GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Dechlorosoma suillum PS

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate Dsui_3199 Dsui_3199 3-isopropylmalate dehydratase, small subunit

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__PS:Dsui_3199
          Length = 212

 Score =  229 bits (585), Expect = 2e-65
 Identities = 114/204 (55%), Positives = 143/204 (70%), Gaps = 8/204 (3%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD------EKGQQ 56
           + FT+  GLV PLD  NVDTDAIIPKQFL+ + R+GFG + F++WR++D      +  ++
Sbjct: 2   QAFTKLDGLVAPLDRNNVDTDAIIPKQFLKSIKRSGFGPNAFDEWRYMDHGEPGMDNSKR 61

Query: 57  P-NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSF 115
           P NP FVLN   YQGAS+LL R NFGCGSSREHAPWAL DYGF+VVIA SFADIF+ N F
Sbjct: 62  PLNPNFVLNQQRYQGASVLLTRSNFGCGSSREHAPWALLDYGFRVVIAESFADIFFNNCF 121

Query: 116 NNQLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQ-VVKAGDKTYSFKIDDFRRHCMLN 174
            N +LP+ L   ++D LF L +  PG K  VDLE Q VV+       F++D FRR C+LN
Sbjct: 122 KNGILPIVLPKTEIDALFGLTEYTPGFKLVVDLEQQKVVRPDGHAIPFEVDAFRRECLLN 181

Query: 175 GLDSIGLTLQHEDAIAAYENKQPA 198
           G D IGLTL+H D I A+E ++ A
Sbjct: 182 GWDDIGLTLRHADKIKAFEERRRA 205


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: 190
Number of extensions: 10
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: 212
Length adjustment: 21
Effective length of query: 180
Effective length of database: 191
Effective search space:    34380
Effective search space used:    34380
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 Dsui_3199 Dsui_3199 (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.8135.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8135.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.