GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate RR42_RS14390 RR42_RS14390 3-isopropylmalate dehydratase

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__Cup4G11:RR42_RS14390
          Length = 216

 Score =  242 bits (618), Expect = 3e-69
 Identities = 122/206 (59%), Positives = 149/206 (72%), Gaps = 8/206 (3%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD------EKGQQ 56
           +KFT H+GL VPLD  NVDTDAIIPKQFL+ + RTGFG +LF++WR+ D      +  ++
Sbjct: 2   DKFTVHSGLTVPLDRENVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYKDVGQPGQDNSRR 61

Query: 57  P-NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSF 115
           P NP+FVLN P YQG SILLAR NFGCGSSREHAPWALT YGF+ VIAPSFADIF+ N +
Sbjct: 62  PLNPDFVLNQPRYQGGSILLARRNFGCGSSREHAPWALTQYGFRAVIAPSFADIFFNNCY 121

Query: 116 NNQLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQ-VVKAGDKTYSFKIDDFRRHCMLN 174
            N LLPV L++ QVD +F    A  G K  +DL+ Q VV  G  +Y F I  FR++CMLN
Sbjct: 122 KNGLLPVVLTELQVDHIFNETNAFNGYKLTIDLDKQLVVTPGGNSYPFDIAPFRKYCMLN 181

Query: 175 GLDSIGLTLQHEDAIAAYENKQPAFM 200
           G D IGL+L+H D I AYE ++ A M
Sbjct: 182 GFDDIGLSLRHADKIKAYEAERVARM 207


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: 201
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: 216
Length adjustment: 21
Effective length of query: 180
Effective length of database: 195
Effective search space:    35100
Effective search space used:    35100
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 RR42_RS14390 RR42_RS14390 (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.7841.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7841.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.