Alignments for a candidate for leuD in Pseudomonas simiae WCS417

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate GFF1851 PS417_09415 3-isopropylmalate dehydratase

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__WCS417:GFF1851
          Length = 204

 Score =  193 bits (490), Expect = 2e-54
 Identities = 101/211 (47%), Positives = 130/211 (61%), Gaps = 9/211 (4%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           ++ FT+ TG  AP+   N+DTD I+PKQFLK I R+G     F + R+L  GEP      
Sbjct: 3   LQPFTLVTGKAAPMLAANIDTDVIMPKQFLKGIDRSGLDRGLFFDLRFLSSGEP------ 56

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
              NP+FVLNQP +QGAS +V   NFGCGSSREHA W L+Q G RA+I  SFA IF++NC
Sbjct: 57  ---NPEFVLNQPAWQGASFMVVGPNFGCGSSREHAVWGLKQMGIRALIGSSFAGIFYDNC 113

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
            +NG+L I L E  +  L       +  Q+++DLEAQ +R  DG    F+I   RK  LL
Sbjct: 114 QRNGVLLITLDEAVLQTLGKTVSQADQAQISVDLEAQQIRLADGEVIAFQIDTLRKSALL 173

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWLN 211
            G D IG TL+ +D+I+ FE   L   PWLN
Sbjct: 174 LGLDAIGSTLQRSDEIKAFERRHLQANPWLN 204


Lambda     K      H
   0.322    0.141    0.437 

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: 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: 216
Length of database: 204
Length adjustment: 21
Effective length of query: 195
Effective length of database: 183
Effective search space:    35685
Effective search space used:    35685
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.3678.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.3678.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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