NGLD IGL
Sbjct: 120 VLPQEQVDLLMKDAEKGANARMTVDLEAQEISTSDGEVIKFEVDAFKKHCLLNGLDDIGL 179

Query: 182 TLQHDDAIAAYEAK 195
           T++   +IA++E K
Sbjct: 180 TMEKATSIASFEDK 193


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: 140
Number of extensions: 6
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: 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 GFF2932 PGA1_c29790 (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.4542.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4542.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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