GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Pseudomonas simiae WCS417

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate GFF1851 PS417_09415 3-isopropylmalate dehydratase

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__WCS417:GFF1851
          Length = 204

 Score =  168 bits (425), Expect = 7e-47
 Identities = 91/194 (46%), Positives = 119/194 (61%), Gaps = 3/194 (1%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           + FT  TG   P+ AAN+DTD I+PKQFL+ + R+G    LF D RFL     +PNPEFV
Sbjct: 4   QPFTLVTGKAAPMLAANIDTDVIMPKQFLKGIDRSGLDRGLFFDLRFLSSG--EPNPEFV 61

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN P +QGAS ++   NFGCGSSREHA W L   G + +I  SFA IFY N   N +L +
Sbjct: 62  LNQPAWQGASFMVVGPNFGCGSSREHAVWGLKQMGIRALIGSSFAGIFYDNCQRNGVLLI 121

Query: 123 TLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGD-KTYSFKIDDFRRHCMLNGLDSIGL 181
           TL +A +  L   V      +  VDLEAQ ++  D +  +F+ID  R+  +L GLD+IG 
Sbjct: 122 TLDEAVLQTLGKTVSQADQAQISVDLEAQQIRLADGEVIAFQIDTLRKSALLLGLDAIGS 181

Query: 182 TLQHEDAIAAYENK 195
           TLQ  D I A+E +
Sbjct: 182 TLQRSDEIKAFERR 195


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: 137
Number of extensions: 7
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: 204
Length adjustment: 21
Effective length of query: 180
Effective length of database: 183
Effective search space:    32940
Effective search space used:    32940
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 GFF1851 PS417_09415 (3-isopropylmalate dehydratase)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.26018.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26018.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.